Sie sind auf Seite 1von 745

www.ck12.

org
_9U3RydWN0dXJl
17

www.ck12.org

CK-12 Biology Advanced


Concepts

Douglas Wilkin, Ph.D.

Say Thanks to the Authors


Click http://www.ck12.org/saythanks
(No sign in required)

www.ck12.org

To access a customizable version of this book, as well as other


interactive content, visit www.ck12.org

AUTHOR
Douglas Wilkin, Ph.D.
EDITOR
Douglas Wilkin, Ph.D.

CK-12 Foundation is a non-profit organization with a mission to


reduce the cost of textbook materials for the K-12 market both in
the U.S. and worldwide. Using an open-source, collaborative, and
web-based compilation model, CK-12 pioneers and promotes the
creation and distribution of high-quality, adaptive online textbooks
that can be mixed, modified and printed (i.e., the FlexBook
textbooks).
Copyright 2015 CK-12 Foundation, www.ck12.org
The names CK-12 and CK12 and associated logos and the
terms FlexBook and FlexBook Platform (collectively
CK-12 Marks) are trademarks and service marks of CK-12
Foundation and are protected by federal, state, and international
laws.
Any form of reproduction of this book in any format or medium,
in whole or in sections must include the referral attribution link
http://www.ck12.org/saythanks (placed in a visible location) in
addition to the following terms.
Except as otherwise noted, all CK-12 Content (including CK-12
Curriculum Material) is made available to Users in accordance
with the Creative Commons Attribution-Non-Commercial 3.0
Unported (CC BY-NC 3.0) License (http://creativecommons.org/
licenses/by-nc/3.0/), as amended and updated by Creative Commons from time to time (the CC License), which is incorporated
herein by this reference.
Complete terms can be found at http://www.ck12.org/about/
terms-of-use.
Printed: May 30, 2015

iii

www.ck12.org
Foreword

Foreword
The study of biology is the study of life. Concept Biology Advanced is the CK-12 Foundations most extensive
material describing the study of life. Concept Biology Advanced presents biology as a set of 18 concepts, with each
concept centered around a specific category, such as cell biology or plants. Each concept is comprised of a series
of lessons, with each lesson focusing on one specific topic. The complete Concept Biology Advanced is comprised
of over 550 lessons. This material has been developed to complement the most advanced secondary-level biology
course.

iv

www.ck12.org

Contents

Contents
Foreword
1

iv

The Study of Life - Advanced


1.1
Goals of Science . . . . . . . . . . . . . .
1.2
A Scientific View of the World . . . . . .
1.3
Scientific Methods - Advanced . . . . . .
1.4
Scientific Reasoning - Advanced . . . . .
1.5
Experiments - Advanced . . . . . . . . .
1.6
Scientific Theories - Advanced . . . . . .
1.7
Scientific Models - Advanced . . . . . . .
1.8
What is a Scientist? - Advanced . . . . . .
1.9
Units of Measurement - Advanced . . . .
1.10
Laboratories - Advanced . . . . . . . . .
1.11
Characteristics of Life - Advanced . . . .
1.12
Unifying Principles of Biology - Advanced
1.13
Interdependence - Advanced . . . . . . .
1.14
Evolution of Life - Advanced . . . . . . .
1.15
Nobel Prizes . . . . . . . . . . . . . . . .
1.16
References . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

1
2
5
9
16
19
27
32
37
44
47
57
62
66
72
78
90

Chemistry of Life - Advanced


2.1
Chemical Substances - Advanced . . . . . .
2.2
The Significance of Carbon - Advanced . .
2.3
Carbohydrates - Advanced . . . . . . . . .
2.4
Lipids - Advanced . . . . . . . . . . . . . .
2.5
Proteins - Advanced . . . . . . . . . . . . .
2.6
Nucleic Acids - Advanced . . . . . . . . . .
2.7
Water - Advanced . . . . . . . . . . . . . .
2.8
Biochemical Properties of Water - Advanced
2.9
Solutions - Advanced . . . . . . . . . . . .
2.10
Water and Life - Advanced . . . . . . . . .
2.11
References . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

93
94
100
104
109
113
119
125
129
135
141
144

Cell Biology - Advanced


3.1
Cells - Advanced . . . . . . . . . .
3.2
Discovery of Cells - Advanced . . .
3.3
Microscopes in Biology - Advanced
3.4
The Cell Theory - Advanced . . . .
3.5
Cell Size and Shape - Advanced . .
3.6
Common Parts of Cells - Advanced .
3.7
Two Types of Cells - Advanced . . .
3.8
Viruses - Advanced . . . . . . . . .

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

145
146
149
153
158
161
166
169
174

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

Contents
3.9
3.10
3.11
3.12
3.13
3.14
3.15
3.16
3.17
3.18
3.19
3.20
3.21
3.22
3.23
3.24
3.25
3.26
3.27
3.28
3.29
3.30
3.31
3.32
3.33
3.34
3.35
3.36
4

vi

www.ck12.org
Cell Structures - Advanced . . . . . . . . . .
The Plasma Membrane - Advanced . . . . . .
The Phospholipid Bilayer - Advanced . . . .
Membrane Proteins - Advanced . . . . . . . .
The Fluid Mosaic Model - Advanced . . . . .
The Cytoplasm and Cytoskeleton - Advanced
External Structures of Cells - Advanced . . .
The Nucleus - Advanced . . . . . . . . . . .
The Mitochondria - Advanced . . . . . . . .
Endoplasmic Reticulum - Advanced . . . . .
Ribosomes - Advanced . . . . . . . . . . . .
The Golgi Apparatus - Advanced . . . . . . .
Vesicles and Vacuoles - Advanced . . . . . .
Other Structures of Cells - Advanced . . . . .
Plant Cells - Advanced . . . . . . . . . . . .
Organization of Cells - Advanced . . . . . . .
Cell Transport - Advanced . . . . . . . . . .
Diffusion - Advanced . . . . . . . . . . . . .
Osmosis - Advanced . . . . . . . . . . . . . .
Facilitated Diffusion - Advanced . . . . . . .
Active Transport - Advanced . . . . . . . . .
The Sodium-Potassium Pump - Advanced . .
The Electrochemical Gradient - Advanced . .
Exocytosis and Endocytosis - Advanced . . .
Cell Communication - Advanced . . . . . . .
Signal Receptors - Advanced . . . . . . . . .
Signal Transduction - Advanced . . . . . . .
References . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

Biochemistry - Advanced
4.1
Biochemical Energy - Advanced . . . . . . . . .
4.2
States of Matter in Biological Systems - Advanced
4.3
Chemical Reactions - Advanced . . . . . . . . .
4.4
Chemical Reactions and Energy - Advanced . . .
4.5
Enzymes and Activation Energy - Advanced . . .
4.6
Enzymes and Biochemical Reactions - Advanced
4.7
References . . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

177
180
183
186
189
191
195
198
201
205
208
211
214
218
222
227
232
235
238
243
247
251
254
258
262
265
269
275

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

277
278
281
285
288
292
295
299

Metabolism - Advanced
5.1
Photosynthesis - Advanced . . . . . . . . . . . . . .
5.2
Autotrophs vs. Heterotrophs - Advanced . . . . . . .
5.3
Energy Carrying Molecules - Advanced . . . . . . .
5.4
The Photosynthesis Reaction - Advanced . . . . . . .
5.5
The Chloroplast - Advanced . . . . . . . . . . . . . .
5.6
The Light Reactions - Advanced . . . . . . . . . . .
5.7
The Calvin Cycle - Advanced . . . . . . . . . . . . .
5.8
Chemosynthesis - Advanced . . . . . . . . . . . . .
5.9
Cellular Respiration - Advanced . . . . . . . . . . .
5.10
Cellular Respiration Overview - Advanced . . . . . .
5.11
Glycolysis - Advanced . . . . . . . . . . . . . . . .
5.12
The Mitochondria in Cellular Respiration - Advanced

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

300
301
305
310
314
320
325
331
337
339
342
351
358

.
.
.
.
.
.
.

www.ck12.org
5.13
5.14
5.15
5.16
5.17
5.18
5.19
6

Contents

The Krebs Cycle - Advanced . . . . . . . . . .


The Electron Transport Chain - Advanced . . .
Anaerobic Respiration - Advanced . . . . . . .
Lactic Acid Fermentation - Advanced . . . . .
Alcoholic Fermentation - Advanced . . . . . .
Aerobic vs. Anaerobic Respiration - Advanced .
References . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

361
367
371
374
378
382
386

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

388
389
392
395
398
404
408
415
420
425
432
435
443
447
452
455

Inheritance - Advanced
7.1
Mendel - Advanced . . . . . . . . . . . . . . . . . . . . .
7.2
Pea Plants - Advanced . . . . . . . . . . . . . . . . . . . .
7.3
Mendels First Experiment - Advanced . . . . . . . . . . .
7.4
Theory of Heredity - Advanced . . . . . . . . . . . . . . .
7.5
Mendels Second Experiment - Advanced . . . . . . . . .
7.6
Molecular Genetics - Advanced . . . . . . . . . . . . . . .
7.7
Inheritance Probability - Advanced . . . . . . . . . . . . .
7.8
Punnett Squares - Advanced . . . . . . . . . . . . . . . . .
7.9
Testcross - Advanced . . . . . . . . . . . . . . . . . . . .
7.10
Dihybrid Crosses - Advanced . . . . . . . . . . . . . . . .
7.11
Mendelian Inheritance in Humans - Advanced . . . . . . .
7.12
Non-Mendelian Inheritance - Advanced . . . . . . . . . .
7.13
Effect of Environment on Genetics - Advanced . . . . . . .
7.14
Human Genetics - Advanced . . . . . . . . . . . . . . . .
7.15
The Human Genome - Advanced . . . . . . . . . . . . . .
7.16
Chromosomes - Advanced . . . . . . . . . . . . . . . . .
7.17
Autosomal Traits - Advanced . . . . . . . . . . . . . . . .
7.18
Sex-Linked Traits - Advanced . . . . . . . . . . . . . . . .
7.19
Genetic Disorders - Advanced . . . . . . . . . . . . . . .
7.20
Complex Traits - Advanced . . . . . . . . . . . . . . . . .
7.21
Multiple-Allele Traits - Advanced . . . . . . . . . . . . .
7.22
Polygenic Traits - Advanced . . . . . . . . . . . . . . . .
7.23
Diagnosis and Treatment of Genetic Disorders - Advanced
7.24
References . . . . . . . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

456
457
461
465
469
472
475
478
482
485
489
492
497
501
504
507
513
519
523
530
539
544
548
553
558

Cell Division - Advanced


6.1
Cell Division - Advanced . . . . . . . .
6.2
Prokaryotic Cell Division - Advanced .
6.3
Eukaryotic Cell Division - Advanced . .
6.4
Chromosomal Division - Advanced . . .
6.5
Cell Cycle - Advanced . . . . . . . . .
6.6
Mitosis - Advanced . . . . . . . . . . .
6.7
Cell Cycle Regulation - Advanced . . .
6.8
Gene Regulation and Cancer - Advanced
6.9
Asexual Reproduction - Advanced . . .
6.10
Sexual Reproduction - Advanced . . . .
6.11
Meiosis - Advanced . . . . . . . . . . .
6.12
Genetic Variation - Advanced . . . . . .
6.13
Gametogenesis - Advanced . . . . . . .
6.14
Sexual Life Cycles - Advanced . . . . .
6.15
References . . . . . . . . . . . . . . . .

Molecular Biology - Advanced

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

560
vii

Contents
8.1
8.2
8.3
8.4
8.5
8.6
8.7
8.8
8.9
8.10
8.11
8.12
8.13
8.14
8.15
8.16
8.17
8.18
8.19
8.20
8.21
8.22
8.23
8.24
8.25
8.26
9

viii

www.ck12.org
DNA - Advanced . . . . . . . . . . . . . . . . . . . . .
The Hereditary Material - Advanced . . . . . . . . . . .
Chargaffs Base-Pairing Rules - Advanced . . . . . . . .
The DNA Double Helix - Advanced . . . . . . . . . . .
DNA Replication - Advanced . . . . . . . . . . . . . . .
RNA - Advanced . . . . . . . . . . . . . . . . . . . . .
RNA Structure - Advanced . . . . . . . . . . . . . . . .
RNA Types - Advanced . . . . . . . . . . . . . . . . . .
Protein Synthesis - Advanced . . . . . . . . . . . . . . .
Transcription - Advanced . . . . . . . . . . . . . . . . .
Messenger RNA - Advanced . . . . . . . . . . . . . . .
The Genetic Code - Advanced . . . . . . . . . . . . . .
Translation - Advanced . . . . . . . . . . . . . . . . . .
Mutations - Advanced . . . . . . . . . . . . . . . . . . .
Causes of Mutations - Advanced . . . . . . . . . . . . .
Mutations Types - Advanced . . . . . . . . . . . . . . .
DNA Repair - Advanced . . . . . . . . . . . . . . . . .
Significance of Mutations - Advanced . . . . . . . . . .
Mutations and Cancer - Advanced . . . . . . . . . . . .
Regulation of Gene Expression - Advanced . . . . . . .
Regulation of Gene Expression Mechanisms - Advanced
Prokaryotic Regulation of Gene Expression - Advanced .
Eukaryotic Regulation of Gene Expression - Advanced .
Transcription Factors - Advanced . . . . . . . . . . . . .
Gene Regulation and Cancer - Advanced . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

561
564
569
572
577
582
585
588
593
597
603
608
613
619
622
624
631
635
640
647
650
655
661
667
672
677

Biotechnology - Advanced
9.1
Biotechnology - Advanced . . . . . . . . . . . . . . . . . . .
9.2
Gene Cloning - Advanced . . . . . . . . . . . . . . . . . . . .
9.3
The Polymerase Chain Reaction - Advanced . . . . . . . . . .
9.4
The Human Genome Project - Advanced . . . . . . . . . . . .
9.5
Biotechnology and Medicine - Advanced . . . . . . . . . . . .
9.6
Biotechnology and Agriculture - Advanced . . . . . . . . . . .
9.7
Cloning - Advanced . . . . . . . . . . . . . . . . . . . . . . .
9.8
Biotechnology and Forensic Science - Advanced . . . . . . . .
9.9
Ethical, Legal, and Social Issues of Biotechnology - Advanced
9.10
References . . . . . . . . . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.

679
680
683
691
695
699
707
713
719
724
727

www.ck12.org

Chapter 1. The Study of Life - Advanced

C HAPTER

The Study of Life Advanced

Chapter Outline
1.1

G OALS OF S CIENCE

1.2

A S CIENTIFIC V IEW OF THE W ORLD

1.3

S CIENTIFIC M ETHODS - A DVANCED

1.4

S CIENTIFIC R EASONING - A DVANCED

1.5

E XPERIMENTS - A DVANCED

1.6

S CIENTIFIC T HEORIES - A DVANCED

1.7

S CIENTIFIC M ODELS - A DVANCED

1.8

W HAT IS A S CIENTIST ? - A DVANCED

1.9

U NITS OF M EASUREMENT - A DVANCED

1.10

L ABORATORIES - A DVANCED

1.11

C HARACTERISTICS OF L IFE - A DVANCED

1.12

U NIFYING P RINCIPLES OF B IOLOGY - A DVANCED

1.13

I NTERDEPENDENCE - A DVANCED

1.14

E VOLUTION OF L IFE - A DVANCED

1.15

N OBEL P RIZES

1.16

R EFERENCES

www.ck12.org

Introduction

Is there a way to define life ?


Scientifically, there is an actual definition of life. Living organisms must have certain characteristics. If they do
not have these characteristics, are they living? This butterfly, like all other insects, animals, plants, and every other
living organism, shares common characteristics with all life. What exactly does it mean to be alive? This concept
will answer this question. These lessons will serve as an introduction to biology, discussing The Study of Life and
fundamental Principles of Biology.

www.ck12.org

Chapter 1. The Study of Life - Advanced

1.1 Goals of Science


Define science.
List the principles that should guide scientific research.
Explain scientific skepticism.

What is science?
The goal of science is to learn how nature works by observing the natural and physical world, and to understand
this world through research and experimentation. Science is a distinctive way of learning about the world through
observation, inquiry, formulating and testing hypotheses, gathering and analyzing data, and reporting and evaluating
findings. We are all part of an amazing and mysterious phenomenon called "life" that thousands of scientists
everyday are trying to better understand. It is surprisingly easy to become part of this great discovery. All you need
is an understanding of how people use the process of science to learn about the world and your natural curiosity.
Goals of Science

The term science is derived from the Latin word, scientia, which means knowledge. Science involves objective,
logical, and repeatable experimental attempts to understand the principles and forces working in the natural universe.
Science is an ongoing process of testing and evaluation, and is guided by a universal set of principles. One of the
intended lessons of "Goals of Science" is for you to become more familiar with the scientific process.
Humans are naturally interested in the world we live in. Young children constantly pose the question "why". The
goal of science is to answer these question . You may not realize it, but you are performing experiments all the time.
For example, when you shop for groceries, you may end up carrying out a type of scientific experiment ( Figure
1.1). If you know you like Brand X of salad dressing but Brand Y is on sale, perhaps you will try Brand Y. If you
end up liking Brand Y, you may buy it again even when it is not on sale. If you did not like Brand Y, not even a sale
would entice you into buying it again. Your conclusions are essentially based on an experiment. To find out why a
3

1.1. Goals of Science

www.ck12.org

person might prefer a salad dressing over another, you might examine the cost, ingredient list, or packaging of the
two salad dressings.

FIGURE 1.1
Shopping sometimes involves a little scientific experimentation. You are
interested in inventing a new type of salad that you can pack for lunch.
You might buy a vegetable or salad dressing that you have not tried before
to discover if it would make an appealing addition to your salad. If you like
it, you will probably buy it again. This is a type of experiment in which you
have discovered a liking for something new.

There are many different areas of science, or scientific disciplines, but all scientific study involves:

asking questions
making observations
relying on evidence to form conclusions
being skeptical about ideas or results

Skepticism is an attitude of doubt about the truthfulness of claims that lack empirical evidence. Scientific skepticism, also referred to as skeptical inquiry, questions claims based on their scientific verifiability rather than simply
accepting claims based on faith or anecdotes. Scientific skepticism uses critical thinking to analyze such claims and
opposes claims which lack scientific evidence.
Vocabulary

experiment: A test that is used to rule out a hypothesis or validate something already known; is used to
eliminate one or more of the possible hypotheses until one hypothesis remains.
science: A distinctive way of learning about the natural world through observation, inquiry, formulating and
testing hypotheses, gathering and analyzing data, and reporting and evaluating findings.
scientific skepticism: Questioning claims based on their scientific verifiability rather than accepting claims
based on faith or anecdotes.
Summary

Scientific skepticism questions claims based on their scientific verifiability rather than accepting claims based
on faith or anecdotes. Scientific skepticism uses critical thinking to analyze such claims and opposes claims
which lack scientific evidence.
Explore More

Use this resource to answer the question that follows.


4

www.ck12.org

Chapter 1. The Study of Life - Advanced

The Aim of a Good Scientist at http://www.5min.com/Video/The-Aim-of-a-Good-Scientist-291035149 (03:27).


1. Describe the goals of the scientist in this video.
Review

1. What is science? What is the goal of science?


2. What is an experiment? Why are experiments performed?
3. Describe scientific skepticism.

1.2. A Scientific View of the World

www.ck12.org

1.2 A Scientific View of the World

Examine a scientists view of the world.


Explain the relationship between science and nature.
Define scientific law.
Discuss why science is unable to answer all questions.

What would be a scientific view of the world ?


It could be said that the scientific view of the world is based on proven answers to specific questions. For example,
"How old are recently identified fossils? What are the consequences of mutations in a certain gene? How does the
endocrine system help maintain homeostasis?". These questions have definite answers which can help expand the
scientific view of the world. Questions that cannot be answered with definitive answers, questions that cannot be
proved with evidence, are not based on science. The scientific view of the world would not include answers to such
questions.

A Scientific View of the World

Science is based on the analysis of observations made either through our senses or by using special equipment.
Science therefore cannot explain anything about the natural world that is beyond what is observable. The term
supernatural refers to entities, events, or powers regarded as being beyond nature, in that such things cannot be
explained by scientific means. They are not measurable or observable in the same way the natural world is, and are
therefore considered to be outside the realm of scientific examination.
When a natural occurrence which was previously considered supernatural is understood in the terms of natural causes
and consequences, it has a scientific explanation. For example, the flickering lights sometimes seen hovering over
damp ground on still evenings or nights are commonly called Will-o-the-wisp. This phenomena looks like a lamp or
flame, and is sometimes said to move away if approached. A great deal of folklore surrounds the legend, such as the
belief that the lights are lost souls or fairies attempting to lead travelers astray. However, science has offered several
6

www.ck12.org

Chapter 1. The Study of Life - Advanced

potential explanations for Will-o-the-wisp from burning marsh gases to glowing fungi, to animals that glow in a
similar way to lightning bugs.
There is no single path that leads to scientific knowledge, and scientists do not follow a fixed set of steps when
attempting to discover the answer to scientific questions. There are, however, certain specific features of scientific
investigation. You do not have to be a professional scientist to think like a scientist. Everyone, including you, can
use certain features of scientific thinking to analyze issues and situations in everyday life.
In science, it is assumed that the universe is a vast single system governed by basic rules and thus, things that are
learned from studying one part of the universe can be applied to other parts of the universe. For example, the same
principles of motion and gravitation that explain the motion of falling objects on Earth also explain the orbit of
the planets around the sun, and galaxies, as shown in the Figure 1.2. Thus nature, and what happens in nature,
can be understood. However, as discussed below, as more and more information and knowledge is collected and
understood, scientific ideas can change. Even though scientific knowledge usually stands the test of time, it cannot
answer all questions.

FIGURE 1.2
With some changes over the years, similar principles of motion have applied to different situations. The same
scientific principles that help explain planetary orbits can be applied to the movement of a Ferris wheel.

Nature Can Be Understood

In science, it is presumed that events in the universe happen in patterns that can be understood by careful study.
Scientists believe that with the help of instruments that extend the human senses and our own careful observation
and analysis, people can discover patterns in all of nature that can help us understand all facets of life, the world,
and the universe.
Scientists think of nature as a single system controlled by natural laws. Scientists strive to increase their understanding of the natural world by discovering natural laws. Laws of nature are expressed as scientific laws. A scientific
law is a statement that describes what always happens under certain conditions in nature.
An example of a scientific law is the law of gravity, which was discovered by Sir Isaac Newton (see Figure 1.3). The
law of gravity states that objects always fall towards Earth because of the pull of gravity. Based on this law, Newton
7

1.2. A Scientific View of the World

www.ck12.org

could explain many natural events. He could explain not only why objects such as apples always fall to the ground,
but he could also explain why the moon orbits Earth. In addition to the laws of gravity, Newton also discovered laws
of motion. His laws of motion allowed him to explain why objects move as they do.

FIGURE 1.3
Did Newton discover the law of gravity when an apple fell from a tree and
hit him on the head? Probably not, but observations of nature are often
the starting points for new ideas about the natural world.

Scientific Ideas Can Change

Science is a process for developing knowledge. Change in knowledge about the natural world is expected because
there is often room for new observations which may challenge current views. No matter how well one theory
explains a set of observations, it is possible that a different theory may explain them just as well or better, or may
also encompass a wider range of observations. Scientists are always testing and attempting to improve theories.
Scientists know that even if there is no way to gain complete knowledge about something, an increasingly accurate
understanding of nature will develop over time.
The ability of scientists to make progressively more accurate predictions about the natural world, from determining
how the smallest living organisms develop antibiotic resistance, to how "non-living" viruses continue to evolve, from
how a cancerous tumor develops its own blood supply, to how mutations lead to cancer and other diseases, from
trying to predict earthquakes, to calculating the orbit of an asteroid, provides evidence that scientists are gaining an
understanding of how the world works.

Scientific Knowledge Can Stand the Test of Time

Continuity and stability are as much characteristics of science as change is. Although scientists accept some
uncertainty as part of nature, most scientific knowledge stands the test of time. A changing of ideas, rather than
a complete rejection of the ideas, is the usual practice in science. Powerful ideas about nature tend to survive, grow
more accurate and become more widely accepted.
For example, in developing the theory of relativity, Albert Einstein did not throw out Issac Newtons laws of motion
but rather, he showed them to be only a small part of the bigger, cosmic picture. That is, the Newtonian laws of
motion have limited use within our more general concept of the universe. For example, the National Aeronautics
and Space Administration (NASA) uses the Newtonian laws of motion to calculate the flight paths of satellites and
space vehicles.
The theory of evolution by natural selection is a classic example of a biological theory that has withstood the test of
time. Developed over 150 years ago, a myriad of data has been collected to support Charles Darwins theory. So far,
no scientific information has been uncovered to contradict or counteract this scientific theory.
8

www.ck12.org

Chapter 1. The Study of Life - Advanced

Science Cannot Offer Answers to All Questions

There are many things that cannot be examined in a scientific way. There are, for instance, beliefs that cannot be
proved or disproved, such as the existence of supernatural powers, supernatural beings, or the meaning of life. In
other cases, a scientific approach to a question and a scientific answer may be rejected by people who hold to certain
beliefs.
Scientists do not have the means to settle moral questions surrounding good and evil, or love and hate, but they can
sometimes contribute to the discussion of such issues by identifying the likely reasons for certain actions by humans
and the possible consequences of these actions.
Vocabulary

science: A distinctive way of learning about the natural world through observation, inquiry, formulating and
testing hypotheses, gathering and analyzing data, and reporting and evaluating findings.
scientific law: A principle which can be used to predict the behavior of the natural world.
scientist: An individual who uses the scientific method; a person who engages in a systematic activity to
acquire knowledge.
Summary

Science is based on the analysis of things that humans can observe either by themselves through their senses,
or by using special equipment. Science therefore cannot explain anything about the natural world that is
beyond what is observable by current means. Supernatural things cannot be explained by scientific means.
Explore More

Use this resource to answer the question that follows.


E.O. Wilson: Advice to young scientists at http://www.ted.com/talks/e_o_wilson_advice_to_young_scientis
ts.html (14:56).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/69290

1. Summarize the principles of biologists E.O. Wilsons presentation.


Review

1.
2.
3.
4.

What makes someone a "scientist?"


Describe a scientific law.
What is meant by nature can be understood?
Discuss why science cannot answer all questions.

1.3. Scientific Methods - Advanced

www.ck12.org

1.3 Scientific Methods - Advanced

Order the general steps of a scientific method.


Outline a set of steps that are used in the scientific method of investigating a problem.
Define hypothesis.
Explain the importance of a hypothesis being falsifiable.
Describe why a control group is used in an experiment.

What is the method of science?


How is science "done?" It can be difficult sometimes to define research methods in a way that will clearly distinguish
science from non-science. However, there is a set of core principles that make up the bones of scientific research.
These principles are widely accepted within the scientific community. Although there is no fixed set of steps that
scientists always follow during an investigation, and there is no single path that leads scientists to knowledge, there
are certain features of science that give it a distinct way of investigating.
10

www.ck12.org

Chapter 1. The Study of Life - Advanced

Scientific Methods

Scientific investigations examine, gain new knowledge, or build on previous knowledge about phenomena. A
phenomenon, is any occurrence that is observable. It can be simply a burning match shown in the Figure 1.4,
as well as the structure of a cell and the prey of a lion. A phenomenon may be a feature of matter, energy, or
time. For example, Isaac Newton made observations of the phenomenon of the moons orbit, Galileo Galilei
made observations of phenomena related to swinging pendulums and Charles Darwin made observations of unique
plant and animal species. Although procedures vary from one field of scientific inquiry to another, certain features
distinguish scientific inquiry from other types of knowledge. Scientific methods are based on gathering observable,
empirical (produced by experiment or observation), and measurable evidence that is critically evaluated.

FIGURE 1.4
The combustion of this match is an
observable event and therefore a phenomenon.

The Scientific Method Video can be seen at http://www.youtube.com/watch?v=BVfI1wat2y8 (4:25).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/151878

Scientific Investigations

The scientific method is not a step by step, linear process. It is a way of learning about the world through the
application of knowledge. Scientists must be able to have an idea of what the answer to an investigation should
be. In order for scientists to make educated guesses about the answers, they will base their guesses on previous
knowledge, with the notion of extending that knowledge. Scientists will often make an observation and then form
a hypothesis to explain why a phenomenon occurred. They use all of their knowledge and a bit of imagination in
their journey of discovery.
A hypothesis is a suggested explanation of a question or problem, based on evidence that can be tested by observation
or experimentation. A hypothesis absolutely must be testable it gains credibility by being tested over and over
11

1.3. Scientific Methods - Advanced

www.ck12.org

again, and by surviving attempts to prove it wrong. Scientists may test and reject several hypotheses before solving
a problem.
Scientific investigations involve the collection of data through observation, the formation and testing of hypotheses
by experimentation, and analysis of the results that involves reasoning. Scientific investigations begin with observations that lead to questions.
We will use an everyday example to show what makes up a scientific investigation. Imagine that you walk into a
room, and the room is dark.
You observe that the room appears dark, and you question why the room is dark.
In an attempt to find explanations to this phenomenon, you develop several different hypotheses. One hypothesis might be that the room does not have a light source at all. Another hypothesis might be that the lights are
turned off. Still, another might be that the light bulb has burnt out. Worse yet, you could be going blind.
To discover the answer, you experiment. You feel your way around the room and find a light switch and turn
it on. No light. You repeat the experiment, flicking the switch back and forth; still nothing.
This means your first two hypotheses, that the room is dark because (1) it does not have a light source; and (2)
the lights are off, have been disproved.
You think of more experiments to test your hypotheses, such as switching on a flashlight to prove that you are
not blind.
In order to accept your last remaining hypothesis as the answer, you could predict that changing the light
bulb will fix the problem. If your predictions about this hypothesis succeed (changing the light bulb fixes the
problem), the original hypothesis is valid and is accepted.
However, in some cases, your predictions will not succeed (changing the light bulb does not fix the problem),
and you will have to start over again with a new hypothesis. Perhaps there is a short circuit somewhere in the
house, or the power might be out.
The general process of a scientific investigation is summed up in Figure 1.6.

TABLE 1.1: Common Terms Used in Scientific Investigations


Term
Scientific Method
Observation

Hypotheses
Scientific Reasoning
Experiment
Rejected Hypothesis
Confirmed Hypothesis

Inference
Theory

12

Definition
The process of scientific investigation.
The act of noting or detecting phenomenon by the
senses. For example, taking measurements is a form
of observation.
A suggested explanation based on evidence that can be
tested by observation or experimentation.
The process of looking for scientific reasons for observations.
A test that is used to rule out a hypothesis or validate
something already known.
An explanation that is ruled out by experimentation.
An explanation that is not ruled out by repeated experimentation, and makes predictions that are shown to be
true.
Developing new knowledge based upon old knowledge.
A widely accepted hypothesis that stands the test of
time. Theories are often tested, and usually not rejected.

www.ck12.org

Chapter 1. The Study of Life - Advanced

FIGURE 1.5
The general pathway of a scientific investigation. A scientific investigation typically
has these steps, though the pathway is
often modified for a specific scientific investigation.

13

1.3. Scientific Methods - Advanced

www.ck12.org

FIGURE 1.6
The general process of scientific investigations.

This diagram illustrates how

scientific investigations move from observation of phenomenon to a theory. The


progress is not as straightforward as it
looks in this diagram.

Many times the

hypothesis is falsified, which means the


investigator will have to redevelop/revise
a hypothesis.

14

www.ck12.org

Chapter 1. The Study of Life - Advanced

The Scientific Method Made Easy explains the scientific method: http://www.youtube.com/watch?v=zcavPAFiG14
(9:55).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/149

Making Observations

Scientists first make observations that raise questions. An observation is the act of noting or detecting phenomenon
through the senses. For example, noting that a room is dark is an observation made through sight.

Developing Hypotheses

In order to explain the observed phenomenon, scientists develop a number of possible explanations, or hypotheses.
A hypothesis is a suggested explanation for a phenomenon or a suggested explanation for a relationship between
many phenomena. Hypotheses are always based on evidence that can be tested by observation or experimentation.
Scientific investigations are required to test hypotheses. Scientists mostly base hypotheses on prior observations or
on extensions of existing scientific explanations.
Though many people describe a hypothesis as an "educated guess," that definition is not scientifically accurate.
To define a hypothesis as "an educated guess" is like calling a tricycle a "vehicle with three." This definition of a
tricycle leaves out its most important and characteristic feature: its wheels. The "educated guess" definition of a
hypothesis also leaves out the concepts most important and characteristic feature: the purpose of the hypotheses.
People generate hypotheses as early attempts to explain patterns observed in nature or to predict the outcomes of
experiments. For example, in science, one could correctly call the following statement a hypothesis: identical twins
can have different personalities because environment influences personality.

Evaluating Hypotheses

Scientific methods require hypotheses that are falsifiable, that is, they must be framed in a way that allows other
scientists to prove them false. Proving a hypothesis to be false is usually done by observation and experimentation.
However, confirming or failing to falsify a hypothesis does not necessarily mean the hypothesis is true.
For example, a person comes to a new country and observes only white sheep. This person might form the
hypothesis: All sheep in this country are white. This statement can be called a hypothesis, because it is falsifiable
- it can be tested and proved wrong; anyone could falsify the hypothesis by observing a single black sheep, shown
in Figure 1.7. If the experimental uncertainties remain small (could the person reliably distinguish the observed
black sheep from a goat or a small horse), and if the experimenter has correctly interpreted the hypothesis, finding a
black sheep falsifies the "only white sheep" hypothesis. However, you cannot call a failure to find non-white sheep
as proof that no non-white sheep exist.

Vocabulary

evidence: Any type of data that may be used to test a hypothesis.


15

1.3. Scientific Methods - Advanced

www.ck12.org

FIGURE 1.7
The statement there are only white
sheep in this country is a hypothesis
because it is open to being falsified. However, failure to see a black sheep does not
necessarily falsify the hypothesis. A better scientific hypothesis may be that "only
white sheep can survive in this country
because of the existing ecosystems."

experiment: A test that is used to rule out a hypothesis or validate something already known; a test that is
used to eliminate one or more of the possible hypotheses until one hypothesis remains.
falsifiable: Can be proved false.
hypothesis (plural, hypotheses): A suggested explanation based on evidence that can be tested by observation
or experimentation.
observation: The act of noting or detecting phenomenon through the senses.
phenomenon: Any occurrence that is observable.
scientific investigation: A plan for asking questions and testing possible answers.
scientific methods: Procedures based on gathering observable, empirical (produced by experiment or observation) and measurable evidence that is critically evaluated.
Summary

Scientific investigations involve the collection of data through observation, the formation and testing of
hypotheses by experimentation, and analysis of the results that involves reasoning.
Review

1.
2.
3.
4.
5.

16

Describe the scientific method.


What is an hypothesis?
How is a hypothesis developed and evaluated?
What is meant by falsifiable?
What happens if a hypothesis is false?

www.ck12.org

Chapter 1. The Study of Life - Advanced

1.4 Scientific Reasoning - Advanced


Outline the role that reasoning plays in examining hypotheses.
Define and compare inductive and deductive reasoning.

What does it mean to reason ?


"What does the data show? Did the experiment work? Is the hypothesis correct?" Reasoning is the human process
used to make sense of things. Reasoning is also used to establish and verify facts. "Scientific reasoning" is no
different than everyday reasoning - it is used to make sense of things related to the scientific process, such as
conclusions based on the results of an experiment.

Scientific Reasoning

Any useful hypothesis will allow predictions based on reasoning. Reasoning can be broken down into two categories:
deduction and induction. Most reasoning in science is done through induction.
17

1.4. Scientific Reasoning - Advanced

www.ck12.org

Deductive Reasoning: Deduction

Deduction involves determining a single fact from a general statement; it is only as accurate as the statement.
For example, we know that all organisms are made of cells and need to maintain homeostasis and must reproduce
to stay alive. Therefore, since humans are organisms, we can then deduce that humans are made of cells, maintain
homeostasis and reproduce.
Deductions are based on valid reasoning. The reasoning in the following argument is valid, because there is no way
in which the reasons 1 and 2, could be true and the conclusion, 3, be false:
Reason 1: All humans are mortal.
Reason 2: Albert Einstein is a human.
Conclusion: Albert Einstein is mortal ( Figure 1.8).

FIGURE 1.8
Albert Einstein (18791955) Deductive
reasoning has helped us determine that
Albert Einstein is a mortal being.

Inductive Reasoning: Induction

Induction involves determining a general statement that is very likely to be true from several facts.
For example, if we have had a test every Tuesday for the past three months, we will have a test next Tuesday (and
every Tuesday after that).
18

www.ck12.org

Chapter 1. The Study of Life - Advanced

Induction contrasts strongly with deduction. Even in the best, strongest cases of induction, the truth of the reason
does not guarantee the truth of the conclusion. Instead, the conclusion of an inductive argument is very likely to be
true, but you cannot be fully sure it is true because you are making a prediction about a fact that has yet to be proven.
A classic example of inductive reasoning comes from the philosopher David Hume:
Reason: The sun has risen in the east every morning up until now.
Conclusion: The sun will also rise in the east tomorrow.
Inductive reasoning involves reaching conclusions about unobserved things on the basis of what has already been
observed. Induction is used regularly in fields such as archaeology, where inferences about the past from present
are made. Inductions could also be made across outer space, as in astronomy, where conclusions about the whole
universe are drawn from the limited number of observations we are able to make.
Vocabulary

deduction: Involves determining a single fact from a general statement.


induction: Involves determining a general statement that is very likely to be true, from several facts; the relief
of repression for a gene or set of genes under negative control.
Summary

Any useful hypothesis will allow predictions based on reasoning. Reasoning can be broken down into two
categories: deduction and induction. Most reasoning in science is formed through induction.
Explore More

Use this resource to answer the questions that follow.


INDUCTIVE AND DEDUCTIVE REASONING at http://www.youtube.com/watch?v=J0OVCgruWDo
(3:47).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/69287

1. What is the difference between inductive and deductive reasoning?


2. What is confirmation bias?
3. Why did investors expect Shrek 3 to be a box office hit?
Review

1. What is meant by scientific reasoning?


2. Outline the difference between inductive and deductive reasoning.

19

1.5. Experiments - Advanced

www.ck12.org

1.5 Experiments - Advanced

Describe what defines a scientific experiment.


Examine the function of the control, dependent and independent variables in an experiment.
Explain Occams razor.
Describe experiments without controls.
Compare natural to field experiments.
Discuss the importance of a scientist communicating results.

So what exactly is an experiment?


Observing lions in their natural habitat. Analyzing DNA for mutations to a particular disease, such as Tay-Sachs
disease or cystic fibrosis. Studying the species of the Galpagos Islands. Are these all experiments? Do all
experiments have to be done in a laboratory? The answers to these questions are yes and no. No, experiments
do not have to be done in a laboratory, but yes, observing lions in their natural habitat, analyzing DNA for mutations,
and studying the species of the Galpagos Islands can all be considered experiments. A common characteristic of
experiments involves trying to answer specific questions posed based on a hypothesis.
Experiments

An experiment is a test that is used to eliminate one or more of the possible hypotheses until one hypothesis
remains. A scientific experiment must have all of the following features:
a control, so variables that could affect the outcome are reduced,
20

www.ck12.org

Chapter 1. The Study of Life - Advanced

the variable being tested reflects the phenomenon being studied,


the variable being tested can be measured accurately, to avoid experimental error,
the experiment must be reproducible.
The experiment is a cornerstone in the scientific approach to gaining deeper knowledge about the natural world.
Scientists use the principles of their hypothesis to make predictions, and then test them to see if their predictions are
to be confirmed or rejected.

FIGURE 1.9
A laboratory experiment studying plant
growth. What might this experiment involve?

Scientific experiments involve controls, or subjects that are not tested during the investigation. In this way, a
scientist limits the factors, or variables that can cause the results of an investigation to differ. A variable is a factor
that can change over the course of an experiment. Independent variables are factors whose values are controlled
by the experimenter to determine their relationship with an observed phenomenon. Dependent variables are the
observed phenomenon, and change in response to the independent variable. Controlled variables are also important
to identify in experiments. They are the variables that are kept constant to prevent them from influencing the effect
of the independent variable on the dependent variable.
For example, if you were to measure the effect that different amounts of fertilizer has on plant growth, the independent variable would be the amount of fertilizer used (the changing factor of the experiment). The dependent
variables would be the growth in height and/or mass of the plant (the factors that are influenced in the experiment).
The controlled variables include the type of plant, the type of fertilizer, the amount of sunlight the plant gets, the size
of the pots you use. The controlled variables are controlled by you, otherwise they would influence the dependent
variable.
In summary:
The independent variable answers the question, "What do I change?"
The dependent variables answer the question, "What do I observe?"
The controlled variables answer the question, "What do I keep the same?"
Experimental Design
Controlled Experiments

In an old joke, a person claims that they are snapping their fingers "to keep tigers away," and justifies their behavior
by saying, "See, it works!" While this experiment does not falsify the hypothesis that "snapping your fingers keeps
21

1.5. Experiments - Advanced

www.ck12.org

tigers away," it does not support the hypothesis either because not snapping your fingers will also keep tigers away.
It also follows that not snapping your fingers will not cause tigers to suddenly appear ( Figure 1.10).

FIGURE 1.10
Are tigers really scared of snapping fingers, or is it more likely they are just
not found in your neighborhood? Considering which of the hypotheses is more
likely to be true can help you arrive at a
valid answer. This principle, called Oc-

cams razor states that the explanation


for a phenomenon should make as few
assumptions as possible. In this case,
the hypothesis there are no tigers in my
neighborhood to begin with is more likely,
because it makes the least number of
assumptions about the situation.

To demonstrate a cause and effect hypothesis, an experiment must often show that, for example, a phenomenon
occurs after a certain treatment is given to a subject, and that the phenomenon does not occur in the absence of the
treatment.
One way to test a cause and effect hypothesis is to perform a controlled experiment. In a controlled experiment,
two identical experiments are carried out side-by-side. In one of the experiments, the independent variable being
tested is used, and in the other experiment, the control, the independent variable is not used.
A controlled experiment generally compares the results obtained from an experimental sample against a control
sample. The control sample is almost identical to the experimental sample except for the one variable whose effect
is being tested. A good example would be a drug trial. The sample or group receiving the drug would be the
experimental group, and the group receiving the placebo would be the control. A placebo is a form of medicine that
does not contain the drug that is being tested.
Controlled experiments can still be conducted when it is difficult to exert complete control over all the conditions
in an experiment. In this case, the experiment begins by creating two or more sample groups that are similar in as
many ways as possible, which means that both groups should respond in the same way if given the same treatment.
Once the groups have been formed, the experimenter tries to treat them identically except for the one variable that
he or she wants to study (the independent variable). Usually, neither the patients nor the doctor knows which group
receives the real drug. This type of experiment is called a double blind experiment, which serves to isolate the
effects of the drug and allow the researchers to be sure the drug does work, and that the effects seen in the patients
are not due to the patients believing they are getting better.
Controlled experiments can be carried out on many subjects other than people; some are even carried out in
space. The wheat plants in Figure 1.11 are being grown in the International Space Station to study the effects
of microgravity on plant growth. Researchers hope to one day be able to grow enough plants during spaceflight
to feed hungry astronauts and cosmonauts. The investigation also measured the amount of oxygen the plants can
produce in the hope that plants could become a cheap and effective way to provide oxygen during space travel.
22

www.ck12.org

Chapter 1. The Study of Life - Advanced

FIGURE 1.11
Spaceflight participant Anousheh Ansari
holds a miniature wheat plant grown in
the Zvezda Service Module of the International Space Station.

Experiments Without Controls

The term experiment usually refers to a controlled experiment, but sometimes, it is difficult or impossible to
completely control experiments. In this case, researchers carry out natural experiments. When scientists conduct
a study in nature instead of the more controlled environment of a lab setting, they cannot control variables such
as sunlight, temperature, or moisture. Natural experiments therefore depend on the scientists observations of the
system under study, rather than the observations of just one or a few variables as in controlled experiments.
In natural experiments, researchers attempt to collect data as consistently as possible. They attempt to ensure that
the effects of the variation remains fairly constant so that the effects of other factors can be determined. Natural
experiments are a common research tool in areas of study where controlled experiments are difficult to carry out.
Examples include:
astronomy - the study of stars, planets, comets, galaxies and phenomena that originate outside Earths atmosphere,
paleontology - the study of prehistoric life forms through the examination of fossils, and
meteorology - the study of Earths atmosphere.
In astronomy it is impossible, when testing the hypothesis "suns are collapsed clouds of hydrogen", to start out with
a giant cloud of hydrogen, and then carry out the experiment of waiting a few billion years for it to form a sun.
However, by observing various clouds of hydrogen in various states of collapse and other phenomena related to the
hypothesis such as the nebula shown in Figure 1.12, researchers can collect the data they need to support (or maybe
falsify) the hypothesis.
An early example of this type of experiment was the first verification in the 1600s that light does not travel from
place to place instantaneously, but instead has a speed that can be measured. Observation of the appearance of the
moons of Jupiter were slightly delayed when Jupiter was farther from Earth, as opposed to when Jupiter was closer
to Earth. This phenomenon was used to demonstrate that the difference in the time of appearance of the moons was
consistent with a measurable speed of light.
Natural Experiments

There are situations where it would be wrong or harmful to carry out an experiment. In these cases, scientists carry
out a natural experiment, or an investigation without an experiment. For example, alcohol can cause developmental
23

1.5. Experiments - Advanced

www.ck12.org

FIGURE 1.12
The Helix nebula, located about 700 lightyears away in the constellation Aquarius,
belongs to a class of objects called plan-

etary nebulae. Planetary nebulae are the


remains of stars that once looked a lot like
our sun. When sun-like stars die, they
puff out their outer gaseous layers. These
layers are heated by the hot core of the
dead star, called a white dwarf, and shine
with infrared and visible colors. Scientists
can study the birth and death of stars
by analyzing the types of light that are
emitted from nebulae.

defects in fetuses, leading to mental and physical problems, through a condition called fetal alcohol syndrome.
Certain researchers want to study the effects of alcohol on fetal development, but it would be considered wrong or
unethical to ask a group of pregnant women to drink alcohol to study its effects on their children. Instead, researchers
carry out a natural experiment in which they study data that is gathered from mothers of children with fetal alcohol
syndrome, or pregnant women who continue to drink alcohol during pregnancy. The researchers will try to reduce
the number of variables in the study (such as the amount or type of alcohol consumed), which might affect their data.
It is important to note that the researchers do not influence or encourage the consumption of alcohol; they collect
this information from volunteers.

Field Experiments

Field experiments are so named to distinguish them from lab experiments. Field experiments have the advantage
that observations are made in a natural setting rather than in a human-made laboratory environment. However, like
natural experiments, field experiments can become contaminated, and conditions like the weather are not easy to
control. Experimental conditions can be controlled with more precision and certainty in the lab.
An introduction to the Prince William Sound Field Experiment can be seen at http://www.youtube.com/watch?v=O
pQngP9HmKo (4:49).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/151

24

www.ck12.org

Chapter 1. The Study of Life - Advanced

Predictions

A prediction is a statement that tells what will happen under specific conditions. It can be expressed in the form: If
A is true, then B will also be true. Predictions are based on confirmed hypotheses shown to be true or not proved to
be false.
For researchers to be confident that their predictions will be useful and descriptive, their data must have as few
errors as possible. Accuracy is the measure of how close a calculated or measured quantity is to its actual value.
Accuracy is closely related to precision, also called reproducibility or repeatability, which is the degree to which
repeated measurements under unchanged conditions show the same results. The reproducibility and repeatability of
experiments are cornerstones of scientific methods. If no other researcher can reproduce or repeat the results of a
certain study, then the results of the study will not be accepted as valid. Results are considered valid only if they are
both accurate and precise.
A useful tool to help explain the difference between accuracy and precision is a target, shown in Figure 1.13. In this
analogy, repeated measurements are the arrows that are fired at a target. Accuracy describes the closeness of arrows
to the bulls eye at the center. Arrows that hit closer to the bulls eye are more accurate. Arrows that are grouped
together more tightly are more precise.
FIGURE 1.13
A visual analogy of accuracy and precision. Left target: High accuracy but low
precision; Right target: low accuracy but
high precision. The results of calculations
or a measurement can be accurate but
not precise; precise but not accurate; neither accurate nor precise; or accurate and
precise. A collection of bulls eyes right
around the center of the target would be
both accurate and precise.

Experimental Error

An error is a boundary on the precision and accuracy of the result of a measurement. Some errors are caused by
unpredictable changes in the measuring devices (such as balances, rulers, or calipers), but other errors can be caused
by reading a measuring device incorrectly or by using broken or malfunctioning equipment. Such errors can have
an impact on the reliability of the experiments results; they affect the accuracy of measurements. For example, you
use a balance to obtain the mass of a 100 gram block. Three measurements that you get are: 93.1 g, 92.0 g, and 91.8
g. The measurements are precise, as they are close together, but they are not accurate.
If the cause of the error can be identified, then it can usually be eliminated or minimized. Reducing the number
of possible errors by careful measurement and using a large enough sample size to reduce the effect of errors will
improve the reliability of your results.
Drawing Conclusions

After experiments have been performed, the results must be analyzed. The data should either agree or disagree with
your hypothesis. Evidence that agrees with your prediction supports your hypothesis. If the hypothesis is supported,
25

1.5. Experiments - Advanced

www.ck12.org

the process moves forward and the scientist begins to think about the next steps. If the data does not support the
hypothesis, the hypothesis may need to be altered.
Does evidence that supports the hypothesis prove that your hypothesis is true? No, not necessarily. A hypothesis
cannot be proven conclusively to be true. This is because you can never examine all of the possible evidence, and
someday evidence might be found that disproves the hypothesis. Nonetheless, the more evidence that supports a
hypothesis, the more likely the hypothesis is to be true.

Communicating Results

The last step in a scientific investigation is communicating what you have learned with others. This is a very
important step because it allows others to test your hypothesis. If other researchers get the same results as yours,
they add support to the hypothesis. However, if they get different results, they may disprove the hypothesis.
When scientists share their results, they should describe their methods and point out any possible problems with
the investigation. Results can be communicated in various ways. A scientist usually contributes material through
publication in a peer-reviewed scientific journal. Peer-review ensures the material is of an acceptable quality for the
scientific community. Scientists also write review articles, book chapters, and even whole books. They also regularly
participate in scientific meetings, presenting their material in front of large audiences of their peers.

Vocabulary

accuracy: The measure of how close a calculated or measured quantity is to its actual value.
control: Something that is not tested during the investigation.
controlled experiment: Two identical experiments are carried out side-by-side; in one of the experiments the
independent variable being tested is used, in the other experiment, the control, or the independent variable is
not used.
controlled variables: Variables that are kept constant to prevent influencing the effect of the independent
variable on the dependent variable.
dependent variable: Variable that changes in response to the independent variable.
double blind experiment: Experiment in which neither the researcher nor the subjects know who receives
the independent variable; common in drug trials.
error: A boundary on the precision and accuracy of the result of a measurement.
experiment: A test that is used to rule out a hypothesis or validate something already known; a test that is
used to eliminate one or more of the possible hypotheses until one hypothesis remains.
hypothesis (plural, hypotheses): A suggested explanation based on evidence that can be tested by observation
or experimentation.
independent variable: Factor(s) whose values are controlled by the experimenter to determine its relationship
to an observed phenomenon (the dependent variable).
Occams razor: States that the explanation for a phenomenon should make as few assumptions as possible.
precision: The degree to which repeated measurements under unchanged conditions show the same results;
reproducibility or repeatability.
prediction: A statement that tells what will happen under specific conditions.
variable: A factor that can change over the course of an experiment.

Summary

A variable is a factor that can change over the course of an experiment. Independent variables are factors
whose values are controlled by the experimenter to determine its relationship to an observed phenomenon (the
dependent variable). Dependent variables change in response to the independent variable.
26

www.ck12.org

Chapter 1. The Study of Life - Advanced

Explore More

Use this resource to answer the questions that follows.


Science Experiment at http://www.youtube.com/watch?v=OgS46ksAawk (5:30).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/69291

1.
2.
3.
4.

What is the hypothesis of this experiment?


Why does the experiment need a control?
What were the results of the experiment?
What is the next step of the experiment?

Review

1.
2.
3.
4.
5.

What is an experiment? Give an example.


Why are controls important?
In taking measurements, what is the difference between accuracy and precision?
Why is it a good idea to try to reduce the chances of errors happening in an experiment?
To ensure that their results are not due to chance, scientists will usually carry out an experiment a number of
times, a process called replication. Devise a practical experimental approach, incorporating replication of the
experiment.

27

1.6. Scientific Theories - Advanced

www.ck12.org

1.6 Scientific Theories - Advanced

Define what is meant by a scientific theory and compare this to the meaning of a hypothesis.
Give examples of scientific theories.
Explain and describe a superseded theory.
Compare scientific theories to scientific laws.

Theory vs. theory. Is a scientific theory different from the everyday use of the word theory?
The Big Bang Theory. The Theory of Gravity. The Plate Tectonic Theory. The Modern Atomic Theory. The Cell
Theory. The Theory of Evolution by Natural Selection. These are all classic scientific theories. So, without a doubt,
yes, a scientific theory is very different from the everyday use of the word theory. A scientific theory is accepted
as a scientific truth, supported by evidence collected by many scientists. Lots of data has been collected to support
theories, and no data has been identified to prove theories incorrect. That does not necessarily mean that evidence
does not exist against a theory does not exist, it simply means that evidence has yet to be identified.
Scientific Theories

Scientific theories are hypotheses which have stood up to repeated attempts at falsification and are thus supported
by a great deal of data and evidence. Some well known biological theories include the theory of evolution by natural
selection, the cell theory (the idea that all organisms are made of cells), and the germ theory of disease (the idea that
certain microbes cause certain diseases). The scientific community holds that a greater amount of evidence supports
these ideas than contradicts them, and so they are referred to as theories. In fact, no evidence has been identified to
disprove these or other scientific theories.
In every day use, people often use the word theory to describe a guess or an opinion. For example, I have a theory
as to why the light bulb is not working. When used in this common way, theory does not have to be based on
facts. It does not have to be based on a true description of reality. This usage of the word theory often leads to a
misconception that can be best summed up by the phrase, "Its not a fact, its only a theory." In such everyday usage,
the word is most similar to the term hypothesis.
28

www.ck12.org

Chapter 1. The Study of Life - Advanced

Scientific theories are the equivalent of what in everyday speech we would refer to as facts. In principle, scientific
theories are always subject to corrections or inclusion in another, wider theory. As a general rule for use of the
term, theories tend to deal with broader sets of phenomena than do hypotheses, which usually deal with much more
specific sets of phenomena or specific applications of a theory.
A video discussing the difference between a hypothesis and a theory can be viewed at http://www.youtube.com/w
atch?v=jdWMcMW54fA (6:39).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/152

Constructing Theories

In time, a confirmed hypothesis may become part of a theory or may grow to become a theory itself. Scientific
hypotheses may be mathematical models. Sometimes they can be statements, stating that some particular instance
of the phenomenon under examination has some characteristic and causal explanations. These theories have the
general form of universal statements, stating that every instance of the phenomenon has a particular characteristic.
A hypothesis may predict the outcome of an experiment in a laboratory or the observation of a natural phenomenon.
A hypothesis should also be falsifiable, and one cannot regard a hypothesis or a theory as scientific if it does not
lend itself to being falsified, even in the future. To meet the falsifiable requirement, it must at least in principle be
possible to make an observation that would disprove the hypothesis. A falsifiable hypothesis can greatly simplify the
process of testing to determine whether the hypothesis can be proven to be false. Scientific methods rely heavily on
the falsifiability of hypotheses by experimentation and observation in order to answer questions. Philosopher Karl
Popper suggested that all scientific theories should be falsifiable, or otherwise they could not be tested by experiment.
A scientific theory must meet the following requirements:
it must be consistent with a pre-existing theory. The pre-existing theory must have been experimentally
verified, though it may often show a pre-existing theory to be wrong in an exact sense,
it must be supported by many strands of evidence rather than a single foundation, ensuring that it is a good
approximation or even completely correct.
Also, a theory is generally only taken seriously if it:
allows for changes to be made as new data is discovered, rather than claiming absolute certainty,
is the most straight forward explanation, and makes the fewest assumptions about a phenomenon (commonly
called passing the Occams razor test).
This is true of such established theories as those of special relativity, general relativity, quantum mechanics, plate
tectonics, and evolution. Theories considered scientific ideally meet all of these extra criteria as well.
In summary, to meet the status of a scientific theory, the theory must be falsifiable or testable. Examples of scientific
theories in different areas of science include:

Astronomy: Big Bang Theory


Biology: Cell Theory; Theory of Evolution; Germ Theory of Disease
Chemistry: Atomic Theory; Kinetic Theory of Gases
Physics: General Relativity; Special Relativity; Theory of Relativity; Quantum Field Theory
Earth Science: Giant Impact Theory; Plate Tectonics
29

1.6. Scientific Theories - Advanced

www.ck12.org

Unverifiable Theories

The term theory is sometimes stretched to refer to theoretical speculation which is currently unverifiable. A couple
examples of such uses include string theory and the theory of everything. String theory is a model of physics,
which predicts the existence of many more dimensions in the universe than the four dimensions that current science
understands (length, width, height, and space-time). The theory of everything is a hypothetical theory in physics that
fully explains and links together all known physical phenomena.
For a scientific theory to be valid, it must be verified experimentally. Many parts of the string theory are currently
untestable due to the large amount of energy that would be needed to carry out the necessary experiments as well as
the high cost of conducting these experiments. Therefore string theory may not be tested in the foreseeable future.
Some scientists have even questioned whether it deserves to be called a scientific theory because it is not falsifiable.
Superseded Theories

A superseded theory, or obsolete scientific theory is a theory that was once commonly accepted, but for a given
reason is no longer considered the most complete description of reality by mainstream science. It can also refer to a
falsifiable theory which has been shown to be false. Giraffes, shown in Figure 1.14, are often used in the explanation
of Lamarcks superseded theory of evolution. In Lamarckism, a giraffe lengthens its neck over the course of its life
in order to, for example, reach higher leaves. That giraffe will then have offspring with longer necks. The theory
has been superseded by the understanding of natural selection on populations of organisms as the main means of
evolution (Darwins theory of evolution by natural selection), not physical changes to a single organism over its
lifetime.

FIGURE 1.14
Superseded theories like Lamarcks theory of evolution are theories that are now
considered obsolete and have been replaced by newer theories that have more
evidence to support them. In Lamarcks
case, his theory was replaced by Darwins
theory of evolution and natural selection,
which will be further discussed in additional concepts.

Scientific Laws

Scientific laws are similar to scientific theories, in that they are principles which can be used to predict the behavior
of the natural world. Both scientific laws and scientific theories are typically well-supported by observations and/or
experimental evidence. Usually scientific laws provide rules for how nature will behave under certain conditions.
Scientific theories are more overarching explanations of how nature works and why it exhibits certain characteristics.
A physical law or law of nature is a scientific generalization based on a sufficiently large number of empirical
observations, so that it is accepted as fully verified.
30

www.ck12.org

Chapter 1. The Study of Life - Advanced

Isaac Newtons law of gravitation is a famous example of an established law that was later found not to be universalit does not hold in experiments involving motion at speeds close to the speed of light or in close proximity of
strong gravitational fields. However, outside these conditions, Newtons laws remain an excellent model of motion
and gravity.
Scientists never claim absolute knowledge of nature or the behavior of the subject of the field of study. A scientific
theory is always open to falsification, if new evidence is presented. Even the most basic and fundamental theories
may turn out to be imperfect if new observations are inconsistent with them. It is critical to make every relevant part
of research publicly available. This allows for and encourages peer review of published results, and it also allows
ongoing reviews, repetition of experiments and observations by many different researchers. Only by meeting these
expectations can it be determined how reliable the experimental results are for possible use by others.
Vocabulary

law of nature: A scientific generalization based on a sufficiently large number of empirical observations so
that it is taken as fully verified; physical law.
physical law: A scientific generalization based on a sufficiently large number of empirical observations so
that it is taken as fully verified; law of nature.
scientific law: A principle which can be used to predict the behavior of the natural world.
scientific theory: A hypothesis which has stood up to repeated attempts at falsification; supported by a great
deal of data and evidence.
superseded theory: A theory that was once commonly accepted, but is no longer considered the most
complete description of reality by mainstream science.
Summary

Scientific theories are hypotheses which have stood up to repeated attempts at falsification and are thus
supported by much data and evidence.
Scientific laws are similar to scientific theories in that they are principles which can be used to predict the
behavior of the natural world.
A scientific theory must be supported by many strands of evidence rather than a single foundation, ensuring
that it is probably a good approximation, if not totally correct.
A superseded scientific theory is a theory that was once commonly accepted, but is no longer considered the
most complete description of reality by mainstream science.
Explore More

Use this resource to answer the questions that follow.


Concepts and Methods in Biology Non-Majors Biology Theories and Laws at : http://www.hippocamp
us.org/Biology .
1. Describe scientific theories and laws. Give examples.
2. What is meant by the following statement: Theories can never be proven absolutely. . .
Review

1. Identify two features that a theory must have, to qualify as a scientific theory.
2. Give an example of a superseded theory.
3. What is meant by the following statement: A hypothesis should be falsifiable.
31

1.6. Scientific Theories - Advanced


4. Distinguish between a scientific theory and a scientific law.
5. Give examples of scientific theory from a variety of scientific fields.

32

www.ck12.org

www.ck12.org

Chapter 1. The Study of Life - Advanced

1.7 Scientific Models - Advanced


Outline the importance of scientific models.
Describe factors important in evaluating models.
List common model organisms.

What is a scientific model?


Looks like a human head, but it is obviously missing certain parts. Of course, this would be a model, and it could
be considered a scientific model as it represents the anatomy of the head and skull. It can be used to teach about this
anatomy.
Scientific Models

To describe particular parts of a phenomenon, or the interactions among a set of phenomena, it is sometimes helpful
to develop a model of the phenomenon. Scientific models are representations of reality. They can be a physical,
mathematical, or logical representations of a system, phenomenon, or process, and they allow scientists to investigate
a phenomenon in a controlled way. For instance, a scale model of a house or of a solar system is clearly not an actual
house or an actual solar system. The parts of an actual house or an actual solar system represented by a scale model
are, only in limited ways, representative of the actual objects ( Figure 1.15).
Scientific modeling is the process of making abstract models of natural phenomena. An abstract model is a theoretical construct that represents something. Models are developed to allow reasoning within a simplified framework
that is similar to the phenomena being investigated. The simplified model may assume certain things that are known
to be incomplete in some details. Such assumptions can be useful in that they simplify the model, while at the same
time, allowing the development of acceptably accurate solutions. These models play an important role in developing
scientific theories.
A simulation is a model that runs over time. A simulation brings a model to life and shows how a particular object
or phenomenon will behave. It is useful for testing, analysis or training where real-world systems or concepts can
33

1.7. Scientific Models - Advanced

www.ck12.org

FIGURE 1.15
A model of planets of the solar system.

This model is clearly not a real

solar system; it is a representation of


the planets Mercury, Venus, Earth, Mars,
Jupiter, Saturn, and Uranus. Scientists
use representations of natural things to
learn more about them. Also, the visitors
to the Griffith Observatory in Los Angeles,
California can get a better idea of the
relative sizes of the planets by observing
this model.

be represented by a model. For the scientist, a model also provides a way for calculations to be expanded to explore
what might happen in different situations. This method often takes the form of models that can be programmed into
computers. The scientist controls the basic assumptions about the variables in the model, and the computer runs the
simulation, eventually coming to a complex answer.
Examples of models include:

Computer models
Weather forecast models
Molecular models
Climate models
Ecosystem models
Geologic models

One of the main aims of scientific modeling is to allow researchers to quantify their observations about the world.
In this way, researchers hope to see new things that may have escaped the notice of other researchers. There are
many techniques that model builders use which allow us to discover things about a phenomenon that may not be
obvious to everyone. The National Weather Service Enhanced Radar Images web site (http://radar.weather.gov/ ) is
an excellent example of a simulation. The site exhibits current weather forecasts across the United States.
Evaluating Models

A person who develops a model must be able to recognize whether a model reflects reality. They must also be able
to identify and work with differences between actual data and theory.
A model is evaluated mostly by how it reflects past observations of the phenomenon. Any model that is not consistent
with reproducible observations must be modified or rejected. However, a fit to observed data alone is not enough for
a model to be accepted as valid. Other factors important in evaluating a model include:

34

its ability to explain past observations,


its ability to predict future observations,
its ability to control events,
the cost of its use, especially when used with other models,
ease of use and how it looks.

www.ck12.org

Chapter 1. The Study of Life - Advanced

FIGURE 1.16
These two food chains represent the flow
of energy in complex systems in nature.
These conceptual models make the systems easier to understand.

Models of

very complex systems are often based


on mathematical equations or computer
simulations.

Some examples of the different types of models that are used by science are shown in Figures 1.17 and 1.18.
Theories as Models

Scientific theories are constructed in order to explain, predict, and understand phenomena. This could include
explanations for the movement of planets, weather patterns, or the behavior of animals. In many instances we are
constructing models of reality. A theory makes generalizations about observations and is made up of a related set of
ideas and models. The important difference between theories and models is that the first is explanatory as well as
descriptive, while the second is only descriptive and predictive in a much more limited sense.
Model Organisms

A model organism is a non-human species that is extensively studied to understand particular biological processes
and concepts. These organisms are chosen because it is believed that discoveries made in the model organism will
35

1.7. Scientific Models - Advanced

www.ck12.org

FIGURE 1.17
A computer model of wind patterns across
the continental United States for 21 June,
2013.

This model is used to forecast

wind speeds and directions. Data on wind


speed, direction, and related data are
entered into a computer which then produces this simulation. This visual model
is much easier for a person to understand
than a large table of numbers.

FIGURE 1.18
Biosphere 2 is an example of a very
large three-dimensional model which biologists built to attempt to recreate a selfsustaining biome. To learn more about
biomes and ecosystems, see Concept
Ecology (Advanced).

provide insight into the workings of other organisms, including humans. Model organisms range from single-celled
bacteria to complex multi-cellular organisms. Even some viruses are utilized as models, though technically a virus
is not considered an organism.
The Table 1.2 lists some common model organisms. All of these organisms listed have had their complete genomes
sequenced.

TABLE 1.2: Common Model Organisms


Prokaryote
Eukaryote, unicellular
36

Organism
Escherichia coli
Saccharomyces cerevisiae

Common Name
E. coli bacteria
Yeast

www.ck12.org

Chapter 1. The Study of Life - Advanced

TABLE 1.2: (continued)


Eukaryote, multicellular

Vertebrate

Organism
Neurospora crassa
Caenorhabditis elegans
Drosophila melanogaster
Arabidopsis thaliana
Danio rerio
Mus musculus
Xenopus laevis
Macaca mulatta

Common Name
bread mold
nematode
fruit fly
thale cress
zebrafish
house mouse
African clawed frog
rhesus monkey

Vocabulary

abstract model: A theoretical construct that represents something.


model organism: A non-human species that is extensively studied to understand particular biological phenomena.
scientific model: A physical, mathematical, or logical representation of a system, phenomenon, or process;
allow scientists to investigate a phenomenon in a controlled way.
scientific modeling: The process of making abstract models of natural phenomena.
simulation: A model that runs over time.
Summary

Scientific models are representations of reality. They can be a physical, mathematical, or logical representation
of a system, phenomenon, or process, and they allow scientists to investigate a phenomenon in a controlled
way.
A simulation is a model that runs over time.
Review

1.
2.
3.
4.
5.

What is a scientific model? Give two examples.


Discuss the importance of scientific models.
What is a model organism? Give three examples.
Why are simulations useful?
What are factors important to evaluating a model?

37

1.8. What is a Scientist? - Advanced

www.ck12.org

1.8 What is a Scientist? - Advanced

Identify the benefits of studying science.


Describe what it means to be a scientist.
List three factors that can influence scientific research.
Examine how ethics are applied to communicating ideas and research.

What is a scientist?
It could be said that a scientist is someone who uses a systematic approach to acquire new knowledge. A scientist
can also be defined as someone who uses the scientific method. A scientist may be an expert in one or more areas
of science, such as biology, or more specifically biochemistry, genetics or ecology. Regardless of the specialty
of the scientist, a common factor that unites all scientists is that they perform research to work towards a more
comprehensive understanding of nature.
What Is a Scientist?
Science and Society

Biology literally means "the study of life." It is also a science that is consistently used in our everyday lives. Biology
is a very broad field, covering topics from the intricate workings of chemical processes inside our cells, to the more
broad concepts of ecosystems and global climate change. Biologists study minute details of the human brain, the
make up of our genes, and even the functioning of our reproductive system. For example, biologists recently finished
decoding the human genome, the sequence of deoxyribonucleic acid (DNA) bases that may determine much of our
abilities and predispositions for certain illnesses and can also play a major role in many court cases. For example,
criminals have been caught, victims identified, and wrongly imprisoned people have been freed based on DNA
evidence.
38

www.ck12.org

Chapter 1. The Study of Life - Advanced

We are constantly being blitzed with headlines about possible health risks from certain foods as well as possible
benefits of eating other foods. Commercials try to sell us the latest miracle pill for easy, fast weight loss. Most
people may choose the conventional medications that can be bought at the pharmacy. However, many people are
turning to herbal remedies to ease arthritis pain, improve memory, as well as improve their mood. It is important to
know the effects that such supplements, such as the ones shown in Figure 1.19, and medications can have on the
body.

FIGURE 1.19
Nutritional supplements. Understanding
how your body works and how nutrients
work will help you decide whether you
need to take a nutritional supplement. It
will also help you make sense of the large
amount of information available about
regular medicines, if and when you need
to take them.

Can just one biology course give you the answers to these everyday questions? No, but it can assist you in learning
how to sift through the biases of investigators, the press, and others in a quest to critically evaluate the question. It is
doubtful you would remember all the details of metabolism, neither are they necessarily very pertinent. However, in
participating in a biology course, you will learn to become a critical thinker. Knowing about the process of science
will also allow you to make a more informed decision. Will you be a scientist? Yes, in a way. You may not be
formally trained as a scientist, but you will be able to think critically, solve problems, have some idea about what
science can and cannot do, and you will also have an understanding of the role of biology in your everyday life.

Biology and You

So why should you study biology? Because you are surrounded by it every day! It is about what happens in your
brain as you read the words on this page, and about how hippopotamuses know to come up to the surface to breathe
even while sleeping. Biology covers topics from the reason why a person with hook worms doesnt sneeze as
much, to why Velcro works. From understanding the benefits of the vitamin-enriched milk or juice that you have
at breakfast, to discerning commercials that promise a fuller head of hair, to snack foods that announce they are the
"healthier option for you," you cannot be fully informed about such claims unless you understand the science behind
them, or can think like a scientist to analyze them. For example, you would need to know the types of fats you need
to get from your food to know why eating salmon, or other foods such as flax seeds and kiwi fruit may be good for
your health.
You may also become a stronger advocate for your community. For example, if a tree planting initiative has begun in
your neighborhood, you can investigate the plan for your area and find out what you can do. You could then explain
what the program is about to your friends and family.
Or, perhaps a city park has fallen into disrepair, and city officials are looking for feedback from the public about
what to do with it. You could use scientific thinking to analyze the issue and options, and develop possible solutions.
39

1.8. What is a Scientist? - Advanced

www.ck12.org

FIGURE 1.20
Salmon has recently been touted as
super-brain food, but do you know why it
is so good for you? Educating yourself on
how science affects your life is important.
It will help you better analyze the validity
of such claims, help you take better care
of your health, and be a wiser healthcare
consumer.

What Is a Scientist?

What exactly makes a person a scientist and what is their role in society? First, we should start with what scientists
are not. They are not crazed geniuses with bad hair and a fondness for hysterical laughter, as the Figure 1.21 might
suggest. Although they may not be on the cutting edge of fashion, they are regular people. They went to school
like you, they studied math, reading, and science like you, and they probably exhibited at science fairs, just like the
students in the Figure 1.21.
FIGURE 1.21
Spot the Scientist.

(a) An example of

what scientists are not. (b) Real-life young


scientists at an exhibition where they are
presenting their research.

Being a scientist does not require you to learn everything in these over 500 concepts or any other science book
by heart, but understanding the important concepts does helps. Instead, being a scientist begins by thinking like a
scientist. Scientists are curious about how the world works; they have many questions and go about answering those
questions using the scientific methods.
If you are fascinated by how things work and why they work a certain way, you too could become a scientist!
Research scientists are the people that do the investigations and make the discoveries that you read or hear about.
To work as a research scientist, a person usually needs an advanced degree in science. An advanced degree is
obtained by attending graduate school after getting a Bachelor of Science, Engineering, or Arts degree. A Bachelor
degree normally takes four years to complete, a graduate Masters degrees usually take two years and a graduate
Doctorate degree takes four or more years to complete.
Scientific research offers much more to a person than just discovering new things. Researchers have the opportunity
to meet with other people (scientists and non-scientists) who care about the same subjects that the scientists research
40

www.ck12.org

Chapter 1. The Study of Life - Advanced

such as cancer research, marine ecology, or human nutrition. Many researchers also teach students who will become
the next generation of scientists. Scientists have many opportunities to work with different people, explore new
fields, and broaden their expertise.
Scientists are part of a community that is based on ideals of trust and freedom, and their work can have a direct
effect on society. As a result, the public usually has an interest in the results of research that will directly affect
them. Therefore it is important that you can understand the meaning of a story about science when you read it, see it,
or hear about it and become an engaged and active member of the public when making decisions involving science.
I Am A Scientist video and song can be viewed at http://www.youtube.com/watch?v=fpOYWdalzTU (3:14).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/153

Science As a Human Endeavor

Conducting science requires part human creativity and part scientific skepticism. Researchers make new observations and develop new ideas with the aim of describing the world more accurately or completely. These observations
and ideas are often based on existing theories and observations that were made by earlier scientists.
The history of molecular biology, for example, is the study of molecules that make up living things, and is a good
example of how scientific knowledge builds on earlier knowledge.
Researchers from chemistry and physics were involved in the early investigations to discover what was responsible
for heredity. Scientists in the late 19th and early 20th century knew that organisms inherited certain characteristics
such as hair color from their parents. What we now call "genes" were then called units of heredity. However
at the time, scientists did not know exactly how these heredity units were inherited or what they were made of.
Following the development of the Mendelian theory of heredity in the 1910s and the development of atomic theory
and quantum mechanics in the 1920s, such explanations began to seem within reach. Researchers from chemistry
and physics turned their attention to this biological question. Still, in the 1930s and 1940s it was not clear which, if
any, area of research would be most successful.
In 1940, geneticists George Beadle and Edward Tatum demonstrated a relationship between genes and proteins. In
1944, physician and researcher Oswald Avery further elaborated on that finding by demonstrating that genes are
made up of DNA. In 1952, geneticist Alfred Hershey and lab assistant Martha Chase confirmed that the genetic
material of a virus that infects bacteria is made up of DNA. And in 1953, biologist James Watson and biophysicist
Francis Crick, with the help of X-ray crystallographer Rosalind Franklin, worked out the three dimensional structure
of DNA and built a model of the double helix structure of the molecule.
There have been many additional discoveries about DNA and heredity since then, which will be discussed in
additional concepts.
Influences on Scientific Research

To nonscientists, the competition, frustration, cooperation, and disagreement between research scientists can seem
disorganized. Scientific knowledge develops from humans trying to figure things out. Scientific research and
discoveries are carried out by peoplepeople who have virtues, values, shortcomings, and limitationsjust like
everyone else. As a result, science and research can be influenced by the values of the society in which the research
is carried out. How do such values influence research?
41

1.8. What is a Scientist? - Advanced

www.ck12.org

This question is of interest to more than just the scientific community. Science is becoming a larger part of everyones
life, from developing more effective medicines, to developing more productive crops, and to designing innovative
air conditioning systems that are modeled after the self-cooling nests of termites. The public has become more
interested in learning more about the areas of science that affect everyday life. As a result, scientists have become
more accountable to a society that expects to benefit from their work.
It costs money to carry out scientific studies. Things such as the cost of equipment, transportation, rent, and salaries
for the people carrying out the research all need to be considered before a study can begin. The systems of financial
support for scientists and their work have been important influences of the type of research and the pace of how that
research is conducted. Today, funding for research comes from many different sources, some of which include:
government, for example, through the National Institutes of Health (NIH), Center for Disease Control and
Prevention (CDC), and the Food and Drug Administration (FDA),
military funding, such as through the Department of Defense,
corporate sponsorship,
non-profit organizations, such as the Muscular Dystrophy Association, the American Cancer Society and
American Heart Association,
private donors.
When the economy of a country slows down, the amount of money available for funding research is usually reduced,
because both governments and businesses try to save funds by reducing certain non-essential expenses.
Many pharmaceutical companies are heavily invested in research and development, on which they spend many
millions of dollars every year. The companies aim to research and develop drugs that can be marketed and sold to
treat certain illnesses, such as diabetes, cancer, or heart disease. Areas of research in which the companies do not
see any hope of a return on their huge investments are not likely to be studied.
For example, two researchers, Evangelos Michelakis and Steven Archer of the University of Alberta, Canada,
recently reported that a drug that has been used for in the treatment of rare metabolic disorders could be an effective
drug for the treatment of several forms of cancer. Dichloroacetic acid, (DCA), is a chemical compound that appears
to change the way cancer cells get energy, without affecting the function of normal cells. The researchers found that
DCA killed cancer cells that were grown in the lab and reduced the size of tumors in rats.
However, DCA is non-patentable as a compound. A patent is a set of rights granted to a person or company (the
patentee) for a certain period of time which allows the patentee the exclusive right to make, use, sell, or offer to sell
the patented item. Because DCA cannot currently be patented, concerns are raised that without the financial security
a patent would ensure, the financial incentive for the pharmaceutical industry to get involved in DCA-cancer research
would be reduced, and therefore clinical trials of DCA may not be funded.
But, other sources of funding exist previous studies of DCA have been funded by government organizations such as
the National Institutes of Health (NIH), the Food and Drug Administration (FDA), the Canadian Institutes of Health
Research and by private charities such as the Muscular Dystrophy Association. Recognizing the possible challenges
to funding, Dr. Michelakiss lab took the unusual step of directly asking for online donations to fund the research.
After six months, his lab had raised over $800,000, which was enough to fund a small clinical study. Dr. Michelakis
and Dr. Archer have since applied for a patent on the use of DCA in the treatment of cancer.
Funding for research can also be influenced by the public and by social issues. An intense amount of public interest
was raised by the DCA study. The story received much media attention in early 2007. As a result, the American
Cancer Society and other medical organizations received a large volume of public interest and questions regarding
DCA. A few months later, the Department of Medicine of Alberta University reported that after the trial funding was
secured, both the Alberta local ethics committee and Health Canada approved the first DCA Clinical Trial in Cancer.
Government funding of research can be indirectly influenced by the public. Funding priorities for specific research
can be influenced by the ethical beliefs or reservations of elected public officials, or influenced by the public during
constitutional amendment elections. Celebrities often campaign to bring public attention to issues that are important
to them.
42

www.ck12.org

Chapter 1. The Study of Life - Advanced

Science and Ethics

Ethics, also called moral philosophy, is the discipline concerned with what is morally good and bad, right and
wrong. The term is also applied to any system or theory of moral values or principles. Personal ethics is the moral
code that a person adheres to, while social ethics includes the moral theory that is applied to groups. Bioethics is the
social ethics of biology and medicine; it deals with the ethical implications of biological research and applications,
especially in medicine. Bioethicists are concerned with the ethical questions that arise in the relationships among
biology, biotechnology, medicine, politics, law, and philosophy.
While scientific research has produced social benefits, it has also posed some troubling ethical questions. For
example, when is it alright to test an experimental cancer drug on people? Developing a new drug takes a long time,
maybe as much as 10 years, or more. There are many rules and regulations that drug researchers need to follow
while developing drugs to treat specific illnesses.
Generally, drugs cannot be tested on people until researchers have evidence that the drug does what they claim it
does, but also that the drug will not make patients more ill or cause death. However, if the drug has tested successfully
in earlier experiments, and scientists are quite confident that the drug does what it is intended to do, is it ethical to
allow patients with a terminal disease, who have no other treatment options, to try the experimental drug?
With new challenges in public health and health policy arising quickly, and with advances in biotechnology being
made, bioethics is a fast-growing academic and professional area of inquiry. Some recent bioethical debates include:
Refusal of medical treatment: the choice of a patient to refuse certain life-saving medical procedures such as
a blood transfusion, or refusal by a parent or guardian for medical treatment for the patient.
Euthanasia: the choice by a terminally ill person to have medical assistance in dying.
Stem cell research: research involving stem cells, which can be harvested from human embryos.
Animal cloning: the ability and usefulness of scientists cloning animals for various needs, such as vaccine
development, tissues for transplant into humans such as heart valves, and increased food production. Dolly
the sheep, probably the most famous animal clone to date, is shown in Figure 1.22.

FIGURE 1.22
Dolly the sheep is seen here on display in the National museum of
Scotland. In 1997, Dolly was the first mammal to be cloned, and quickly
became world-famous. She was euthanized in 2003 after she developed
a common, but serious lung disease.

To grow her, researchers at

the Roslin Institute in Scotland, collected DNA from a mammary cell of


another sheep (technically her (older) twin sister), and then injected the
DNA into a stem cell which had its own DNA removed. That stem cell
then developed into an embryo.

Because research may have a great effect on the well-being of individual people and society in general, scientists
are required to behave ethically. Scientists who conduct themselves ethically treat people (called subjects) who are
involved in their research respectfully. Subjects are not allowed to be exploited deliberately, exposed to harm, or
forced to do something they do not agree to.
43

1.8. What is a Scientist? - Advanced

www.ck12.org

Vocabulary

bioethicists: Individuals concerned with the ethical questions that arise in the relationships among biology,
biotechnology, medicine, politics, law, and philosophy.
bioethics: The social ethics of biology and medicine; deals with the ethical implications of biological research
and applications, especially in medicine.
biologists: Scientists who study biology.
biology: The study of life.
ethics: The discipline concerned with what is morally good and bad, right and wrong.
molecular biology: The study of molecules that make up living organisms.
patent: A set of rights granted to a person or company (the patentee) for a certain period of time; allows the
patentee the exclusive right to make, use, sell, or offer to sell the patented item.
research scientist: People that do the scientific investigations and make scientific discoveries.
scientist: An individual who uses the scientific method; a person who engages in a systematic activity to
acquire knowledge.
Summary

Biology is the study of life.


Scientists are regular people who chose to study science. They are experts in done or more fields of science.
Science can be influenced by numerous agencies and organizations.
Ethics has a significant role in the science of today.

Explore More

Use this resource to answer the questions that follow.


Symphony of Science - the Quantum World! at http://www.youtube.com/watch?v=DZGINaRUEkU .

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/69289

1. What aspects of science do the actors and scientists in this video discuss?
2. According to this video, what is a main goal of science?
Review

1.
2.
3.
4.
5.

44

What is a scientist?
What would a molecular biologist study?
List three potential influences on science.
Where does most funding for research come from in the United States?
Discuss the role of ethics in science.

www.ck12.org

Chapter 1. The Study of Life - Advanced

1.9 Units of Measurement - Advanced


Identify the units of measurement that scientists use.
List common SI base units.
Name common SI prefixes.

How do you measure something really really small?


If we are talking about a cell, then not with a ruler. Units must exist that can describe sizes many times smaller than
the smallest marking on a ruler.
Units of Measurement

The measurements that scientists use are based on the International System of Units (SI), which is a form of the
metric system. The term SI is shortened from the French term Le Systme international dunits. It is the worlds
most widely used system of units, both in science and business. It is useful to scientists because it is based on
multiples of 10. The SI was developed in 1960 from an older metric system and is used in almost every country.
The SI is not static, as the technology of measurement progresses, units are created and definitions are changed
through international agreement among many nations. The international system of units is made up of a seven base
units, shown in the SI Base Units Table 1.3. From these seven base units several other units are derived.

TABLE 1.3: SI Base Units


Name
meter

Symbol
m

Quantity
length
45

1.9. Units of Measurement - Advanced

www.ck12.org

TABLE 1.3: (continued)


Name
kilogram
second
ampere
kelvin
mole
candela

Symbol
kg
s
A
K
mol
cd

Quantity
mass
time
electric current
thermal energy (temperature)
amount of substance
uminous intensity

A prefix may be added to SI units to make a multiple of the original unit. An SI prefix is a name or symbol that
is put before a unit of measure (or its symbol) to form a decimal or a multiple of the unit. For example, kilo- is a
multiple of a thousand and milli- is a multiple of a thousandth, so there are one thousand millimeters in a meter, and
one thousand meters in a kilometer. All prefixes are multiples of 10, as you can see from the SI Prefixes Table 1.4.
The prefixes are never combined; a millionth of a kilogram is a milligram not a microkilogram.

TABLE 1.4: SI Prefixes


Name
teragigamegakilohectodecadecicentimillimicronanopico-

Symbol
T
G
M
k
h
da
d
c
m

n
p

Factor of 10
1,000,000,000,000 (1012 )
1,000,000,000 (109 )
1,000,000 (106 )
1000 (103 )
100 (102 )
10 (101 )
1 (101 )
0.1 (102 )
0.01 (103 )
0.00001 (106 )
0.00000001 (109 )
0.00000000001 (1012 )

trillion (thousand billion)


billion (thousand million)
million
thousand
hundred
ten
tenth
hundredth
thousandth
millionth
billionth
trillionth

Vocabulary

International System of Units (SI): The modern form of the metric system; a system of units of measurement
devised around seven base units and the convenience of the number ten.
SI prefixes: A name or symbol that is put before a unit of measure (or its symbol) to form a decimal or a
multiple of the unit.

Summary

The measurements that scientists use are based on the International System of Units (SI), which is form of the
metric system. Based on multiples of ten, it is the worlds most widely used system of units, both in science
and business.

Explore More

Use this resource to answer the questions that follow.


46

www.ck12.org

Chapter 1. The Study of Life - Advanced

International System of Units at http://www.mashpedia.com/International_System_of_Units .


1. When was the SI system established?
2. What is the SI system based on?
Review

1. What is SI?
2. Why is it important that scientists use common units of measurement?
3. Which one of the following units of measurement would be the most appropriate in determining the mass of a
banana? Kilograms, micrograms, or grams.
4. What is the standard SI unit for measuring volume, weight, time, and length?
5. What is the shorthand unit for .000056 grams, 5600000000 seconds, .56 liter, and 560 meter.

47

1.10. Laboratories - Advanced

www.ck12.org

1.10 Laboratories - Advanced


Identify items that are common to science labs.
Contrast light microscopes and electron microscopes.
Outline what students and researchers can do to stay safe while working in the lab.

What is a laboratory?
When most people think of a scientific laboratory, they picture images similar to those shown here. And its true that
a laboratory must be a controlled environment, but what if certain studies cannot be done in a laboratory setting?
How do you observe penguins or elephants in their natural environments? What is the lab then?
The Laboratory

A laboratory is a place that has controlled conditions in which scientific research, experiments, and measurement
may be carried out. Scientific laboratories can be found in schools and universities, in industries, in government
facilities, and even aboard ships and spacecraft, such as the one shown in Figure 1.23.
Because of the different areas of science, there are many different types of science labs that each include different
scientific equipment. For example, a physics lab might contain a particle accelerator, in which the particles that
48

www.ck12.org

Chapter 1. The Study of Life - Advanced

FIGURE 1.23
Labs are not always Earth-bound, like
the biochemistry lab to the left is. This
astronaut is working in a lab on the International Space Station (right).

make up atoms are studied. A chemistry or biology lab most likely contains a fume hood where substances with
poisonous fumes can be worked. A particle accelerator and a fume hood are both shown in Figure 1.24. Despite the
great differences among labs, some features are common among them.
Most labs have workbenches or counter tops at which the scientist may sit or stand to do work comfortably. This
is important because scientists can spend all day working in the lab. A scientist usually records an experiments
progress in a lab notebook, but modern labs almost always contain a computer for data collection and analysis. In
many labs computers are also used for lab simulations (modeling or imitating an experiment or a natural process),
and for presenting results in the form of graphs or tables.
FIGURE 1.24
Different fields of science need different
types of equipment, such as the particle accelerator at left, found in a physics
lab, and the fume hood, at right, found
in chemistry labs, but also sometimes in
biology labs.

View http://www.nasa.gov/centers/dryden/aircraft/DC-8/index.html to read about a flying DC-8 laboratory.


Lab Equipment

Lab techniques include the procedures and equipment used in science to carry out an experiment. Lab techniques
follow scientific methods; some of them involve the use of simple laboratory equipment such as glassware (shown
on the shelves in Figure 1.23), and some use more complex and expensive equipment such as electrical and
computerized machines such as the particle accelerator shown in Figure 1.24.
Equipment commonly found in biology labs includes microscopes, weighing scales or balances, water baths, glassware (such as test tubes, flasks, and beakers), Bunsen burners, pipettes shown in Figure 1.25, chemical reagents,
and equipment such as centrifuges and PCR machines.
Light Microscopes

Microscopes are instruments used to view objects that are too small to be seen by the naked eye. Optical microscopes, such as the one shown in Figure 1.26, use visible light and lenses to magnify objects. They are the simplest
and most widely used type of microscopes. Compound microscopes are optical microscopes which have a series of
49

1.10. Laboratories - Advanced

www.ck12.org
FIGURE 1.25
Pipettes are small, but important tools in many biology labs. Micropipettes,
such as the ones shown here, are calibrated to measure very small
amounts of liquids. For example, 100 microliters (100 L) is about half
the volume of your little finger tip; or even 1 L, which is much smaller
than a drop of water.

lenses: the ocular lens (in the eyepiece) and the objective lenses (close to the sample). These microscopes have uses
in many fields of science particularly biology and geology. The scientist in Figure 1.27 is looking through a stereo
microscope (notice the two lenses). This type of microscope uses the two lenses to produce a three-dimensional
visualization of the sample being examined.

FIGURE 1.26
Compound light microscopes use lenses to focus light. Typical magnification of a light microscope is up to 1500x. The various parts of the
microscope are labeled. This specifically is a phase contrast microscope.
Phase contrast microscopy is particularly important in biology, as it reveals
many cellular structures that are not visible with a simpler bright field
microscope.

FIGURE 1.27
This scientist is using a stereo microscope, which is a light microscope
with two ocular lenses.

Resolution is a measure of the clarity of an image; it is the minimum distance two points can be separated and still be
distinguished as two separate points. Because light beams have a physical size, which is described in wavelengths,
it is difficult to see an object that is about the same size or smaller than the wavelength of light. Objects smaller than
50

www.ck12.org

Chapter 1. The Study of Life - Advanced

about 0.2 micrometers appear fuzzy, and objects below that size cannot be seen.
Magnification involves enlarging the image of an object so that it appears much bigger than its actual size. Magnification also refers to the number of times an object is magnified. For example, a lens that magnifies 100X, magnifies
an object 100 times larger than its actual size. Light microscopes have three objective lenses that have different
magnifications, as shown in Figure 1.28. The ocular lens has a magnification of 10X, so a 100X objective lens and
the ocular lens together will magnify an object by 1000X.

FIGURE 1.28
Objective lenses of a light microscope.

Visible light has wavelengths of 400 to 700 nanometers, which is larger than many objects of interest such as the
insides of cells. Scientists use different types of microscopes in order to get better resolution and magnification
of objects that are smaller than the wavelength of visible light. Objects that are to be viewed under an electron
microscope may need to be specially prepared to make them suitable for magnification.

Electron Microscopes

Electron microscopes use electrons instead of photons (light), because electrons have a much shorter wavelength
than photons and thus allow a researcher to see things at much higher magnification, far higher than an optical
microscope can possibly magnify.
There are two general types of electron microscopes: the Transmission Electron Microscope and the Scanning
Electron Microscope. The Transmission Electron Microscope shoots electrons through the sample and measures
how the electron beam changes because it is scattered in the sample. The Scanning Electron Microscope scans an
electron beam over the surface of an object and measures how many electrons are scattered back.
Transmission electron microscopy (TEM) is an imaging method in which a beam of electrons is passed through
a specimen. An image is formed on photographic film or a fluorescent screen by the electrons that scatter when
passing through the object. TEM images show the inside of the object.
The scanning electron microscope (SEM) is a type of electron microscope capable of producing high-resolution
images of a sample surface. Due to the manner in which the image is created, SEM images have a characteristic
three-dimensional appearance and are useful for judging the surface structure of the sample. Sometimes objects need
to be specially prepared to make them better suited for imaging under the scanning electron microscope, as shown
with the insect in Figure 1.29.
Electron microscopes are usually used in vacuum chambers under low pressures to avoid scattering the electrons in
the gas. This makes the microscopes considerably larger and more expensive than optical microscopes. The different
types of images from the two electron microscopes are shown in Figure 1.30. Zoom into a Leaf at http://www.daily
motion.com/video/x4mtsz_zoom-into-a-leaf_tech .

Aseptic Technique

In the microbiology lab, aseptic technique refers to the procedures that are carried out under sterile conditions.
Scientists who study microbes are called microbiologists. Microbiologists must carry out their lab work using the
51

1.10. Laboratories - Advanced

www.ck12.org

FIGURE 1.29
This fish has been coated in gold, as
part of the preparation for viewing with an
SEM.

FIGURE 1.30
SEM and TEM images of the algae
Chlamydomonas.

The SEM image,

shown at the right, is a three-dimensional


image of the surface of the organism, whereas the TEM image is a twodimensional image of the interior of the
organism.

aseptic technique to prevent microbial contamination of themselves, contamination of the environment they are
working in, including work surfaces or equipment, and contamination of the sample they are working on. Bacteria
live on just about every surface on Earth, so if a scientist wants to grow a particular type of bacterium in the lab, he
or she needs to be able to sterilize their equipment to prevent contamination by other bacteria or microorganisms.
The aseptic technique is also used in medicine, where it is important to keep the human body free of contamination.
Aseptic technique is used whenever bacteria or other microbes are transferred between nutrient media or in the
preparation of the nutrient media. Some equipment that is used in the aseptic technique includes Bunsen burners,
autoclaves ( Figure 1.31), hand and surface sanitizers, neoprene gloves, and fume hoods.
Students of microbiology are taught the principles of aseptic technique by hands-on laboratory practice. Practice is
essential in learning how to handle the lab tools without contaminating them.

Lab Safety

In some laboratories, conditions are no more dangerous than in any other room. In many labs, though, additional
hazards are present. Laboratory hazards are as varied as the subjects of study in laboratories, and might include
poisons, infectious agents, flammable, explosive, or radioactive materials, moving machinery, extreme temperatures,
52

www.ck12.org

Chapter 1. The Study of Life - Advanced

FIGURE 1.31
A worktop autoclave.

Autoclaves com-

monly use steam heated to 121C


(250F), at 103 kPa (15 psi) above atmospheric pressure. Solid surfaces are
effectively sterilized when heated to this
temperature. Liquids can also be sterilized by this process, though additional
time is required to reach sterilizing temperature.

or high voltage. The hazard symbols for corrosive, explosive, and flammable substances are shown in Figure 1.32.
In laboratories where conditions might be dangerous, safety precautions are important. Lab safety rules minimize a
persons risk of getting hurt, and safety equipment is used to protect the lab user from injury or to help in responding
to an emergency.

FIGURE 1.32
The hazard symbols for corrosive, explosive, and flammable substances.

Some safety equipment that you might find in a biology lab includes:
Sharps Container: A container that is filled with used medical needles and other sharp instruments such as
blades, shown in Figure 1.33. Needles or other sharp items that have been used are dropped into the container
without touching the outside of the container. Objects should never be pushed or forced into the container, as
damage to the container or injuries may result.
Laminar Flow Cabinet: A carefully enclosed bench designed to prevent contamination of biological samples.
Air is drawn through a fine filter and blown in a very smooth, laminar (streamlined) flow towards the user.
The cabinet is usually made of stainless steel with no gaps or joints where microorganisms might collect.
Gloves: Due to possible allergic reactions to latex, latex gloves are not recommended for lab use. Instead,
vinyl or nitrile gloves, shown in Figure 1.34, are often used. Gloves protect the wearers hands and skin from
getting contaminated by microorganisms or stained or irritated by chemicals.

Lab Coat: A knee-length overcoat is usually worn while working in the lab. The coat helps to protect the
researchers clothes from splashes or contamination. The garment is made from white cotton or linen to allow
it to be washed at high temperatures and to make it easy to see if it is clean.
53

1.10. Laboratories - Advanced

www.ck12.org

FIGURE 1.33
Immediate disposal of used needles, and
other sharp equipment into a sharps container is standard procedure.

FIGURE 1.34
A nitrile glove. Latex gloves are no longer recommended so vinyl gloves
or nitrile gloves, which are usually green or blue in color, are preferred.

Safe Laboratory Practice

Safety precautions are in place to help prevent accidents. Always wear personal protective equipment such as goggles
and gloves when recommended to do so by your teacher.
Tell your teacher immediately if an accident happens.
The production of aerosols due to poor technique such as squirting the last drop out of pipettes, and the spread
of contamination due to spills is completely avoidable and especially important if you are handling infectious
material or chemicals.
Wear enclosed toe shoes, instead of sandals or flip flops, or thongs ( Figure 1.35). Your feet and toes could
easily get hurt or broken or if you dropped something.
Do not wear loose, floppy clothes in the lab; they can get caught in or knock over equipment, causing an
accident.
If you have long hair, tie it up for the same reasons listed above.
54

www.ck12.org

Chapter 1. The Study of Life - Advanced

Do not eat or drink in the lab.


Do not use cell phones in the lab, even if you are only sending a text message. You can easily contaminate
your phone with whatever you have been working with. Consider where your hands have been, and where
your face will be the next time you talk on the phone.
Sweep up broken glass immediately and dispose in a designated area or container, or notify your teacher.
Always listen carefully to your teachers instructions.

FIGURE 1.35
Although they may be comfy and casual,
flip-flops and other open-toed shoes are
not suitable footwear in the lab.

Accidents

In the case of an accident, it is important to begin by telling your teacher and to know where to find safety equipment.
Some common safety equipment in a school lab:

Fire Extinguishers
Fire Blanket
Eye-Wash Fountain ( Figure 1.36)
First-Aid Kit
55

1.10. Laboratories - Advanced

www.ck12.org

FIGURE 1.36
Symbol for the eyewash fountain.

Through the first three lessons, we have discussed what science is and how science is done. Now we need to turn
our attention to Biology. Biology is the study of life. As the study of life, a knowledge of biology is an extremely
important aspect of your education. Biology includes the identification and analysis of characteristics common to all
living organisms. What is known about biology is discovered or identified through the same processes as all other
sciences, including the scientific method and peer review process.

Vocabulary

aseptic technique: Laboratory procedures that are carried out under sterile conditions.
compound microscope: An optical microscopes that has a series of lenses; has uses in many fields of science,
particularly biology and geology.
electron microscope: A microscope that uses electrons instead of light; allows a researcher to see things at
very high magnification, far higher than an optical microscope can possibly magnify.
lab techniques: The procedures used in science to carry out an experiment.
laboratory: A place with controlled conditions in which scientific research, experiments, and measurement
can be carried out.
magnification: Enlarging an image of an object so that it appears much bigger than its actual size; also refers
to the number of times an object is magnified.
microscope: An instrument used to view objects that are too small to be seen by the naked eye.
optical microscope: A microscope that uses visible light and lenses to magnify objects.
resolution: A measure of the clarity of an image; the minimum distance that two points can be separated and
still be distinguished as two separate points.
scanning electron microscope (SEM): Electron microscope that scans an electron beam over the surface of
an object; measures how many electrons are scattered back.
transmission electron microscope (TEM): Electron microscope that shoots electrons through the sample;
56

www.ck12.org

Chapter 1. The Study of Life - Advanced

measures how the electron beam changes because it is scattered in the sample.
Summary

Equipment commonly found in a biology labs include microscopes, weighing scales or balances, water baths,
glassware (such as test tubes, flasks, and beakers), Bunsen burners, tongs, pipettes, chemical reagents, lab
coats, goggles, and biohazard waste containers.
Always wear personal protective equipment such as goggles and gloves, wear enclosed shoes, and do not eat
or drink in the lab.
Explore More

Use this resource to answer the question that follows.


Science Lab Safety Rules at http://www.youtube.com/watch?v=yclOrqEv7kw (2:24).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/57466

1. List the laboratory rules described in this video.


Review

1.
2.
3.
4.
5.
6.

What is a laboratory? Where can they be found?


What is the main difference between a light microscope and an electron microscope.
What is an aseptic technique and what equipment does it require?
Name three pieces of safety equipment that you should wear while carrying out an investigation in the lab.
What should you first do if an accident happens in the lab?
If you saw this hazard sign on a chemical container, what do you think it might mean?

57

1.11. Characteristics of Life - Advanced

www.ck12.org

1.11 Characteristics of Life - Advanced

Identify the seven characteristics of living things.


Define cell.
Describe an adaptation.
Explain a complex chemistry.
Describe the importance of homeostasis.

What do a bacterium and a whale have in common?


Do they share characteristics with us? All living organisms, from the smallest bacterium to the largest whale, share
certain characteristics of life. For example, all living things are made of cells and they must reproduce to make the
next generation. Without these characteristics, there is no life.
Characteristics of Life

Biology examines the structure, function, growth, origin, evolution, and distribution of living things. It classifies
and describes organisms, their functions, how species come into existence, and the interactions they have with each
other and with the natural environment. Four unifying principles form the foundation of modern biology: cell theory,
evolution, genetics and homeostasis.
A powerful introductory video, Characteristics of Life, choreographed to dramatic music, highlighting the wonder
of life, and how it is defined can be seen at http://vimeo.com/15407847 (3:40).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/84744

Most biological sciences are specialized areas of study. Biology includes biochemistry, cell biology, microbiology,
immunology, genetics, physiology, zoology, ecology, evolutionary biology, and botany. Biochemistry is the study of
the chemicals that make up life. Cell biology is the study of life at the level of the cell. Microbiology is the study
of microscopic organisms. Immunology is the study of an organisms resistance to disease. Genetics is the study of
58

www.ck12.org

Chapter 1. The Study of Life - Advanced

how organisms pass traits to their offspring. The study of how the human body works is called physiology. Zoology
is the study of animals. The study of how organisms interact with their environment and each other is called ecology.
Evolutionary biology is the study of how populations and species change over time. Botany is the study of plants.
The four unifying principles are important foundations for each and every field of biology. Applied fields of biology
such as medicine and genetic research involve many specialized areas of study.

What is Life?

Not all scientists agree exactly about what makes up life. Many characteristics describe most living things. However,
with most of the characteristics listed below we can think of one or more examples that would seem to break the
rule, with something non-living being classified as living or something living being classified as non-living.
There is not just one distinguishing feature that separates a living thing from a non-living thing. A cat moves but so
does a car. A tree grows bigger, but so does a cloud. A cell has structure, but so does a crystal. Biologists define life
by listing characteristics that living things share. Something that has all of the characteristics of life is considered
to be alive. The duck decoy in Figure 1.37 may look like a duck, act like a duck in that it floats about, but it is not
alive. The decoy cannot reproduce, respond to its environment, or breathe.

FIGURE 1.37
Is it a duck? Both of these objects move
across the waters surface. But, how can
you tell which one is alive and which is
not? You can tell by seeing which of them
have all of the characteristics of life.

An individual living creature is called an organism. There are many characteristics that living organisms share.
They all:

respond to their environment


grow and change
reproduce and have offspring
have a complex chemistry
maintain homeostasis
are built of structures called cells
pass their traits onto their offspring

Responding to the Environment

All living organisms respond to their environment. If you step on a rock, it will just lie there, but if you step on a
turtle, it may move or even snap at you. Living things know what is going on around them, and respond to changes
in the environment. An adaptation refers to the process of becoming adjusted to an environment. Adaptations may
include structural, physiological, or behavioral traits that improve an organisms likelihood of survival, and thus,
reproduction.
59

1.11. Characteristics of Life - Advanced

www.ck12.org

Growth and Change

All living organisms have the ability to grow and change. A seed may look like a pebble, but under the right
conditions it will sprout and form a seedling that will grow into a larger plant. The pebble of course will not grow.
Even the smallest bacteria must grow. This bacteria will reproduce by dividing into two separate bacterium. If the
parent bacterium does not grow, then each subsequent generation will just be smaller then the previous generation.
Eventually the bacteria will be too small to function properly.
FIGURE 1.38
Tadpoles, like those shown here, go
through many changes to become adult
frogs.

Reproduction

All living organisms must have the ability to reproduce. Living things make more organisms like themselves.
Whether the organism is a rabbit, or a tree, or a bacterium, life will create more life. If a species cannot create
the next generation, the species will go extinct. Reproduction is the process of making the next generation and may
be a sexual or an asexual process. Sexual reproduction involves two parents and the fusion of gametes, haploid
sex cells from each parent. Sexual reproduction produces offspring that are genetically unique and increases genetic
variation within a species. Asexual reproduction involves only one parent. It occurs without a fusion of gametes
and produces offspring that are all genetically identical to the parent.
Have Complex Chemistry

All living organisms have a complex chemistry. A flower has a complicated and beautiful structure. So does a
crystal. But if you look closely at the crystal, you see no change. The flower, on the other hand, is transporting water
through its petals, producing pigment molecules, breaking down sugar for energy, and undergoing a large number of
other biochemical reactions that are needed for living organisms to stay alive. The sum of all the chemical reactions
in a cell is metabolism.
Maintain Homeostasis

A human body has a temperature of 37 degrees Celsius, (about 98.6 degrees Fahrenheit). If you step outside on a
cold morning, the temperature might be below freezing. Nevertheless, you do not become an ice cube. You shiver
and the movement in your arms and legs allows you to stay warm. Eating food also gives your body the energy
it needs to keep warm. Living organisms keep their internal environments within a certain range (they maintain a
stable internal condition), despite changes in their external environment. This process is called homeostasis, and is
an important characteristic of all living organisms.
Built of Cells

If you look closely at any organism you can see that it is made of structures called cells. Organisms that are very
different such as ferns, fish, and elephants all look similar at the cellular level. A cell is the basic unit of structure
60

www.ck12.org

Chapter 1. The Study of Life - Advanced

and function of all living organisms. All living organisms are made of one or more cells: a simple bacterium will
consist of just one cell, whereas you are made of trillions of cells.

FIGURE 1.39
Representations of human cells (left) and
onion cells (right). If you looked at human
and onion cells under a microscope, this
is what you might see.

Organisms are organized in the microscopic level from atoms up to cells. The matter is structured in an ordered way.
Atoms are arranged into molecules, then into macromolecules, which make up organelles, which work together to
form cells. Beyond this, cells are organized in higher levels to form entire multicellular organisms, as shown in
Figure 1.40. Cells together form tissues, which make up organs, which are part of organ systems, which work
together to form an entire organism. Of course, beyond this, organisms form populations which make up parts of an
ecosystem. All of Earths ecosystems together form the diverse environment that is Earth.

FIGURE 1.40
Levels of organization in a tree. (a) The tree is the organism; (b) a leaf is an organ, (c) a leaf tissue is made up
of different types of cells; (d) a plant cell; (e) chloroplast is an organelle inside a plant cell; (f) chlorophyll is the
photosynthetic molecule that is found in chloroplasts.

61

1.11. Characteristics of Life - Advanced

www.ck12.org

Vocabulary

adaptation: The process of becoming adjusted to an environment; a characteristic which helps an organism
survive in a specific habitat.
asexual reproduction: Reproduction involving only one parent; occurs without a fusion of gametes; produces
offspring that are all genetically identical to the parent.
cell: The basic unit of structure and function of all living organisms.
gamete: A sexually reproducing organisms reproductive cells, such as sperm and egg cells.
homeostasis: The process of maintaining a stable environment inside a cell or an entire organism.
metabolism: The sum of all the chemical reactions in a cell and/or organism.
organism: An individual living creature; a life form consisting of one or more cells.
reproduction: Process by which living organisms give rise to offspring; making the next generation.
sexual reproduction: Reproduction involving the joining of haploid gametes, producing genetically diverse
individuals.
Summary

The seven characteristics of life include: responsiveness to the environment; growth and change; ability to
reproduce; have a metabolism and breathe; maintain homeostasis; being made of cells; passing traits onto
offspring.
Explore More

Use this resource to answer the questions that follow.


http://www.hippocampus.org/Biology . Non-Majors Biology Search: Defining Biology
1.
2.
3.
4.

What does "biology" encompass?


What characteristics define life?
Define metabolism and homeostasis
Are viruses living? Explain your answer.

Review

1.
2.
3.
4.
5.

62

What are the four unifying principles that form the foundation of modern biology?
Identify three of the seven characteristics of living things.
What is adaptation?
Distinguish between metabolism and homeostasis.
What is a cell?

www.ck12.org

Chapter 1. The Study of Life - Advanced

1.12 Unifying Principles of Biology - Advanced

Identify and explain the four unifying principles of modern biology.


Briefly explain the cell theory and the gene theory.
Explain homeostasis.
Define evolution and natural selection.

What is a biological principle?


The word principle can be defined as "a fundamental truth or proposition that serves as the foundation for a system
of belief or behavior or for a chain of reasoning." A principle of biology is a fundamental concept that is just as true
for a bee or a sunflower as it is for us. All life, including that sunflower and bee, is made of at least one cell. The
traits of a particular organism are embedded within its genes, that organism must maintain homeostasis to survive,
and that organism has evolved from previously existing species.
Unifying Principles of Biology

There are four unifying principles of biology that are important to all life and form the foundation of modern biology.
These are:
1.
2.
3.
4.

the cell theory,


the gene theory,
homeostasis,
evolutionary theory.

The Cell Theory

The cell is the basic unit of structure and function of all organisms. The Cell Theory states that all living things
are made of one or more cells, or the secretions of those cells, such as the organisms shown in Figure 1.41. For
63

1.12. Unifying Principles of Biology - Advanced

www.ck12.org

example, shell and bone are built by cells from substances that they secrete into their surroundings. Cells come from
cells that already exist, that is, they do not suddenly appear from nowhere. In organisms that are made of many cells
(called multicellular organisms), every cell in the organisms body derives from the single cell that results from a
fertilized egg. You will learn more about cells and the Cell Theory in Cells: The Cell Theory (Advanced) concept.
FIGURE 1.41
Tiny diatoms and whale sharks are all
made of cells. Diatoms are about 20 m
in diameter and are made up of one cell,
whereas whale sharks can measure up to
12 meters in length, and are made up of
billions of cells.

Gene Theory

An organisms traits are encoded in their DNA, the large molecule, or macromolecule, that holds the instructions
needed to build cells and organisms. DNA makes up the genes of an organism. Traits are passed on from one
generation to the next by way of these genes. Information for how the organism appears and how its cells work
come from the organisms genes. Although the appearance and cell function of the organism may change due to
the organisms environment, the environment does not change its genes. The only way that genes can change in
response to a particular environment is through the process of evolution in populations of organisms. You will learn
more about DNA and genes in Concept Molecular Biology (Advanced).

Homeostasis

Homeostasis is the ability of an organism to control its body functions in order to uphold a stable internal environment even when its external environment changes. All living organisms perform homeostasis. For example, cells
maintain a stable internal acidity (pH); and warm-blooded animals maintain a constant body temperature. You will
learn more about homeostasis in the The Human Body: Homeostasis (Advanced) concept.
Homeostasis is a term that is also used when talking about the environment. For example, the atmospheric concentration of carbon dioxide on Earth has been regulated by the concentration of plant life on Earth, because plants
remove more carbon dioxide from the atmosphere during the daylight hours than they emit to the atmosphere at
night.

Evolution

Evolution by natural selection, is the theory that maintains that a populations inherited traits change over time,
and that all known organisms have a common origin. This theory, initially described by Charles Darwin, describes
why organisms must adapt to their environments. Evolutionary theory can explain how specialized features, such as
the geckos sticky foot pads shown in Figure 1.42, develop in different species. More about evolution is discussed in
Concept Evolution (Advanced).
64

www.ck12.org

Chapter 1. The Study of Life - Advanced

FIGURE 1.42
A Tokay Gecko. The pads at the tip of the
Tokay geckos foot are covered in microscopic hairs, each split into hundreds of
tips that measure about 200 nanometers
in diameter.

By using these tiny hairs

that can cling to smooth surfaces, the


geckos are able to support their entire
body weight while climbing walls This is
evidence of a product of evolution.

KQED: Bio-Inspiration: Nature as Muse

For hundreds of years, scientists have been using design ideas from structures in nature. Now, biologists and
engineers at the University of California, Berkeley are working together to design a broad range of new products,
such as life-saving milli-robots modeled on the way cockroaches run and adhesives based on the amazing design
of a geckos foot. This process starts with making observations of nature, which lead to asking questions and to the
additional aspects of the scientific process. Bio-Inspiration: Nature as Muse can be observed at http://www.kqed.
org/quest/television/bioinspiration-nature-as-muse (11:01).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/430

Vocabulary

cell: The basic unit of structure and function of all living organisms.
DNA (deoxyribonucleic acid): Double-stranded nucleic acid that composes genes and chromosomes; the
hereditary material.
evolution: The change in the characteristics of living organisms over time; the change in species over time.
gene: A segment of DNA that contains information to encode an RNA molecule or a single polypeptide.
homeostasis: The process of maintaining a stable environment inside a cell or an entire organism.
natural selection: Evolutionary process by which certain beneficial traits becomes more common within a
population, changing the characteristics (traits) of a species over time.

Summary

Four unifying principles form the foundation of modern biology: cell theory, evolutionary theory, the gene
theory and the principle of homeostasis. These four principles are important to each and every field of biology.
65

1.12. Unifying Principles of Biology - Advanced

www.ck12.org

Explore More

Use this resource to answer the questions that follow.


http://www.hippocampus.org/Biology . Non-Majors Biology Search: Cell Theory
1.
2.
3.
4.
5.

What is the Cell Theory?


What are the three basic tenets of the Cell Theory?
Describe the findings of Schwann, Schleiden, and Virchow.
What has led to the "modernization" of the Cell Theory?
What are the main differences between the classic cell theory and the modern cell theory?

Review

1. Identify and describe the four unifying principles of modern biology.


2. Why do you believe the four unifying principles of modern biology form the foundation of modern biology.

66

www.ck12.org

Chapter 1. The Study of Life - Advanced

1.13 Interdependence - Advanced

Explain the concept of interdependence.


List different types of interactions that organisms can have with each other.
Identify levels of organization within a biological system.
Define biodiversity.

What does it mean to be interdependent ?


Do species live alone, or do many live in communities with other organisms? All species rely on other species in
some way in order to survive. They may rely on other species for food, shelter or to help them reproduce. Here the
bee is helping the flower spread its pollen. Species are not independent, they are interdependent.
Interdependence of Living Things

Biological interactions are the interactions between different organisms in an environment. In the natural world,
no organism is cut off from its surroundings. Organisms are a part of their environment which is rich in living and
non-living elements that interact with each other in some way. The interactions of an organism with its environment
are vital to its survival, and the functioning of the ecosystem as a whole.
These relationships can be categorized into many different classes. The interactions between two species do not
necessarily need to be through direct contact. Due to the connected nature of ecosystems, species may affect each
other through such relationships involving shared resources or common enemies.
The term symbiosis comes from a Greek word that means living together. Symbiosis can be used to describe
various types of close relationships between organisms of different species, such as mutualism and commensalism,
which are relationships in which neither organism is harmed. Sometimes the term symbiosis is used only for cases
67

1.13. Interdependence - Advanced

www.ck12.org

where both organisms benefit, sometimes it is used more generally to describe all kinds of close relationships,
even when one organism is killed by another, as shown in Figure 1.43. Symbiosis can also be used to describe
relationships where one organism lives on or in another, called parasitism, or when one organism kills and eats
another organism, called predation. These relationships will be further described in Concept Ecology (Advanced).
FIGURE 1.43
There are many different types of symbiotic interactions between organisms.
Clockwise from top left: Escherichia coli
bacteria live inside your intestines in a
mutualistic relationship: the bacteria produce Vitamin K for you, and they get
their food from what you eat.

Clown-

fish that live among the tentacles of


sea anemones protect the anemone from
anemone-eating fish, and in turn the
stinging tentacles of the anemone protect
the clownfish from its predators (a special
mucus on the clownfish protects it from
the stinging tentacles). Similar to the E.
coli, this bee has a mutualistic relationship
with the flower, the bee feeds from the
flower, and the flower gets pollinated by
the bee. Lions are predators that feed
on other organisms such as this Cape
buffalo.

FIGURE 1.44
A flock of starlings looks out, before
searching for parasites on a red deer
stag.

Competition is as an interaction between organisms or species, for the same resources such as water, food, or
hunting grounds in an environment, shown in Figure 1.45. Eventually, the species that is less able to compete for
resources will either adapt or die out. According to evolutionary theory, competition for resources plays an important
68

www.ck12.org

Chapter 1. The Study of Life - Advanced

role in natural selection.


FIGURE 1.45
Competition between organisms and
species. These male deer are competing
for females during rutting (mating) season. Trees in this forest are in competition
for light.

Animals that eat decomposing organic material also have an important interaction with the environment. They help
to decompose dead matter and assist with the recycling of nutrients. By burying and eating dung, dung beetles, such
as the one shown in Figure 1.46, improve nutrient cycling and soil structure. They make the dead organic matter
available to bacteria that break it down even further.

FIGURE 1.46
Dung beetles have important interactions with the environment, through which
many other organisms benefit.

Organisms are not independent, they are interdependent. They cannot live alone; they need other organisms to
survive. The same is true for species. All species need other species to survive.

Levels of Organization

In studying how organisms interact with each other, biologists often find it helpful to classify the organisms and
interactions into levels of organization. Similar to the way an organism itself has different levels of organization,
the ways in which organisms interact with their environment and each other can also be divided into levels of
organization. For example:
The biosphere includes all living things within all of their environments. It includes every part of the environment
where life exists, from the upper reaches of the atmosphere to the top few meters of soil, to the bottoms of the
69

1.13. Interdependence - Advanced

www.ck12.org

oceans. An ecosystem is made up of the relationships among smaller groups of organisms with each other, and with
their environment. Scientists often speak of the interrelatedness of living things, because, according to evolutionary
theory, organisms adapt to their environment, and they must also adapt to other organisms in that environment.
A community is made up of the relationships between groups of different species. For example, the desert communities consist of rabbits, coyotes, snakes, birds, mice and such plants as sahuaro cactus, ocotillo, and creosote bush.
Community structure can be disturbed by such dynamics as fire, human activity, and over-population.
A population is a group of individuals of a single species that mate and interact with one another in a limited
geographic area. For example, a field of flowers which is separated from another field by a hill or other area where
none of these flowers occur.
It is thus possible to study biology at many levels, from collections of organisms or communities, to the inner
workings of a cell (organelle). More about the interactions of organisms will be discussed in Concept Ecology
(Advanced).

FIGURE 1.47
This picture shows the levels of organization in nature, from the individual organism to the biosphere.

The Diversity of Life

Evolutionary theory and the cell theory give us the basis for how and why organisms relate to each other. The
diversity of life found on Earth today is the result of 4 billion years of evolution. Some of this diversity is shown
in Figure 1.48. The origin of life is not completely understood by science, though limited evidence suggests that
life may already have been well-established a few 100 million years after Earth formed. Until approximately 600
million years ago, all life was made up of single-celled organisms.
The level of biodiversity found in the fossil record suggests that the last few million years include the period
of greatest biodiversity in the Earths history. However, not all scientists support this view, since there is a lot
of uncertainty as to how strongly the fossil record is biased by the greater availability and preservation of more
recent fossil-containing rock layers. Some researchers argue that modern biodiversity is not much different from
biodiversity 300 million years ago. Estimates of the present global species diversity vary from 5 million to 30
million species, with a best estimate of somewhere near 10 million species. All living organisms are classified
into one of the six kingdoms: Archaebacteria (Archaea), Eubacteria (Bacteria), Protista (Protists), Fungi, Plantae
70

www.ck12.org

Chapter 1. The Study of Life - Advanced

(Plants), and Animalia (Animals).


New species are regularly discovered and many, though already discovered, are not yet classified. One estimate
states that about 40 percent of freshwater fish from South America are noa few of the many members of the animal
kingdom are shown in Figure 1.48. The animal kingdom is just a tiny portion ot yet classified. Every year, scientists
discover the existence of many hundreds more archaea and bacteria than were previously known. Just f the total
diversity of life. More about the diversity of living creatures will be discussed throughout numerous concepts.

FIGURE 1.48
Animal diversity. This figure shows just
a fraction of the diversity of life.

The

diversity of organisms found in the five


kingdoms of life, dwarf the number of
organisms found in the animal kingdom.
The other kingdoms of life are Eubacteria, Archaebacteria, Protista, Fungi, and
Plantae.

Vocabulary

biodiversity: The variety of life and its processes; including the variety of living organisms, the genetic
differences among them, and the communities and ecosystems in which they occur.
biological interactions: The interactions between different organisms in an environment.
biosphere: The areas of Earth where all organisms live; extends from about 11,000 meters below sea level to
15,000 meters above sea level.
commensalism: A symbiotic relationship in which one species benefits while the other species is not affected.
community: The populations of different species that live in the same habitat and interact with one another;
the biotic component of an ecosystem.
competition: The relationship between organisms that strive for the same limited resources.
ecosystem: A natural unit consisting of a community (the biotic factors) functioning together with all the
nonliving (abiotic) physical factors of the environment.
interdependent: The notion that organisms (species) cannot live alone; they need other organisms (species)
to survive.
mutualism: A type of symbiotic relationship in which both species benefit.
71

1.13. Interdependence - Advanced

www.ck12.org

parasitism: A symbiotic relationship in which one species (the parasite) benefits while the other species (the
host) is harmed.
population: A group of individuals of a single species that mate and interact with one another in a limited
geographic area.
predation: A relationship in which members of one species (the predator) consume members of other species
(the prey).
symbiosis: A close relationship/association between organisms of different species in which at least one of
the organisms benefits from the relationship.
Summary

The interactions of an organism with its environment are vital to its survival, and the functioning of the
ecosystem as a whole.
An ecosystem consists of the relationships among smaller groups of organisms with each other, and with their
environment.
Symbiosis can be used to describe various types of close relationships between organisms of different species.
Competition is as an interaction between organisms or species for the same resources in an environment.
Explore More

Use this resource to answer the questions that follow.


http://www.hippocampus.org/Biology Non-Majors Biology Search: Interactions Within Communities
1.
2.
3.
4.

How do organisms within a community interact with each other?


Describe and give examples of the two types of competition.
How may predation benefit the prey population?
Describe the various types of symbiotic relationships. Provide examples of each.

Review

1.
2.
3.
4.
5.

72

What is biological interactions?


What is the difference between mutualism and commensalism?
What is predation?
What are the levels of organization that organisms interact with their environment and explain them.
Give an example of how you are interdependent from another organism.

www.ck12.org

Chapter 1. The Study of Life - Advanced

1.14 Evolution of Life - Advanced

Identify Charles Darwin and Alfred Russel Wallace.


Describe the relationship between evolution and natural selection.
Outline the formation of modern evolutionary theory.
Discuss common misconceptions of evolution.

What is a dinosaur?
A dinosaur is from a class of reptiles. They are diverse reptiles that first appeared during the Triassic period,
approximately 230 million years ago, and were the dominant land vertebrates for 135 million years, from the
beginning of the Jurassic period (about 200 million years ago) until they went extinct, at the end of the Cretaceous
period, 65.5 million years ago. They are very strong evidence of evolution, the change in species over time.
Dinosaurs went extinct because they could not adapt to a catastrophic environmental change. The ability to adapt to
a changing environment is a key feature of natural selection, the process of evolution.
Evolution of Life

Evolution is the process by which populations of organisms change over time. It is a process that began on this
planet well over 3.5 billion years ago and continues to this day, as populations of organisms continue to change.
Evolution occurs as organisms acquire and pass on new traits from one generation to the next generation. Its
occurrence over large stretches of time explains the origin of new species and the great diversity of the biological
world. Extant species are related to each other through common descent, and products of evolution over billions of
years. Analysis of the DNA of different organisms indicates there is a similarity among very different organisms in
the genetic code that help make proteins and other molecules. This genetic code is used by all known forms of life
on Earth. The theory of evolution suggests that the genetic code was established very early in the history of life,
and some studies suggest it was established soon after the formation of Earth. The timeline of the evolution of life,
shown in Figure 1.49, outlines the major events in the development of life.
How do scientists know Earth is so old? The answer is in the rocks. Contained in rocks that were once molten,
shown in Figure 1.50, are chemical elements that act like an atomic clock. The atoms of different forms of elements
73

1.14. Evolution of Life - Advanced

www.ck12.org

FIGURE 1.49
According to recent estimates, the Earth
is about 4.5 billion years old. Most of the
evidence for an ancient Earth is contained
in the rocks that form the Earths crust.
The rock layers themselves, like pages
in thick history book, record the surface
shaping events of the past. Buried within
them are traces of life, including the plants
and animals that evolved from organic
structures that existed perhaps as many
as 3 to 3.5 billion years ago.

(called isotopes) break down at different rates over time. Parent isotopes within these rocks decay at a predictable
rate to form daughter isotopes. By determining the relative amounts of parent and daughter isotopes, the age of these
rocks can be calculatedforming the so-called atomic clock.
Thus, the results of studies of rock layers ( stratigraphy), and of fossils ( paleontology), along with the ages of
certain rocks as measured by atomic clocks ( geochronology), indicate that the Earth is over 4.5 billion years old,
with the oldest known rocks being 3.96 billion years old. More about the history of life on Earth will be discussed
in History of Life: Introduction (Advanced) concept.

FIGURE 1.50
Molten rock, called lava, is expelled by
a volcano during an eruption. The lava
will eventually cool to become solid rock.
When first expelled from a volcanic vent,
it is a liquid at temperatures from 700 C
to 1,200 C (1,300 F to 2,200 F). Not all
types of rocks come from cooled lava, but
many do.

Additional images/videos of volcanic eruptions can be seen at Hawaii Volcanic Eruption with Lightning and USGS
Kilauea Volcano: http://hvo.wr.usgs.gov/gallery/kilauea/volcanomovies/ .
74

www.ck12.org

Chapter 1. The Study of Life - Advanced

FIGURE 1.51
This timeline shows the history of life on
Earth.

In the entire span of the time,

humans are a relatively new addition.

History of Evolutionary Thought

The theory of evolution by natural selection was proposed at about the same time by both Charles Darwin and Alfred
Russel Wallace, shown in Figure 1.52, and was set out in detail in Darwins 1859 book On the Origin of Species.
Natural selection is a process that causes heritable traits that are helpful for survival and reproduction to become
more common, and harmful traits, or traits that are not helpful or advantageous for survival to become more rare
in a population of organisms. This occurs because organisms with advantageous traits are more "fit" to survive in
a particular environment and have "adapted" to the conditions of that environment. These individuals will have
greater reproductive success than organisms less fit for survival in the environment. This will lead to an increase in
the number of organisms with the advantageous trait(s) over time. Over many generations, adaptations occur through
a combination of successive, small, random changes in traits, and natural selection of those variants best-suited for
their environment. Natural selection is one of the cornerstones of modern biology.

FIGURE 1.52
Charles Darwin, left (1809-1882), and Alfred Russel Wallace, right (1823-1913).
Both scientists proposed a process of
evolution by natural selection at about the
same time. However, Darwin is primarily
associated with the theory of evolution by
natural selection due to his abundance of
data.

75

1.14. Evolution of Life - Advanced

www.ck12.org

The theory of evolution encountered initial resistance from religious authorities who believed humans were divinely
set apart from the animal kingdom. There was considerable concern about Darwins proposal of an entirely scientific
explanation for the origin of humans. Many people found such an explanation to be in direct conflict with their
religious beliefs. A caricature of Darwin as a monkey, shown in Figure 1.53, reflects the controversy that arose over
evolutionary theory. In the 1930s, Darwinian natural selection was combined with Mendelian inheritance to form
the basis of modern evolutionary theory.

FIGURE 1.53
An 1871 caricature portraying Darwin with an ape body and the bushy
beard he grew in 1866. Such satire reflected the cultural backlash against
evolution.

The identification of DNA as the genetic material by Oswald Avery and colleagues in the 1940s, as well as the
publication of the structure of DNA by James Watson and Francis Crick in 1953, demonstrated the physical basis
for inheritance. Since then, genetics and molecular biology have become core aspects of evolutionary biology.
Currently the study of evolutionary biology involves scientists from fields as diverse as biochemistry, ecology,
genetics and physiology, and evolutionary concepts are used in even more distant disciplines such as psychology,
medicine, philosophy and computer science.

Misconceptions About Evolution

The following list includes some common misconceptions about evolution.

The term evolution describes the changes that occur in populations of living organisms over time. Describing
these changes does not address the origin of life. The two are commonly and mistakenly confused. Biological
evolution likewise says nothing about cosmology, the Big Bang, or where the universe, galaxy, solar system,
or Earth came from.
Humans did not evolve from chimpanzees or any other modern ape; instead they share a common ancestor
that existed around 7 million years ago.
The process of evolution is not necessarily slow. Millions of years are not required to see evolution in action.
Indeed, it has been observed multiple times under both controlled laboratory conditions and in nature.
Evolution is not a progression from "lower" to "higher" forms of life, and it does not increase in complexity.
For example, bacteria have simpler structures and a smaller amount of genetic material than humans do. This
does not mean however, that bacteria are less evolved than humans are. Bacteria have evolved over many
millions of years and are well adapted to their own environments.
76

www.ck12.org

Chapter 1. The Study of Life - Advanced

After Darwin

Since Darwins time, scientists have gathered a more complete fossil record, including microorganisms and chemical
fossils. These fossils have supported and added more information to Darwins theories. However, the age of the
Earth is now held to be much older than Darwin thought. Researchers have also uncovered some of the preliminary
mysteries of the mechanism of heredity as carried out through genetics and DNA, which were areas unknown to
Darwin. Another growing subject is the study of comparative anatomy, which looks at how different organisms have
similar body structures. Molecular biology studies of slowly changing genes reveal an evolutionary history that is
consistent with fossil and anatomical records.
Vocabulary

evolution: The change in the characteristics of living organisms over time; the change in species over time.
geochronology: The study of the age of rocks.
isotope: An atom of a different form of the same element.
natural selection: Evolutionary process by which certain beneficial traits becomes more common within a
population, changing the characteristics (traits) of a species over time.
paleontology: The study of fossils.
stratigraphy: The study of rock layers.

Summary

Analysis of the DNA of different organisms indicate that there is a similarity in the genetic codes that help
make proteins and other molecules in very different organisms.
The theory of evolution by natural selection is based on the concept of the survival of the fittest, where
individuals with beneficial traits are better able to survive and reproduce in the environment in which they
live.
Explore More

Use this resource to answer the questions that follow.


Introduction to Evolution and Natural Selection at http://www.youtube.com/watch?v=GcjgWov7mTM
(17:39).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/156

1.
2.
3.
4.
5.

What is meant by evolution?


Describe natural selection.
What is meant by variation?
Describe the "evolution" of the peppered moth.
What is a virus? Do viruses evolve? Why or why not?
77

1.14. Evolution of Life - Advanced

www.ck12.org

Review

1.
2.
3.
4.
5.

78

What is evolution and natural selection?


Outline the formation of modern evolutionary theory.
How have more recent scientific findings fit with evolutionary theory since Darwins time?
What are the misconceptions about evolution?
Large animals are more evolved than single-celled organisms such as bacteria. Do you agree with this
statement? Explain your answer.

www.ck12.org

Chapter 1. The Study of Life - Advanced

1.15 Nobel Prizes


Explain what the Nobel Prize is.

What is the highest honor a scientist can be awarded?


The Nobel Prize, awarded each October in six categories, including physiology or medicine and chemistry.
The Nobel Prize

The Nobel Prize is an international award given each year to honor outstanding achievements in physics, chemistry,
medicine, literature and for work in peace. The award is maintained by the Nobel Foundation in Stockholm, Sweden,
named after Alfred Nobel (1833-1896), a scientist, inventor, entrepreneur, author and pacifist. At the age of 17,
Alfred Nobel spoke five languages fluently. He went on to become an inventor and businessman, and at the time of
his death, he had 355 patents worldwide, one which was the patent for dynamite. More importantly, he had started 87
companies world-wide. He had an unprecedented idea for his wealth. See http://www.nobelprize.org for additional
information.
In his last will, dated November 27, 1895, Nobel left instructions for the prize. After leaving sums of monies to
various friends and relatives, Nobel stated in his will, "The whole of my remaining realizable estate shall be dealt with
in the following way: the capital, invested in safe securities by my executors, shall constitute a fund, the interest on
which shall be annually distributed in the form of prizes to those who, during the preceding year, shall have conferred
the greatest benefit to mankind. The said interest shall be divided into five equal parts, which shall be apportioned
as follows: one part to the person who shall have made the most important discovery or invention within the field
79

1.15. Nobel Prizes

www.ck12.org

of physics; one part to the person who shall have made the most important chemical discovery or improvement;
one part to the person who shall have made the most important discovery within the domain of physiology or
medicine; one part to the person who shall have produced in the field of literature the most outstanding work in an
ideal direction; and one part to the person who shall have done the most or the best work for fraternity between
nations, for the abolition or reduction of standing armies and for the holding and promotion of peace congresses.
The prizes for physics and chemistry shall be awarded by the Swedish Academy of Sciences; that for physiological
or medical work by the Caroline Institute in Stockholm; that for literature by the Academy in Stockholm, and that
for champions of peace by a committee of five persons to be elected by the Norwegian Storting. It is my express
wish that in awarding the prizes no consideration whatever shall be given to the nationality of the candidates, but
that the most worthy shall receive the prize, whether he be a Scandinavian or not."
The first five Nobel Prizes were awarded in 1901. In 1969, another prize was added: "The Sveriges Riksbank Prize
in Economic Sciences in Memory of Alfred Nobel."
Many of the contributions of Nobel laureates are discussed throughout these concepts. The contributions from the
physiology or medicine are directly related to the life sciences, as are selected contributions from the chemistry
prize.
Physiology or Medicine

TABLE 1.5: Nobel Laureates in Physiology or Medicine, 1950 to present


Year
2014

Laureates
John OKeefe, May-Britt
Moser, Edvard I. Moser

2013

James
E.
Rothman,
Randy W. Schekman,
Thomas C. Sdhof

2012

Sir John B. Gurdon,


Shinya Yamanaka

2011

Bruce A. Beutler, Jules


A. Hoffmann, Ralph M.
Steinman

2010

Robert G. Edwards

2009

Elizabeth H. Blackburn,
Carol W. Greider, Jack W.
Szostak

80

Contribution
for their discoveries of
cells that constitute a positioning system in the
brain
for their discoveries of
machinery
regulating
vesicle traffic, a major
transport system in our
cells
for the discovery that mature cells can be reprogrammed to become
pluripotent
for their discoveries concerning the activation of
innate immunity (BAB,
JAH) and for his discovery of the dendritic cell
and its role in adaptive
immunity (RMS)
for the development of in
vitro fertilization
for the discovery of
how
chromosomes
are
protected
by
telomeres and the enzyme
telomerase

Concept

Active Transport: Exocytosis and Endocytosis


(Advanced)

www.ck12.org

Chapter 1. The Study of Life - Advanced

TABLE 1.5: (continued)


Year
2008

Laureates
Harald
zur
Hausen,
Franoise Barr-Sinoussi,
Luc Montagnier

2007

Mario R. Capecchi, Sir


Martin J. Evans, Oliver
Smithies

2006

Andrew Z. Fire, Craig C.


Mello

2005

Barry J. Marshall,
Robin Warren

2004

Richard Axel, Linda B.


Buck

2003

Paul C. Lauterbur, Sir Peter Mansfield

2002

Sydney Brenner,
H.
Robert Horvitz, John E.
Sulston

2001

Leland H. Hartwell, Tim


Hunt, Sir Paul M. Nurse
Arvid Carlsson, Paul
Greengard,
Eric
R.
Kandel
Gnter Blobel

2000

1999

1998

J.

Robert F. Furchgott,
Louis J. Ignarro, Ferid
Murad

Contribution
for his discovery of human papilloma viruses
causing cervical cancer
(HzH) and for their discovery of human immunodeficiency virus (FB-S,
LM)
for their discoveries of
principles for introducing specific gene modifications in mice by the use
of embryonic stem cells
for their discovery of RNA
interference - gene silencing by double-stranded
RNA
for their discovery of the
bacterium Helicobacter
pylori and its role in
gastritis and peptic ulcer
disease
for their discoveries of
odorant receptors and the
organization of the olfactory system
for their discoveries concerning magnetic resonance imaging
for their discoveries concerning genetic regulation
of organ development and
programmed cell death
for their discoveries of key
regulators of the cell cycle
for their discoveries concerning signal transduction in the nervous system
for the discovery that proteins have intrinsic signals that govern their
transport and localization
in the cell
for their discoveries concerning nitric oxide as a
signalling molecule in the
cardiovascular system

Concept

Human
Genetics:
The Human Genome
(Advanced)

RNA: Types (Advanced)

81

1.15. Nobel Prizes

www.ck12.org

TABLE 1.5: (continued)


Year
1997

Laureates
Stanley B. Prusiner

1996

Peter C. Doherty, Rolf M.


Zinkernagel

1995

Edward
B.
Lewis,
Christiane
NssleinVolhard,
Eric
F.
Wieschaus
Alfred G. Gilman, Martin
Rodbell

1994

1993
1992

Richard
J.
Roberts,
Phillip A. Sharp
Edmond H. Fischer, Edwin G. Krebs

1991

Erwin Neher, Bert Sakmann

1990

Joseph E. Murray,
Donnall Thomas

1989

J. Michael Bishop, Harold


E. Varmus

1988

Sir James W. Black,


Gertrude
B.
Elion,
George H. Hitchings
Susumu Tonegawa

1987

1986
1985

82

E.

Stanley Cohen, Rita LeviMontalcini


Michael S. Brown, Joseph
L. Goldstein

Contribution
for his discovery of Prions
- a new biological principle of infection
for their discoveries concerning the specificity of
the cell mediated immune
defense
for their discoveries concerning the genetic control of early embryonic
development
for their discovery of Gproteins and the role of
these proteins in signal
transduction in cells
for their discoveries of
split genes
for their discoveries concerning reversible protein
phosphorylation as a biological regulatory mechanism
for their discoveries concerning the function of
single ion channels in
cells
for their discoveries
concerning organ and
cell transplantation in
the treatment of human
disease
for their discovery of the
cellular origin of retroviral oncogenes
for their discoveries of
important principles for
drug treatment
for his discovery of the genetic principle for generation of antibody diversity
for their discoveries of
growth factors
for their discoveries concerning the regulation of
cholesterol metabolism

Concept

Regulation of Gene Expression:Eukaryotic (Advanced)

DNA Technology: Gene


Cloning (Advanced)

Cell Cycle: Cancer (Advanced)

www.ck12.org

Chapter 1. The Study of Life - Advanced

TABLE 1.5: (continued)


Year
1984

Laureates
Niels K. Jerne, Georges
J.F. Khler, Csar Milstein

1983

Barbara McClintock

1982

Sune K. Bergstrm, Bengt


I. Samuelsson, John R.
Vane

1981

Roger W. Sperry, David


H. Hubel, Torsten N.
Wiesel

1980

Baruj Benacerraf, Jean


Dausset, George D. Snell

1979

Allan M. Cormack, Godfrey N. Hounsfield

1978

Werner Arber, Daniel


Nathans, Hamilton O.
Smith

1977

Roger Guillemin, Andrew


V. Schally,
Rosalyn
Yalow

1976

Baruch S. Blumberg, D.
Carleton Gajdusek

Contribution
for theories concerning
the specificity in development and control of the
immune system and the
discovery of the principle
for production of monoclonal antibodies
for her discovery of mobile genetic elements
for their discoveries
concerning
prostaglandins
and
related biologically active
substances
for
his
discoveries
concerning the functional
specialization of the
cerebral
hemispheres
(RWS), and for their
discoveries concerning
information processing in
the visual system (DHH,
TNW)
for their discoveries concerning genetically determined structures on the
cell surface that regulate
immunological reactions
for the development of
computer assisted tomography
for the discovery of
restriction enzymes and
their
application
to
problems of molecular
genetics
for their discoveries concerning the peptide hormone production of the
brain (RG, AVS) and for
the development of radioimmunoassays of peptide hormones (RY)
for their discoveries concerning new mechanisms
for the origin and dissemination of infectious diseases

Concept

DNA Technology: Gene


Cloning (Advanced)

83

1.15. Nobel Prizes

www.ck12.org

TABLE 1.5: (continued)


Year
1975

Laureates
David Baltimore, Renato
Dulbecco, Howard Martin
Temin

1974

Albert Claude, Christian


de Duve, George E.
Palade

1973

Karl von Frisch, Konrad


Lorenz, Nikolaas Tinbergen

1972

Gerald M. Edelman, Rodney R. Porter

1971

Earl W. Sutherland, Jr.

1970

Sir Bernard Katz, Ulf von


Euler, Julius Axelrod

1969

Max Delbrck, Alfred


D. Hershey, Salvador E.
Luria

1968

Robert W. Holley, Har


Gobind Khorana, Marshall W. Nirenberg

1967

Ragnar Granit, Haldan


Keffer Hartline, George
Wald

1966

Peyton Rous, Charles


Brenton Huggins

84

Contribution
for their discoveries concerning the interaction
between tumour viruses
and the genetic material
of the cell
for their discoveries concerning the structural and
functional organization of
the cell
for their discoveries concerning organization and
elicitation of individual
and social behavior patterns
for their discoveries
concerning the chemical
structure of antibodies
for his discoveries concerning the mechanisms
of the action of hormones
for their discoveries
concerning the humoral
transmittors
in
the
nerve terminals and the
mechanism for their
storage,
release and
inactivation
for their discoveries concerning the replication
mechanism and the genetic structure of viruses
for their interpretation of
the genetic code and its
function in protein synthesis
for their discoveries concerning the primary physiological and chemical visual processes in the eye
for
his
discovery
of
tumour-inducing
viruses (PR) and for his
discoveries concerning
hormonal treatment of
prostatic cancer (CBH)

Concept
Viruses:
Classification
(Advanced)

www.ck12.org

Chapter 1. The Study of Life - Advanced

TABLE 1.5: (continued)


Year
1965

Laureates
Franois Jacob, Andr
Lwoff, Jacques Monod

1964

Konrad Bloch, Feodor Lynen

1963

Sir John Carew Eccles,


Alan Lloyd Hodgkin, Andrew Fielding Huxley

1962

Francis Harry Compton


Crick, James Dewey Watson, Maurice Hugh Frederick Wilkins

1961

Georg von Bksy

1960

Sir Frank Macfarlane


Burnet,
Peter Brian
Medawar
Severo Ochoa, Arthur Kornberg

1959

1958

George Wells Beadle,


Edward Lawrie Tatum,
Joshua Lederberg

Contribution
for their discoveries concerning genetic control of
enzyme and virus synthesis
for their discoveries
concerning
the
mechanism
and
regulation
of
the
cholesterol and fatty
acid metabolism
for their discoveries concerning the ionic mechanisms involved in excitation and inhibition in
the peripheral and central
portions of the nerve cell
membrane
for their discoveries
concerning the molecular
structure of nucleic acids
and its significance for
information transfer in
living material
for his discoveries of the
physical mechanism of
stimulation within the
cochlea
for discovery of acquired
immunological tolerance

Concept
Regulation
of
Gene
Expression: Introduction
(Advanced)

DNA: The Double Helix


(Advanced)

for their discovery of the


mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid
for their discovery that
genes act by regulating
definite chemical events
(GWB, ELT) and for his
discoveries concerning
genetic
recombination
and the organization of
the genetic material of
bacteria

85

1.15. Nobel Prizes

www.ck12.org

TABLE 1.5: (continued)


Year
1957

Laureates
Daniel Bovet

1956

Andr Frdric Cournand,


Werner Forssmann, Dickinson W. Richards

1955

Axel Hugo Theodor Theorell

1954

John Franklin Enders,


Thomas Huckle Weller,
Frederick
Chapman
Robbins
Hans Adolf Krebs, Fritz
Albert Lipmann

1953

1952

Selman Abraham Waksman

1951

Max Theiler

1950

Edward Calvin Kendall,


Tadeus Reichstein, Philip
Showalter Hench

Contribution
for his discoveries relating to synthetic compounds that inhibit the action of certain body substances, and especially
their action on the vascular system and the skeletal
muscles
for their discoveries concerning heart catheterization and pathological
changes in the circulatory
system
for his discoveries concerning the nature and
mode of action of oxidation enzymes
for their discovery of the
ability of poliomyelitis
viruses to grow in cultures
of various types of tissue
for his discovery of the
citric acid cycle (HAK)
and for his discovery of
co-enzyme A and its importance for intermediary
metabolism (FAL)
for his discovery of streptomycin, the first antibiotic effective against tuberculosis
for his discoveries concerning yellow fever and
how to combat it
for their discoveries relating to the hormones of
the adrenal cortex, their
structure and biological
effects

Concept

TABLE 1.6: Selected Nobel Laureates in Physiology or Medicine, 1901-1949


Year
1945

86

Laureates
Sir Alexander Fleming,
Ernst B. Chain, Sir
Howard Florey

Contribution
for the discovery of penicillin and its curative effect in various infectious
diseases

Concept
Fungi: Uses (Advanced)

www.ck12.org

Chapter 1. The Study of Life - Advanced

TABLE 1.6: (continued)


Year
1935

Laureates
Hans Spemann

1933

Thomas H. Morgan

1905

Robert Koch

1902

Ronald Ross

Contribution
for his discovery of the
organizer effect in embryonic development
for his discoveries concerning the role played by
the chromosome in heredity
for his investigations and
discoveries in relation to
tuberculosis
for his work on malaria,
by which he has shown
how it enters the organism
and thereby has laid the
foundation for successful
research on this disease
and methods of combating
it

Concept

Human Genetics: Chromosomes (Advanced)

Prokaryotes:
(Advanced)

Diseases

Animal-like Protists: Diseases (Advanced)

Chemistry

The following are the Nobel Prizes in Chemistry that have significance to the life sciences.

TABLE 1.7: Chemistry


Year
2013

Laureates
Martin Karplus, Michael
Levitt, Arieh Warshel

2012

Robert J. Lefkowitz,
Brian K. Kobilka
Venkatraman Ramakrishnan, Thomas A. Steitz,
Ada E. Yonath
Roger D. Kornberg

2009

2006

2004

2003

Aaron
Ciechanover,
Avram Hershko, Irwin
Rose
Peter Agre, Roderick
MacKinnon

Contribution
for the development of
multiscale models for
complex chemical systems
for studies of G-proteincoupled receptors
for studies of the structure
and function of the ribosome
for his studies of the
molecular basis of eukaryotic transcription
for the discovery of
ubiquitin-mediated
protein degradation
for discoveries concerning channels in cell membranes

Concept

The Chromosome - Advanced

87

1.15. Nobel Prizes

www.ck12.org

TABLE 1.7: (continued)


Year
1997

Laureates
Paul D. Boyer, John E.
Walker, Jens C. Skou

1993

Kary B. Mullis, Michael


Smith

1989
1988

Sidney Altman, Thomas


R. Cech
Johann
Deisenhofer,
Robert Huber, Hartmut
Michel

1982

Aaron Klug

1980

Paul Berg, Walter Gilbert,


Frederick Sanger

88

Contribution
for their elucidation of
the enzymatic mechanism
underlying the synthesis
of adenosine triphosphate
(PDB, JEW) and for
the first discovery of an
ion-transporting enzyme,
Na+ , K+ -ATPase (JCS)
for
his
invention
of
the
polymerase
chain reaction (PCR)
method
(KBM)
and
for
his
fundamental
contributions
to
the
establishment
of
oligonucleotide-based,
site-directed mutagenesis
and its development for
protein studies (MS)
for their discovery of catalytic properties of RNA
for the determination of
the
three-dimensional
structure
of
a
photosynthetic reaction
centre
for his development of
crystallographic electron
microscopy and his structural elucidation of biologically important nucleic acid-protein complexes
for
his
fundamental
studies
of
the
biochemistry of nucleic
acids, with particular
regard to recombinantDNA (PB) and for their
contributions concerning
the determination of base
sequences in nucleic
acids (WG, FS)

Concept

The Polymerase Chain


Reaction - Advanced

Biotechnology
Advanced

www.ck12.org

Chapter 1. The Study of Life - Advanced

TABLE 1.7: (continued)


Year
1978

Laureates
Peter D. Mitchell

1972

Christian B. Anfinsen,
Stanford Moore, William
H. Stein

1970

Luis F. Leloir

1962

Max Ferdinand Perutz,


John Cowdery Kendrew

1961

Melvin Calvin

1958

Frederick Sanger

1954

*Linus Carl Pauling

Contribution
for his contribution to
the understanding of biological energy transfer
through the formulation
of the chemiosmotic theory
for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active conformation
(CBA) and for their contribution to the understanding of the connection
between chemical structure and catalytic activity of the active centre of
the ribonuclease molecule
(SM, WHS)
for his discovery of sugar
nucleotides and their role
in the biosynthesis of carbohydrates
for their studies of the
structures of globular
proteins
for his research on the
carbon dioxide assimilation in plants
for his work on the structure of proteins, especially that of insulin
for his research into the
nature of the chemical
bond and its application
to the elucidation of the
structure of complex substances

Concept

Linus Pauling was also awarded the Nobel Peace Prize in 1962.
Vocabulary

Alfred Nobel: A Swedish chemist, engineer, innovator, and armaments manufacturer who used his fortune to
posthumously institute the Nobel Prizes.
Nobel Prize: A set of annual international awards given in recognition of cultural and scientific advances.
89

1.15. Nobel Prizes

www.ck12.org

Summary
How are the life sciences studied? The scientific method is the process by which biological information, like that
of all other sciences, has been identified. This method has produced scientific theories and laws, including the cell
theory and the theory of evolution. All life, from the smallest bacteria to the largest whale, and all other prokaryotes,
protists, fungi, plants and animals in between, have characteristics of life in common. All life responds to their
environment, grows and changes, reproduces and has offspring, has a complex chemistry, maintains homeostasis, is
built of structures called cells and passes their traits onto their offspring.

90

www.ck12.org

Chapter 1. The Study of Life - Advanced

1.16 References
1. Flickr: Polycart. An experiment does not have to involve laboratory equipment; it can be as simple as trying
new items while shopping . CC BY 2.0
2. Solar system: Courtesy of Harman Smith and Laura Generosa (nee Berwin), NASA; Ferris wheel: Flickr:
mjtmail (tiggy). Solar system: http://commons.wikimedia.org/wiki/File:Solar_sys.jpg; Ferris wheel: http:/
/www.flickr.com/photos/mjtmail/2589115469/ . Solar system: Public Domain; Ferris wheel: CC BY 2.0
3. Image copyright Dennis Cox, 2014. http://www.shutterstock.com . Used under license from Shutterstock.com
4. Jeff Turner. The combustion of this match is an observable event and therefore a phenomenon . CC BY 2.0
5. Hana Zavadska. A simple summary of the steps of a scientific investigation . CC BY-NC 3.0
6. Laura Guerin. A broader summary of how scientific investigations move from observation of a phenomena to
a theory . CC BY-NC 3.0
7. David Schiersner. http://www.flickr.com/photos/freaky_designz/8732089237 . CC BY 2.0
8. Oren Jack Turner. http://commons.wikimedia.org/wiki/File:Albert_Einstein_1947a.jpg . Public Domain
9. Eric Schmelz, U.S. Department of Agriculture. http://www.flickr.com/photos/usdagov/8424943726/ . CC
BY 2.0
10. Peter Harrison. http://www.flickr.com/photos/devcentre/327942590 . CC BY 2.0
11. Courtesy of NASA. http://commons.wikimedia.org/wiki/File:Anousheh_Ansari_in_the_ISS.jpg . Public Domain
12. Courtesy of NASA/JPL-Caltech/Univ. of Ariz. http://commons.wikimedia.org/wiki/File:169141main_piaa09
178.jpg . Public Domain
13. User:DarkEvil/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:High_accuracy_Low_precisi
on.svg; http://commons.wikimedia.org/wiki/File:High_precision_Low_accuracy.svg . Public Domain
14. Sergio Cambelo. http://commons.wikimedia.org/wiki/File:Giraffe.JPG . Public Domain
15. Rachel Titiriga. http://www.flickr.com/photos/pocait/5920996538/ . CC BY 2.0
16. Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/File:S
implified_food_chain.svg . Public Domain
17. Courtesy of NOAA - Air Resources Laboratory. http://ready.arl.noaa.gov/READY_animations.php . Public
Domain
18. Colin Marquardt. http://commons.wikimedia.org/wiki/File:Biosphere2_Inside_big.jpg . Public Domain
19. Steven Depolo. http://www.flickr.com/photos/stevendepolo/7315153342/ . CC BY 2.0
20. Maggie Hoffman. http://www.flickr.com/photos/maggiejane/3359690235/ . CC BY 2.0
21. Mad scientist: Image copyright Art Prestige studio, 2013; Students: George Jumara/US Army Corps of
Engineers Savannah District; No and Yes icons: Pixabay:OpenClips. Mad scientist: http://www.shutterstock.c
om; Students: http://www.flickr.com/photos/savannahcorps/6916922975/; No icon: http://pixabay.com/en
/abort-delete-cancel-icon-cross-no-146072/; Yes icon: http://pixabay.com/en/approved-button-check-greenround-151676/ . Mad scientist: Used under license from Shutterstock.com; Students: CC BY 20; No and Yes
icons: Public Domain
22. Colin and Sarah Northway. http://www.flickr.com/photos/46174988@N00/4822043093/ . CC BY 2.0
23. (left) User:Magnus Manske/Wikimedia Commons; (right) Courtesy of NASA. (left) http://commons.wikime
dia.org/wiki/File:Lab_bench.jpg; (right) http://commons.wikimedia.org/wiki/File:Iss013e56052.jpg . (left)
CC BY 1.0; (right) Public Domain
24. (left) Matt Brown (Flickr: Matt from London); (right) User:Deglr6328/Wikimedia Commons. (left) http:
//www.flickr.com/photos/londonmatt/4980007220/; (right) http://commons.wikimedia.org/wiki/File:Fume_hood.jpg . (left) CC BY 2.0; (right) Public Domain
25. User:Newbie/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Pipetten.JPG . Public Domain
26. User:GcG/Wikimedia Commons, modified by User:Rozzychan/Wikimedia Commons. http://commons.wikim
91

1.16. References

27.
28.
29.
30.
31.
32.

33.
34.
35.
36.

37.
38.
39.

40.

41.

42.

43.

44.
45.

46.
47.
92

www.ck12.org

edia.org/wiki/File:Phase_contrast_microscope_labelled1.jpg . Public Domain


Courtesy of Neil Sanscrainte and the ARS/USDA. http://commons.wikimedia.org/wiki/File:Scientists_inject
_Nucleic_acids_into_Mosquitoes_to_%22silence%22_specific_genes_-_USDA-ARS.jpg . CC BY 2.0
Image copyright Leigh Prather, 2014. Objective lenses of a light microscope. . Used under license from
Shutterstock.com
User:Toutates/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Salaria_fluviatilis_SEM_imagi
ng.jpg . CC BY 3.0
Elizabeth Smith, Louisa Howard, Erin Dymek. (left) http://remf.dartmouth.edu/images/algaeSEM/source/4.ht
ml; (right) http://remf.dartmouth.edu/images/algaeTEM/source/1.html . Public Domain
Tom Beatty (Flickr: North Coast Outfitters, Ltd.). http://www.flickr.com/photos/northcoastoutfitters/829151
9767/ . CC BY 2.0
User:Phrood/Wikimedia Commons and User:Matthias M./Wikimedia Commons. (left) http://commons.wi
kimedia.org/wiki/File:Hazard_C.svg; (middle) http://commons.wikimedia.org/wiki/Image:Hazard_E.svg; (righ
t) http://commons.wikimedia.org/wiki/Image:Hazard_F.svg . Public Domain
William Rafti. http://commons.wikimedia.org/wiki/File:Sharps_Container.jpg . CC BY 2.5
User:Tjwood/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Disposable_nitrile_glove.jpg .
Public Domain
Steve Johnson. http://www.flickr.com/photos/artbystevejohnson/4618667796/ . CC BY 2.0
Rafal Konieczny. http://commons.wikimedia.org/wiki/File:Sign_eyewash.svg . The copyright holder of this
work allows anyone to use it for any purpose including unrestricted redistribution, commercial use, and
modification
Ducks: Jrgen from Sandesneben, Germany; Decoy: Peter Shanks (Flickr: BotheredByBees). A duck decoy
may look like a duck, but it does not have all the characteristics of life . CC BY 2.0
Tadpole: Dan Century; Frog: Greg Schechter (Flickr:GregTheBusker). Tadpoles go through visible changes
that show growth and development, a characteristic of life . CC BY 2.0
Human cells image copyright Sebastian Kaulitzki, 2014; onion cells image copyright Jubal Harshaw, 2014.
Humans and onions look very different, but when comparing the cells, you might notice some similarities .
Used under licenses from Shutterstock.com
(a) Taz (Flickr: sporkist); (b) Jon Sullivan, pdphoto.org; (c) Louisa Howard; (d) Mariana Ruiz Villarreal
(Wikimedia: LadyofHats); (e) User:Ollin/Wikipedia; (f) Ben Mills (Wikimedia: Benjah-bmm27). Illustrates
how cells are organized to form multicellular organisms . (a) CC-BY 2.0; (b) Public Domain; (c) Public
Domain; (d) Public Domain; (e) Public Domain; (f) Public Domain
(a) Mary Ann Tiffany, San Diego State University; (b) Flickr: istolethetv. (a) http://commons.wikimedia.org
/wiki/File:Diatoms.png; (b) http://commons.wikimedia.org/wiki/File:Whale_Shark_diagonal.jpg . (a) CC BY
2.5; (b) CC BY 2.0
Tokay gecko: Nick Hobgood; Tokay foot: User:Shimbathesnake/Wikipedia. Tokay gecko: http://commons.
wikimedia.org/wiki/File:Tokay.jpg; Tokay foot: http://commons.wikimedia.org/wiki/File:Tokay_foot.jpg .
Tokay gecko: CC BY 2.0; Tokay foot: Public Domain
E. coli: Courtesy of Rocky Mountain Laboratories, NIAID, NIH; Clownfish: Jan Derk; Lions: Flickr:
paulshaffner; Bee: Jon Sullivan and pdphoto.org. E. coli: http://commons.wikimedia.org/wiki/File:Esch
erichiaColi_NIAID.jpg; Clownfish: http://commons.wikimedia.org/wiki/File:Common_clownfish.jpg; Lions:
http://www.flickr.com/photos/paulshaffner/1867661393/; Bee: http://commons.wikimedia.org/wiki/File:Bee
s_Collecting_Pollen_cropped.jpg . E. coli: Public Domain; Clownfish: Public Domain; Lions: CC-BY 2.0;
Bee: Public Domain
Image copyright Godrick, 2014. http://www.shutterstock.com . Used under license from Shutterstock.com
Deers: Heinz Seehagel (User:HaSee/De.Wikipedia); Forest: Flickr:baronsquirrel. Deers: http://common
s.wikimedia.org/wiki/File:Hirschkampf.jpg; Forest: https://www.flickr.com/photos/baronsquirrel/106337895
. Deers: Public Domain; Forest: CC BY 2.0
User:LiquidGhoul/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Dung_beetle.jpg . CC
BY 2.5
Christopher Auyeung, modified by Mariana Ruiz Villarreal. CK-12 Foundation . CC BY-NC 3.0

www.ck12.org

Chapter 1. The Study of Life - Advanced

48. Bird: Kevin Cole; Moose: Courtesy Hagerty Ryan, US Fish and Wildlife Service; Frog: User:Zandberg/Wikimedia
Commons; Snake: Kelley Minars (Flickr: greaterumbrage); Fish: Adrian Pingstone; LadyBug: Jon Sullivan. Bird: http://commons.wikimedia.org/wiki/File:Recurvirostra_americana_2.jpg; Moose: http://common
s.wikimedia.org/wiki/File:Male_Moose.jpg; Frog: http://commons.wikimedia.org/wiki/File:Groene_kikker_achter_Bekaert-draad.jpg; Snake: http://commons.wikimedia.org/wiki/File:Rattlesnake_copperhead.jpg; Fis
h: http://commons.wikimedia.org/wiki/File:Clown.fish.arp.750pix.jpg; Ladybug: http://commons.wikimed
ia.org/wiki/File:Ladybug_%281%29.jpg . Bird: CC BY 2.0; Moose: Public Domain; Frog: Public Domain;
Snake: CC BY 2.0; Fish: Public Domain; Ladybug: Public Domain
49. Courtesy of the US Geological Survey. http://commons.wikimedia.org/wiki/File:Geological_time_spiral.png
. Public Domain
50. Courtesy of Jim D. Griggs, HVO, US Geological Survey. http://commons.wikimedia.org/wiki/File:Pahoeoe_f
ountain_original.jpg . Public Domain
51. Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/Fi
le:Timeline_evolution_of_life.svg . Public Domain
52. . Darwin: http://commons.wikimedia.org/wiki/File:Charles_Darwin.jpg; Wallace: http://commons.wikim
edia.org/wiki/File:Alfred_Russel_Wallace.jpg . Public Domain
53. . http://commons.wikimedia.org/wiki/File:Editorial_cartoon_depicting_Charles_Darwin_as_an_ape_%281871%
29.jpg . Public Domain

93

www.ck12.org

C HAPTER

Chemistry of Life Advanced

Chapter Outline
2.1

C HEMICAL S UBSTANCES - A DVANCED

2.2

T HE S IGNIFICANCE OF C ARBON - A DVANCED

2.3

C ARBOHYDRATES - A DVANCED

2.4

L IPIDS - A DVANCED

2.5

P ROTEINS - A DVANCED

2.6

N UCLEIC ACIDS - A DVANCED

2.7

WATER - A DVANCED

2.8

B IOCHEMICAL P ROPERTIES OF WATER - A DVANCED

2.9

S OLUTIONS - A DVANCED

2.10

WATER AND L IFE - A DVANCED

2.11

R EFERENCES

Introduction

94

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

What do you see when you look at this picture? Is it just a mass of tangled ribbons? Look closely. Its actually a
complex pattern of three-dimensional shapes. It represents the structure of a common chemical found inside living
cells. The chemical is a protein called hemoglobin. It is the protein in red blood cells which transports oxygen
around the body.
What are proteins? What other chemicals are found in living things? You will learn the answers to these questions
as you read about the chemistry of life.

95

2.1. Chemical Substances - Advanced

www.ck12.org

2.1 Chemical Substances - Advanced

Distinguish between atoms, elements, and ions.


Compare ionic bonds to covalent bonds.
Define organic compound.
Describe elements and compounds, and explain how mixtures differ from compounds.

Take some Cs, Hs, Ns, Os, Ps and Ss, combine them in many different combinations, and what do you get?
In just the right combinations, you get life. Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur. Some of the
most basic of elements, but some of the most important. Together they can form countless combinations of organic
compounds. And in just the right combinations, anything can happen.
Chemical Substances

Living things are made of matter. In fact, matter is the stuff of which all things are made. Anything that occupies
space and has mass is known as matter. Matter, in turn, consists of chemical substances. A chemical substance is
a material that has a definite chemical composition. It is also homogeneous, so the same chemical composition is
found uniformly throughout the substance. A chemical substance may be an element or a chemical compound.

Elements

An element is a pure substance that cannot be broken down into different types of substances. There are almost 120
known elements ( Figure 2.1), each with its own personality. The chemical and physical properties of one element
differ from any other. Elements are arranged according to their properties in the Periodic Table.
96

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

FIGURE 2.1
The Periodic Table.

Examples of elements include carbon, oxygen, hydrogen, gold, silver and iron. Each element is made up of just
one type of atom. An atom is the smallest particle of an element that still characterizes the element. As shown in
Figure 2.2, at the center of an atom is a nucleus. The nucleus contains positively charged particles called protons
and electrically neutral particles called neutrons. Surrounding the nucleus is a much larger electron cloud consisting
of negatively charged electrons. Electrons are arranged into distinct energy levels, at various distances from the
nucleus. An atom is electrically neutral if it has the same number of protons as electrons. Each element has atoms
with a characteristic number of protons, which defines the atomic number of the element. For example, all carbon
atoms have six protons, and all oxygen atoms have eight protons. A combination of the number of protons and
neutrons in the nucleus gives the approximate atomic mass of the atom, measured in an amu, or atomic mass unit.
For example, hydrogen has an atomic number of 1 and an atomic mass of 1.00794 amu; carbon has an atomic number
of 6 and an atomic mass of 12.0107 amu; oxygen has an atomic number of 8 and an atomic mass of 15.9994 amu.
See the Dynamic Periodic Table at http://www.ptable.com for additional information.
Over 100 elements can be seen in this video http://www.youtube.com/watch?v=LFsdbLFHgY8 (10:00).

97

2.1. Chemical Substances - Advanced

www.ck12.org

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/193

FIGURE 2.2
Model of an Atom.

The protons and

neutrons of this atom make up its nucleus.


Electrons surround the nucleus.

The majority of known elements are classified as metals. Metals are elements that are lustrous, or shiny. They
are also good conductors of electricity and heat. Examples of metals include iron, gold, and copper. Fewer than
20 elements are classified as nonmetals. Nonmetals lack the properties of metals. Examples of nonmetals include
oxygen, hydrogen, and sulfur. Certain other elements have properties of both metals and nonmetals. They are known
as metalloids. Examples of metalloids include silicon and boron.
The Element Song can be heard at http://www.youtube.com/watch?v=DYW50F42ss8 (1:24).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/194

Chemical Compounds

A chemical compound is a new substance that forms when atoms of two or more elements react with one another. A
chemical reaction is a process that changes some chemical substances into other chemical substances. A compound
that results from a chemical reaction always has a unique and fixed chemical composition. The substances in the
compound can be separated from one another only by another chemical reaction. This is covered further in Concept
Biochemistry (Advanced). Atoms bond with each other through the interactions of their electrons, specifically their
outermost or valence electrons.
98

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

The atoms of a compound are held together by chemical bonds. Chemical bonds form when atoms share electrons.
There are different types of chemical bonds, and they vary in how strongly they hold together the atoms of a
compound. Two of the strongest types of bonds are covalent and ionic bonds. Covalent bonds form between
atoms that have little if any difference in electronegativity, and result when atoms share electrons. Electronegativity
is the power of an atom to attract electrons toward itself. Ionic bonds, in contrast, form between atoms that are
significantly different in electronegativity. An ion is an atom that has gained or lost at least one electron. Ionic bonds
form between ions of opposite charges.
An example of a chemical compound is water. A water molecule forms when oxygen (O) and hydrogen (H)
atoms react and are held together by covalent bonds. Like other compounds, water always has the same chemical
composition: a 2:1 ratio of hydrogen atoms to oxygen atoms. This is expressed in the chemical formula H2 O. A
model of a water molecule is shown in Figure 2.3.

FIGURE 2.3
Model of a water molecule, showing the
arrangement of hydrogen and oxygen
atoms. The protons (8 in oxygen, 1 in
hydrogen) and neutrons (8 in oxygen) are
depicted in the nucleus.

Compounds that contain mainly the elements carbon and hydrogen are called organic compounds. This is because
they are found mainly in living organisms. Most organic compounds are held together by covalent bonds. An
example of an organic compound is glucose (C6 H12 O6 ), which is shown in Figure 2.4. Glucose is a simple sugar
that living cells use for energy. All other compounds are called inorganic compounds. Water is an example of an
inorganic compound.
A short animation describing chemical compounds can be seen at http://www.youtube.com/watch?v=-HjMoTthEZ0
(3:53).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/195

99

2.1. Chemical Substances - Advanced

www.ck12.org

FIGURE 2.4
Glucose Molecule. This model represents
a molecule of glucose, an organic compound composed of carbon, hydrogen,
and oxygen.

The chemical formula for

glucose is C6 H12 O6 .

This means that

each molecule of glucose contains six


carbon atoms, twelve hydrogen atoms,
and six oxygen atoms. NOTE: Each unlabeled point where lines intersect represents another carbon atom. Some of
these carbons and the oxygen atom are
bonded to another hydrogen atom, not
shown here.

Mixtures vs. Compounds

Like a chemical compound, a mixture consists of more than one chemical substance. Unlike a compound, a mixture
does not have a fixed chemical composition. The substances in a mixture can be combined in any proportions. A
mixture also does not involve a chemical reaction. Therefore, the substances in a mixture are not changed into unique
new substances, and they can be separated from each other without a chemical reaction.
The following examples illustrate these differences between mixtures and compounds. Both examples involve the
same two elements: the metal iron (Fe) and the nonmetal sulfur (S).
When iron filings and sulfur powder are mixed together in any ratio, they form a mixture. No chemical reaction
occurs, and both elements retain their individual properties. A magnet can be used to mechanically separate
the two elements by attracting the iron filings out of the mixture and leaving the sulfur behind.
When iron and sulfur are mixed together in a certain ratio and heated, a chemical reaction occurs. This
results in the formation of a unique new compound, called iron sulfide (FeS). A magnet cannot be used to
mechanically separate the iron from the iron sulfide because metallic iron does not exist in the compound.
Instead, another chemical reaction is required to separate the iron and sulfur.
Vocabulary

atom: The smallest particle of an element that still characterizes the element.
100

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

chemical compound: Unique substance with a fixed composition that forms when atoms of two or more
elements react.
chemical reaction: A process that changes some chemical substances into other chemical substances.
chemical substance: A material that has a definite chemical composition; may be an element or a chemical
compound.
element: Pure substance made up of just one type of atom.
ion: An atom that has gained or lost at least one electron.
matter: All the substances of which things are made.
mixture: Combination of chemical substances that does not have a fixed composition and does not result from
a chemical reaction.
organic compound: Compound found in living organisms; contains mainly carbon.
periodic table: A tabular display of the chemical elements; organized on the basis of their atomic numbers,
electron configurations, and chemical properties.
Summary

Matter consists of elements and compounds.


A compound forms when elements combine in fixed proportions and undergo a chemical reaction.
A mixture forms when substances combine in any proportions without a chemical reaction.
Explore More

Use this resource to answer the questions that follow.


Elements and Atoms at http://www.khanacademy.org/science/chemistry/v/elements-and-atoms .

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139351

1.
2.
3.
4.
5.
6.

What is an element?
How do elements relate to atoms?
Most of all living organisms is made out of what element?
What are the fundamental particles of an atom? What defines an element?
How many protons does carbon have?
What is the role of the electrons?

Review

1.
2.
3.
4.

Define element, and give an example of an element.


State how a compound differs from an element, and give an example of a compound.
Compare and contrast mixtures and compounds.
Describe the difference between an ionic bond and a covalent bond.

101

2.2. The Significance of Carbon - Advanced

www.ck12.org

2.2 The Significance of Carbon - Advanced

Explain why carbon is essential to life on Earth.


Give examples of carbohydrates, lipids, proteins, and nucleic acids.
List the functions of carbohydrates, lipids, proteins, and nucleic acids.
Name the monomers of the four classes of organic compounds.
Compare condensation to hydrolysis reactions.

Carbon. Element number six. Right in the middle of the first row of the Periodic Table. So what?
Carbon is the most important element to life. Without this element, life as we know it would not exist. As you will
see, carbon is the central element in compounds necessary for life-organic compounds. These compounds include
carbohydrates, lipids, proteins and nucleic acids.
The Significance of Carbon

Why is carbon so important to organisms? The answer lies with carbons unique properties. Carbon has an
exceptional ability to bind with a wide variety of other elements. Carbon makes four electrons available to form
covalent chemical bonds, allowing carbon atoms to form multiple stable bonds with other small atoms, including
hydrogen, oxygen, and nitrogen. Carbon atoms can also form stable bonds with other carbon atoms. In fact, a carbon
atom may form single, double, or even triple bonds with other carbon atoms. This allows carbon atoms to form a
tremendous variety of very large and complex molecules.
Organic Compounds

Carbon has the ability to form very long chains of interconnecting C-C bonds. This property allows carbon to form
the backbone of organic compounds, carbon-containing compounds, which are the basis of all known organic life.
Nearly 10 million carbon-containing organic compounds are known. Types of carbon compounds in organisms
102

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

include carbohydrates, lipids, proteins, and nucleic acids. The elements found in each type are listed in the table
below. Elements other than carbon and hydrogen usually occur within organic compounds in smaller groups of
elements called functional groups. When organic compounds react with other compounds, generally just the
functional groups are involved. Therefore, functional groups generally determine the nature and functions of organic
compounds.
When combined with oxygen and hydrogen, carbon can form many groups of important biological compounds
including carbohydrates (sugars), lignans (important in plants), chitins (the main component of the cell walls of
fungi, the exoskeletons of arthropods), alcohols, lipids and fats (triglycerides), and carotenoids (plant pigment). With
nitrogen it forms alkaloids, and with the addition of sulfur in addition to the nitrogen, it forms amino acids which
bind together to form proteins, antibiotics, and rubber products. With the addition of phosphorus to these other
elements, carbon forms nucleotides which bond into nucleic acids (DNA and RNA), and adenosine triphosphate
(ATP), which is known as the energy currency of the cell. The properties of all these organic molecules is related to
the composition of the elements that compose the molecule. Certain carbohydrates, proteins and nucleic acids are
known as macromolecules, as they are very large polymers made of individual monomers.
The Miracle of Life: Carbohydrates, Proteins, Lipids Nucleic Acids video can be viewed at http://www.youtube.c
om/watch?v=nMevuu0Hxuc (3:28).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/196

A Comparison

TABLE 2.1: Organic Compounds


Type of Compound
Carbohydrates

Elements It Contains
carbon, hydrogen, oxygen

Examples
Glucose, Starch, Glycogen

Lipids

carbon, hydrogen, oxygen

Cholesterol, Triglycerides
(fats), Phospholipids

Proteins

carbon, hydrogen, oxygen, nitrogen, sulfur

Enzymes, Antibodies

Nucleic Acids

carbon, hydrogen, oxygen, nitrogen, phosphorus

Deoxyribonucleic
acid
(DNA),
Ribonucleic
acid (RNA), Adenosine
Triphosphate (ATP)

Functions
provides energy to cells,
stores energy, forms body
structures
stores energy, forms cell
membranes, carries messages
helps cells keep their
shape/structure,
makes
up muscles, catalyzes
chemical
reactions,
carries messages and
materials
contains instructions for
proteins, passes instructions from parents to offspring, helps make proteins

103

2.2. The Significance of Carbon - Advanced

www.ck12.org

The Table 2.1 lists the four types of organic compounds, the elements they contain, and examples and functions of
each type of compound.
Condensation and Hydrolysis

Condensation reactions are the chemical processes by which large organic compounds are synthesized from their
monomeric units. Hydrolysis reactions are the reverse process. During condensation reactions, water is produced
from the two molecules being bonded together; an H from one monomer is joined to an -OH from another molecule,
producing H2 O.

TABLE 2.2: title


Polymer
carbohydrates
lipids
proteins
nucleic acids

Monomer
monosaccharides
fatty acid
amino acids
nucleotides

Bond
glycosidic
ester*
peptide
phosphodiester**

The ester linkage is between a glycerol molecule and fatty acid chain.
See http://www.biotopics.co.uk/as/condensation_and_hydrolysis.html for additional information.

Vocabulary

adenosine triphosphate (ATP): Energy-carrying molecule that cells use to power their metabolic processes;
energy-currency of the cell.
amino acid: Small molecule that is a building block of proteins; the monomer of a polypeptide.
carbohydrate: Organic compound such as sugar or starch; major source of energy to living cells.
condensation reaction: A chemical reaction in which two molecules combine to form one single molecule,
together with the loss of a small molecule, often water.
functional group: Part of organic compound that generally determines the nature and functions of the
compound.
hydrolysis reaction: A chemical process in which a molecule of water is split, resulting in the separation of a
large molecule into two smaller molecules.
lipid: Organic compound such as fat or oil.
macromolecule: A large molecule composed of individual monomer units.
nucleic acid: Organic compound such as DNA or RNA.
nucleotide: Monomer of nucleic acids, composed of a nitrogen-containing base, a five-carbon sugar, and a
phosphate group.
organic compound: Compound found in living organisms; contains mainly carbon.
protein: Organic compound made of amino acids.

Summary

Carbons exceptional ability to form bonds with other elements and with itself allows it to form a huge number
of large, complex molecules called organic molecules. These molecules make up organisms and carry out life
processes.
104

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

Review

1.
2.
3.
4.
5.

Why is carbon essential to all known life on Earth?


What is an organic compound? Give an example.
List the four main classes of organic compounds. What are examples of each?
What is condensation of hydrolysis?
What is a phosphodiester bond?

105

2.3. Carbohydrates - Advanced

www.ck12.org

2.3 Carbohydrates - Advanced

Describe the structure and function of carbohydrates.


State the formula of glucose.
Distinguish between monosaccharides, disaccharides, and polysaccharides.
Describe the structure and function of complex carbohydrates.

Sugar. Does this look like biological energy?


As a child, you may have been told that sugar is bad for you. Well, thats not exactly true. Essentially, carbohydrates
are made of sugar, from a single sugar molecule to thousands of sugar molecules all attached together. Why? One
reason is to store energy. But that does not mean you should eat it by the spoonful.
Carbohydrates

Carbohydrates are organic compounds that contain only carbon (C), hydrogen (H), and oxygen (O). They are the
most common of the four major types of organic compounds. There are thousands of different carbohydrates, but
they all consist of one or more smaller units called monosaccharides.
Monosaccharides and Disaccharides

The general formula for a monosaccharide is (CH2 O)n , where n can be any number greater than two. For example,
if n is 6, then the formula can be written C6 H12 O6 . This is the formula for the monosaccharide glucose. Another monosaccharide, fructose, has the same chemical formula as glucose, but the atoms are arranged differently.
Molecules with the same chemical formula but with atoms in a different arrangement are called isomers. Compare
the glucose and fructose molecules in Figure 2.5. Can you identify their differences? The only differences are the
positions of some of the atoms. These differences affect the properties of the two monosaccharides.
106

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

Monosaccharides can be classified by the number of carbon atoms they contain: diose (2), triose (3), tetrose (4),
pentose (5), hexose (6), heptose (7), and so on.
In addition to glucose, other common monosaccharides include fructose ("fruit sugar"), galactose, xylose ("wood
sugar") and ribose (in RNA) and deoxyribose (in DNA).
If two monosaccharides bond together, they form a carbohydrate called a disaccharide. Two monosaccharides
will bond together through a dehydration reaction, in which a water molecule is lost. A dehydration reaction is a
condensation reaction, a chemical reaction in which two molecules combine to form one single molecule, losing
a small molecule in the process. In the dehydration reaction, this small molecule is water. The bond between two
monosaccharides is known as a glycosidic bond.
An example of a disaccharide is sucrose (table sugar), which consists of the monosaccharides glucose and fructose
( Figure 2.5). Other common disaccharides include lactose ("milk sugar") and maltose. Monosaccharides and
disaccharides are also called simple sugars. They provide the major source of energy to living cells.

FIGURE 2.5
Sucrose Molecule. This sucrose molecule
is a disaccharide. It is made up of two
monosaccharides: glucose on the left and
fructose on the right.

Sucrose forms

through a condensation reaction: glucose


(C6 H12 O6 ) + fructose (C6 H12 O6 ) sucrose
(C12 H22 O11 ).

Oligosaccharides

An oligosaccharide is a saccharide polymer containing a small number (typically two to ten) of monosaccharides.
Oligosaccharides can have many functions; for example, they are commonly found on the plasma membrane of
animal cells where they can play a role in cellcell recognition. In general, they are found attached to compatible
amino acid side-chains in proteins or to lipids.
Oligosaccharides are often found as a component of glycoproteins or glycolipids. They are often used as chemical
markers on the outside of cells, often for cell recognition. An example is ABO blood type specificity. A and B
blood types have two different oligosaccharide glycolipids embedded in the cell membranes of the red blood cells,
AB-type blood has both, while O blood type has neither.

Polysaccharides

Polysaccharides are long carbohydrate molecules of repeated monomer units joined together by glycosidic bonds. A
polysaccharide may contain anywhere from a few monosaccharides to several thousand monosaccharides. Polysaccharides are also called complex carbohydrates. Polysaccharides have a general formula of Cx (H2O)y , where x is
107

2.3. Carbohydrates - Advanced

www.ck12.org

usually a large number between 200 and 2500. Considering that the repeating units in the polymer backbone are
often six-carbon monosaccharides, the general formula can also be represented as (C6 H10 O5 )n , where 40n3000.
Starches are one of the more common polysaccharides. Starch is made up of a mixture of amylose (1520%) and
amylopectin (8085%). Amylose consists of a linear chain of several hundred glucose molecules and amylopectin
is a branched molecule made of several thousand glucose units. Starches can be digested by hydrolysis reactions,
catalyzed by enzymes called amylases, which can break the glycosidic bonds. Humans and other animals have
amylases, so they can digest starches. Potato, rice, wheat, and maize are major sources of starch in the human diet.
The formations of starches are the ways that plants store glucose. Glycogen is sometimes referred to as animal
starch. Glycogen is used for long-term energy storage in animal cells. Glycogen is made primarily by the liver and
the muscles.
The main functions of polysaccharides are to store energy and form structural tissues. Examples of several other
polysaccharides and their roles are listed in the Table 2.3. These complex carbohydrates play important roles in
living organisms.

TABLE 2.3: Complex Carbohydrates


Complex Carbohydrate
Starch

Function
Stores energy

Organism
Plants

Amylose
Glycogen

Stores energy
Stores energy

Plants
Animals

Cellulose

Forms cell walls

Plants

Chitin

Forms an exoskeleton

Some animals

108

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

KQED: Biofuels: From Sugar to Energy

For years theres been buzz both positive and negative about generating ethanol fuel from corn. But thanks to
recent developments, the Bay Area of California is rapidly becoming a world center for the next generation of
green fuel alternatives. The Joint BioEnergy Institute is developing methods to isolate biofeuls from the sugars
in cellulose. See Biofuels: Beyond Ethanol at http://www.kqed.org/quest/television/biofuels-beyond-ethanol for
further information.

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/466

Vocabulary

amylase: An enzyme that catalyses the breakdown of starch into sugars; present in human saliva.
carbohydrate: Organic compound such as sugar or starch; major source of energy to living cells.
complex carbohydrate: Carbohydrates with three or more monosaccharides bonded together.
condensation reaction: A chemical reaction in which two molecules combine to form one single molecule,
together with the loss of a small molecule, often water.
disaccharide: A carbohydrate composed of two monosaccharides.
glycogen: A carbohydrate used for long-term energy storage in animal cells; human muscle and liver cells
store energy in this form.
glycolipid: A lipid with a carbohydrate attached; provides energy and serves as markers for cellular recognition.
glycoprotein: A protein that contain oligosaccharide chains (glycans) covalently attached to polypeptide sidechains; often important integral membrane proteins, where they play a role in cellcell interactions.
glycosidic bond: A covalent bond that joins a carbohydrate molecule to another group, which may or may not
be another carbohydrate.
hydrolysis reaction: A chemical process in which a molecule of water is split, resulting in the separation of a
large molecule into two smaller molecules.
isomers: Molecules with the same chemical formula but with differently arranged atoms.
monosaccharide: A simple sugar such as glucose; the building block of carbohydrates.
oligosaccharide: A saccharide polymer containing a small number (typically two to ten) of monosaccharides.
polysaccharide: A chain of monosaccharides; a complex carbohydrate such as starch or glycogen.
starch: A carbohydrate used for long-term energy storage in plant cells.

Summary

Carbohydrates are organic molecules that consist of carbon, hydrogen, and oxygen. They are made up of
repeating units called saccharides. They provide cells with energy, store energy, and form structural tissues.
Review

1. What are carbohydrates?


2. State the function of monosaccharides, such as glucose and fructose.
3. Compare and contrast simple sugars and complex carbohydrates.
109

2.3. Carbohydrates - Advanced


4. What are glycoproteins and glycolipids?
5. Give examples of polysaccharides.

110

www.ck12.org

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

2.4 Lipids - Advanced


Describe the structure and function of lipids.
Distinguish between saturated and unsaturated fatty acids.
Name and describe various types of lipids.

Oil. Does it mix with water? No. Biologically, why is this important?
Oil is a lipid. The property of chemically not being able to mix with water gives lipids some very important biological
functions. A particular type of lipid - the phospholipid - is the main component of the outer membrane of all cells.
Why?
Lipids

Lipids are organic compounds that contain mainly carbon, hydrogen, and oxygen. They include substances such as
fats and oils, as well as waxes, sterols, some vitamins (A, D, E and K) and phospholipids. Lipid molecules consist of
fatty acids, with or without additional molecules. Fatty acids are organic compounds that have the general formula
CH3 (CH2 )n COOH, where n usually ranges from 2 to 28 and is always an even number.
A distinguishing feature of lipids is that they are insoluble in water. The main biological functions of lipids include
energy storage, as the major structural component of cell membranes, and as important signaling molecules.
Saturated and Unsaturated Fatty Acids

Fatty acids can be saturated or unsaturated. The term saturated refers to the placement of hydrogen atoms around
the carbon atoms. In a saturated fatty acid, all the carbon atoms (other than the carbon in the -COOH group) are
111

2.4. Lipids - Advanced

www.ck12.org

bonded to as many hydrogen atoms as possible (usually two hydrogens). Saturated fatty acids do not contain any
other groups except the -COOH. This is why they form straight chains, as shown in Figure 2.6. Because of this
structure, saturated fatty acids can be packed together very tightly. This allows organisms to store chemical energy
very densely. The fatty tissues of animals contain mainly saturated fatty acids.

FIGURE 2.6
Saturated and Unsaturated Fatty Acids.
Saturated fatty acids include arachidic,
stearic, and palmitic fatty acids. Unsaturated fatty acids include all the other fatty
acids in the figure.

Notice how all the

unsaturated fatty acids have bent chains,


whereas the saturated fatty acids have
straight chains.

In an unsaturated fatty acid, some carbon atoms are not bonded to the maximum number of hydrogen atoms.
This is because they are bonded to one or more additional groups, including double and triple bonds between
carbons. Wherever these other groups bind with carbon, they cause the chain to bend - they do not form straight
chains ( Figure 2.6). This gives unsaturated fatty acids different properties than saturated fatty acids. For example,
unsaturated fatty acids are liquids at room temperature whereas saturated fatty acids are solids. Unsaturated fatty
acids are found mainly in plants, especially in fatty tissues such as nuts and seeds.
Unsaturated fatty acids occur naturally in the bent shapes shown in Figure 2.6. However, unsaturated fatty acids
can be artificially manufactured to have straight chains like saturated fatty acids. Called trans fatty acids, these
synthetic lipids were commonly added to foods until it was found that they increased the risk for certain health
problems. Many food manufacturers no longer use trans fatty acids for this reason.

FIGURE 2.7
These plant products all contain unsaturated fatty acids.

112

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

Types of Lipids

Lipids may consist of fatty acids alone or in combination with other compounds. Several types of lipids consist of
fatty acids combined with a molecule of alcohol:
Triglycerides are the main form of stored energy in animals. This type of lipid is commonly called fat.
Triglycerides are composed of a glycerol and three fatty acid chains. An example is shown in Figure 2.8.
In humans, triglycerides are a mechanism for storing unused calories, and their high concentration in blood
correlates with the consumption of excess starches and other carbohydrate-rich foods.
Phospholipids are a major component of the membranes surrounding the cells of all organisms, as they have
the ability to form bilayers. The structure of the phospholipid molecule consists of two hydrophobic tails (a
diglyceride made of two fatty acid chains) and a hydrophilic head (a phosphate group, PO4 3 ).
Steroids (or sterols) have several functions. Sterols are a subgroup of steroids. The sterol cholesterol is an
important part of cell membranes and plays other vital roles in the body. Cholesterol is a precursor to fatsoluble vitamins and steroid hormones. Steroid hormones include the male and female sex hormones. Sterols
also have roles as second messengers in signalling pathways.
FIGURE 2.8
Triglyceride Molecule. The left part of this
triglyceride molecule represents glycerol.
Each of the three long chains on the right
represents a different fatty acid. From top
to bottom, the fatty acids are palmitic acid,
oleic acid, and alpha-linolenic acid. The
chemical formula for this triglyceride is
C55 H98 O6 . KEY: H=hydrogen, C=carbon,
O=oxygen

Lipids and Diet

Humans need lipids for many vital functions such as storing energy and forming cell membranes. Lipids can also
supply cells with energy. In fact, a gram of lipids supplies more than twice as much energy as a gram of carbohydrates
or proteins. Lipids are necessary in the diet for most of these functions. Although the human body can manufacture
most of the lipids it needs, there are others, called essential fatty acids, that must be consumed in food. Essential
fatty acids include omega-3 and omega-6 fatty acids. Both of these fatty acids are needed for important biological
processes, not just for energy.
Although some lipids in the diet are essential, excess dietary lipids can be harmful. Because lipids are very high
in energy, eating too many may lead to unhealthy weight gain. A high-fat diet may also increase lipid levels in the
blood. This, in turn, can increase the risk for health problems such as cardiovascular disease. The dietary lipids
of most concern are saturated fatty acids, trans fats, and cholesterol. For example, cholesterol is the lipid mainly
responsible for narrowing arteries and causing the disease atherosclerosis.
Vocabulary

cholesterol: A steroid alcohol that is present in animal cells and body fluids, regulates membrane fluidity, and
functions as a precursor molecule in various metabolic pathways.
113

2.4. Lipids - Advanced

www.ck12.org

essential fatty acids: Fatty acids that humans and other animals must ingest.
fatty acids: A component of triglycerides and phospholipids; a carboxylic acid (-COOH) with a long hydrocarbon tail, which is either saturated or unsaturated.
lipid: Organic compound such as fat or oil.
phospholipid: A major component of the cell membrane; consists of two hydrophobic tails and a hydrophilic
phosphate head group.
saturated fatty acid: Fatty acid (lipid) with carbon atoms bonded to the maximum number of hydrogen
atoms; contains only single bonds between carbon atoms.
second messenger: A molecule that relays a signal from a receptor on the cell surface to target molecules
inside the cell.
steroid: A type of lipid; examples include cholesterol and the sex hormones.
trans fatty acid: Unsaturated fatty acid artificially manufactured to have straight fatty acid chains, like
saturated fatty acids.
triglycerides: The main form of stored energy in animals; commonly called fat; composed of a glycerol and
three fatty acid chains.
unsaturated fatty acid: Fatty acid (lipid) with double or triple bonds between carbon atoms; does not contain
the maximum number of hydrogen atoms.
Summary

Lipids are organic compounds that consist of carbon, hydrogen, and oxygen. They are made up of fatty acids
and other compounds. They provide cells with energy, store energy, and help form cell membranes.
Review

1.
2.
3.
4.
5.

114

What are lipids? Give examples of lipids?


Why do molecules of saturated and unsaturated fatty acids have different shapes?
Describe the structure and role of phospholipids.
What type of organic compound is represented by the formula CH3 (CH2 )4 COOH? How do you know?
What are essential fatty acids?

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

2.5 Proteins - Advanced


Give examples of protein functions.
Identify the general structure of an amino acid.
Describe the four levels of protein structure.

You may have been told proteins are good for you. Do these look good to you?
Proteins as food? To you, these may not look appetizing (or they might), but they do provide a nice supply of amino
acids, the building blocks of proteins. Proteins have many important roles, from transporting, signaling, receiving,
and catalyzing to storing, defending, and allowing for movement. Where do you get the amino acids needed so your
cells can make their own proteins? If you cannot make the amino acids yourself - and some of them you cannot
make - then you must eat them.
Proteins

Proteins are organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and, in some cases, sulfur. These
compounds may many essential functions within the cell (see below). Proteins are made of smaller units called
amino acids. There are 20 different common amino acids needed to make proteins. All amino acids have the same
basic structure, which is shown in Figure 2.9. Only the side chain (labeled R in the figure) differs from one amino
acid to another. These side chains can vary in size from just one hydrogen atom in glycine to a large heterocyclic
group in tryptophan. The variable side chain gives each amino acid unique properties. The side chains can also
characterize the amino acid as (1) nonpolar or hydrophobic, (2) neutral (uncharged) but polar, (3) acidic, with a net
negative charge, and (4) basic, with a net positive charge at neutral pH.
Proteins can differ from one another in the number and sequence (order) of amino acids. It is because of the side
chains of the amino acids that proteins with different amino acid sequences have different shapes and different
chemical properties. Small proteins can contain just a few hundred amino acids. Yeast proteins average 466 amino
115

2.5. Proteins - Advanced

www.ck12.org

acids. The largest known proteins are the titins, found in muscle, which are composed from over 27,000 amino acids.

FIGURE 2.9
General Structure of Amino Acids. This
model shows the general structure of all
amino acids.

Only the side chain, R,

varies from one amino acid to another.


For example, in the amino acid glycine,
the side chain is simply hydrogen (H). In
glutamic acid, in contrast, the side chain
is CH2 CH2 COOH. Variable side chains
give amino acids acids different chemical
properties.

The order of amino acids,

together with the properties of the amino


acids, determines the shape of the protein, and the shape of the protein determines the function of the protein. KEY: H
= hydrogen, N = nitrogen, C = carbon, O
= oxygen, R = variable side chain

Protein Structure

Amino acids can bond together through peptide bonds to form short chains called peptides or longer chains called
polypeptides ( Figure 2.10). A peptide bond is a covalent bond formed from a condensation reaction between two
molecules, causing the release of a molecule of water. This bond usually forms between two amino acids, hence
forming a peptide or polypeptide. Peptide bonds between amino acids are formed during the process of translation.
Polypeptides may have as few as 40 amino acids or as many as several thousand. A protein consists of one or more
polypeptide chains. The sequence of amino acids in a proteins polypeptide chain(s) determines the overall structure
and chemical properties of the protein.
The amino acid sequence is the primary structure of a protein. As explained in Figure 2.11, a protein may have up
to four levels of structure, from primary to quaternary. The complex structure of a protein allows it to carry out its
biological functions.
Secondary structure refers to local sub-structures generated from the primary structure, usually involving alpha helix
and beta pleated sheet structures. These secondary structures form through hydrogen bonding between amino acids.
Tertiary structure refers to the three-dimensional structure of a single polypeptide. The alpha-helices and beta-sheets
are folded into a compact globule structure. Stability is maintained through hydrogen bonds, disulfide bonds and
other interactions.
Quaternary structure is a larger assembly of several polypeptide chains, now referred to as subunits of the protein.
The quaternary structure is stabilized by the same interactions as the tertiary structure. Complexes of two or more
polypeptides are called multimers. Specifically, a dimer contains two subunits, a trimer contains three subunits, and
a tetramer contains four subunits.
The atomic mass of proteins is measured in kilodaltons (kDa). One dalton (Da) is approximately equal to the mass
of one proton or one neutron, so a carbon atom has a mass of approximately 12 Da. The molecular weights of amino
116

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

FIGURE 2.10
Polypeptide. This polypeptide is a chain
made up of many linked amino acids.

FIGURE 2.11
Protein Structure. Primary protein structure is the sequence of amino acids in
a single polypeptide.

Secondary pro-

tein structure refers to internal shapes,


such as alpha helices and beta pleated
sheets, that a single polypeptide takes
on due to bonds between atoms in different parts of the polypeptide.

Ter-

tiary protein structure is the overall threedimensional shape of a protein consisting of one polypeptide. Quaternary protein structure is the shape of a protein
consisting of two or more polypeptides.
For a brief animation of protein structure,
see www.stolaf.edu/people/giannini/flash
animat/proteins/protein%20structure.swf
.

acids range from 75 Da for glycine to 204 for tryptophan. Human proteins may have molecular weights ranging
from a low of about 3.7 kDA to titian, the largest known human protein with 34,350 amino acids and a molecular
weight of approximately 3,816.2 kDa.

Functions of Proteins

Proteins are an essential part of all organisms. They play many roles in living things. Certain proteins provide a
scaffolding that maintains the shape of cells (structural proteins). Proteins also make up the majority of muscle
tissues. Many proteins are enzymes that speed up chemical reactions in cells. Enzymes interact with the substrates
(reactants) of a biochemical reaction, helping the reaction proceed at a much faster rate. Other proteins are antibodies that protect you from pathogens. Antibodies bond to foreign substances in the body and target them for
117

2.5. Proteins - Advanced

www.ck12.org

destruction. Still other proteins help carry messages or materials in and out of cells (transport proteins) or around
the body. For example, the blood protein hemoglobin (see Figure 2.12) bonds with oxygen and carries it from the
lungs to cells throughout the body.

FIGURE 2.12
Hemoglobin Molecule. This model represents the protein hemoglobin. The red
parts of the molecule contain iron. The
iron binds with oxygen molecules.

A short video describing protein function can be viewed at http://www.youtube.com/watch?v=T500B5yTy58 (4:02).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/197

One of the most important traits of proteins, allowing them to carry out these functions, is their ability to bond with
other molecules. They can bond with other molecules very specifically and tightly. This ability, in turn, is due to the
complex and highly specific structure of protein molecules. The structure-function relationship of proteins is an
important principle of biology. A slight difference in the structure of a protein can lead to a difference in the function
of that protein, and this can have devastating effects on the cell or organism.

Proteins and Diet

Proteins in the diet are necessary for life. Dietary proteins are broken down into their component amino acids
when food is digested. Cells can then use the components to build new proteins. Humans are able to synthesize
all but nine of the twenty common amino acids. These nine amino acids, called essential amino acids, must be
consumed in foods. Like dietary carbohydrates and lipids, dietary proteins can also be broken down to provide cells
with energy. The amino acids regarded as essential for humans are phenylalanine, valine, threonine, tryptophan,
118

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

isoleucine, methionine, leucine, lysine, and histidine. Additionally, cysteine, tyrosine and arginine are required by
infants and growing children.
In addition, certain amino acids (arginine, cysteine, glycine, glutamine, histidine, proline, serine and tyrosine) are
considered conditionally essential, meaning they are not normally required in the diet, but must be supplied to
specific populations that do not synthesize them in adequate amounts. An example would be with the disease
phenylketonuria (PKU). Individuals with PKU must keep their intake of phenylalanine extremely low to prevent
mental retardation and other metabolic complications. However, they cannot synthesize tyrosine from phenylalanine,
so tyrosine becomes essential in the diet of PKU patients. PKU can be easily detected with a simple blood
test. All states in the US require a PKU screening test for all newborns as part of the newborn screening panel.
These individuals are placed on a special diet as soon as the disease is detected, a diet that is extremely low in
phenylalanine, particularly when the child is growing. The diet must be strictly followed. Those who continue the
diet into adulthood have better physical and mental health. Maintaining the diet for life has become the standard
recommended by most experts.

Vocabulary

amino acid: Small molecule that is a building block of proteins; the monomer of a polypeptide.
antibody: A large, Y-shaped protein produced by B cells; recognizes and binds to antigens in a humoral
immune response; also known as immunoglobulins (Ig).
enzyme: Chemical, usually a protein, that speeds up chemical reactions in organisms; a biological catalyst.
essential amino acid: An amino acid that cannot be synthesized by the organism, and therefore must be
supplied in the diet.
hemoglobin: The iron-containing oxygen-transport protein found in red blood cells; allows oxygen to be
transported in the blood.
kilodalton: 1,000 daltons; a unit that is used for indicating mass on an atomic or molecular scale; a dalton is
defined as one twelfth of the mass carbon-12 atom.
peptide bond: A covalent chemical bond formed between two molecules; usually occurs between amino
acids; forms through the release of a molecule of water.
phenylketonuria (PKU): An autosomal recessive genetic disorder characterized the inability to metabolize
the amino acid phenylalanine.
polypeptide: A chain of amino acids that alone or with other such chains makes up a protein.
protein: Organic compound made of amino acids.
structure-function relationship: Principle that states the function of a biological item (molecule, protein,
cell) is determined by its structure.

Summary

Proteins are organic compounds that consist of carbon, hydrogen, oxygen, nitrogen, and, in some cases, sulfur.
They are made up of repeating units called amino acids. They provide cells with energy, form tissues, speed
up chemical reactions throughout the body, and perform many other cellular functions.

Explore More

Additional information can be found at:


Biomolecules - The Proteins at http://www.wisc-online.com/Objects/ViewObject.aspx?ID=AP13304 .
What is a Protein? at http://learn.genetics.utah.edu/content/begin/dna/ .
119

2.5. Proteins - Advanced

www.ck12.org

Review

1.
2.
3.
4.

120

What is a protein?
What determines the primary structure of a protein?
Describe the structural levels of proteins.
State three functions of proteins, and explain how the functions depend on the ability of proteins to bind other
molecules to them.

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

2.6 Nucleic Acids - Advanced

Describe the structure and function of nucleic acids.


Name the components of a nucleotide.
Compare DNA to RNA.
Describe the structure and function of ATP.

You may have heard that "its in your DNA." What does that mean?
Nucleic acids. Essentially the "instructions" or "blueprints" of life. Deoxyribonucleic acid, or DNA, is the unique
blueprints to make the proteins that give you your traits. Half of these blueprints come from your mother, and half
from your father. And they come in different combinations every time. In fact, every couple - every man and woman
that has every lived - together has over 64,000,000,000,000 combinations of their chromosomes, which is where the
DNA is found. Therefore, every person that has ever lived - except for identical twins - has his or her own unique
set of blueprints - or instructions - or DNA.
Nucleic Acids

Nucleic acids are organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. They are
made of smaller units called nucleotides. Nucleic acids are named for the nucleus of the cell, where some of them
are found. Nucleic acids are found not only in all living cells but also in viruses. Types of nucleic acids include
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Structure of Nucleic Acids

A nucleic acid consists of one chain (in RNA) or two chains (in DNA) of nucleotides held together by chemical
bonds. Each individual nucleotide unit consists of three parts:
121

2.6. Nucleic Acids - Advanced

www.ck12.org

a base (containing nitrogen)


a sugar (ribose in RNA, deoxyribose in DNA)
a phosphate group (containing phosphorus)

The sugar of one nucleotide binds to the phosphate group of the next nucleotide. Alternating sugars and phosphate
groups form the backbone of a nucleotide chain, as shown in Figure 2.13. The bases, which are bound to the sugars,
protrude from the backbone of the chain. In DNA, pairs of bases-one from each of two nucleotides-form the middle
section of the molecule.

FIGURE 2.13
Part of a Nucleic Acid (DNA). This small
section of a nucleic acid shows how phosphate groups and sugars alternate to form
the backbone of a nucleotide chain. The
bases that jut out to the side from the
backbone are adenine, thymine, cytosine,
and guanine. Hydrogen bonds between
complementary bases, such as between
adenine and thymine, hold the two chains
of nucleotides together.

An animation of DNA structure can be viewed at http://www.youtube.com/watch?v=qy8dk5iS1f0 (1:19).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/198

An overview of DNA can be seen at http://www.youtube.com/watch?v=_-vZ_g7K6P0 (28:05).

122

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/199

RNA consists of a single chain of nucleotides, and DNA consists of two chains of nucleotides. Bonds form between
the bases on the two chains of DNA and hold the chains together ( Figure 2.13). There are four different types of
bases in a nucleic acid molecule: cytosine (C), adenine (A), guanine (G), and either thymine (T) (in DNA) or uracil
(U) (in RNA). Each type of base bonds with just one other type of base. Cytosine and guanine always bond together,
and adenine and thymine (or uracil) always bond with one another. The pairs of bases that bond together are called
complementary bases.
The binding of complementary bases allows DNA molecules to take their well-known shape, called a double helix.
Figure 2.14 shows how two chains of nucleotides form a DNA double helix. A simplified double helix is illustrated
in Figure 2.15. It shows more clearly how the two chains are intertwined. The double helix shape forms naturally
and is very strong. Being intertwined, the two chains are difficult to break apart. This is important given the
fundamental role of DNA in all living organisms.

FIGURE 2.14
DNA Molecule. Hydrogen bonds between
complementary bases help form the double helix of a DNA molecule. The letters
A, T, G, and C stand for the bases adenine, thymine, guanine, and cytosine. The
sequence of these four bases in DNA is a
code that carries instructions for making
proteins. Shown is a representation of
how the double helix folds into a chromosome. In this double-stranded nucleic
acid, complementary bases (A and T, C
and G) form hydrogen bonds that hold
the two nucleotide chains together in the
shape of a double helix.

Notice that

A always bonds with T and C always


bonds with G. The hydrogen bonds help
maintain the double helix shape of the
molecule.

A brief overview of DNA, stressing the base-pairing rules, can be seen in the following animation: http://www.y
outube.com/watch?v=cwfO6SzGaEg (1:28).

123

2.6. Nucleic Acids - Advanced

www.ck12.org

FIGURE 2.15
Simple Model of DNA. In this simple
model of DNA, each line represents a
nucleotide chain. The double helix shape
forms when the two chains wrap around
the same axis.

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/200

Role of Nucleic Acids

The order of bases in nucleic acids is highly significant. The bases are like the letters of a four-letter alphabet. These
"letters" can be combined to form "words." Groups of three bases form words of the genetic code. Each code word,
called a codon, stands for a different amino acid. A series of many codons spells out the sequence of amino acids
in a polypeptide or protein ( Figure 2.16). In short, nucleic acids contain the information needed for cells to make
proteins. This information is passed from a body cell to its daughter cells when the cell divides. It is also passed
from parents to their offspring when organisms reproduce.
How RNA codes for Proteins

FIGURE 2.16
The letters G, U, C, and A stand for the
bases in RNA, specifically mRNA or messenger RNA. Each group of three bases
makes up a codon, and each codon represents one amino acid (represented here
by a single letter, such as V (valine), H
(histidine), or L (leucine)).

A string of

codons specifies the sequence of amino


acids in a protein.

DNA and RNA have different functions relating to the genetic code and proteins. Like a set of blueprints, DNA
contains the genetic instructions for the correct sequence of amino acids in proteins. RNA uses the information in
124

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

DNA to assemble the amino acids and make the proteins. More about the genetic code and the role of nucleic acids
will be discussed in Concept Molecular Biology (Advanced).

Adenosine Triphosphate

Adenosine Triphosphate (ATP), or Adenosine-5-triphosphate, is another important nucleic acid. ATP is described
as the "energy currency" of the cell or the "molecular unit of currency." One molecule of ATP contains three
phosphate groups, and it is produced by ATP synthase from inorganic phosphate and adenosine diphosphate (ADP)
or adenosine monophosphate (AMP). The structure of ATP consists of the purine base adenine, attached to the
1 carbon atom of the pentose sugar ribose. Three phosphate groups are attached at the 5 carbon atom of the
pentose sugar. It is the removal of these phosphate groups that convert ATP to ADP (adenosine diphosphate) and to
AMP (adenosine monophosphate). ATP is produced during cellular respiration, and will be further discussed in the
Cellular Respiration (Advanced) concepts.
ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and lipids, as
well as by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP (cAMP). The
ratio between ATP and AMP determines the amount of available energy. This regulates the metabolic pathways
that produce and consume ATP. Apart from its roles in energy metabolism and signaling, ATP is also incorporated
into DNA and RNA by polymerases during both DNA replication and transcription. When ATP is used in DNA
synthesis, the ribose sugar is first converted to deoxyribose by ribonucleotide reductase.

FIGURE 2.17
ATP. The ATP molecule clearly shows the
three phosphate groups.

See DNA and proteins are key molecules of the cell nucleus at http://www.dnaftb.org/15/animation.html for a
description of early work (starting in 1869) on DNA and proteins.

Vocabulary

Adenosine Triphosphate ( ATP): Energy-carrying molecule that cells use to power their metabolic processes;
energy-currency of the cell.
codon: A sequence of three nucleotides within mRNA; encodes for a specific amino acid or termination (stop)
sequence.
complementary bases: A pair of nucleotide bases that bond togethereither adenine and thymine (or uracil)
or cytosine and guanine; complementary base pair.
deoxyribonucleic acid ( DNA): Double-stranded nucleic acid that composes genes and chromosomes; the
hereditary material.
double helix: The double spiral shape of the DNA molecule; resembles a spiral staircase.
genetic code: The universal code of three-base codons; encodes the genetic instructions for the amino acid
sequence of proteins.
nucleic acid: organic compound such as DNA or RNA
125

2.6. Nucleic Acids - Advanced

www.ck12.org

nucleotide: Monomer of nucleic acids, composed of a nitrogen-containing base, a five-carbon sugar, and a
phosphate group.
ribonucleic acid ( RNA): Single-stranded nucleic acid; involved in protein synthesis.
Summary

Nucleic acids are organic compounds that consist of carbon, hydrogen, oxygen, nitrogen, and phosphorus.
DNA, RNA and ATP are important nucleic acids.
DNA and RNA are made up of repeating units called nucleotides. They contain genetic instructions for
proteins, help synthesize proteins, and pass genetic instructions on to daughter cells and offspring.
Explore More

Use this resource to answer the questions that follow.


http://www.youtube.com/watch?v=_-vZ_g7K6P0 : DNA: An Introduction to DNA.

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/199

1.
2.
3.
4.
5.
6.

What is DNA? Describe its shape.


What makes the "sides" and the "bridges" of the double helix?
What are the 2 base pairs?
How many base pairs are in 1 cell?
Briefly describe the process of transcription.
How many chromosomes are in a human cell?

Additional information can be viewed at


What is DNA? at http://learn.genetics.utah.edu/content/begin/dna/ .
Review

1.
2.
3.
4.

What is a nucleic acid?


Identify the three parts of a nucleotide.
What is the structure of DNA?
Bases in nucleic acids are represented by the letters A, G, C, and T (or U). How are the bases in nucleic acids
like the letters of an alphabet.
5. Describe the role and structure of ATP.

126

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

2.7 Water - Advanced


Describe the distribution of Earths water.
Give a brief outline of the water cycle.

Dihydrogen oxide or dihydrogen monoxide. Does this chemical sound dangerous?


Another name for this compound is. . . water. Water can create some absolutely beautiful sights. Iguassu Falls is
the largest series of waterfalls on the planet, located in Brazil, Argentina, and Paraguay. And water is necessary for
life. Water, like carbon, has a special role in biology because of its importance to organisms. Water is essential to
all known forms of life. Water, H2 O, such a simple molecule, yet it is this simplicity that gives water its unique
properties and explains why water is so vital for life.
The Wonder of Water video can be viewed at http://vimeo.com/7508571 http://vimeo.com/7508571 .

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139352

Water, Water Everywhere

"Water is the driving force of all nature," Leonardo da Vinci.


Water is a common chemical substance on Earth. The term water generally refers to its liquid state. Water is a liquid
over a wide range of standard temperatures and pressures. However, water can also occur as a solid (ice) or gas
(water vapor).
127

2.7. Water - Advanced

www.ck12.org

Where Is All the Water?

Of all the water on Earth, about two percent is stored underground in spaces between rocks. A fraction of a percent
exists in the air as water vapor, clouds, or precipitation. Another fraction of a percent occurs in the bodies of plants
and animals. So where is most of Earths water? Its on the surface of the planet. In fact, water covers about 70
percent of Earths surface. Of water on Earths surface, 97 percent is salt water, mainly in the ocean. Only 3 percent
is fresh water. Most of the fresh water is frozen in glaciers and polar ice caps. The remaining fresh water occurs in
rivers, lakes, and other fresh water features.

FIGURE 2.18
Most of the water on Earth consists of
saltwater in the oceans. What percent of
Earths water is fresh water? Where is
most of the fresh water found?

Although clean fresh water is essential to human life, in many parts of the world it is in short supply. The amount of
fresh water is not the issue. There is plenty of fresh water to go around, because water constantly recycles on Earth.
However, fresh water is not necessarily located where it is needed, and clean fresh water is not always available.

How Water Recycles

Like other matter on Earth, water is continuously recycled. Individual water molecules are always going through
the water cycle, in which molecules of water cycle through both the living and non-living parts of the biosphere
(discussed in the Recycling Matter: The Water Cycle (Advanced) concept). In fact, water molecules on Earth have
been moving through the water cycle for billions of years. In this cycle, water evaporates from Earths surface (or
escapes from the surface in other ways), forms clouds, and falls back to the surface as precipitation. This cycle keeps
repeating. Several processes change water from one state to another during the water cycle. They include:

128

EvaporationLiquid water on Earths surface changes into water vapor in the atmosphere.
SublimationSnow or ice on Earths surface changes directly into water vapor in the atmosphere.
TranspirationPlants give off liquid water, most of which evaporates into the atmosphere.
CondensationWater vapor in the atmosphere changes to liquid water droplets, forming clouds or fog.

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

PrecipitationWater droplets in clouds are pulled to Earths surface by gravity, forming rain, snow, or other
type of falling moisture.

FIGURE 2.19
Like other biogeochemical cycles, there is
no beginning or end to the water cycle. It
just keeps repeating.

Vocabulary

condensation: The process by which water vapor in the atmosphere changes to liquid water droplets, forming
clouds or fog.
evaporation: Liquid water on Earths surface changes into water vapor in the atmosphere.
fresh water: Naturally occurring water on the Earths surface in ice sheets, ice caps, glaciers, bogs, ponds,
lakes, rivers and streams, and underground as groundwater in aquifers and underground streams; characterized
by having low concentrations of dissolved salts and other total dissolved solids.
precipitation: Forms when water droplets in clouds become large enough to fall, forming rain, snow, or other
type of falling moisture.
sublimation: The transformation of snow and ice directly into water vapor; occurs as the snow and ice are
heated by the sun.
transpiration: A process by which plants lose water; occurs when stomata in leaves open to take in carbon
dioxide for photosynthesis and lose water to the atmosphere in the process.
water cycle: The continuous movement of water on, above and below the surface of the Earth; also called the
hydrologic cycle.
Summary

Most of Earths water is salt water located on the planets surface.


Water is constantly recycled through the water cycle, cycling through both the living and non-living parts of
the biosphere.
Explore More

Use this resource to answer the questions that follow.


129

2.7. Water - Advanced

www.ck12.org

http://www.hippocampus.org/Biology Non-Majors Biology Search: Properties of Water


1. What are all the physical properties of water that make is important to living things? Describe two properties.
2. Why is the specific heat of water important?
3. Why does ice float?
Review

1.
2.
3.
4.
5.

130

Where is most of Earths water? What percent of that is salt water?


Where is most of the fresh water on Earth?
What are the two concerns of fresh water?
What is the water cycle?
Draw a circle diagram to represent basic components of the water cycle. Identify the states of water and the
processes in which water changes state throughout the cycle.

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

2.8 Biochemical Properties of Water - Advanced

Identify the chemical structure of water.


Describe a polar molecule.
Deine hydrogen bond.
Explain how waters structure related to its unique properties.

What may be the most important molecule for life?


Some may argue DNA. Some may argue certain proteins. But many would argue water. And what makes water so
important? Its properties. The nature of the three atoms and how they interact with each other. This allows water to
be a polar molecule, which allows it to interact with many other molecules necessary for life. Most of the substances
in a cell are floating around in a water-based cytoplasmic environment.
Chemical Structure and Properties of Water

You are probably already familiar with many of waters properties. For example, you no doubt know that water is
tasteless, odorless, and transparent. In small quantities, it is also colorless. However, when a large amount of water
is observed, as in a lake or the ocean, it is actually light blue in color. The blue hue of water is an intrinsic property
and is caused by selective absorption and scattering of white light. These and other properties of water depend on
its chemical structure.
The transparency of water is important for organisms that live in water. Because water is transparent, sunlight can
pass through it. Sunlight is needed by water plants and other water organisms for photosynthesis.
Chemical Structure of Water

Each molecule of water consists of one atom of oxygen and two atoms of hydrogen, so it has the chemical formula
H2 O. The arrangement of atoms in a water molecule, shown in Figure 2.20, explains many of waters chemical
131

2.8. Biochemical Properties of Water - Advanced

www.ck12.org

properties. In each water molecule, the nucleus of the oxygen atom (with 8 positively charged protons) attracts
electrons much more strongly than do the hydrogen nuclei (with only one positively charged proton). This results in
a negative electrical charge near the oxygen atom (due to the "pull" of the negatively charged electrons toward the
oxygen nucleus) and a positive electrical charge near the hydrogen atoms. A difference in electrical charge between
different parts of a molecule is called polarity. A polar molecule is a molecule in which part of the molecule is
positively charged and part of the molecule is negatively charged.
FIGURE 2.20
This model shows the arrangement of
oxygen and hydrogen atoms in a water
molecule. A water molecule has a bent or
angular (non-linear) shape, with an angle
of about 105. The nucleus of the oxygen atom attracts electrons more strongly
than do the hydrogen nuclei. As a result, the middle part of the molecule near
oxygen has a negative charge, and the
other parts of the molecule have a positive
charge.

In essence, the electrons are

"pulled" toward the nucleus of the oxygen


atom and away from the hydrogen atom
nuclei. Water is a polar molecule, with an
unequal distribution of charge throughout
the molecule.

FIGURE 2.21
This model is an atomic diagram of water,
showing the two hydrogen atoms and oxygen atom in the center. The protons (red)
are in the center (nucleus) of each atom,
and the electrons (light blue) circle each
nucleus.

132

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

FIGURE 2.22
This diagram shows the positive and negative parts of a water molecule. It also
depicts how a charge, such as on an ion
(Na or Cl, for example) can interact with a
water molecule.

Hydrogen Bonding

Opposite electrical charges attract one another. Therefore, the positive part of one water molecule is attracted to the
negative parts of other water molecules. Because of this attraction, bonds form between hydrogen and oxygen atoms
of adjacent water molecules, as demonstrated in Figure below. This type of bond always involves a hydrogen atom,
so it is called a hydrogen bond. Hydrogen bonds are bonds between molecules, and they are not as strong as bonds
within molecules. Nonetheless, they help hold water molecules together.
Hydrogen bonds can also form within a single large organic molecule. For example, hydrogen bonds that form
between different parts of a protein molecule bend the molecule into a distinctive shape, which is important for the
proteins functions. Hydrogen bonds also hold together the two nucleotide chains of a DNA molecule.

Sticky, Wet Water

Water has some unusual properties due to its hydrogen bonds. One property is cohesion, the tendency for water
molecules to stick together. The cohesive forces between water molecules are responsible for the phenomenon
known as surface tension. The molecules at the surface do not have other like molecules on all sides of them and
consequently they cohere more strongly to those directly associated with them on the surface. For example, if you
drop a tiny amount of water onto a very smooth surface, the water molecules will stick together and form a droplet,
rather than spread out over the surface. The same thing happens when water slowly drips from a leaky faucet. The
water doesnt fall from the faucet as individual water molecules but as droplets of water. The tendency of water to
stick together in droplets is also illustrated by the dew drops in Figure 2.24.
133

2.8. Biochemical Properties of Water - Advanced

www.ck12.org

FIGURE 2.23
Hydrogen bonds form between positively
and negatively charged parts of water
molecules.

The bonds hold the water

molecules together. How do you think this


might affect waters properties?

FIGURE 2.24
Droplets of dew cling to a spider web,
demonstrating cohesion, the tendency of
water molecules to stick together because
of hydrogen bonds.

Another important physical property of water, is adhesion. In terms of water, adhesion is the bonding of a water
molecule to another substance, such as the sides of a leafs veins. This process happens because hydrogen bonds
are special in that they break and reform with great frequency. This constant rearranging of hydrogen bonds allows
a percentage of all the molecules in a given sample to bond to another substance. This grip-like characteristic that
water molecules form causes capillary action, the ability of a liquid to flow against gravity in a narrow space. An
example of capillary action is when you place a straw into a glass of water. The water seems to climb up the straw
before you even place your mouth on the straw. The water has created hydrogen bonds with the surface of the straw,
causing the water to adhere to the sides of the straw. As the hydrogen bonds keep interchanging with the straws
surface, the water molecules interchange positions and some begin to ascend the straw.
Adhesion and capillary action are necessary to the survival of most organisms. It is the mechanism that is responsible
134

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

for water transport in plants through roots and stems, and in animals through small blood vessels.
Hydrogen bonds also explain why waters boiling point (100C) is higher than the boiling points of similar substances without hydrogen bonds. Because of waters relatively high boiling point, most water exists in a liquid state
on Earth. Liquid water is needed by all living organisms. Therefore, the availability of liquid water enables life to
survive over much of the planet.
Furthermore, water has a high specific heat because it takes a lot of energy to raise or lower the temperature of
water. As a result, water plays a very important role in temperature regulation. Since cells are made up of water, this
property helps to maintain homeostasis.

Density of Ice and Water

The melting point of water is 0C. Below this temperature, water is a solid (ice). Unlike most chemical substances,
water in a solid state has a lower density than water in a liquid state. This is because water expands when it freezes.
Again, hydrogen bonding is the reason. Hydrogen bonds cause water molecules to line up less efficiently in ice than
in liquid water. As a result, water molecules are spaced farther apart in ice, giving ice a lower density than liquid
water. A substance with lower density floats on a substance with higher density. This explains why ice floats on
liquid water, whereas many other solids sink to the bottom of liquid water.
In a large body of water, such as a lake or the ocean, the water with the greatest density always sinks to the bottom.
Water is most dense at about 4C. As a result, the water at the bottom of a lake or the ocean usually has temperature
of about 4C. In climates with cold winters, this layer of 4C water insulates the bottom of a lake from freezing
temperatures. Lake organisms such as fish can survive the winter by staying in this cold, but unfrozen, water at the
bottom of the lake.

Vocabulary

adhesion: The force of attraction between unlike molecules, or the attraction between the surfaces of contacting bodies.
boiling point: The temperature at which a liquid changes state into a gas.
capillary action: The ability of a liquid to flow against gravity in a narrow space.
cohesion: The tendency for water molecules to stick together.
homeostasis: The process of maintaining a stable environment inside a cell or an entire organism.
hydrogen bond: A weak bond between two molecules resulting from an electrostatic attraction between a
proton in one molecule and an electronegative atom in the other; always involves a hydrogen atom.
melting point: The temperature at which a solid changes state into a liquid.
polarity: A difference in electrical charge between different parts of a molecule.
polar molecule: A molecule with an unequal distribution of charge throughout the molecule.
specific heat: The amount of heat per unit mass required to raise the temperature by one degree Celsius.
surface tension: The energy required to increase the surface area of a liquid due to intermolecular forces.

Summary

Water molecules are polar, so they form hydrogen bonds. This gives water unique properties, such as a
relatively high boiling point, high specific heat, cohesion, adhesion and density.

Explore More

Use this resource to answer the questions that follow.


135

2.8. Biochemical Properties of Water - Advanced


Water at http://johnkyrk.com/H2O.html .
1.
2.
3.
4.
5.
6.

How do hydrogen and oxygen bind to form water?


Why is water a polar molecule?
What are Van der Waals forces?
Describe the bond between water molecules.
What happens to water molecules as the temperature increases?
What is hydronium?

Review

1.
2.
3.
4.
5.

136

Describe the structure of a water molecule.


What is polarity, and why is water polar?
Explain how hydrogen bonds cause molecules of liquid water to stick together.
What is capillary action and give an example.
What property of water helps to maintain homeostasis and how?

www.ck12.org

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

2.9 Solutions - Advanced

Define solution, and describe waters role as a solvent.


State how water is used to define acids and bases.
Identify the pH ranges of acids and bases.
Describe a neutralization reaction.
Give examples of acids and bases in organisms.

Acids and bases. Why are these important in biology?


It comes back to a number of biological and biochemical processes. For example, some enzymes work best at
specific pH levels of acids. Other biochemical reactions need a relatively neutral environment to function properly.
Take your stomach, a very acidic environment. The enzyme pepsin that works best in that acidic environment could
not work in your mouth. What would your food taste like if your mouth was also a very acidic environment? Other
biochemical reactions need a relatively neutral environment to function properly.
Solutions

Water is one of the most common ingredients in solutions. A solution is a homogeneous mixture composed of two
or more substances. In a solution, one substance is dissolved in another substance, forming a mixture that has the
same proportion of substances throughout. The dissolved substance in a solution is called the solute. The substance
in which it is dissolved is called the solvent. An example of a solution in which water is the solvent is salt water. In
this solution, a solidsodium chlorideis the solute. In addition to a solid dissolved in a liquid, solutions can also
form with solutes and solvents in other states of matter. Examples are given in the Table 2.4.

137

2.9. Solutions - Advanced

www.ck12.org

TABLE 2.4: Solutions and Three States of Matter


Gas
Liquid
Solid

Gas
Oxygen and other gases in
nitrogen (air)
Carbon dioxide in water
(carbonated water)
Hydrogen gas in metals

Liquid

Solid

Ethanol (an alcohol) in


water
Mercury in silver and
other metals (dental fillings)

Sodium chloride in water


(salt water)
Iron in carbon (steel)

The ability of a solute to dissolve in a particular solvent is called solubility. Many chemical substances are soluble in
water. In fact, so many substances are soluble in water that water is called the universal solvent. Water is a strongly
polar solvent, and polar solvents are better at dissolving polar solutes. Many organic compounds and other important
biochemicals are polar, so they dissolve well in water. On the other hand, strongly polar solvents like water cannot
dissolve strongly nonpolar solutes like oil. Did you ever try to mix oil and water? Even after being well shaken, the
two substances quickly separate into distinct layers.
Acids and Bases

Water is the solvent in solutions called acids and bases. To understand acids and bases, it is important to know more
about pure water, in which nothing is dissolved. In pure water (such as distilled water), a tiny fraction of water
molecules naturally breaks down, or dissociates, to form ions. An ion is an electrically charged atom or molecule.
The dissociation of pure water into ions is represented by the chemical equation:
2 H2 O H3 O+ + OH .
The products of this reaction are a hydronium ion (H3 O+ ) and a hydroxide ion (OH ). The hydroxide ion is
negatively charged. It forms when a water molecule donates, or gives up, a positively charged hydrogen ion. The
hydronium ion, modeled in Figure 2.25, is positively charged. It forms when a water molecule accepts a positively
charged hydrogen ion (H+ ).
An introduction to acid and bases, Acid Base Introduction, can be seen at http://www.youtube.com/watch?v=v
ShCnTY1-T0 .

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/69285

Acidity and pH

Acidity refers to the hydronium ion concentration of a solution. It is measured by pH. In pure water, the hydronium
ion concentration is very low. Only about one in ten million water molecules naturally dissociates to form a
hydronium ion in pure water. This gives water a pH of 7. The hydronium ions in pure water are also balanced
by hydroxide ions, so pure water is neutral (neither an acid nor a base).
Because pure water is neutral, any other solution with the same hydronium ion concentration and pH is also
considered to be neutral. If a solution has a higher concentration of hydronium ions and lower pH than pure water,
138

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

FIGURE 2.25
A hydronium ion has the chemical formula
H3 O+ . The plus sign (+ ) indicates that the
ion is positively charged. How does this
molecule differ from a water molecule?

it is called an acid. If a solution has a lower concentration of hydronium ions and higher pH than pure water, it is
called a base. Several acids and bases and their pH values are identified on the pH scale, which ranges from 0 to 14,
in Figure 2.26.
The pH scale is a negative logarithmic scale. Because the scale is negative, as the ion concentration increases, the
pH value decreases. In other words, the more acidic the solution, the lower the pH value. Because the scale is
logarithmic, each one-point change in pH reflects a ten-fold change in the hydronium ion concentration and acidity.
For example, a solution with a pH of 6 is ten times as acidic as pure water with a pH of 7.

Acids

An acid can be defined as a hydrogen ion donor. The hydrogen ions bond with water molecules, leading to a higher
concentration of hydronium ions than in pure water. For example, when hydrochloric acid (HCl) dissolves in pure
water, it donates hydrogen ions (H+ ) to water molecules, forming hydronium ions (H3 O+ ) and chloride ions (Cl ).
This is represented by the chemical equation:
HCl + H2 O Cl + H3 O+ .
Strong acids can be harmful to organisms and damaging to materials. Acids have a sour taste and may sting or burn
the skin. Testing solutions with litmus paper is an easy way to identify acids. Acids turn blue litmus paper red.

Bases

A base can be defined as a hydrogen ion acceptor. It accepts hydrogen ions from hydronium ions, leading to a lower
concentration of hydronium ions than in pure water. For example, when the base ammonia (NH3 ) dissolves in pure
water, it accepts hydrogen ions (H+ ) from hydronium ions (H3 O+ ) to form ammonium ions (NH4 + ) and hydroxide
ions (OH ). This is represented by the chemical equation:
139

2.9. Solutions - Advanced

www.ck12.org

FIGURE 2.26
Acidity and the pH Scale. Water has a
pH of 7, so this is the point of neutrality
on the pH scale. Acids have a pH less
than 7, and bases have a pH greater
than 7. Approximate pHs of examples are
depicted.

NH3 + H2 O NH4 + + OH .
Like strong acids, strong bases can be harmful to organisms and damaging to materials. Bases have a bitter taste and
feel slimy to the touch. They can also burn the skin. Bases, like acids, can be identified with litmus paper. Bases
turn red litmus paper blue.
Neutralization

What do you think would happen if you mixed an acid and a base? If you think the acid and base would cancel each
other out, you are right. When an acid and base react, they form a neutral solution of water and a salt (a molecule
140

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

composed of a positive and negative ion). This type of reaction is called a neutralization reaction. For example,
when the base sodium hydroxide (NaOH) and hydrochloric acid (HCl) react, they form a neutral solution of water
and the salt sodium chloride (NaCl). This reaction is represented by the chemical equation:
NaOH + HCl NaCl + H2 O.
In this reaction, hydroxide ions (OH ) from the base combine with hydrogen ions (H+ ) from the acid to form water.
The other ions in the solution (Na+ ) and (Cl ) combine to form sodium chloride.
Acids and Bases in Organisms

Enzymes are needed to speed up biochemical reactions. Most enzymes require a specific range of pH in order to do
their job. For example, the enzyme pepsin, which helps break down proteins in the human stomach, requires a very
acidic environment in order to function. Strong acid is secreted into the stomach, allowing pepsin to work. Once the
contents of the stomach enter the small intestine, where most digestion occurs, the acid must be neutralized. This is
because enzymes that work in the small intestine need a basic environment. An organ near the small intestine, called
the pancreas, secretes bicarbonate ions (HCO3 ) into the small intestine to neutralize the stomach acid.
Bicarbonate ions play an important role in neutralizing acids throughout the body. Bicarbonate ions are especially
important for protecting tissues of the central nervous system from changes in pH. The central nervous system
includes the brain, which is the bodys control center. If pH deviates too far from normal, the central nervous system
cannot function properly. This can have a drastic effect on the rest of the body.
Vocabulary

acid: A solution with a pH lower than 7.


acidity: A measure of the ability of a solution to neutralize a base; refers to the hydronium ion concentration
of a solution.
base: A solution with a pH higher than 7.
neutralization reaction: A chemical reaction where a base and an acid react to form a salt.
pepsin: The main digestive enzyme in the stomach; degrades food proteins into peptides.
pH: The negative logarithm of the hydrogen ion concentration; the scale that is used to measure acidity.
solubility: The ability of a solute to dissolve in a particular solvent.
solute: The substance that is dissolved in a solvent.
solution: Mixture that has the same composition throughout; mixture of a solute in a solvent.
solvent: A substance that dissolves another substance to form a solution.
Summary

A solution is a homogeneous mixture in which a solute dissolves in a solvent. Water is a very common solvent,
especially in organisms.
The ion concentration of neutral, pure water gives water a pH of 7 and sets the standard for defining acids and
bases. Acids have a pH lower than 7, and bases have a pH higher than 7.
Explore More

Use this resource to answer the questions that follow.


Water at http://johnkyrk.com/H2O.html .
1. What is hydronium? What is the charge of a hydroxyl ion?
141

2.9. Solutions - Advanced


2.
3.
4.
5.
6.
7.

www.ck12.org

What does HCl do to the hydrogen:hydroxyl ratio?


What is a strong acid?
What is the definition of pH?
Describe the pH scale.
At what pHs do most cellular processes function?
Give an example of a strong acid and strong base.

Review

1.
2.
3.
4.

What is pH?
Define solution, and give an example of a solution.
What is the pH of a neutral solution? Why?
What type of reaction is represented by this chemical equation: KOH + HCl KCl + H2 O? Defend your
answer.
5. What is pepsin and give an example of how the body neutralizes its environment?

142

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

2.10 Water and Life - Advanced


Explain why water is essential for life processes.
Describe various biochemical reactions involving water.

Condensation. Just in clouds?


Condensation occurs in your cells constantly. It occurs in the form of a chemical reaction. These condensation
reactions involve the formation of a water molecule from two other molecules. Water forms when two molecules,
such as amino acids or monosaccharides, are joined together. The amino acids join together to form peptides (or
polypeptides or proteins) and the monosaccharides join together to form disaccharides or polysaccharides.

Water and Life

Humans are composed of about 60-70 percent water (not counting water in body fat). This water is crucial for normal
functioning of the body. Waters ability to dissolve most biologically significant compoundsfrom inorganic salts
to large organic moleculesmakes it a vital solvent inside organisms and cells.
Water is an essential part of most metabolic processes within organisms. Metabolism is the sum total of all body
reactions, including those that build up molecules ( anabolic reactions) and those that break down molecules (
catabolic reactions). In anabolic reactions, water is generally removed from small molecules in order to make
larger molecules. In catabolic reactions, water is used to break bonds in larger molecules in order to make smaller
molecules.
Water is central to two related, fundamental metabolic reactions in organisms: photosynthesis and cellular respiration. All organisms depend directly or indirectly on these two reactions. In photosynthesis, cells use the energy in
143

2.10. Water and Life - Advanced

www.ck12.org

sunlight to change water and carbon dioxide into glucose (C6 H12 O6 ) and oxygen (O2 ). This is an anabolic reaction,
represented by the chemical equation:
6 CO2 + 6 H2 O + energy C6 H12 O6 + 6 O2 .
In cellular respiration, cells break down glucose in the presence of oxygen and release energy, water, and carbon
dioxide. This is a catabolic reaction, represented by the chemical equation:
C6 H12 O6 + 6 O2 6 CO2 + 6 H2 O + energy
Two other types of reactions that occur in organisms and involve water are dehydration and hydration reactions. A
dehydration reaction occurs when molecules combine to form a single, larger molecule and also a molecule of
water. (If some other small molecule is formed instead of water, the reaction is called by the more general term,
condensation reaction.) It is a type of anabolic reaction. An example of a dehydration reaction is the formation
of peptide bonds between amino acids in a polypeptide chain. When two amino acids bond together, a molecule of
water is lost. This is shown in Figure 2.27.

FIGURE 2.27
In this dehydration reaction, two amino
acids form a peptide bond.

A water

molecule also forms.

A hydration reaction is the opposite of a dehydration reaction. A hydration reaction adds water to an organic
molecule and breaks the large molecule into smaller molecules. Hydration reactions occur in an acidic water
solution. An example of hydration reaction is the breaking of peptide bonds in polypeptides. A hydroxide ion
(OH ) and a hydrogen ion (H+ ) (both from a water molecule) bond to the carbon atoms that formed the peptide
bond. This breaks the peptide bond and results in two amino acids.
Water is essential for all of these important chemical reactions in organisms. As a result, virtually all life processes
depend on water. Clearly, without water, life as we know it could not exist.

Vocabulary

anabolic reaction: Endothermic reaction that occurs in organisms; chemical reaction that builds new molecules
and/or stores energy.
catabolic reaction: Chemical reaction that breaks down more complex organic molecules into simpler substances; usually releases energy.
cellular respiration: Metabolic process which transfers chemical energy from glucose (a deliverable fuel
molecule) to ATP (a usable energy-rich molecule); most efficient in the presence of oxygen (aerobic).
condensation reaction: A chemical reaction in which two molecules combine to form one single molecule,
together with the loss of a small molecule, often water.
dehydration reaction: A condensation reaction that involves the loss of water from the reacting molecule
(product).
hydration reaction: A chemical reaction in which a water molecule is added to a molecule, breaking the
reactant into two separate products.
metabolism: The sum of all the chemical reactions in a cell and/or organism.
photosynthesis: The process by which carbon dioxide and water are converted to glucose and oxygen, using
sunlight for energy.
144

www.ck12.org

Chapter 2. Chemistry of Life - Advanced

Summary

Water is essential for most life processes, including photosynthesis, cellular respiration, and other important
chemical reactions that occur in organisms.
Review

1.
2.
3.
4.
5.

What percent of humans are composed of water?


Summarize how metabolism in organisms depends on water.
What is a condensation reaction?
Distinguish between anabolic and catabolic reactions.
Distinguish between between hydration and dehydration reactions.

Summary
The cell is the basic unit of life. A cell is made of molecules, which are made of elements. All life-which means all
bacteria and archaea, all protists, fungi, plants and animals-is built around the element carbon, and four categories
of organic compounds: carbohydrates, lipids, proteins, and nucleic acids. These molecules come together to form a
cell, which is the basis of life. One particular type of protein, enzymes, are biological catalysts, allowing biochemical
reactions to proceed at the rate necessary to maintain life. One other molecule, water, is also essential to life, though
water is not an organic compound.

145

2.11. References

www.ck12.org

2.11 References
1.
2.
3.
4.
5.
6.
7.

8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.

146

Christopher Auyeung. CK-12 Foundation . CC BY-NC 3.0


Christopher Auyeung. CK-12 Foundation . CC BY-NC 3.0
Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
User:NEUROtiker/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Alpha-D-Glucopyranose
.svg . Public Domain
User:Booyabazooka/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Saccharose.svg . Public Domain
Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Seeds: Lebensmittelfotos; Olives: Steve Jurvetson; Nuts: Petr Kratochvil. Seeds: http://pixabay.com/en
/barley-grain-cereals-whole-wheat-74247/; Olives: http://www.flickr.com/photos/jurvetson/454873761/; Nut
s: http://www.publicdomainpictures.net/view-image.php?image=424&picture=nuts . Seeds: Public Domain;
Olives: CC BY 2.0; Nuts: Public Domain
Wolfgang Schaefer (User:WS62/Wikimedia Commons). http://commons.wikimedia.org/wiki/File:Fat_trigl
yceride_shorthand_formula.PNG . Public Domain
User:YassineMrabet/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:AminoAcidball.svg .
Public Domain
Courtesy of the National Human Genome Research Institute. http://commons.wikimedia.org/wiki/File:Prote
in_primary_structure.svg . Public Domain
Hana Zavadska, based on image from the National Human Genome Research Institute. CK-12 Foundation .
CC BY-NC 3.0
Image copyright ynse, 2014. http://www.shutterstock.com . Used under license from Shutterstock.com
Marianna Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Marianna Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
User:Honeymane/Wikimedia Commons and User:LucasVB/Wikimedia Commons. http://commons.wikim
edia.org/wiki/File:Double_Helix.png . Public Domain
Madeleine Price Ball (User:Madprime/Wikimedia Commons), modified by CK-12 Foundation. http://commo
ns.wikimedia.org/wiki/File:Genetic_code.svg . Public Domain
User:NEUROtiker/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Adenosintriphosphat_proto
niert.svg . Public Domain
Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Rupali Raju. CK-12 Foundation . CC BY-NC 3.0
Ben Mills (User:Benjah-bmm27/Wikimedia Commons), modified by CK-12 Foundation. http://commons.w
ikimedia.org/wiki/File:Water-elpot-transparent-3D-balls.png . Public Domain
Laura Guerin. CK-12 Foundation . CC BY-NC 3.0
Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. Water Molecule . CC BY-NC 3.0
Jodi So. Hydrogen Bonding in Water Molecule . CC BY-NC 3.0
Courtesy of the US Fish and Wildlife Service. http://commons.wikimedia.org/wiki/File:Water_drops_on_sp
ider_web.jpg . Public Domain
User:Bensacoount/Wikipedia. http://commons.wikimedia.org/wiki/File:Hydronium.png . Public Domain
Hana Zavadska and Marianna Ruiz Villarreal (LadyofHats). CK-12 Foundation . CC BY-NC 3.0
User:LukeSurl/Wikipedia and User:DMacks/Wikipedia. http://commons.wikimedia.org/wiki/File:2-amino-a
cidsb.png . Public Domain

www.ck12.org

Chapter 3. Cell Biology - Advanced

C HAPTER

Cell Biology - Advanced

Chapter Outline
3.1

C ELLS - A DVANCED

3.2

D ISCOVERY OF C ELLS - A DVANCED

3.3

M ICROSCOPES IN B IOLOGY - A DVANCED

3.4

T HE C ELL T HEORY - A DVANCED

3.5

C ELL S IZE AND S HAPE - A DVANCED

3.6

C OMMON PARTS OF C ELLS - A DVANCED

3.7

T WO T YPES OF C ELLS - A DVANCED

3.8

V IRUSES - A DVANCED

3.9

C ELL S TRUCTURES - A DVANCED

3.10

T HE P LASMA M EMBRANE - A DVANCED

3.11

T HE P HOSPHOLIPID B ILAYER - A DVANCED

3.12

M EMBRANE P ROTEINS - A DVANCED

3.13

T HE F LUID M OSAIC M ODEL - A DVANCED

3.14

T HE C YTOPLASM AND C YTOSKELETON - A DVANCED

3.15

E XTERNAL S TRUCTURES OF C ELLS - A DVANCED

3.16

T HE N UCLEUS - A DVANCED

3.17

T HE M ITOCHONDRIA - A DVANCED

3.18

E NDOPLASMIC R ETICULUM - A DVANCED

3.19

R IBOSOMES - A DVANCED

3.20

T HE G OLGI A PPARATUS - A DVANCED

3.21

V ESICLES AND VACUOLES - A DVANCED

3.22

OTHER S TRUCTURES OF C ELLS - A DVANCED

3.23

P LANT C ELLS - A DVANCED

3.24

O RGANIZATION OF C ELLS - A DVANCED

3.25

C ELL T RANSPORT - A DVANCED

3.26

D IFFUSION - A DVANCED

3.27

O SMOSIS - A DVANCED

3.28

FACILITATED D IFFUSION - A DVANCED

3.29

ACTIVE T RANSPORT - A DVANCED

3.30

T HE S ODIUM -P OTASSIUM P UMP - A DVANCED

3.31

T HE E LECTROCHEMICAL G RADIENT - A DVANCED

3.32

E XOCYTOSIS AND E NDOCYTOSIS - A DVANCED

3.33

C ELL C OMMUNICATION - A DVANCED

147

www.ck12.org
3.34

S IGNAL R ECEPTORS - A DVANCED

3.35

S IGNAL T RANSDUCTION - A DVANCED

3.36

R EFERENCES

Introduction

What is a cell?
It could easily be said that a cell is the fundamental unit of life, the smallest unit capable of life or the structural and
functional unit necessary for life. But whatever it is, a cell is necessary for life. This concept will discuss some of
the fundamental properties of the cell with lessons that include the cell structure, transport in and out of the cell and
cell communication.

148

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.1 Cells - Advanced


Describe the importance of cells to biology.

Why is a cell so complex?


Cells have lots of things to do. Some cells make the whole organism, so that one cell must do everything that
organism needs to do to live. Other cells perform specific functions, so they must be designed to do that specific
activity.

Introduction to Cells

The cell is the smallest unit of structure and function of all living organisms. A cell is also the smallest unit of life,
with single-celled organisms present on this planet for over 3.5 billion years. Single-celled ( unicellular) organisms
like bacteria are obviously composed of just one cell, whereas multicellular organisms can be composed of trillions
of cells. Multicellular organisms include protists (though single-celled protists also exist), fungi, plants and animals.
Most plant and animal cells are between 1 and 100 m and therefore can only be observed under the microscope.
The one cell of a unicellular organism must be able to perform all the functions necessary for life. These functions
include metabolism, homeostasis and reproduction. Specifically, these single cells must transport materials, obtain
and use energy, dispose of wastes, and continuously respond to their environment. The cells of a multicellular
organism also perform these functions, but they may do so in collaboration with other cells.
149

3.1. Cells - Advanced

www.ck12.org

Cells are essentially carbohydrates, lipids, proteins and nucleic acids in a water-based environment. It is the
lipid (phospholipid) membrane that keeps the water-based environment in the cell separate from the water-based
environment outside the cell. But a cell, even the single cell of a unicellular organism, must be able to interact with
its external environment. The cell must be able to bring molecules in from the outside, and expel unwanted waste
products. Knowing the components of cells and how cells work is necessary to all of the biological sciences.
Learning about the similarities and differences between cell types is particularly important to the fields of cell biology
and molecular biology. Cell biology is the field of biology that studies cells. In particular, cell biologists study a cells
physiological properties, structure, organelles, interactions with the extracellular environment, life cycle, division
and death. Molecular biology concerns itself with understanding the interactions between the various systems of a
cell, including the relationships between DNA, RNA and proteins.
Research in cell biology is closely linked to molecular biology, as well as genetics, biochemistry and developmental
biology. The importance of the similarities and differences between cell types is a unifying theme in biology. They
allow the principles learned from studying one cell type to be applied when learning about other cell types. For
example, learning about how single-celled bacteria function can help us understand more about how human cells
function. Understanding basic cellular processes, such as cell division or metabolism in bacteria, gives information
about similar processes in our cells.
Vocabulary

cell: The basic unit of structure and function of all living organisms.
cell biology: The field of biology that studies cells.
molecular biology: The field of biology that deals with the molecular basis of biological activity; the study
of molecules that make up living organisms.
multicellular organism: Organism made up of more than one type of cell; most have specialized cells that
are grouped together to carry out specialized functions.
organelle: A structure within the cytoplasm of a cell; may be enclosed within a membrane; performs a specific
function.
unicellular organism: An organism that consists of only one cell; also known as a single-celled organism.
Summary

A cell is the smallest unit of structure and function of all living organisms.
The understanding of cells is integral to other biological fields, including molecular biology, genetics, biochemistry and developmental biology.
Explore More

Use this resource to answer the questions that follow.


Introduction to Cells at http://www.youtube.com/watch?v=gFuEo2ccTPA

150

www.ck12.org

Chapter 3. Cell Biology - Advanced

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139336

1.
2.
3.
4.

Concerning cells, what does all life have in common?


How many cells are in the human body?
How big is a cell?
Each second, what is happening in your cells that keeps you alive?

Review

1. What is a cell?
2. List some of the functions of a cell.
3. Describe the relationship between cell biology and molecular biology.

151

3.2. Discovery of Cells - Advanced

www.ck12.org

3.2 Discovery of Cells - Advanced


Identify the scientists that first observed cells.
Describe the first cells identified.

What was needed to discover the cell?


The microscope of course. Objects that were too small to be seen with the human eye were unknown until the
microscope was developed. Once this instrument was developed, a whole new field of science was initiated.
Discovery of Cells

If you look at living organisms under a microscope you will see they are made up of cells. The word cell, derived
from the Latin word cellula meaning small compartment, was first used by Robert Hooke, a British biologist and
early microscopist. Hooke looked at thin slices of cork under a microscope. The structure he saw looked like
a honeycomb as it was made up of many tiny units. Hookes drawing is shown in Figure 3.1. In 1665 Hooke
published his book Micrographia, in which he wrote:
... I could exceedingly plainly perceive it to be all perforated and porous, much like a Honey-comb, but that the pores
of it were not regular.... these pores, or cells, ... were indeed the first microscopical pores I ever saw, and perhaps,
that were ever seen, for I had not met with any Writer or Person, that had made any mention of them before this...
During the 1670s, the Dutch tradesman Antony van Leeuwenhoek, shown in Figure 3.2, used microscopes to observe
many microbes and body cells. Leeuwenhoek developed an interest in microscopy and ground his own lenses to
make simple microscopes. Leeuwenhoek was so good at making lenses that his simple microscopes were able
to magnify much more clearly than the compound microscopes of his day. His microscopes increased ability to
152

www.ck12.org

Chapter 3. Cell Biology - Advanced

FIGURE 3.1
This figure is a drawing of the structure
of cork from Micrographia as it appeared
under the microscope to Robert Hooke.

magnify over 200x is comparable to a modern compound light microscope. Compound microscopes, which are
microscopes that use more than one lens, had been invented around 1595 by Zacharias Jansen, a Dutch spectaclemaker. Several people, including Robert Hooke, had built compound microscopes and were making important
discoveries with them during Leeuwenhoeks time.
Fortunately, Leeuwenhoek took great care in writing detailed reports of what he saw under his microscope. He was
the first person to report observations of many microscopic organisms. Some of his discoveries included tiny animals
such as ciliates, foraminifera, roundworms, and rotifers, shown in Figure 3.3. He discovered blood cells and was
the first person to see living sperm cells. In 1683, Leeuwenhoek wrote to the Royal Society of London about his
observations on the plaque between his own teeth, "a little white matter, which is as thick as if twere batter." He
called the creatures he saw in the plaque animacules, or tiny animals. This report was among the first observations
on living bacteria ever recorded.
Vocabulary

cell: The basic unit of structure and function of all living organisms.
compound microscope: An optical microscopes that has a series of lenses; has uses in many fields of science,
particularly biology and geology.
microscope: An instrument used to view objects that are too small to be seen by the naked eye.
microscopist: A scientist who specializes in research with the use of microscopes.
153

3.2. Discovery of Cells - Advanced

www.ck12.org

FIGURE 3.2
Antony van Leeuwenhoek (1632-1723).
His carefully crafted microscopes and insightful observations of microbes led to
the title the "Father of Microscopy."

FIGURE 3.3
A rotifer,

the microscopic organism

Leeuwenhoek saw under his microscope.

154

www.ck12.org

Chapter 3. Cell Biology - Advanced

Summary

Before the development of microscopes, the existence of cellular life was unknown.
By examining a piece of cork, Robert Hooke first saw and named cells.
Antony van Leeuwenhoek was the first person to see living cells.
Explore More

Use this resource to answer the questions that follow.


Discovering Cells at http://www.youtube.com/watch?v=FUqORLDDwVM

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139342

1. How did Hooke first observe cells?


2. What did Leeuwenhoek look at through his microscope?
Review

1. Describe the contributions of Hooke and Leeuwenhoek to cell biology.


2. What enabled Leeuwenhoek to observe things that nobody else had seen before?

155

3.3. Microscopes in Biology - Advanced

www.ck12.org

3.3 Microscopes in Biology - Advanced


Outline the importance of microscopes in the discovery of cells.
Describe contemporary microscopes that are used for biological research.

How do you see something that is too small to be seen by a light microscope?
Use an electron microscope. This instrument has a resolution many times greater than a light microscope, and can
be used to see the details on the outside of a cell. Some electron microscopes can also be used to see the details
inside a cell.
Microscopes

Hookes and Leeuwenhoeks studies and observations filled people with wonder because their studies were of life
forms that were everywhere, but too small to see with the naked eye. Just think how amazed you would be if
you were to read about the first accounts of a newly discovered microorganism from the moon or Mars. Your first
thought might be "Things can live there?!" which was probably the first thought of the people who read Hookes and
Leeuwenhoeks accounts. The microscope literally opened up an amazing new dimension in the natural sciences,
and became a critical tool in the progress of biology.
Magnifying glasses had been in use since the 1300s, but the use of lenses to see very tiny objects was a slowlydeveloping technology. The magnification power of early microscopes was very limited by the glass quality used
in the lenses and the amount of light reflected off the object. These early light microscopes had poor resolution
and a magnification power of about 10 times. Compare this to the over 200 times magnification that Leeuwenhoek
156

www.ck12.org

Chapter 3. Cell Biology - Advanced

was able to achieve by carefully grinding his own lenses. However, in time the quality of microscopes was much
improved with better lighting and resolution. It was through the use of light microscopes that the first discoveries
about the cell and the cell theory (1839) were developed. The Figure 3.4 is an example of an early light microscope
used by Robert Hooke (1665), the microscopist who was the first to discover cells.
However, by the end of the 19th century, light microscopes had begun to hit resolution limits, and microscopy
became a significant tool in the biological sciences. Resolution is a measure of the clarity of an image; it is the
minimum distance that two points can be separated by and still be distinguished as two separate points. Because
light beams have a physical size, it is difficult to see an object that is about the same size as the wavelength of light.
Objects smaller than about 0.2 micrometers appear fuzzy, and objects below that size just cannot be seen. Light
microscopes were still useful, but most organelles and tiny cell structures were invisible to the light microscope.

FIGURE 3.4
(A) English Scientist and Microscopist
Robert Hookes light microscope.

(B)

Modern electron microscope.

Electron Microscopes

In the 1930s, a new system was developed that could use a beam of electrons to resolve very tiny dimensions at the
molecular level. Electron microscopes, one of which is shown in Figure 3.4, have been used to produce images
of molecules and atoms. They have been used to visualize the tiny sub-cellular structures that were invisible to
light microscopes. Many of the discoveries made about the cell since the 1950s have been made with electron
microscopes. The first electron microscope was the transmission electron microscope (TEM). The TEM works
on the same principle as an optical microscope, but uses electrons instead of light and electromagnets in the place
of glass lenses. Electrons have a much lower wavelength, which makes it possible to get a resolution a thousand
times better than with a light microscope. The TEM allows scientists to study the topographical, morphological,
compositional and crystalline details in the cell or different materials near the atomic levels, as seen in the Figure
3.5.
Development of the TEM was quickly followed in 1935 by the development of the scanning electron microscope
(SEM). The SEM forms an image of a sample by scanning it with a beam of electrons. The electrons interact with
the atoms that make up the sample producing signals that contain information about the samples surface topography,
morphology and composition. Although it is not as powerful as its TEM counterpart, the interactions that take place
on the surface of the specimen provide a greater depth of view, higher resolution and more detailed surface picture.
The 1980s saw the development of the first scanning probe microscopes. The first was the scanning tunneling
microscope in 1981. Scanning Probe Microscopy forms images of surfaces using a physical probe that scans the
specimen. The most recent developments in light microscope largely center on the rise of fluorescence microscopy.
A fluorescence microscope is an optical microscope that uses fluorescence and phosphorescence instead of (or
157

3.3. Microscopes in Biology - Advanced

www.ck12.org

FIGURE 3.5
Electron
Organelles.

Microscope

Image

of

An electron microscope

produced this image of a cell.

sometimes, in addition to) reflection and absorption to study properties of organic or inorganic samples.
How to use a microscope can be viewed at http://www.youtube.com/watch?v=FuDcge0Zuak (1:52).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/246

KQED: The Worlds Most Powerful Microscope

Lawrence Berkeley National labs uses a $27 million electron microscope to make images to a resolution of half
the width of a hydrogen atom. This makes it the worlds most powerful microscope. See http://www.kqed.org/ques
t/television/the-worlds-most-powerful-microscope and http://www.kqed.org/quest/slideshow/web-extra-images-fro
m-the-worlds-most-powerful-microscope for more information.

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/494

158

www.ck12.org

Chapter 3. Cell Biology - Advanced

KQED: Confocal Microscopy

Confocal microscopy is an optical imaging technique used to increase optical resolution and contrast of a micrograph by using point illumination and a spatial pinhole to eliminate out-of-focus light in specimens that are
thicker than the focal plane. These important features also allow confocal microscopes to collect double and
triple labels(most commonly used for detecting fluorescent labels), since precise colocalizations can be performed.
Examples of specific uses of the confocal microscope are:
1. to resolve the structure of various complex three-dimensional objects, such as networks of cytoskeletal fibers
in the cytoplasm of cells
2. the arrangements of chromosomes and genes in a cells nucleus during different points in the cell division
cycle
3. observing pollen grains whose complex cell wall can only be seen clearly using confocal microscopy
Cutting-edge confocal microscopes, at the University of California, San Francisco are helping scientists create threedimensional images of cells, and may help lead to new medical breakthroughs, including a treatment for Type 1
diabetes. For a description of this work, see http://www.kqed.org/quest/television/super-microscope

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139335

Vocabulary

confocal microscopy: An optical imaging technique used to increase optical resolution and contrast of a
micrograph by using point illumination and a spatial pinhole to eliminate out-of-focus light in specimens that
are thicker than the focal plane.
electron microscope: A microscope that uses electrons instead of light; allows a researcher to see things at
very high magnification, far higher than an optical microscope can magnify.
magnification: Enlarging an image of an object so that it appears much bigger than its actual size; also refers
to the number of times an object is magnified.
microscopist: A scientist who specializes in research with the use of microscopes.
microscopy: The scientific field of using microscopes to view samples and objects that cannot be seen with
the unaided eye.
optical microscope: A microscope that uses visible light and lenses to magnify objects.
organelle: A structure within the cytoplasm of a cell; may be enclosed within a membrane; performs a specific
function.
resolution: A measure of the clarity of an image; the minimum distance that two points can be separated by
and still be distinguished as two separate points.
159

3.3. Microscopes in Biology - Advanced

www.ck12.org

scanning electron microscope (SEM): Electron microscope that scans an electron beam over the surface of
an object; measures how many electrons are scattered back.
transmission electron microscope (TEM): Electron microscope that shoots electrons through the sample;
measures how the electron beam changes because it is scattered in the sample.
Summary

The development of light microscopes and later electron microscopes helped scientists learn about the cell.
Early light microscopes had poor resolution and a magnification power of only about 10 times.
Electron microscopes have much higher resolution and magnification; they have been used to produce images
of molecules and atoms.
Many of the discoveries about cell structure since the 1950s have been made with the use of electron microscopes.
Explore More

Use the three videos within this resource to answer the questions that follow.
Types of Microscopy at http://www.wellcome.ac.uk/Education-resources/Teaching-and-education/Big-Picture
/All-issues/The-Cell/Videos-Types-of-microscopy/index.htm
1. Differentiate between light and electron microscopy.
2. What is the role of the objective lenses of a light microscope?
3. What is the upper magnification of an electron microscope?
Review

1. Relate resolution to magnification.


2. Compare the different types of electron microscopy.

160

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.4 The Cell Theory - Advanced


Summarize the principle points of the Cell Theory.

Where do cells come from?


All cells come from other cells. It was the advent of the microscope that allowed this discovery to be made. And it is
one of the three basic points of the Cell Theory. This picture represents cell division, the process of one cell dividing
into two cells.
The Cell Theory

Over the next two centuries after the discoveries of Hooke and Leeuwenhoek, biologists found cells everywhere.
Biologists in the early part of the 19th century suggested that all living things were made of cells, but the role of cells
as the primary building block of life was not discovered until 1839 when two German scientists, Theodor Schwann,
a zoologist, and Matthias Jakob Schleiden, a botanist, suggested that cells were the basic unit of structure and
function of all living things. Later, in 1858, the German doctor Rudolf Virchow observed that cells divide to produce
more cells. He proposed that all cells arise only from other cells. The collective observations of all three scientists
form the Cell Theory, which states that:
all organisms are made up of one or more cells,
all the life functions of an organism occur within cells,
all cells come from preexisting cells.
Though no one point of the Cell Theory is more important than another, the theory clearly states that the functions
necessary for life occur in the cell. Findings since the time of the original Cell Theory have enabled scientists to
"modernize" the theory, including points related to biochemistry and molecular biology. The modern version of
the Cell Theory includes:
all known living things are made up of one or more cells,
all living cells arise from pre-existing cells by division,
161

3.4. The Cell Theory - Advanced

www.ck12.org

the cell is the fundamental unit of structure and function in all living organisms,
the activity of an organism depends on the total activity of independent cells,
energy flow ( metabolism and biochemistry) occurs within cells,
cells contain hereditary information ( DNA) which is passed from cell to cell during cell division,
all cells are basically the same in chemical composition in organisms of similar species.

The Cell Theory is one of the main principles of biology. The points of the theory have been found to be true for all
life. As with any scientific theory, the Cell Theory is based on observations that over many years upheld the basic
conclusions of Schwanns 1839 paper. However, one of Schwanns original conclusions stated that cells formed in
a similar way to crystals. This observation, which refers to spontaneous generation of life, was discounted when
Virchow proposed that all cells arise only from other cells. The Cell Theory has withstood intense examination
of cells by modern powerful microscopes and other instruments. Scientists continue to use new techniques and
equipment to look into cells to discover additional explanations for how they work.

Vocabulary

biochemistry: The study of the structure, composition, and chemical reactions of substances in living systems.
botanist: A person engaged in botany, the science of plant life.
cell: The basic unit of structure and function of all living organisms.
cell division: The process of cell formation from the division of older cells.
cell theory: One of the foundations of biology; refers to the idea that cells are the basic unit of structure and
function of all life.
deoxyribonucleic acid (DNA): Double-stranded nucleic acid that composes genes and chromosomes; the
hereditary material.
metabolism: The sum of all the chemical reactions in a cell and/or organism.
molecular biology: The field of biology that deals with the molecular basis of biological activity; the study
of molecules that make up living organisms.
spontaneous generation: An obsolete principle regarding the origin of life from inanimate matter.
zoologist: A person engaged in zoology, the branch of biology that focuses on the animal kingdom; studies the
structure, embryology, evolution, classification, habits, and distribution of all animals, both living and extinct.

Summary

The Cell Theory states that all living things are made of one or more cells, that cells are the basic unit of life,
and that cells come only from other cells.
The Cell Theory has been updated to include findings based on more recent findings.
162

www.ck12.org

Chapter 3. Cell Biology - Advanced

Explore More

Use this resource to answer the questions that follow.


The wacky history of cell theory at http://ed.ted.com/lessons/the-wacky-history-of-cell-theory
1.
2.
3.
4.
5.

What are the three parts of the Cell Theory?


Who was Zacharias Jensen?
How was bacteria discovered?
Who were Matthias Schleiden and Theodore Schwann? Discuss their agreements and disagreements.
Who was Rudolf Virchow? What was his role in the formation of the cell theory?

Review

1. What three things does the original Cell Theory propose?


2. Compare the modern Cell Theory to the original Cell Theory.
3. How has the theory developed?

163

3.5. Cell Size and Shape - Advanced

www.ck12.org

3.5 Cell Size and Shape - Advanced


Identify the limitations on cell size. Describe the relationship between volume and surface area.
Discuss cell shape and its relationship to cell function.

What determines a cells function?


The cells structure has a lot to do with it. Notice in the representation of skin that there are different layers. These
layers have different functions. Also notice the difference in cell shape within the different layers. The structurefunction relationship is a central theme running throughout biology.

Diversity of Cells

Different cells within a single organism can come in a variety of sizes and shapes. They may not be very big, but
their shapes can be very different from each other. However, these cells all have common abilities, such as obtaining
and using food energy, responding to the external environment, and reproducing. In part, a cells shape determines
its function.
164

www.ck12.org

Chapter 3. Cell Biology - Advanced

Cell Size

If cells are the main structural and functional unit of an organism, why are they so small? And why are there no
organisms with huge cells? The answers to these questions lie in a cells need for fast, easy food. The need to be
able to pass nutrients and gases into and out of the cell sets a limit on how big cells can be. The larger a cell gets,
the more difficult it is for nutrients and gases to move in and out of the cell.
As a cell grows, its volume increases more quickly than its surface area. If a cell was to get very large, the small
surface area would not allow enough nutrients to enter the cell quickly enough for the cells needs. This idea is
explained in Figure 3.6. However, large cells have a way of dealing with some size challenges. Big cells, such
as some white blood cells, often grow more nuclei so that they can supply enough proteins and RNA for the cells
requirements. Large, metabolically active cells often have lots of cell protrusions, resulting in many folds throughout
the membrane. These folds increase the surface area available for transport of materials into or out of the cell. Such
cell types are found lining your small intestine, where they absorb nutrients from your food through protrusions
called microvilli.
Scale of Measurements

1 centimeter (cm) = 10 millimeters (mm) = 102 meters (m)


1 mm = 1000 micrometers (m) = 103 m
1 m = 1000 nanometers (nm) = 106 m
1 nm = 103 m

FIGURE 3.6
A small cell (left), has a larger surfacearea to volume ratio than a bigger cell
(center). The greater the surface-area to
volume ratio of a cell, the easier it is for
the cell to get rid of wastes and take in
essential materials such as oxygen and
nutrients. In this example, the large cell
has the same area as 27 small cells, but
much less surface area.

Imagine cells as little cube blocks. If a small cube cell like the one in the Figure 3.6 is one unit (u) in length, then
the total surface area of this cell is calculated by the equation:
height width number of sides number of boxes
1u 1u 6 1 = 6u2
The volume of the cell is calculated by the equation:
height width length number of boxes
1u 1u 1u 1 = 1u3
The surface-area to volume ratio is calculated by the equation:
area volume
165

3.5. Cell Size and Shape - Advanced

www.ck12.org

61=6
A larger cell that is 3 units in length would have a total surface area of
3u 3u 6 1 = 54u2
and a volume of:
3u 3u 3u 1 = 27u3
The surface-area to volume ratio of the large cell is:
54 27 = 2
Now, replace the three unit cell with enough one unit cells to equal the volume of the single three unit cell. This can
be done with 27 one unit cells. Find the total surface area of the 27 cells:
1u 1u 6 27 = 162u2
The total volume of the block of 27 cells is:
1 1 1 27 = 27u3
The surface-area to volume ratio of the 27 cells is:
162 27 = 6
An increased surface area to volume ratio means increased exposure to the environment. This means that nutrients
and gases can move in and out of a small cell more easily than in and out of a larger cell.

FIGURE 3.7
Ostrich eggs (A) can weigh as much as
1.5 kg and be 13 cm in diameter, whereas
each of the mouse cells (B) shown at right
are each about 10 m in diameter, much
smaller than the period at the end of this
sentence.

The cells you have learned about so far are much smaller than the period at the end of this sentence, so they are
normally measured on a very small scale. The smallest prokaryotic cell currently known has a diameter of only 400
nm. Eukaryotic cells normally range between 1100m in diameter. The mouse cells in Figure 3.7 are about 10
m in diameter. One exception, however, is eggs. Eggs contain the largest known single cell, and the ostrich egg is
the largest of them all. The ostrich egg in Figure 3.7 is over 10,000 times larger than the mouse cell.
166

www.ck12.org

Chapter 3. Cell Biology - Advanced

Cell Shape

The variety of cell shapes seen in prokaryotes and eukaryotes reflects the functions that each cell has, confirming
the structure-function relationship seen throughout biology. Each cell type has evolved a shape that is best related
to its function. For example, the neuron in Figure 3.8 has long, thin extensions ( axons and dendritres) that reach
out to other nerve cells. The extensions help the neuron pass chemical and electrical messages quickly through the
body. The shape of the red blood cells ( erythrocytes) enable these cells to easily move through capillaries. The
spikes on the pollen grain help it stick to a pollinating insect or animal so that it can be transferred to and pollinate
another flower. The long whip-like flagella (tails) of the algae Chlamydomonas help it swim in water.

FIGURE 3.8
Cells come in very different shapes. Left
to right, top row: Long, thin nerve cells;
biconcave red blood cells; curved-rod
shaped bacteria.

Left to right, bottom

row: oval, flagellated algae and round,


spiky pollen grains are just a sample of
the many shapes.

Vocabulary

axon: A long, slender projection of a neuron that conducts electrical impulses away from the neurons cell
body.
capillary: The smallest of a bodys blood vessels.
dendrite: Branched projections of a neuron; conducts the electrochemical stimulation received from other
cells to the cell body.
egg (Latin, ovum): Cell in which an embryo first begins to develop.
erythrocyte: Flattened, doubly concave cells that carry oxygen; also known as red blood cells.
eukaryotic cell: Typical of multi-celled organisms; have membrane bound organelles; usually larger than
prokaryotic cells.
flagella (singular, flagellum): A "tail-like" appendage that protrudes from the cell body of certain prokaryotic
and eukaryotic cells; used for locomotion.
167

3.5. Cell Size and Shape - Advanced

www.ck12.org

microvilli: Cellular membrane protrusions that increase the surface area of cells.
neuron: An electrically excitable cell that processes and transmits information by electrical and chemical
signaling; a nerve cell.
prokaryotic cell: Typical of simple, single-celled organisms, such as bacteria; lack a nucleus and other
membrane bound organelles.
structure-function relationship: Principle that states the function of a biological item (molecule, protein,
cell) is determined by its structure.
Summary

Cell size is limited by a cells surface area to volume ratio. A smaller cell is more effective and transporting
materials, including waste products, than a larger cell.
Cells come in many different shapes. A cells function is determined, in part, by its shape.
Explore More

Use this resource to answer the questions that follow.


Cell Shape and Size at http://www.youtube.com/watch?v=wgnG64ieUkE

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139343

1. Describe the relationship between the cell surface area and cell membrane.
2. Why is a smaller volume of the cell better?
3. What are ways to "get around" the SA:V ratio?
Review

1. What limits the size of a cell? Why?


2. A cell has a volume of 64 units, and total surface area of 96 units. What is the cells surface area to volume
ratio?
3. What is the largest single cell?
4. Describe the relationship between cell shape and function? Give an example of cell shape influencing cell
function.

168

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.6 Common Parts of Cells - Advanced


Identify the parts common to all cells.

What do your cells share with a bacterium?


This bacterial cell has the features all cells have in common-the ribosomes and DNA can be seen floating around in
the cytoplasm, which is surrounded by the plasma membrane.
Parts of a Cell

There are many different types of cells, but all cells fall into two general categories: prokaryotic and eukaryotic.
These cells can be vastly different, but still similar in some ways. All cells, whether from a simple bacterium or a
cell from a large whale, have a few things in common. These are:

a cell membrane (also known as the plasma membrane)


cytoplasm
ribosomes
DNA (genetic information)

The cell membrane (also called the plasma membrane) is the physical boundary between the intracellular space
(the inside of the cell) and the extracellular environment. It acts almost like the "skin" of the cell, controlling the
movement of substances in and out of cells. The cell membrane is semi-permeable, allowing only select ions and
169

3.6. Common Parts of Cells - Advanced

www.ck12.org

organic molecules to enter and/or leave the cell. The cell membrane consists of two layers of phospholipids (a lipid
bilayer) with embedded proteins which have numerous functions. More about the cell membrane will be discussed
in the The Plasma Membrane (Advanced) concepts.
Cytoplasm is the general term for all of the material inside the cell, excluding the nucleus of eukaryotic cells. All
the contents of a prokaryotic cell are contained within the cytoplasm. Cytoplasm is made up of cytosol, a watery
fluid that contains cytoskeletal fragments, dissolved particles and organelles. Organelles are structures that carry
out specific functions inside the cell. It is within the cytoplasm that most cellular activities occur, such as many
metabolic pathways and processes such as cell division. More about the cytoplasm will be discussed in the Cell
Structures: The Cytoplasm and Cytoskeleton (Advanced) concept.
Ribosomes are the organelles on which proteins are made during protein synthesis. Ribosomes are found throughout the cytosol of the cell and attached to the endoplasmic reticulum organelle. Ribosomes order amino acids using
messenger RNA (mRNA) as a template in a process called translation. Ribosomes are made from complexes of
ribosomal RNAs (rRNA) and proteins called ribonucleoproteins. Each ribosome is divided into two subunits.
The smaller subunit binds to the mRNA pattern, while the larger subunit binds to the transfer RNA (tRNA) and the
growing polypeptide chain. More about the ribosome will be discussed in the Cell Structures: Ribosomes (Advanced)
concept.
All cells also have DNA. DNA contains the genetic information needed for building structures such as proteins and
RNA molecules in the cell.
An introduction to the cell, discussing various parts of the cell, is available at http://www.youtube.com/user/khan
academy#p/c/7A9646BC5110CF64/33/Hmwvj9X4GNY (21:03).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/247

Vocabulary

cell membrane: Thin coat of lipids (phospholipids) that surrounds and encloses a cell; physical boundary
between the intracellular space and the extracellular environment; also called the plasma membrane.
cytoplasm: The gel-like material inside the plasma membrane of a cell; holds the cells organelles (excluding
the nucleus).
cytosol: A watery cytoplasmic fluid that contains cytoskeletal fragments, dissolved particles and organelles.
deoxyribonucleic acid (DNA): Double-stranded nucleic acid that composes genes and chromosomes; the
hereditary material.
eukaryotic: From an organism that has cells containing a nucleus and other membrane-bound organelles;
eukaryote.
messenger RNA (mRNA): Type of RNA that copies genetic instructions from DNA in the nucleus and carries
them to the cytoplasm.
170

www.ck12.org

Chapter 3. Cell Biology - Advanced

organelle: A structure within the cytoplasm of a cell; may be enclosed within a membrane; performs a specific
function.
plasma membrane: Thin coat of lipids (phospholipids) that surrounds and encloses a cell; physical boundary
between the intracellular space and the extracellular environment; also called the cell membrane.
prokaryotic: From a single-celled organism that lacks a nucleus; prokaryote.
protein synthesis: The process in which cells make proteins; includes transcription of DNA and translation
of mRNA.
ribonucleoprotein: A nucleoprotein that contains RNA; includes the ribosome, vault ribonucleoproteins, and
small nuclear RNPs (snRNPs).
ribosomal RNA: Type of RNA that helps form ribosomes and assemble proteins.
ribosome: A non-membrane bound organelle inside all cells; site of protein synthesis (translation).
semi-permeable: The feature of a cell membrane that allows only select molecules (ions and organic molecules)
to enter and/or leave the cell.
transfer RNA (tRNA): Type of RNA that brings amino acids to ribosomes where they are joined together to
form proteins.
translation: The process of synthesizing a polypeptide/protein from the information in a mRNA sequence;
occurs on ribosomes.
Summary

Parts common to all cells are the plasma membrane, the cytoplasm, ribosomes, and genetic material.
Review

1.
2.
3.
4.

What are the common parts of all cells?


What is one general feature of the plasma membrane?
What occurs on the ribosomes? What are the three types of RNAs?
What is the relationship between cytosol and cytoplasm?

171

3.7. Two Types of Cells - Advanced

www.ck12.org

3.7 Two Types of Cells - Advanced


Define prokaryotic and eukaryotic.
Describe common features of prokaryotic cells.
Compare prokaryotic and eukaryotic cells.

How many different types of cells are there?


There are many different types of cells. For example, in you there are blood cells and skin cells and bone cells and
even bacteria. Here we have drawings of bacteria and animal cells. Can you tell which depicts various types of
bacteria? However, all cells - whether from bacteria, human, or any other organism - will be one of two general
types: prokaryotic or eukaryotic. In fact, all cells other than bacteria will be one type, and bacterial cells will be the
other. And it all depends on how the cell stores its DNA.
Two Types of Cells

There are two cell types: prokaryotes and eukaryotes. Prokaryotic cells are usually single-celled and smaller than
eukaryotic cells. Eukaryotic cells are usually found in multicellular organisms, but there are some single-celled
eukaryotes.
Prokaryotic Cells

The bacterium in Figure 3.9 is a prokaryote. Prokaryotes are microscopic organisms that have neither a membranebound nucleus nor membrane-bound organelles. Some cell biologists consider the term "organelle" to describe
membrane-bound structures only, whereas other cell biologists define organelles as discrete structures that have a
specialized function. Prokaryotes have ribosomes, which are not surrounded by a membrane but do have a specialized function, and could therefore be considered organelles. All metabolic functions carried out by a prokaryote take
place in the plasma membrane or the cytosol.
Prokaryotes are the smallest types of cells, averaging 2-5m in diameter. Despite their small size, inside each cell
there is chemical and biochemical machinery necessary for growth, reproduction, and the acquisition and utilization
of energy. The common features of prokaryotic cells are:

172

cell wall
plasma membrane
ribosomes
genetic material

www.ck12.org

Chapter 3. Cell Biology - Advanced

FIGURE 3.9
Diagram of a typical prokaryotic cell.
Among other things, prokaryotic cells
have a plasma membrane, cytoplasm, ribosomes, and DNA. Prokaryotes do not
have membrane-bound organelles or a
cell nucleus.

capsule (most, but not all)


flagella (most, but not all)
pili (most, but not all)
lack of compartmentalization
plasmid (most, but not all)
binary fission

All prokaryotes have a cell wall that adds structural support, acts as a barrier against outside forces and anchors the
whip-like flagella. Some prokaryotes have an extra layer outside their cell wall called a capsule, which protects the
cell when it is engulfed by other organisms, assists in retaining moisture, and helps the cell adhere to surfaces and
nutrients. Pili are hair-like structures on the surface of the cell that attach to other bacterial cells or surfaces.
Within the plasma membrane, the cytoplasm is not subdivided by membranes into organelles, a lack of compartmentalization that is most evident in the organization of the genetic material. Prokaryotic cells contain only a single
circular piece of chromosomal DNA stored in an area called the nucleoid. Some prokaryotes also carry smaller
circles of DNA called plasmids. Plasmids are physically separate from, and can replicate independently of, the
chromosomal DNA. The genetic information on the plasmids is transferable between cells, allowing prokaryotes to
share abilities, such as antibiotic resistance.
Scientists have discovered that plasmids serve as important tools in genetics and biotechnology labs, most commonly
for their ability to amplify (make many copies of) or to express particular genes. For example, the pGLO plasmid
is a genetically engineered plasmid used in biotechnology as a vector for creating genetically modified organisms.
Below is a video that will demonstrate the pGLO transformation.
pGLO Transformation at http://www.youtube.com/watch?v=yI9IXHw0j1U

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139337

173

3.7. Two Types of Cells - Advanced

www.ck12.org

Reproduction in prokaryotic cells is by binary fission; a process of growth, enlargement and division. This will be
discussed in the Cell Division: Prokaryotic (Advanced) concept.
Prokaryotes have a large array of characteristics, that enable them to withstand different conditions, environments
and resources. Some live in the absence of oxygen, some in extreme cold or hot temperatures, and some in the
bottom of the ocean where their only resource is hot hydrogen sulfide, bubbling up from the core of the Earth. They
are spectacularly resourceful organisms.
Eukaryotic Cells

FIGURE 3.10
A eukaryotic cell, represented here by a
model animal cell is much more complex
than a prokaryotic cell. Eukaryotic cells
contain many organelles that do specific
jobs. No single eukaryotic cell has all the
organelles shown here, and this model
shows all eukaryotic organelles.

A eukaryote is an organism whose cells are organized into complex structures by internal membranes and a
cytoskeleton, as shown in Figure 3.10. The most characteristic membrane-bound structure of eukaryotes is the
nucleus. This feature gives them their name, which comes from Greek and means "true nucleus." The nucleus is the
membrane-enclosed organelle that contains DNA. Eukaryotic DNA is organized in one or more linear molecules,
called chromosomes. Some eukaryotes are single-celled, but many are multicellular. Eukaryotes include all protists,
fungi, plants and animals.
In addition to having a plasma membrane, cytoplasm, a nucleus and ribosomes, eukaryotic cells also contain
membrane-bound organelles. Each organelle in a eukaryote has a distinct function. Because of their complex level
of organization, eukaryotic cells can carry out many more functions than prokaryotic cells. The main differences
between prokaryotic and eukaryotic cells are shown in Figure 3.11 and listed in Table 3.1. Keep in mind that some
eukaryotic cells may have characteristics or features that other eukaryotic cells lack, such as the cell wall.
A Comparison

Eukaryotic cells are about 10 times the size of a typical prokaryote; they range between 10 and 100 m in diameter
while prokaryotes range between 1 and 10 m in diameter, as shown in Figure 3.12. Scientists believe that
eukaryotes developed about 1.6 2.1 billion years ago. The earliest fossils of multicellular organisms that have
been found are 1.2 billion years old.

174

www.ck12.org

Chapter 3. Cell Biology - Advanced


FIGURE 3.11
The main differences between prokaryotic
and eukaryotic cells.

Eukaryotic cells

have membrane bound organelles, shown


here as a mitochondria, while prokaryotic
cells do not.

The nucleoid is the area

within the cytoplasm of a prokaryotic cell


that contains the genetic material.

FIGURE 3.12
The relative scale of prokaryotic and eukaryotic cells. See how eukaryotic cells
are generally 10 to 100 times larger than
prokaryotic cells.

TABLE 3.1: Structural Differences Between Prokaryotic Cells and Eukaryotic Cells
Presence of
Plasma membrane
Genetic material (DNA)
Cytoplasm
Ribosomes
Nucleus
Nucleolus
Mitochondria
Other membrane-bound organelles
Cell wall
Capsule
Flagellum
Pili
Average diameter

Prokaryote
yes
yes
yes
yes
no
no
no
no
yes
yes
yes
yes
0.4 to 10 m

Eukaryote
yes
yes
yes
yes
yes
yes
yes
yes
some (plant cells)
no
yes
no
1 to 100 m

Vocabulary

175
binary fission: Asexual reproduction in prokaryotic organisms; produces two identical cells.

3.7. Two Types of Cells - Advanced

www.ck12.org

Summary

There are only two main types of cells: prokaryotic and eukaryotic.
Prokaryotic cells lack a nucleus and other membrane-bound organelles.
Eukaryotic cells have a nucleus and other membrane-bound organelles. This allows these cells to have
complex functions.
Review

1. What is a prokaryotic cell? What is an eukaryotic cell? What is the major difference between the two cell
types?
2. What are the common features of prokaryotic cells?
3. Give examples of prokaryotic and eukaryotic cells.
4. Identify three differences between prokaryotic and eukaryotic cells.

176

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.8 Viruses - Advanced


Explain why viruses are not considered living organisms.

What is a virus? Is it even a living organism?


This alien-looking thing is a representation of a virus. But is it prokaryotic or eukaryotic? Or neither? Or both? A
virus is essentially genetic material surrounded by protein. Thats it. So, is a virus prokaryotic or eukaryotic? Or
neither? Or both?
Are Viruses Prokaryotic or Eukaryotic?

A virus is a sub-microscopic particle that can infect living cells. Viruses are much smaller than prokaryotic
organisms. In essence, a virus is simply a nucleic acid surrounded by a protein coat, as seen in the Figure 8.3.
This outer coat is called a capsid. Viruses will be discussed in more detail in the Viruses concepts.
Are viruses prokaryotic or eukaryotic? Neither. Viruses are not made up of cells, so they do not have a cell membrane
or any cytoplasm, ribosomes, or other organelles, nor do they have their own metabolism. The viral DNA (or
sometimes RNA) encodes for proteins that make the capsid. However, viruses cannot make their own proteins; they
use the ribosomes of a host cell to make proteins. A host cell is a cell infected by a virus.
Viruses do not reproduce by themselves, instead, they use their host cell to make additional copies of themselves.
The host cell both replicates the viral genome (DNA) and produces the viral capsid. The viral genome is then
packaged into the capsid, resulting in new viruses. So most virologists consider viruses non-living. But, they do
evolve, which is a characteristic of living organisms.
Viruses do have significant use in research and medicine, including gene therapy. Understanding the structure of
viruses and understanding their interaction with host organisms (including how they infect and exploit host cells to
reproduce) and understanding their physiology and immunity is beneficial to human health.
An overview of viruses can be seen at http://www.youtube.com/watch?v=0h5Jd7sgQWY (23:17).

177

3.8. Viruses - Advanced

www.ck12.org

FIGURE 3.13
Structural overview of a virus, the T2
phage. A 2-dimensional representation
is on the left, and a 3-dimensional representation is on the right. The virus is
essentially nucleic acid surrounded by a
protein coat.

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/248

Viruses were first described by Dmitri Ivanovsky in 1892. He described a "non-bacterial pathogen" infecting tobacco
plants. This was soon followed by the identification of the tobacco mosaic virus by Martinus Beijerinck in 1898.
Since then, about 5,000 viruses have been described in detail, although it is believed that there are millions of
different types. Viruses are found in almost every ecosystem on Earth, and are the most abundant type of biological
entity. Viruses can be classified with a taxonomic structure from order to species. No kingdom classification exists.
Viruses, not being made of cells, do not fall into any of the six prokaryotic or eukaryotic kingdoms.
Vocabulary

capsid: The protective protein coat that surrounds the DNA or RNA of a virus particle.
gene therapy: Process to potentially cure genetic disorders; involves inserting normal genes into cells with
mutant genes.
genome: The complete set of an organisms hereditary information; may be either DNA or, for many types of
virus, RNA; includes both the genes and the non-coding sequences of the DNA/RNA.
virologist: A scientist who studies viruses and virus-like agents.
virus: A sub-microscopic particle that can infect living cells; contains DNA (or RNA) and can evolve, but
lacks other characteristics of living organisms.
Summary

Viruses are neither prokaryotic or eukaryotic.


178

www.ck12.org

Chapter 3. Cell Biology - Advanced

Viruses are not made of cells. Viruses cannot replicate on their own.
Most scientists do not consider viruses to be living.
Explore More

Use this resource to answer the questions that follow.


http://www.hippocampus.org/Biology Non-Majors Biology Search: Viruses
1. Describe a virus.
2. What are the two types of replication a viral genome can undergo? Explain.
Review

1. What is a virus?
2. Are viruses considered living? Explain your answer.

179

3.9. Cell Structures - Advanced

www.ck12.org

3.9 Cell Structures - Advanced


Describe the cellular structure-function relationship.

What are cell structures?


The contents of the cell, or the structures of the cell, allow the cell to be "specialized." Together with the cells
proteins, they allow the cell to do specific things. They allow a cell to act like a neuron or a bone cell or a skin cell.
Introduction to Cellular Structures

The invention of the microscope opened up a previously unknown world. Before the invention of the microscope,
very little was known about what made up living things and non-living things, or where living things came from.
During the discovery of cells, spontaneous generation the belief that living organisms grow directly from
decaying organic substances was the accepted explanation for the appearance of small organisms. For example,
people accepted that mice spontaneously appeared in stored grain, and maggots formed in meat with no apparent
external influence. Once cells were discovered, the search for answers to such questions as "What are cells made
of?" and "What is the function of cells?" became the focus of study.
Cell Function

Cells share the same needs: the need to get energy from their environment, the need to respond to their environment,
and the need to reproduce. Cells must also be able to separate their relatively stable interior from the ever-changing
180

www.ck12.org

Chapter 3. Cell Biology - Advanced

FIGURE 3.14
The structure and contents of a typical
animal cell. Every animal cell has a cell
membrane, cytoplasm, ribosomes, and a
nucleus, but not all cells have every structure shown here. For example, some cells
such as red blood cells do not have any
mitochondria, yet others such as muscle
cells may have thousands of mitochondria.

external environment. They do this by coordinating many processes that are carried out within organelles, or other
cellular structures. Structures that are common to many different cells indicate the common history shared by cellbased life. Examples of these common structures include the components of both the cell (or plasma) membrane
and the cytoskeleton, and other structures shown in Figure 3.14.
Is there a relationship between the cell structure and its function? Of course there is. The structure-function
relationship describes a pattern evident throughout biological systems. This relationship is evident in proteins
(protein structure determines its function), nucleic acids (nucleic acid structure results in a genetic code), anatomy
(longer necked giraffes are more functional than short neck giraffes), as well as cells. Using the human body as an
example, specialized cells perform many diverse functions, from digestion and excretion to message transmission
and oxygen distribution. The structure of each type of human cell depends on what function it will perform. This
structure-function relationship can be extended to all other organisms, from the largest whale to the smallest bacteria.
The variability between cell function is related to the proteins expressed in a particular type of cell. For example,
though they do have many proteins in common, a neuron is going to use select different proteins than muscle cell.
A direct relationship exists between the proteins expressed, the size and shape of every cell and the tasks it needs to
accomplish. Examples can easily be seen in red blood cells, neurons muscle cells and sperm cells.
Red blood cells are flat, round, and very small. Their small size allows easy maneuverability through the
capillaries, the narrowest blood vessels, where oxygen is transferred into body cells.
Neurons have a long, thin cellular extension, allowing for very quick and accurate communication and
responses. The long length allows a neuron to send electrical messages extremely quickly.
Skeletal muscle cells have an arrangement of linear protein fibers. The elongated shape allows for muscle
contraction.
Sperm cells are the only human cell with flagella. This is because of their need to "swim" long distances to
reach an egg for fertilization.
Vocabulary

flagella (singular, flagellum): A tail-like appendage that protrudes from the cell body of certain prokaryotic
and eukaryotic cells; used for locomotion.
181

3.9. Cell Structures - Advanced

www.ck12.org

neuron: An electrically excitable cell that processes and transmits information by electrical and chemical
signaling; a nerve cell.
organelle: A structure within the cytoplasm of a cell; may be enclosed within a membrane; performs a specific
function.
spontaneous generation: An obsolete principle regarding the origin of life from inanimate matter.
structure-function relationship: Principle that states the function of a biological item (molecule, protein,
cell) is determined by its structure.
Summary

A cells function is usually directly related to its structure; this is known as the structure-function relationship.
The structure-function relationship is evident throughout biology.
Explore More

Use this resource to answer the questions that follow.


The Theme of Structure and Function in Cells at http://www.shmoop.com/biology-cells/structure-functi
on.html .
1. What is meant by structure dictates function?
2. Describe how the structure-function relationships relates to the following:
a. mitochondria.
b. chloroplasts.
c. ribosomes.
Review

1. Describe the structure-function relationship of cells. Give two examples.


2. Discuss the role of proteins in the structure-function relationship of cells.

182

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.10 The Plasma Membrane - Advanced


Outline the structure of the plasma membrane.

All cells have a plasma membrane. This membrane surrounds the cell. So what is its role?
Can molecules enter and leave the cell? Yes. Can anything or everything enter or leave? No. So, what determines
what can go in or out? Is it the nucleus? The DNA? Or the plasma membrane?
Plasma Membrane

The plasma membrane (also called the cell membrane) is a lipid bilayer that is common to all living cells. Its
function is to keep the cell as a distinct entity in a water-based environment. A phospholipid bilayer is a double
layer of closely-packed phospholipid molecules. It is this orientation of the phospholipids into the bilayer that
biochemically gives the membrane its specific functional characteristics.
Organelle membranes are also composed of phospholipids. For example, mitochondria are bounded by a double
membrane. Each membrane has a phospholipid bilayer with embedded proteins. This division from the rest of the
cell makes the mitochondria only partially dependent on the cell. More on the structure of the phospholipid bilayer
will be presented in the The Plasma Membrane: The Phospholipid Bilayer (Advanced) concept.
Along the phospholipid bilayer, numerous proteins are embedded within the membrane. This structure is called the
Fluid Mosaic Model which will be discussed in the The Plasma Membrane: The Fluid Mosaic Model (Advanced)
concept. These proteins have a variety of important roles; hormone binding sites, electron carriers, pumps for active
transport, channels for passive transport, enzymes, cell signaling and cell adhesion.
The plasma membranes allows only certain molecules, such as ions and small organic molecules, into and out of
the cell. The ability to allow only certain molecules in or out of the cell is referred to as selective permeability or
semipermeability. This characteristic helps the cell to regulate its interactions between the internal machinery and
the external surroundings, helping to maintain homeostasis.
The plasma membrane also acts as the attachment point for both the intracellular cytoskeleton and, if present, the
cell wall.
183

3.10. The Plasma Membrane - Advanced

www.ck12.org

The plasma membrane is discussed at http://www.youtube.com/watch?v=4Ug5Vf_lxtI . The video is below.

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139345

Vocabulary

cell membrane: Thin coat of lipids (phospholipids) that surrounds and encloses a cell; physical boundary
between the intracellular space and the extracellular environment; also called the plasma membrane.
Fluid Mosaic Model: Model of the plasma membrane; proposes that the membrane behaves like a fluid with
an embedded mosaic of proteins.
phospholipid bilayer: A bilayer (2 layers) of phospholipids that surrounds and encloses a cell; physical
boundary between the intracellular space and the extracellular environment.
plasma membrane: Thin coat of lipids (phospholipids) that surrounds and encloses a cell; physical boundary
between the intracellular space and the extracellular environment; also called the cell membrane.
selective permeability: The ability to allow only certain molecules in or out of the cell; characteristic of the
cell membrane; also called semipermeability.
semipermeability: The ability to allow only certain molecules in or out of the cell; characteristic of the cell
membrane; also called selective permeability.
Summary

The plasma membrane forms a barrier between the cytoplasm and the environment outside the cell.
A main characteristic of the plasma membrane is selective permeability.
Explore More

Use these resources to answer the questions that follow.


Cell Membranes at http://johnkyrk.com/cellmembrane.html .
1.
2.
3.
4.

Are all cells surrounded by a membrane?


Why are phospholipids considered an amphipathic molecule?
What is a glycolipid?
Describe the role of cholesterol in the cell membrane.

http://www.hippocampus.org/Biology Non-Majors Biology Search: Plasma Membrane Structure


184

www.ck12.org

Chapter 3. Cell Biology - Advanced

5. What are the roles of the plasma membrane?


Construction of the Cell Membrane at http://www.wisc-online.com/Objects/ViewObject.aspx?ID=AP1101
.
6. What are the two main components of the cell membrane?
Review

1. Describe the role of the plasma membrane.


2. What is meant by semipermeable?

185

3.11. The Phospholipid Bilayer - Advanced

www.ck12.org

3.11 The Phospholipid Bilayer - Advanced


Describe the structure and function of the plasma membrane.

Why a bilayer?
Whats on the inside of the cell and on the outside? Mostly water. As you can see here, the water-based interior of
the cell has lots of components. These need to be kept inside the cell. And it is the nature of the phospholipid bilayer
to keep the inside of the cell separate from the outside.
Phospholipids

The cell membrane (or plasma membrane) is composed mainly of phospholipids with embedded proteins. The
membrane is a lipid bilayer, with the phospholipids oriented in a distinct manner to provide qualities necessary to
maintain a cell in a water-based environment.
A phospholipid is made up of a polar, phosphorus-containing head, and two long fatty acid (hydrocarbon), non-polar
"tails." That is, the head of the molecule is hydrophilic (water-loving), and the tail is hydrophobic (water-fearing).
Cytosol and extracellular fluid - the insides and outsides of the cell - are made up of mostly water. In this watery
environment, the water loving heads point out towards the water, and the water fearing tails point inwards, and push
the water out. The resulting double layer is called a phospholipid bilayer. A phospholipid bilayer is made up of
two layers of phospholipids, in which hydrophobic fatty acids are in the middle of the plasma membrane, and the
hydrophilic heads are on the outside. An example of a simple phospholipid bilayer is illustrated in Figure 3.15.
The cell membrane also decides what may enter or leave a cell. The membrane is said to be semipermeable
or selectively permeable, allowing only certain ions and organic molecules to cross the membrane. The plasma
membrane contain many proteins, as well as other lipids called sterols. The proteins have various functions, such as
channels (channel proteins) that allow certain molecules into the cell, and receptors (receptor proteins) that bind to
186

www.ck12.org

Chapter 3. Cell Biology - Advanced


FIGURE 3.15
Phospholipid Bilayer.

The phospholipid

bilayer consists of two layers of phospholipids, with a hydrophobic, or waterhating, interior and a hydrophilic, or waterloving, exterior. The hydrophilic (polar)
head group and hydrophobic tails (fatty
acid chains) are depicted in the single
phospholipid molecule. The polar head
group and fatty acid chains are attached
by a 3-carbon glycerol unit.

The hy-

drophobic fatty acids point towards the


middle of the plasma membrane, and the
hydrophilic heads point outwards.

The

membrane is stabilized by cholesterol


molecules (green). This self-organization
of phospholipids results in a semipermeable membrane which allows only certain
molecules in or out of the cell.

signal molecules. In Figure 3.15, the smaller (green) molecules shown between the phospholipids are cholesterol
molecules. Cholesterol helps keep the plasma membrane firm and stable over a wide range of temperatures. At least
ten different types of lipids are commonly found in plasma membranes. Each type of cell or organelle will have a
different percentage of each lipid, protein and carbohydrate.
Vocabulary

cholesterol: A steroid alcohol that is present in animal cells and body fluids, regulates membrane fluidity, and
functions as a precursor molecule in various metabolic pathways.
hydrophilic: Characteristic of the phospholipid head group; water-loving.
hydrophobic: Characteristic of the phospholipid tails; water-hating.
phospholipid: A major component of the cell membrane; consists of two hydrophobic tails and a hydrophilic
phosphate head group.
phospholipid bilayer: A bilayer (2 layers) of phospholipids that surrounds and encloses a cell; physical
boundary between the intracellular space and the extracellular environment.
plasma membrane: Thin coat of lipids (phospholipids) that surrounds and encloses a cell; physical boundary
between the intracellular space and the extracellular environment; also called the cell membrane.
Summary

A phospholipid is a lipid molecule with a polar head group ( a phosphate group) and two non-polar hydrocarbon tails.
187

3.11. The Phospholipid Bilayer - Advanced

www.ck12.org

The plasma membrane is a selectively permeable lipid bilayer that contains mostly lipids and proteins. These
lipids and proteins are involved in many cellular processes.
Explore More

Use this resource to answer the questions that follow.


What Is the Phospholipid Bilayer? at http://www.wisegeek.com/what-is-the-phospholipid-bilayer.htm .
1. What is the phospholipid bilayer?
2. Describe the structure of a phospholipid.
3. What are the phospholipid bilayers problems?
Review

1. Why can hydrophobic (water-hating) molecules easily cross the plasma membrane, while hydrophilic (waterloving) molecules cannot?
2. Describe the composition of the plasma membrane.
3. Describe the orientation of the phospholipids in the cell membrane.
4. What is the role of cholesterol in the plasma membrane?

188

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.12 Membrane Proteins - Advanced


Describe the structures and roles of proteins associated with the cell membrane.

Membrane Proteins

The second main component of plasma membranes are the variety of proteins. A membrane protein is a protein
molecule that is attached to, or associated with the membrane of a cell or an organelle. Membrane proteins can be
put into two groups based on how the protein is associated with the membrane: (1) integral membrane proteins and
(2) peripheral membrane proteins.
Integral membrane proteins, also called intrinsic proteins, are permanently embedded within the plasma membrane. Structurally, the integral proteins contain residues with hydrophobic side chains that penetrate the fatty acyl
regions of the phospholipid bilayer, thus anchoring the protein to the membrane. The only way to remove the integral
proteins from the membrane are with synthetic detergents, nonpolar solvents and denaturing agents that disrupt the
hydrophobic interactions of the bilayer.
Integral membrane proteins can be classified according to their relationship with the bilayer:
Transmembrane proteins span the entire plasma membrane. Their function is mainly to regulate the transport
189

3.12. Membrane Proteins - Advanced

www.ck12.org

of specific molecules across the membrane. There are two basic types of transmembrane proteins, alphahelical and beta-barrels, which are discussed in Organic Compounds: Proteins (Advanced).
Integral monotopic proteins are permanently attached to the membrane from only one side.
Examples of integral membrane proteins and their functions are:
1. glycoprotein (cell-to-cell interactions)
2. Na+/K+ ATPase (responsible for establishing and maintaining the electrochemical gradients of Sodium and
Potassium ions across the plasma membrane)
3. glucose permease (the reversible transporter protein of glucose)
4. ion channels gates (the flow of ions across the cell membrane)
5. gap junction proteins (a direct connection between the cytoplasm of two cells, which allows various molecules
and ions to pass freely between cells)
6. Bacterial rhodopsins (a protein in archaeans that uses the energy of light to pump protons across the membrane)
Peripheral membrane proteins, also called extrinsic proteins, are only temporarily associated with the membrane.
Most peripheral membrane proteins are hydrophilic so usually they are either attached to integral membrane proteins,
or they can directly bound to a polar head group of the bilayer. This way they can be easily removed, which allows
them to be involved in cell signaling. Peripheral membrane proteins are often associated with ion channels and
transmembrane receptors.
Examples of peripheral membrane proteins and their functions are:
1. spectrin (links the plasma membrane to the actin cytoskeleton for determination of cell shape, arrangement of
transmembrane proteins, and organization of organelles)
2. Kinase C (enzyme that helps mediate signal transduction cascades by hydrolyzing lipids)
3. phospholipases (hydrolyze various bonds in the the polar head group of phospholipids which are vital to the
degredation of damaged or aged cell membranes)
4. hormone receptors (binds a hormone outside the cell membrane and activates a protein kinase inside the cell)
Glycoproteins and glycolipids, in particular, have a carbohydrate chain that acts as a label to identify the cell
type. Specifically, A, B, O blood groups result from having different carbohydrate chains on the cell surface of
red blood cells and other types of cells. Everyone has glycolipids and glycoproteins with the particular type of
carbohydrate chain that signals type O. However, people with type A also have an additional carbohydrate called
N-Acetylgalactosamine and those with type B have an added galactose. Those with type AB have some glycolipids
and glycoproteins with N-Acetylgalactosamine added and others with galactose added.
Shown in Figure 3.16 are two different types of membrane proteins and associated molecules.
Vocabulary

integral membrane proteins: Proteins that are permanently embedded within the plasma membrane of a cell
or organelle.
membrane protein: A protein molecule that is attached to, or associated with, the membrane of a cell or
organelle.
peripheral membrane proteins: Proteins that are only temporarily associated with the cell membrane; can
be easily removed.
plasma membrane: Thin coat of lipids (phospholipids) that surrounds and encloses a cell; physical boundary
between the intracellular space and the extracellular environment; also called the cell membrane.
190

www.ck12.org

Chapter 3. Cell Biology - Advanced

FIGURE 3.16
Some of the membrane proteins make up a major transport system that moves molecules and ions through the
polar phospholipid bilayer.

Summary

The plasma membrane has many proteins that assist other substances in crossing the membrane.
Membrane proteins may be permanently attached/embedded (integral membrane proteins) to the membrane,
or just temporarily associated with the membrane (peripheral membrane proteins).
Explore More

Use this resource to answer the questions that follow.


Cell Membranes at http://www.sparknotes.com/biology/cellstructure/cellmembranes/section2.rhtml
1. Distinguish between integral and peripheral proteins.
2. List three facts about integral proteins.
3. What is the glycocalyx?
Review

1. What are the main differences between the types of proteins associated with the plasma membrane?
2. Name three membrane protein functions.

191

3.13. The Fluid Mosaic Model - Advanced

www.ck12.org

3.13 The Fluid Mosaic Model - Advanced


Describe the Fluid Mosaic Model of the plasma membrane.

Fluid and mosaic?


In this artistic impression of a plasma membrane of a human cell, the plasma membrane is shown as a bilayer
composed of phospholipids with transmembrane and surface proteins. The phospholipids create a fluid environment
full of a mosaic of proteins.
The Fluid Mosaic Model

In 1972, S. J. Singer and G. L. Nicolson proposed the now widely accepted Fluid Mosaic Model of the structure
of cell membranes (Science, 175: 720-731). Remember, it is the cell membrane that keeps the cells internal
environment separate from its surroundings, but it is also this membrane that constantly and consistently allows
the cell to interact and exchange materials with its environment.
The Fluid Mosaic Model proposes that integral membrane proteins are embedded in the phospholipid bilayer, as
seen in the opening image. The bilayer results from the chemical nature of the phospholipids in a polar environment.
The phospholipids create a double layer - or bilayer - when placed in a polar environment like water. Some of these
proteins associated with the membrane extend all the way through the bilayer, and some only partially across it. In
this model, the integral membrane proteins have their polar groups protruding from the membrane into the aqueous
environment, while the non polar regions of the protein are buried within the hydrophobic interior of the membrane.
This model also proposed that the membrane behaves like a fluid. Scanning electron microscope images demonstrated that the embedded molecules can move sideways throughout the membrane, meaning the membrane is not
solid, but more like a fluid. The membrane proteins and lipids of the membrane can move laterally around the
membrane, much like buoys in water, or sideways throughout the membrane. Such movement causes a constant
change in the "mosaic pattern" of the plasma membrane. The mosaic pattern results from the many different components of the bilayer. These components include the phospholipids, integral and peripheral proteins, glycoproteins
192

www.ck12.org

Chapter 3. Cell Biology - Advanced

and glycolipids, which aid in their location and identification of food, water, waste, and other membrane traffic.
Each cell has a particular glycoprotein structure extruding from the cell membrane, based on its need to attract or
repel membrane traffic. The cell is constantly interacting with its environment, bring certain molecules such as ions,
hormones and food into the cell, and exporting materials, such as wastes, out of the cell.
A further description of the fluid mosaic model can be viewed in Fluid Mosaic Model of the Cell Membrane at http
://www.youtube.com/watch?v=LKN5sq5dtW4 (1:27).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139341

Vocabulary

Fluid Mosaic Model: Model of the plasma membrane; proposes that the membrane behaves like a fluid with
an embedded mosaic of proteins.
integral membrane proteins: Proteins that are permanently embedded within the plasma membrane of a cell
or organelle.
phospholipid bilayer: A bilayer (2 layers) of phospholipids that surrounds and encloses a cell; physical
boundary between the intracellular space and the extracellular environment.
Summary

The Fluid Mosaic Model depicts the biological nature of the plasma membrane, with a fluid phospholipid
bilayer and a mosaic of proteins.
Review

1. Describe the Fluid Mosaic Model.

193

3.14. The Cytoplasm and Cytoskeleton - Advanced

www.ck12.org

3.14 The Cytoplasm and Cytoskeleton - Advanced


Distinguish cytoplasm from cytosol.
Name and describe three types of protein fibers that make up the cytoskeleton.

Does a cell have, or even need, a "skeleton"?


What do you get if you take some tubing, and make the tubes smaller and smaller and smaller? You get very
small tubes, or microtubes. Very small tubes, or microtubules, together with microfilaments, form the basis of the
"skeleton" inside the cell.
Cytoplasm

Cytoplasm is one component of cells that is common to all cells. Cytoplasm is the gel-like material between the cell
membrane and the nucleus. The cytoplasm plays an important role in a cell, serving as a "jelly" in which organelles
are suspended and held together by the cell membrane. Though prokaryotic cells do not have organelles (though
they do have ribosomes), they still have cytoplasm. It is within the cytoplasm that most cellular activities occur,
including the many metabolic pathways that occur within organelles, such as photosynthesis and aerobic respiration.
The cytosol, which is the watery substance that does not contain organelles, is made up of 80% to 90% water. The
cytosol plays a mechanical role by exerting pressure against the cells plasma membrane. This helps keep the shape
of the cell. Cytosol also acts as the site of biochemical reactions such as anaerobic glycolysis and protein synthesis.
In prokaryotes all chemical reactions take place in the cytosol.
Cytoskeleton

The cytoskeleton is a cellular "scaffolding" or "skeleton" that crisscrosses the cytoplasm. All eukaryotic cells
have a cytoskeleton, and recent research has shown that prokaryotic cells also have a cytoskeleton. The eukaryotic
cytoskeleton is made up of a network of long, thin protein fibers and has many functions. It helps to maintain cell
194

www.ck12.org

Chapter 3. Cell Biology - Advanced

shape, holds organelles in place, and for some cells, it enables cell movement. The cytoskeleton plays important roles
in both the intracellular movement of substances and in cell division. Certain proteins act like a path that vesicles and
organelles move along within the cell. The threadlike proteins that make up the cytoskeleton continually rebuild to
adapt to the cells constantly changing needs. Three main kinds of cytoskeleton fibers are microtubules, intermediate
filaments, and microfilaments.
Microtubules, shown as (a) in Figure 3.17, are hollow cylinders and are the thickest of the cytoskeleton
structures. They are most commonly made of filaments which are polymers of alpha and beta tubulin, and
radiate outwards from an area near the nucleus called the centrosome. Tubulin is the protein that forms
microtubules. Two forms of tubulin, alpha and beta, form dimers (pairs) which come together to form the
hollow cylinders. The cylinders are twisted around each other to form the microtubules. Microtubules help
the cell keep its shape. They hold organelles in place and allow them to move around the cell, and they form
the mitotic spindle during cell division. Microtubules also make up parts of cilia and flagella, the organelles
that help a cell move.
Microfilaments, shown as (b) in Figure 3.17, are made of two thin actin chains that are twisted around
one another. Microfilaments are mostly concentrated just beneath the cell membrane, where they support the
cell and help the cell keep its shape. Microfilaments form cytoplasmatic extentions, such as pseudopodia
and microvilli, which allow certain cells to move. The actin of the microfilaments interacts with the protein
myosin to cause contraction in muscle cells. Microfilaments are found in almost every cell, and are numerous
in muscle cells and in cells that move by changing shape, such as phagocytes (white blood cells that search
the body for bacteria and other invaders).
Intermediate filaments differ in make-up from one cell type to another. Intermediate filaments organize the
inside structure of the cell by holding organelles and providing strength. They are also structural components
of the nuclear envelope. Intermediate filaments made of the protein keratin are found in skin, hair, and nails
cells.
FIGURE 3.17
(a) The eukaryotic cytoskeleton. Microfilaments are shown in red, microtubules
in green, and the nuclei are in blue. By
linking regions of the cell together, the
cytoskeleton helps support the shape of
the cell. (b) Microscopy of microfilaments
(actin filaments), shown in green, inside
cells. The nucleus is shown in blue.

TABLE 3.2: Cytoskeleton Structure


Fiber Diameter
Protein Composition

Shape

Microtubules
About 25 nm
Tubulin, with two subunits, alpha and beta tubulin
Hollow cylinders made of
two protein chains twisted
around each other

Intermediate Filaments
8 to 11 nm
One of different types of
proteins such as lamin, vimentin, and keratin
Protein fiber coils twisted
into each other

Microfilaments
Around 7 nm
Actin

Two actin chains twisted


around one another

195

3.14. The Cytoplasm and Cytoskeleton - Advanced

www.ck12.org

TABLE 3.2: (continued)


Main Functions

Microtubules
Organelle and vesicle
movement; form mitotic
spindles
during
cell
reproduction;
cell
motility (in cilia and
flagella)

Intermediate Filaments
Organize cell shape; positions organelles in cytoplasm structural support
of the nuclear envelope
and sarcomeres; involved
in cell-to-cell and cell-tomatrix junctions

Microfilaments
Keep cellular shape; allows movement of certain
cells by forming cytoplasmatic extensions or contraction of actin fibers; involved in some cell-tocell or cell-to-matrix junctions

Representation

The cytoskeleton is discussed in the following video: http://www.youtube.com/watch?v=5rqbmLiSkpk (4:50).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/251

Vocabulary

actin: A thin, threadlike protein filament found in muscle; the protein component of microfilaments.
cytoplasm: The gel-like material inside the plasma membrane of a cell; holds the cells organelles (excluding
the nucleus).
cytoskeleton: The structure of filaments and tubules in the cytoplasm; provides a cell with an internal
framework.
cytosol: A watery cytoplasmic fluid that contains cytoskeletal fragments, dissolved particles and organelles.
intermediate filaments: Intermediate component of the cytoskeleton; made of protein fiber coils twisted into
each other.
microfilaments: Smallest component of the cytoskeleton; made of two actin chains twisted around one
another.
microtubules: Largest component of the cytoskeleton; hollow protein cylinders made of alpha and beta
tubulin; also found in flagella.
microvilli: Cellular membrane protrusions that increase the surface area of cells.
tubulin: Protein component of microtubules; alpha-tubulin and beta-tubulin combine to form components of
microtubules.
196

www.ck12.org

Chapter 3. Cell Biology - Advanced

Summary

The cytoplasm consists of everything between the plasma membrane of the cell and the nucleus (of an
eukaryotic cell).
The cytoskeleton is a cellular "skeleton" that crisscrosses the cytoplasm. Three main cytoskeleton fibers are
microtubules, intermediate filaments, and microfilaments.
Microtubules are the thickest of the cytoskeleton structures and are most commonly made of filaments which
are polymers of alpha and beta tubulin.
Microfilament are the thinnest of the cytoskeleton structures and are made of two thin actin chains that are
twisted around one another.
Review

1. What is the difference between cytoplasm and cytosol?


2. Name the three main parts of the cytoskeleton.
3. List two functions of the eukaryotic cytoskeleton.

197

3.15. External Structures of Cells - Advanced

www.ck12.org

3.15 External Structures of Cells - Advanced


Distinguish between cilia and flagella.

What propels a bacteria along?


Bacteria, being single-celled organisms, cannot just get up and walk from place to place. So they have to "swim." To
do this, they must have some sort of structure that propels them through their environment. Such a tail-like structure
is a flagellum or set of flagella. These protein containing structures spin around a biological motor, allowing the
bacteria to move.
External Structures of the Cell

Flagella ( flagellum, singular) are long, thin structures that protrude from the cell membrane. Both eukaryotic and
prokaryotic cells can have flagella. Flagella help single-celled organisms move or swim towards food. The flagella
of eukaryotic cells are normally used for movement too, such as in the movement of sperm cells, which have only
a single flagellum. The flagella of either group are very different from each other. Prokaryotic flagella, shown in
Figure 3.18, are spiral-shaped and stiff. They spin around in a fixed base much like a screw does, which moves the
cell in a tumbling fashion. Eukaryotic flagella are made of microtubules that bend and flex like a whip.
Cilia ( cilium, singular) are made up of microtubule containing extensions of the cell membrane. Although both
cilia and flagella are used for movement, cilia are much shorter than flagella. Cilia cover the surface of some singlecelled organisms, such as paramecium. Their cilia beat together to move the little animal-like protists through the
water. In multicellular animals, including humans, cilia are usually found in large numbers on a single surface of
cells. Multicellular animals cilia usually move materials inside the body. For example, the mucociliary escalator of
the respiratory system is made up of mucus-secreting ciliated cells that line the trachea and bronchi. These ciliated
cells, shown in Figure 3.19, move mucus away from the lungs. This mucus catches spores, bacteria, and debris and
moves to the esophagus, where it is swallowed.
A video showing flagella and cilia can be viewed at http://www.youtube.com/watch?v=QGAm6hMysTA (3:12).

198

www.ck12.org

Chapter 3. Cell Biology - Advanced

FIGURE 3.18
Bacterial flagella spin about in place,
which causes the bacterial cell to "tumble."

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/252

FIGURE 3.19
Left:

Scanning electron micrograph

(SEM), of the cilia protruding from human


lung cells.

Right: Electron micrograph

of cross-section of two cilia, showing the


positions of the microtubules inside. Note
how there are nine groups of two microtubules (called dimers) in each cilium.
Each dimer is made up of an alpha and
a beta tubulin protein that are connected
together.

Vocabulary

cilia (singular, cilium): Short, hairlike projection, similar to flagella, that allows some cells to move.
199

3.15. External Structures of Cells - Advanced

www.ck12.org

flagella (singular, flagellum): A "tail-like" appendage that protrudes from the cell body of certain prokaryotic
and eukaryotic cells; used for locomotion.
microtubules: Largest component of the cytoskeleton; hollow protein cylinders made of alpha and beta
tubulin; also found in flagella.
Summary

Cilia and flagella are extensions of the cell membrane that contain microtubules, and are usually used for
movement.
Cilia cover the surface of some single-celled animals, such as paramecium, but cover only one side of cells in
some multicellular organisms.
Explore More

Use this resource to answer the questions that follow.


Structure and Function of Bacterial Cells at http://textbookofbacteriology.net/structure_2.html .
1.
2.
3.
4.

What is the role of the flagellum motor?


What powers the flagulla motor?
Describe the process needed to propel the bacterium.
Describe the structure and function of the basal body and hook of the flagella.

Review

1. Compare and contrast cilia and flagella.

200

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.16 The Nucleus - Advanced


Outline the form and function of the nucleus.

Where does the DNA live?


The answer depends on if the cell is prokaryotic or eukaryotic. The main difference between the two types of cells
is the presence of a nucleus. In eukaryotic cells, DNA lives in the nucleus.
The Nucleus

The nucleus is a membrane-enclosed organelle found in most eukaryotic cells. The nucleus is the largest organelle
in the cell and contains most of the cells genetic information (mitochondria also contain DNA, called mitochondrial
DNA, but it makes up just a small percentage of the cells overall DNA content). The genetic information, which
contains the information for the structure and function of the organism, is found encoded in DNA in the form of
genes. A gene is a short segment of DNA that contains information to encode an RNA molecule or a protein strand.
DNA in the nucleus is organized in long linear strands that are attached to different proteins. These proteins help
the DNA to coil up for better storage in the nucleus. Think how a string gets tightly coiled up if you twist one end
while holding the other end. These long strands of coiled-up DNA and proteins are called chromosomes. Each
chromosome contains many genes. Humans have about 20,000 to 22,000 genes scattered among 23 chromosomes.
Essentially, the nucleus is the control center of the cell. The function of the nucleus is to maintain the integrity of
the genes and to control the activities of the cell by regulating gene expression. Gene expression is the process by
which the information in a gene is "decoded" by various cell molecules to produce a functional gene product, such as
a protein molecule or an RNA molecule. Gene expression is a highly regulated process, ensuring RNA and proteins
are only produced when necessary.
The degree of DNA coiling determines whether the chromosome strands are short and thick or long and thin. Between cell divisions, the DNA in chromosomes is more loosely coiled and forms long thin strands called chromatin.
DNA is in this uncoiled form during the majority of the cell cycle, making the DNA available to the proteins
201

3.16. The Nucleus - Advanced

www.ck12.org

involved in DNA replication and transcription. Before the cell divides, the chromatin coils up more tightly and form
chromosomes. Only chromosomes stain clearly enough to be seen under a microscope. The word chromosome
comes from the Greek word chroma (color), and soma (body) due to its ability to be stained strongly by dyes.
Nuclear Envelope

The nuclear envelope is a double membrane of the nucleus that encloses the genetic material. It separates the
contents of the nucleus from the cytoplasm. The nuclear envelope is made of two phospholipid bilayers, an inner
membrane and an outer membrane. The outer membrane is continuous with the rough endoplasmic reticulum. Many
tiny holes called nuclear pores are found in the nuclear envelope. These nuclear pores help to regulate the exchange
of materials (such as RNA and proteins) between the nucleus and the cytoplasm.
Nucleolus

The nucleus of many cells also contains an organelle called a nucleolus, shown in Figure 3.20. The nucleolus
is mainly involved in the assembly of ribosomes. Ribosomes are organelles made of protein and ribosomal RNA
(rRNA), and they build cellular proteins in the cytoplasm. The function of the rRNA is to provide a way of decoding
the genetic messages within another type of RNA, called mRNA for messenger RNA, into amino acids. After being
made in the nucleolus, ribosomes are exported to the cytoplasm where they direct protein synthesis.

FIGURE 3.20
The eukaryotic cell nucleus. Visible in this
diagram are the ribosome-studded double
membranes of the nuclear envelope, the
DNA (as chromatin), and the nucleolus.
Within the cell nucleus is a viscous liquid
called nucleoplasm, similar to the cytoplasm found outside the nucleus.

The

chromatin (which is normally invisible), is


visible in this figure only to show that it is
spread out throughout the nucleus.

Vocabulary

chromatin: Grainy material form of uncoiled DNA; form of DNA during interphase of the cell cycle.
chromosome: The coiled structure of DNA and histone proteins; allows for the precise separation of replicated
DNA; forms during prophase of mitosis and meiosis.
202

www.ck12.org

Chapter 3. Cell Biology - Advanced

gene: A segment of DNA that contains information to encode an RNA molecule or a single polypeptide.
gene expression: The process by which the information in a gene is "decoded" to produce a functional gene
product, such as an RNA molecule or a polypeptide/protein molecule.
nuclear envelope: Double phospholipid membrane of the nucleus; encloses the genetic material.
nuclear pore: Tiny hole in the nuclear envelope.
nucleolus: Section of the nucleus; site of ribosome assembly.
nucleus (plural, nuclei): The membrane-enclosed organelle found in most eukaryotic cells that contains the
genetic material (DNA); control center of the cell.
ribosome: A non-membrane bound organelle inside all cells; site of protein synthesis (translation).
Summary

The nucleus is a membrane-enclosed organelle, found in most eukaryotic cells, which stores the genetic
material (DNA).
The nucleus is surrounded by a double lipid bilayer, the nuclear envelope, which is embedded with nuclear
pores.
The nucleolus is inside the nucleus, and is where ribosomes are made.
Review

1.
2.
3.
4.

What is the role of the nucleus of a eukaryotic cell?


Describe the nuclear envelope.
What are nuclear pores?
What is the role of the nucleolus?

203

3.17. The Mitochondria - Advanced

www.ck12.org

3.17 The Mitochondria - Advanced


Outline the form and function of the mitochondria.

Sperm cells and muscle cells need lots of energy. What do they have in common?
They have lots of mitochondria. Mitochondria are called the power plants of the cell, as these organelles are where
most of the cells energy is produced. Cells that need lots of energy have lots of mitochondria.
The Mitochondria

A mitochondrion ( mitochondria, plural), is a membrane-enclosed organelle that is found in most eukaryotic cells.
Mitochondria are called the "power plants" of the cell because they are the site of cellular respiration. In cellular
respiration, the energy from organic compounds such as glucose, is used to make ATP ( adenosine triphosphate).
ATP is the cells energy source that is used for such things such as movement and cell division. Some ATP is made
in the cytosol of the cell, but most of it is made inside mitochondria. The number of mitochondria in a cell depends
on the cells energy needs. For example, active human muscle cells may have thousands of mitochondria, while less
active red blood cells do not have any.
5 Compartments

As the Figure 3.21 (a) and (b) shows, a mitochondrion has two phospholipids membranes. The smooth outer
membrane separates the mitochondrion from the cytosol. The inner membrane has many folds, called cristae.
204

www.ck12.org

Chapter 3. Cell Biology - Advanced

These cristae greatly increase the membrane surface area for integral proteins. Many proteins involved in cellular
respiration are embedded in this inner membrane. The greater surface area allows more proteins to be located
there, resulting in more cellular respiration reactions, and more ATP synthesis. ATP is produced by the enzyme
ATP synthase, which is a membrane protein of the mitochondria inner membrane. The fluid-filled inside of the
mitochondrian, called matrix, is where most of the cells ATP is made.

FIGURE 3.21
(a): Electron micrograph of a single mitochondrion within which you can see many cristae. Mitochondria range
from 1 to 10 m in size. (b): This model of a mitochondrian shows the organized arrangement of the outer
membrane and folded inner membrane with cristae, the inter membrane space, the mitochondrial matrix, and
ATP synthase protein complex.

The mitochondria essentially has five compartments, each with its own function:
1.
2.
3.
4.
5.

the outer mitochondrial membrane,


the intermembrane space (the space between the outer and inner membranes),
the inner mitochondrial membrane,
the cristae space (formed by infoldings of the inner membrane), and
the matrix (space within the inner membrane).

The outer membrane contains large numbers of integral proteins called porins. These porins form channels that
allow small molecules to freely diffuse across the membrane to the other. The inner mitochondrial membrane is
highly impermeable to all molecules. Almost all ions and molecules require special membrane transporters to enter
or exit the matrix. ATP synthase, which produces ATP in the matrix, is embedded within this membrane. The cristae
greatly expand the surface area of the inner mitochondrial membrane, enhancing the ability of the mitochondria
to produce ATP. The matrix contains a highly-concentrated mixture of hundreds of enzymes, the mitochondrial
ribosomes, tRNAs, and several copies of the mitochondrial genome. Of the enzymes, the Krebs cycle enzymes are
located here.
205

3.17. The Mitochondria - Advanced

www.ck12.org

Mitochondria Genome

Although most of a cells DNA is contained in the cell nucleus, mitochondria have their own DNA. Mitochondria
also have the machinery to manufacture their own RNAs and proteins. The human mitochondrial DNA sequence
has 16,569 base pairs encoding 37 total genes: 22 tRNA genes, 2 rRNA genes, and 13 peptide genes. The 13
mitochondrial peptides in humans are integrated into the inner mitochondrial membrane, along with proteins encoded
by nuclear genes.
Mitochondria are able to reproduce asexually, like bacteria, and scientists think that they are descended from prokaryotic organisms. According to the Theory of Endosymbiosis, mitochondria were once free-living prokaryotes that
infected other prokaryotic cells. The invading prokaryotes were protected inside the host cell, and in turn the
prokaryote supplied extra ATP to its host. Eventually these two cells turned into one eukaryotic cell, as the two
organisms evolved so that they could no longer live without each other. Over time, the ancient internal prokaryote
turned into an organelle, resulting in a large cell with an internal organelle. By definition, this is an eukaryotic cell.
Unlike nuclear DNA which is inherited from the father and mother, mitochondrial DNA (mtDNA is most often
inherited from mothers. However paternal mtDNA occasionally slips through with sperm. The technical process
is still unclear but a study was down using Caenorhabditis elegans that showed double membrane vesicles, called
autophagosomes, engulf paternal mitochondria and destroy them.
Since mothers provide the mtDNA and fathers will never pass on a mtDNA, a child shares the same or similar
mtDNA sequence as does his/her siblings and mother. This direct inheritance has allowed biologists to track the
origin of modern human and to draw maternal lineages.
Unfortunately, maternal mt(DNA)is susceptible to mutations which are a cause of inherited disease, such as breast
cancer. Although, it is important to note that most mutations do not lead to defected mtDNA. Heteroplasmy is
the presence of a mixture of more than one type of mtDNA. Most people have homoplasmic cells, meaning that
their cells contain only normal, undefected mtDNA. However, people with both normal, undefected mtDNA and not
normal, defected mtDNA, may inherit mitochondrial diseases. The ultimate condition leading to disease is when the
proportion of mutant mtDNA reaches a threshold, after which the cell can no longer cope, resulting in disease. This
threshold varies among different tissues and different mutations.
Vocabulary

ATP ( adenosine triphosphate): Energy-carrying molecule that cells use to power their metabolic processes;
energy-currency of the cell.
ATP synthase: Ion channel and enzyme complex; chemically bonds a phosphate group to ADP, producing
ATP as H+ ions flow through the ion channel.
cellular respiration: Metabolic process which transfers chemical energy from glucose (a deliverable fuel
molecule) to ATP (a usable energy-rich molecule); most efficient in the presence of oxygen (aerobic).
cristae: Inner membrane folds of the mitochondrion.
Heteroplasmy: the presence of a mixture of more than one type of mtDNA (normal or defected).
Krebs cycle: Stage 2 of aerobic cellular respiration; a series of chemical reactions which completes the
breakdown of glucose begun in stage 1, releasing more chemical energy and producing carbon dioxide; also
called the Citric Acid Cycle.
matrix: Fluid-filled inside of the mitochondrion; space inside of the inner membrane.
206

www.ck12.org

Chapter 3. Cell Biology - Advanced

mitochondria (singular, mitochondrion): Membrane-enclosed organelles that are found in most eukaryotic
cells; called the "power plants" of the cell because they use energy from organic compounds to make ATP.
porin: Integral membrane proteins that act as a pore through which molecules can diffuse.
Theory of Endosymbiosis: Theory that proposes that eukaryotic organelles, such as mitochondria, evolved
from ancient, free-living prokaryotes that invaded other prokaryotic cells.
Summary

Mitochondria are where energy from organic compounds is used to make ATP.
Mitochondria have a double-membrane, resulting in five distinct compartments within the mitochondrion.
They are:

The outer mitochondrial membrane.


The intermembrane space (the space between the outer and inner membranes).
The inner mitochondrial membrane.
The cristae space (formed by infoldings of the inner membrane).
The matrix (space within the inner membrane).

Mitochondria are thought to have evolved from ancient prokaryotic cells.


Mitochondria are most often maternally inherited.
Review

1. Identify the reason why mitochondria are called "power plants" of the cell.
2. What are the five compartments of a mitochondria?
3. If muscle cells become more active than they usually are, they will grow more mitochondria. Explain why
this happens.
4. What determines whether a child inherits a mitochondrial disease?

207

3.18. Endoplasmic Reticulum - Advanced

www.ck12.org

3.18 Endoplasmic Reticulum - Advanced


Outline the form and function of the endoplasmic reticulum.

Does a cell have its own ER?


Yes, but in this case, the ER is not just for emergencies. True, there might be times when the cell responds to
emergency conditions and the functions of the ER may be needed, but usually the cells ER is involved in normal
functions. Proteins are also made on the outside of the ER, and this starts a whole process of protein transport, both
around the inside of the cell and to the cell membrane and out.
The Endoplasmic Reticulum

The endoplasmic reticulum (ER) (plural, reticuli) is a network of phospholipid membranes that form hollow tubes,
flattened sheets, and round sacs. These flattened, hollow folds and sacs are called cisternae. The membrane of the
ER is continuous with the outer layer of the nuclear envelope. The ER has two major functions:
1. Transport: Molecules, such as proteins, can move from place to place inside the ER, much like on an
intracellular highway.
2. Synthesis: Ribosomes that are attached to ER, similar to unattached ribosomes, make proteins. Lipids are
also produced in the ER.
There are two types of endoplasmic reticulum, rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER).
Rough endoplasmic reticulum is studded with ribosomes which gives it a "rough" sandpaper-like appearance. The ribosomes on the RER make proteins that are then transported from the ER in small phospholipid
208

www.ck12.org

Chapter 3. Cell Biology - Advanced

sacs called transport vesicles. The transport vesicles pinch off the ends of the ER. These vesicles can easily
shuttle proteins between the ER and the Golgi apparatus. The RER works with the Golgi apparatus to move
new proteins to their proper destinations in the cell or to the cell membrane. Proteins that are made on the
RER are inserted directly into the ER and then are transported to their various cellular destinations, including
the cell membrane.
Smooth endoplasmic reticulum does not have any ribosomes attached to it, and so it has a smooth appearance. SER has many different functions some of which are: lipid synthesis, carbohydrate metabolism,
calcium ion storage, steroid metabolism and drug detoxification. Smooth endoplasmic reticulum is found
in both animal and plant cells and it serves different functions in each. The SER is made up of tubules
and vesicles that branch out to form a network. In some cells there are dilated areas like the sacs of RER.
Smooth endoplasmic reticulum and RER form an interconnected network of membranous cisternae, tubules
and vesicles.

FIGURE 3.22
Image of nucleus, endoplasmic reticulum
and Golgi apparatus, and how they work
together. The process of secretion from
endoplasmic reticuli (orange) to Golgi apparatus (pink) is shown.

Protein Transport

The ER plays a significant role in protein transport. Proteins are transported through the ER and then throughout the
cell are marked with a signal sequence. This sequence is usually a short peptide of a few amino acids attached to
the N-terminal end of the protein. This short sequence acts as an address "tag," directing the protein to its correct
destination in the cell. At this time, the signal sequence is removed. These proteins packed into transport vesicles
and moved along the cytoskeleton toward their destination.
209

3.18. Endoplasmic Reticulum - Advanced

www.ck12.org

Vocabulary

cisternae (singular, cisterna): Flattened membranous regions of the rough endoplasmic reticulum and the
Golgi apparatus.
endoplasmic reticulum (ER): A network of phospholipid membranes that form hollow tubes, cisternae, and
vesicles; involved in transport of molecules, such as proteins, and the synthesis of proteins and lipids.
rough endoplasmic reticulum: Endoplasmic reticulum embedded with ribosomes.
smooth endoplasmic reticulum: Endoplasmic reticulum without embedded ribosomes.
transport vesicle: A vesicle that is able to move molecules between locations inside the cell.
Summary

The endoplasmic reticulum is a network of phospholipid membranes that form hollow tubes, cisternae, and
vesicles.
The ER is involved in transport of molecules, such as proteins, and the synthesis of proteins and lipids.
The ER can be rough, with embedded ribosomes, or smooth, without ribosomes.
Review

1. What are the main structural and functional differences between rough endoplasmic reticulum and smooth
endoplasmic reticulum?

210

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.19 Ribosomes - Advanced


Outline the form and function of ribosomes.

Where are proteins made?


Proteins are made on ribosomes. The chemical structure of a ribosome is shown above. A ribosome is an organelle
made out of just protein and RNA. Its role in protein synthesis is extremely important. And it is the structure of the
ribosome that allows it to function as it does.
Ribosomes

Ribosomes are small organelles and are the site of protein synthesis (translation). Ribosomes can be found alone or
in groups within the cytoplasm. They can also be attached to the endoplasmic reticulum, and others are attached to
the nuclear envelope. Unlike other organelles, ribosomes are not surrounded by a membrane.
Translation is the process of ordering the amino acids in the assembly of a protein. The word ribosome comes from
ribonucleic acid and the Greek soma (meaning body). Two Nobel Prizes have been awarded for work relating to
the ribosome. The 1974 Nobel Prize in Physiology or Medicine was awarded to Albert Claude, Christian de Duve
and George Emil Palade for the discovery of the ribosome, and the 2009 Nobel Prize in Chemistry was awarded
to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for discovering the detailed structure and
mechanism of the ribosome.
Ribozymes are RNA molecules that catalyze chemical reactions, such as translation. Ribosomes, which are just made
out of rRNA (ribosomal RNA) and protein, have been classified as ribozymes, because the rRNA has enzymatic
211

3.19. Ribosomes - Advanced

www.ck12.org

activity. The rRNA is important for the peptidyl transferase activity that bonds amino acids. Briefly, the ribosomes
interact with other RNA molecules to make chains of amino acids called polypeptide chains, due to the peptide bond
that forms between individual amino acids. Inside the ribosome, three sites participate in the translation process, the
A, P and E sites. Translation will be discussed in detail the Protein Synthesis: Translation (Advanced) concept.

Ribosome Structure

Ribosomes from bacteria, archaea and eukaryotes, have significantly different structures and RNA sequences. The
ribosomes in the mitochondria of eukaryotic cells significantly resemble those in bacteria, reflecting the likely
evolutionary origin of mitochondria.
Ribosomes are produced in the nucleolus, and then transported to the cytoplasm. Ribosomes are made of ribosomal
proteins, called ribonucleoproteins, and ribosomal RNA (rRNA). Each ribosome has two parts, a large and a small
subunit, as shown in Figure 3.23. The subunits are attached to each other. During translation, the smaller subunit
binds to the mRNA, while the larger subunit binds to the tRNA with attached amino acids. When a ribosome finishes
reading an mRNA molecule, the two ribosomal subunits disassociate.

FIGURE 3.23
The two subunits that make up a ribosome, small organelles that are intercellular protein factories.

The two ribosomal subunits are named base on their sedmentation rate in a centrifuge. The unit of measurement is
the Svedberg unit, a measure of the rate of sedimentation, not the size. This accounts for why fragment names do
not add up (70S is made of 50S and 30S).

Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. Their small
subunit has a 16S RNA subunit (consisting of 1540 nucleotides) bound to 21 proteins. The large subunit is
composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins.
Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S) subunit. Their 40S subunit
has an 18S RNA (1900 nucleotides) and 33 proteins. The large subunit is composed of a 5S RNA (120
nucleotides), 28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and about 49 proteins.
The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and small subunits
bound together with proteins into one 70S particle. These organelles are believed to be descendants of bacteria
and as such their ribosomes are similar to those of bacteria.
212

www.ck12.org

Chapter 3. Cell Biology - Advanced

Vocabulary

ribonucleoprotein: A nucleoprotein that contains RNA; includes the ribosome, vault ribonucleoproteins, and
small nuclear RNPs (snRNPs).
ribosome: A non-membrane bound organelle inside all cells; site of protein synthesis (translation).
ribozyme: An RNA molecule with a tertiary structure that enables it to catalyze a chemical reaction.
Svedberg unit: A non-SI unit for sedimentation rate; technically a measure of time that offers a measure of
particle size; 1013 seconds (100 fs).
translation: The process of synthesizing a polypeptide/protein from the information in a mRNA sequence;
occurs on ribosomes.
Summary

Ribosomes are small organelles and are the site of protein synthesis. They are found in all cells.
Ribosomes are composed of a large and small subunit. Prtokaryotic ane eukaryotic ribosomal subunits differ
in size.
Review

1. What is the role of the ribosome?


2. What is a significant difference between the structure of a ribosome and other organelles?
3. Describe the structural differences between prokaryotic and eukayrotic ribosomes.

213

3.20. The Golgi Apparatus - Advanced

www.ck12.org

3.20 The Golgi Apparatus - Advanced


Outline the form and function of the Golgi apparatus.

Why balloons?
The Golgi apparatus is said to look like a stack of deflated balloons. In essence, that is what the Golgi apparatus is.
Not balloons, but plasma membrane. The Golgi apparatus is a series of stacks of membrane, with some extremely
important functions.
The Golgi Apparatus

The Golgi apparatus, which is also known as the Golgi complex or Golgi body, is a large organelle found in most
eukaryotic cells. It was identified in 1898 by the Italian physician Camillo Golgi.
The Golgi apparatus is usually made up of five to eight cup-shaped, membrane-covered stacks of discs called
cisternae (singular, cisterna), as shown in Figure 3.26. Both plant and animal cells have a Golgi apparatus. A
typical mammalian cell will have 40 to 80 of these stacks. While plant cells can have up to several hundred Golgi
stacks scattered throughout the cytoplasm. In plants, the Golgi apparatus contains enzymes that synthesize some of
the cell wall polysaccharides.
The Golgi apparatus modifies, sorts, and packages different substances for secretion out of the cell, or for use within
the cell. The Golgi apparatus is found close to the nucleus of the cell where it modifies proteins that have been
delivered in transport vesicles from the RER. It is also involved in the transport of lipids around the cell. Pieces of
the Golgi membrane pinch off to form vesicles that transport molecules around the cell. The Golgi apparatus can
be thought of as similar to a post office; it packages and labels "items" and then sends them to different parts of the
cell. The Golgi apparatus tends to be larger and more numerous in cells that synthesize and secrete large quantities
of materials; for example, the plasma B cells and the antibody-secreting cells of the immune system have prominent
Golgi complexes.
The stack of cisternae has four functional regions: the cis-Golgi network, medial-Golgi, endo-Golgi, and trans-Golgi
network. Vesicles from the ER fuse with the network and subsequently progress through the stack from the cis- to
the trans-Golgi network, where they are packaged and sent to their destination. Each cisterna includes special Golgi
214

www.ck12.org

Chapter 3. Cell Biology - Advanced

enzymes which modify or help to modify proteins that travel through it. Proteins may be modified by the addition
of a carbohydrate group (glycosylation) or phosphate group (phosphorylation). These modifications may form a
signal sequence on the protein, which determines the final destination of the protein. For example, the addition of a
mannose-6-phosphate signals the protein for lysosomes.

FIGURE 3.24
This animal cell depicts the Golgi apparatus as a stack of flattened discs. The nucleus with the adjacent endoplasmic reticulum, and numerous mitochondria are
also easily identifiable.

The Endomembrane System

Together with the ER and transport vesicles, the Golgi apparatus is part of the cells endomembrane system, which
transports molecules around the cell. This system transports molecules, such as proteins, in vesicles. The vesicles
that leave the RER are transported to the cis face of the Golgi apparatus, where they fuse with the Golgi membrane
and empty their contents into the lumen. Once inside the lumen, the molecules are modified, then sorted for transport
to their next destinations. In addition to the ER, Golgi apparatus, the endomembrane system includes the nuclear
envelope, lysosomes, vacuoles, vesicles, peroxisomes and the cell membrane.
Those proteins destined for areas of the cell other than the ER or Golgi apparatus are moved towards the trans face of
the Golgi complex, to a complex network of membranes and associated vesicles known as the trans-Golgi network
(TGN). This area of the Golgi is the point at which proteins are sorted and shipped to their intended destinations by
their placement into one of at least three different types of vesicles, depending upon the molecular signal they carry.

Vocabulary

cisternae (singular, cisterna): Flattened membranous regions of the rough endoplasmic reticulum and the
Golgi apparatus.
215

3.20. The Golgi Apparatus - Advanced

www.ck12.org

FIGURE 3.25
The secretory process (vesicular transport) from endoplasmic reticulum to Golgi
apparatus. Note how the ER is attached
to the nuclear envelope and the flow of
vesicles from the cis to the trans face of
the Golgi apparatus.

endomembrane system: Divide the cell into functional and structural compartments (organelles); composed
of the different membranes that are suspended in the cytoplasm within a eukaryotic cell; includes the nuclear
envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, vacuoles, vesicles, peroxisomes and the
cell membrane.
Golgi apparatus: A large organelle that is usually made up of five to eight cup-shaped, membrane-covered
discs called cisternae; modifies, sorts, and packages different substances for secretion out of the cell, or for
use within the cell.
trans-Golgi network (TGN): A major sorting pathway that directs newly synthesized proteins to different
subcellular destinations.
Summary

The Golgi apparatus is a large organelle that is usually made up of five to eight cup-shaped, membrane-covered
discs called cisternae.
The Golgi apparatus modifies, sorts, and packages different substances for secretion out of the cell, or for use
within the cell.
Review

1. Describe the structure and role of the Golgi apparatus.


2. Describe the endomembrane system.

216

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.21 Vesicles and Vacuoles - Advanced


Outline the form and function of organelles.

Whats a little ball of plasma membrane?


A vesicle. Because vesicles are made of phospholipids, they can break off of and fuse with other membraneous
material. This allows them to serve as small transport containers, moving substances around the cell and to the cell
membrane.
Vesicles

A vesicle is a small, spherical compartment that is separated from the cytosol by at least one lipid bilayer. Many
vesicles are made in the Golgi apparatus and the endoplasmic reticulum, or are made from parts of the cell membrane
by endocytosis. Vesicles can also fuse with the cell membrane and release their contents to the outside. This process
is called exocytosis. In addition to the Golgi apparatus and ER, vesicles can also fuse with other organelles within
the cell.
Vesicles from the Golgi apparatus can be seen in Figure 3.26. Because a vesicle is essentially a small organelle,
the space inside the vesicle can be chemically different from the cytosol. It is within the vesicles that the cell can
perform various metabolic activities, as well as transport and store molecules.
Types of Vesicles

Vesicles can be classified by their contents and function.


Transport vesicles are part of the endomembrane system. They are able to move molecules such as proteins
between locations inside the cell. For example, transport vesicles move proteins from the rough endoplasmic
reticulum to the Golgi apparatus.
217

3.21. Vesicles and Vacuoles - Advanced

www.ck12.org

FIGURE 3.26
Vesicles from the Golgi apparatus can be
seen in this figure.

Lysosomes are vesicles that are formed by the Golgi apparatus. They contain powerful enzymes that could
break down (digest) the cell. Lysosomes break down harmful cell products, waste materials, and cellular
debris and then force them out of the cell. They also digest invading organisms such as bacteria. Lysosomes
also break down cells that are ready to die, a process called autolysis.

Peroxisomes are vesicles that use oxygen to break down toxic substances in the cell. Unlike lysosomes,
which are formed by the Golgi apparatus, peroxisomes self-replicate by growing bigger and then dividing.
They are common in liver and kidney cells that break down harmful substances. Peroxisomes are named
for the hydrogen peroxide (H2 O2 ) that is produced when they break down organic compounds. Hydrogen
peroxide is toxic, and in turn is broken down into water (H2 O) and oxygen (O2 ) molecules.

Secretory Vesicles contain materials that are to be excreted from the cell, such as wastes or hormones.
Secretory vesicles include synaptic vesicles and vesicles in endocrine tissues. Synaptic vesicles store neurotransmitters. They are located at presynaptic terminals in neurons. When a signal reaches the end of an
axon, the synaptic vesicles fuse with the cell membrane and release the neurotransmitter. The neurotransmitter
crosses the synaptic junction, and binds to a receptor on the next cell. Some cells also produce molecules, such
as hormones produced by endocrine tissues, needed by other cells. These molecules are stored in secretory
vesicles and released when needed. Secretory vesicles also hold enzymes needed to make extracellular
structures, such as the extracellular matrix of animal cells.
218

www.ck12.org

Chapter 3. Cell Biology - Advanced

Vesicles and Transport

Most vesicles are involved in transporting some sort of molecule, such as a hormone or neurotransmitter. These
vesicles must first form around the substance being transported. This requires numerous vesicle coats to surround
and bind to the proteins being transported. They also trap various transmembrane receptor proteins, called cargo
receptors, which in turn trap the cargo molecules.

The Vesicle Coat

The vesicle coat selects specific proteins as cargo. It selects cargo proteins by binding to sorting signals. These
complexes cluster in the membrane, forming a vesicle buds, or coated pit. There are three types of vesicle coats:
clathrin, COPI and COPII. Clathrin coats are found on vesicles trafficking between the Golgi and plasma membrane,
the Golgi and endosomes, and the plasma membrane and endosomes. COPI ( coat protein complex) coated vesicles
are responsible for transport from the cis-Golgi to the ER (retrograde transport), while COPII coated vesicles are
responsible for transport from the ER to the Golgi (anterograde transport). Low-density lipoprotein (LDL) receptors
aggregate in clathrin coated pits prior to internalization.

SNAREs

The vesicle fuses to the membrane phospholipids to release its materials. This process is mediated by a class
of proteins known as SNAREs, for Soluble NSF Attachment Protein Receptors. SNAREs are divided into two
categories, depending on their location. Vesicle or v-SNAREs are incorporated into the membranes of transport
vesicles, and target or t-SNAREs are located in the membranes of target compartments. The v-SNAREs identify
the vesicles cargo, while the t-SNAREs on the target membrane cause the fusion of the vesicle with the target
membrane.

Vesicle Fusion

For a vesicle to release its contents to a cell organelle or to the outside of the cell, the vesicle and target membrane
must fuse. This process is called vesicle fusion. Fusion between the vesicle and a target membrane occurs in one of
two ways: full fusion or "kiss-and-run" fusion. In a full fusion process, the vesicle phospholipids fully incorporate
into the plasma membrane. The vesicle can only be reformed and by a clathrin-coat-dependent process. With kissand-run fusion, the vesicle reforms after the release of its material. This allows the rapid release of materials from
a synaptic vesicle. In this type of fusion, the vesicle forms a fusion pore or porosome in the presynaptic membrane
and releases its neurotransmitters across the synapse, after which the vesicle reforms, allowing it to be reused.

Vacuoles

Vacuoles are membrane-bound organelles that can have secretory, excretory, and storage functions. Vacuoles are
usually much larger than vesicles. Many organisms will use vacuoles as storage areas and some plant cells have
very large vacuoles. The large central vacuole of the plant cell is used for osmotic control (storage of water) and
nutrient storage. Contractile vacuoles are found in certain protists. These vacuoles take water from the cytoplasm
and excrete it from the cell to avoid bursting due to osmotic pressure.

Vocabulary

clathrin: A protein that plays a major role in the formation of coated vesicles.
219

3.21. Vesicles and Vacuoles - Advanced

www.ck12.org

contractile vacuole: An organelle found in freshwater protists involved in osmoregulation; pumps excess
water out of a cell.
endocytosis: The cellular process of capturing a material/substance from outside the cell by vesicle formation.
exocytosis: The cellular process of secreting materials by vesicle fusion.
hormone: A chemical messenger molecule.
lysosome: A vesicle that contains powerful digestive enzymes.
neurotransmitter: Chemical messages which are released at the synapse; relay the message/signal onto the
next neuron or other type of cell.
peroxisome: Vesicles that use oxygen to break down toxic substances in the cell.
porosome: A cup-shaped structure in the cell membranes of eukaryotic cells where vesicles dock in the
process of vesicle fusion and secretion.
secretory vesicle: Vesicle with materials that are to be excreted/secreted from the cell.
SNARE: Soluble NSF Attachment Protein Receptor; mediate vesicle fusion through full fusion exocytosis or
kiss-and-run fusion exocytosis.
synaptic vesicle: Vesicle located at presynaptic terminals in neurons; store neurotransmitters.
transport vesicle: A vesicle that is able to move molecules between locations inside the cell.
vacuole: Membrane-bound organelle that can have secretory, excretory, and storage functions; plant cells have
a large central vacuole.
vesicle: A small, spherical compartment that is separated from the cytosol by at least one lipid bilayer; used
for transport and storage.
vesicle coat: Clusters selected membrane cargo proteins into regions of the plasma membrane for internalization; develops vesicle buds.
Summary

Vesicles store and transport materials with the cell. Some of these materials are transported to other organelles,
other materials are secreted from the cell.
Examples of vesicles include secretory vesicles, transport vesicles, synaptic vesicles and lysosomes.
Vacuoles are membrane-bound organelles that can have secretory, excretory, and storage functions.They are
usually larger than vesicles.
Review

1. Compare vesicles to vacuoles.


2. Describe three types of vesicles.
3. How does a vesicle export materials from the cell?

220

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.22 Other Structures of Cells - Advanced


Outline the form and function of cellular structures.

How are chromosomes separated during cell division?


They are pulled apart by spindle fibers. The fibers are made of microtubules and are organized by the centrioles.
Two pairs of centrioles are seen on opposite sides of the cell during prophase, the first phase of mitosis.

Centrioles

Centrioles are rod-like structures made of short microtubules. Though they are found in most eukaryotic cells,
centrioles are absent in some plants and most fungi.
Nine groups of three microtubules (nine triplets) make up each centriole. The nine triplets are arranged in a
cartwheel-like orientation. Two perpendicularly placed centrioles make up the centrosome. Centrioles are very
important in cellular division, where they arrange the mitotic spindles that pull the chromosome apart during
mitosis. The position of the centriole determines the position of the nucleus, thus playing a crucial role in the
spatial arrangement of the cell.
Centrioles are a very important part of centrosomes, which are involved in organizing microtubules in the cytoplasm.
Centrosomes are associated with the nuclear membrane during prophase of the mitosis. In mitosis, the nuclear
membrane breaks down and the microtubule organizing center (MTOC) of the centrosome arranges microtubules
such that they interact with the chromosomes to build the mitotic spindle.
221

3.22. Other Structures of Cells - Advanced

www.ck12.org

FIGURE 3.27
Here the centrosome is shown as a pair
of orange cylindrical centrioles. They are
made of nine triplets of microtubules.

Junctions

Junctions are areas between cells that either allow or prevent the movement of materials. Junctions are usually
composed of numerous proteins, forming a large molecular complex. Gap junctions, desmosomes and tight junctions
are three examples of junctions.
Gap Junctions

A gap junction or nexus is a specialized intercellular connection between a variety of animal cell-types. This
junction is a type of "opening," or channel, directly connecting the cytoplasm of two cells, which allows various
molecules and ions to pass freely between these cells. One gap junction channel is composed of two connexons
which connect across the intercellular space. Six connexins proteins create one connexon (hemichannel) channel.
Each connexin protein has four transmembrane domains. The complete gap junction is a macromolecular complex
composed of several to hundreds of individual junctions. Gap junctions are especially important in cardiac muscle
cells. The action potential signaling contraction is passed efficiently and effortlessly through gap junctions, allowing
the heart muscle cells to contract in tandem. Electrical synapses in the brain also pass through gap junctions. This
allows action potentials at the synaptic terminals to be transmitted across to the postsynaptic cell without the need
of a neurotransmitter.
Gap junctions are analogous to the plasmodesmata that join plant cells.
Desmosomes

A desmosome is a cell junction specialized for cell-to-cell adhesion. They are found in simple and stratified squamous epithelium, and in muscle tissue where they bind muscle cells to one another. These junctions are composed
of complexes of cell surface adhesion proteins and linking proteins. These proteins have both an intracellular and
extracellular region. Inside the cell, they attach to intracellular filaments of the cytoskeleton. Outside the cell, they
attach to other adhesion proteins.
222

www.ck12.org

Chapter 3. Cell Biology - Advanced

The cell adhesion proteins of the desmosome, desmoglein and desmocollin, are members of the cadherin family
of adhesion proteins. These proteins are transmembrane proteins that bridge the space between adjacent epithelial
cells. The extracellular domains of these cells bind to other cadherin proteins on an adjacent cell. The extracellular
domain of the desmosome is called the Extracellular Core Domain (ECD). This is where the two adhesion proteins
interact.
Tight Junction

Tight junctions are the closely associated areas of two cells. It is a type of junctional complex present only in
vertebrates. The corresponding junctions that occur in invertebrates are septate junctions. An example of a tight
junction is between epithelial cells in the distal convoluted tubule and the collecting duct part of the nephron in the
kidney.
Tight junctions are common at epithelia, which are sheets of cells that form a boundary between a mass of cells
and a cavity or space (a lumen). The membranes of these cells join together, forming a virtually impermeable
barrier to fluid. Tight junctions essentially seal adjacent epithelial cells in a narrow layer just beneath their apical
surface, which is the portion of the cell exposed to the lumen. The rest of the cell surface is known as the basolateral
surface. Tight junctions prevent integral membrane proteins from moving between the apical and basolateral surface,
maintaining the properties of those distinct surfaces. For example, receptor-mediated endocytosis occurs at the apical
surface and exocytosis at the basolateral surface.
Tight junctions are composed of strands of transmembrane proteins embedded in the plasma membranes of two
adjacent cells. The extracellular domains of these proteins directly join to one another. These joining proteins
associate with peripheral membrane proteins located on the intracellular side of plasma membrane. These peripheral
proteins anchor the strands to the actin component of the cytoskeleton, effectively forming a molecular complex
that joins together the cytoskeletons of adjacent cells. The major types anchoring proteins of tight junctions are the
claudins and the occludins.
In addition to holding cells together, tight junctions play a role in the transport of materials. Tight junctions prevent
the passage of molecules and ions through the space between cells. So these molecules and ions must actually
enter cells (either by diffusion or active transport) in order to proceed through a tissue. This allows tight junctions
to indirectly play a role over what substances are allowed into a specific cell. Tight junctions play this role in
maintaining the blood-brain barrier.
Vocabulary

centriole: A cylindrical shaped cell structure composed of nine triplets of microtubules; structure from which
spindle fibers originate.
centrosome: An organelle that serves as the main microtubule organizing center (MTOC) of the animal cell.
connexon: An assembly of six connexin proteins; part of a gap junction channel between the cytoplasm of
two adjacent cells.
desmosome: A junctional complex cell structure specialized for cell-to-cell adhesion.
gap junction: A specialized intercellular connection between a various animal cell-types; directly connects
the cytoplasm of two cells; the narrow gap between the pre- and post-synaptic cells in electrical synapses.
microtubule organizing center (MTOC): A structure found in eukaryotic cells from which microtubules
emerge.
223

3.22. Other Structures of Cells - Advanced

www.ck12.org

plasmodesmata: Microscopic channels which traverse the cell walls of plant cells; enables transport and
communication between them.
tight junction: The closely associated areas of two cells whose membranes join together; forms a virtually
impermeable barrier to fluid.
Summary

Centrioles are made of short microtubules and are very important in cell division.
Cellular junctions allow cell association communication, and adhesion.
Explore More

Use this resource to answer the questions that follow. Inter Cellular Junctions - The Tissue Level of Organization
at https://www.youtube.com/watch?v=ARaj3Kz1cCQ .
1. List the 5 types of intercellular junctions.
2. Briefly describe each type of junction.
3. What is a connexon?
Review

1. What is a cell junction?


2. Describe the structure of a gap junction. How does the structure relate to its function?
3. Distinguish between tight junctions and desmosomes.

224

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.23 Plant Cells - Advanced


Identify and describe three structures that are present solely in plant cells.

What do plants have to do that animals dont?


When an animal needs energy, it eats food. Thats why animals use mitochondria to convert food into energy.
Plants, on the other hand, dont seem to eat anything. Instead, they receive energy from water and sunlight. They
use chloroplasts to convert light into energy through photosynthesis. The focus of this concept is to delineate the
distinct differences between plant and animal cells.
Special Structures in Plant Cells

Most of the organelles that have been discussed in other concepts, such as ribosomes, the mitochondria, endoplasmic
reticulum, and Golgi complex, are common to both animal and plant cells. However, plant cells also have features
that animal cells do not have; they have a cell wall, a large central vacuole, and plastids such as chloroplasts. They
also have junctions called plasmodesmata.
Plants have very different lifestyles from animals, and these differences are apparent when you examine the structure
of the plant cell. Plants have to make their own food, and they do so in a process called photosynthesis. They take
225

3.23. Plant Cells - Advanced

www.ck12.org

in carbon dioxide (CO2 ) and water (H2 O) and convert them into sugars. The features unique to plant cells can be
seen in Figure 3.28.

FIGURE 3.28
In addition to containing most of the organelles found in animal cells, plant cells
also have a cell wall, a large central vacuole, and plastids. These three features
are not found in animal cells.

Cell Wall

A cell wall is a rigid layer that is found outside the cell membrane and surrounds the cell. The cell wall contains
not only cellulose and protein, but other polysaccharides as well. In fact, two other classes of polysaccharides,
hemicelluloses and pectic polysaccharides, can comprise 30% of the dry mass of the cell wall. The cell wall provides
structural support and protection. Pores in the cell wall allow water and nutrients to move into and out of the cell.
The cell wall also prevents the plant cell from bursting when water enters the cell.
Microtubules guide the formation of the plant cell wall. Cellulose is laid down by enzymes to form the primary cell
wall. Some plants also have a secondary cell wall. The secondary wall contains a lignin, a secondary cell component
in plant cells that have completed cell growth/expansion.
Central Vacuole

Most mature plant cells have a central vacuole that occupies more than 30% of the cells volume, but can also
occupy as much as 90% of the volume of certain cells. The central vacuole is surrounded by a membrane called the
tonoplast. The central vacuole has many functions. Aside from storage, the main role of the vacuole is to maintain
turgor pressure against the cell wall. Proteins found in the tonoplast control the flow of water into and out of the
vacuole. The central vacuole also stores the pigments that color flowers.
The central vacuole contains large amounts of a liquid called cell sap, which differs in composition to the cell cytosol.
Cell sap is a mixture of water, enzymes, ions, salts, and other substances. Cell sap may also contain toxic byproducts
that have been removed from the cytosol. Toxins in the vacuole may help to protect some plants from being eaten.
Plastids

Plant plastids are a group of closely related membrane-bound organelles that carry out many functions. They
are responsible for photosynthesis, for storage of products such as starch, and for the synthesis of many types of
226

www.ck12.org

Chapter 3. Cell Biology - Advanced

molecules that are needed as cellular building blocks. Plastids have the ability to change their function between
these and other forms. Plastids contain their own DNA and some ribosomes, and scientists think that plastids are
descended from photosynthetic bacteria that allowed the first eukaryotes to make oxygen. The main types of plastids
and their functions are:
Chloroplasts are the organelle of photosynthesis. They capture light energy from the sun and use it with water
and carbon dioxide to make food (sugar) for the plant. The arrangement of chloroplasts in a plants cells can
be seen in Figure 3.29.
Chromoplasts make and store pigments that give petals and fruit their orange and yellow colors.
Leucoplasts do not contain pigments and are located in roots and non-photosynthetic tissues of plants. They
may become specialized for bulk storage of starch, lipid, or protein. However, in many cells, leucoplasts do
not have a major storage function; instead they make molecules such as fatty acids and many amino acids.

FIGURE 3.29
Plant cells with visible chloroplasts.

The Chloroplast

Chloroplasts capture light energy from the sun and use it with water and carbon dioxide to produce sugars for food.
Chloroplasts look like flat discs that are usually 2 to 10 micrometers in diameter and 1 micrometer thick. A model of
a chloroplast is shown in Figure 3.30. The chloroplast is enclosed by an inner and an outer phospholipid membrane.
Between these two layers is the intermembrane space. The fluid within the chloroplast is called the stroma, and it
contains one or more molecules of small circular DNA. The stroma also has ribosomes. Within the stroma are stacks
of thylakoids, the sub-organelles which are the site of photosynthesis. The thylakoids are arranged in stacks called
grana (singular: granum). A thylakoid has a flattened disk shape. Inside it is an empty area called the thylakoid
space or lumen. Photosynthesis takes place on the thylakoid membrane.
Within the thylakoid membrane is the complex of proteins and light-absorbing pigments, such as chlorophyll
and carotenoids. This complex allows capture of light energy from many wavelengths because chlorophyll and
carotenoids both absorb different wavelengths of light. More about how chloroplasts convert light energy into
chemical energy will be presented in the Photosynthesis (Advanced) concepts.
Plasmodesmata

Plasmodesmata (singular, plasmodesma) are microscopic channels which traverse the cell walls of plant cells
and some algal cells. These junctions enable two cells to transport materials and communication between them.
227

3.23. Plant Cells - Advanced

www.ck12.org

FIGURE 3.30
The internal structure of a chloroplast,
with a granal stack of thylakoids circled.

Plasmodesmata are similar to gap junctions of animal cells. Like gap junctions, plasmodesmata enable direct
intercellular transport of substances between cells. However, unlike other junctions, plasmodesmata do not seem
to be protein based. Rather, they are made from membrane and cell wall material. Plasmodesmata move various
types of molecules, including transport proteins (including transcription factors), short interfering RNA, messenger
RNA and viral genomes from cell to cell. A typical plant cell may have between 1,000 and 100,000 plasmodesmata
connecting it with adjacent cells.
There are two forms of plasmodesmata: primary plasmodesmata, which are formed during cell division, and
secondary plasmodesmata, which can form between mature cells. As plant cells are surrounded by a polysaccharide
cell wall, movement of materials and communication between cells is more complicated than in animal cells.
Neighboring plant cells are separated by a pair of cell walls and the space between them, forming an extracellular
domain known as the apoplast.
Primary plasmodesmata form during cell division. These junctions form as portions of the endoplasmic reticulum
are trapped in the apoplast as new cell wall is formed between two newly divided plant cells. This eventually
become the cytoplasmic connections between cells (primary plasmodesmata). Secondary plasmodesmata form as
plasmodesmata are inserted into existing cell walls between non-dividing cells. This process forms a cytoplasmic
sleeve, a fluid-filled space enclosed by the cell membrane. The cytoplasmic sleeve is a continuous extension of
the cytosol of the two adjacent cells. Molecules and ions pass through plasmodesmata using this passage. These
molecules move by diffusion without the need for additional chemical energy.
Vocabulary

apoplast: The space outside the plasma membrane of plant cells; formed by the continuum of cell walls of
adjacent cells.
cell wall: Rigid layer that surrounds the plasma membrane of prokaryotic cells and plant cells; helps support
and protect the cell.
central vacuole: Large saclike organelle in plant cells; stores substances such as water; helps keep plant
tissues rigid.
chloroplast: The organelle of photosynthesis; site of photosynthesis.
228

www.ck12.org

Chapter 3. Cell Biology - Advanced

chromoplast: Plastid responsible for pigment synthesis and storage in specific photosynthetic eukaryotes.
cytoplasmic sleeve: A fluid-filled space enclosed by the plasmalemma and a continuous extension of the
cytosol.
grana (singular: granum): Structure within the chloroplast; consists of stacks of sac-like thylakoid membranes.
leucoplast: Non-pigmented plastid specialized for bulk storage of starch, lipid or protein; located in roots and
non-photosynthetic tissues of plants.
photosynthesis: The process by which carbon dioxide and water are converted to glucose and oxygen, using
sunlight for energy.
plasmodesmata (singular, plasmodesma): Microscopic channels which traverse the cell walls of plant cells;
enables transport and communication between them.
plastid: Organelle found in the cells of plants and algae; the site of manufacture and storage of important
chemical compounds used by the cell; often contain pigments.
stroma: Space outside the thylakoid membranes of a chloroplast; site of the Calvin cycle of photosynthesis.
thylakoid: Sub-organelle within the chloroplast; site of the light reactions of photosynthesis.
tonoplast: Membrane that surrounds the central vacuole.
Summary

Plant cells have a cell wall, a large central vacuole, and plastids such as chloroplasts.
The cell wall is a rigid layer that is found outside the cell membrane and surrounds the cell, providing structural
support and protection.
The central vacuole maintains turgor pressure against the cell wall.
Chloroplasts capture light energy from the sun and use it with water and carbon dioxide to produce sugars for
food.
Plasmodesmata are gaps between plant cells, connecting the cytoplasms of plant cells.
Explore More

Eucaryotic Cell Interactive Animation: Plant Cell at http://www.cellsalive.com/cells/cell_model.htm .


Review

1.
2.
3.
4.

List three structures that are found in plant cells but not in animal cells.
Identify two functions of plastids in plant cells.
What is the role of the cell wall?
Describe plasmodesmata.

229

3.24. Organization of Cells - Advanced

www.ck12.org

3.24 Organization of Cells - Advanced


Distinguish between a colonial organism and a multicellular organism.
Outline the relationship between cells, tissues, organs, and organ systems.

Why be organized?
It can be said organization leads to efficiency. And in you, cells are organized into tissues, which are organized into
organs, which are organized into organ systems, which form you. And it can be said that the human body is a very
organized and efficient system.

Organization of Cells

Biological organization exists at all levels in organisms. It can be seen at the smallest level, in the molecules that
make up such compounds as DNA and proteins, to the largest level, in an organism such as a blue whale, the largest
mammal on Earth. Similarly, single celled prokaryotes and eukaryotes show order in the way their cells are arranged.
Single-celled organisms such as an amoeba are free-floating and independent-living. Their single-celled "bodies"
are able to carry out all the processes of life such as metabolism and respiration without help from other cells.
Some single-celled organisms such as bacteria can group together and form a colony. A colony refers to a group of
individual organisms of the same species that live closely together. This is usually done to benefit the group, such
as by providing a stronger defense or the ability to attack bigger prey. A colony can also form from organisms other
than bacteria. A bacterial colony often defends from a single organism, producing a colony of genetically identical
individuals.
230

www.ck12.org

Chapter 3. Cell Biology - Advanced

A specific type of colony of microorganisms is a biofilm. A biofilm is a large grouping of many microorganisms
that sticks to a surface and makes a protective coating over itself. Biofilms can show similarities to multicellular
organisms, in the sense that a biofilm will have properties and capabilities greater than the capabilities of the
individual organisms.
Division of labor is the process in which one group of cells does one job (such as making the "glue" that sticks the
biofilm to the surface), while another group of cells does another job (such as taking in nutrients). Multicellular
organisms carry out their life processes through division of labor and they have specialized cells that have specific
functions. However, biofilms are not considered a multicellular organism, but this and other colonial organisms were
probably the first step toward the evolution of multicellular organisms.

FIGURE 3.31
Colonial algae of the genus Volvox.

Colonial Organisms

A colony of single-cell organisms is known as colonial organisms. The difference between a multicellular organism
and a colonial organism is that the individual organisms that form a colony or biofilm can, if separated, survive on
their own, while cells from a multicellular organism (e.g., liver cells) cannot.
Colonial organisms were probably one of the first evolutionary steps towards multicellular organisms. Algae of the
genus Volvox are an example of the bridge between colonial organisms and multicellular organisms. Each Volvox,
shown in Figure 3.31, is a colonial organism. It is made of up to 50,000 photosynthetic flagellate algae that are
grouped together into a hollow sphere. Volvox live in a variety of freshwater habitats, and were first reported by
Antonie van Leeuwenhoek in 1700.
The Volvox sphere has a distinct front and back end. The colony of cells can swim in a coordinated fashion. The
cells have eyespots, which are more developed in the cells near the front. This enables the colony to swim towards
light.
231

3.24. Organization of Cells - Advanced

www.ck12.org

Origin of Multicellularity

The oldest known multicellular organism is a red algae Bangiomorpha pubescens, fossils of which were found in
1.2 billion year old rock. However, the first organisms were single celled. How multicellular organisms developed
is the subject of much debate.
Scientists think that multicellularity arose from cooperation between many organisms of the same species. The
Colonial Theory proposes that this cooperation led to the development of a multicellular organism. Many examples
of cooperation between organisms in nature have been observed. For example, a certain species of amoeba (a
single-celled protist) groups together during times of food shortage and forms a colony that moves as one to a new
location. Some of these amoebas then become slightly differentiated from each other. Volvox, shown in Figure 3.31,
is another example of a colonial organism. Most scientists accept that the Colonial theory explains how multicellular
organisms evolved.
Multicellular organisms are organisms that are made up of more than one type of cell and have specialized cells
that are grouped together to carry out specialized functions. Most life that you can see without a microscope is
multicellular. As discussed earlier, the cells of a multicellular organism would not survive as independent cells. The
body of a multicellular organism, such as a tree or a cat, exhibits organization at several levels: tissues, organs, and
organ systems. Similar cells are grouped into tissues, groups of tissues make up organs, and organs with a similar
function are grouped into an organ system.
Levels of Organization in Multicellular Organisms

The simplest living multicellular organisms, sponges, are made of many specialized types of cells that work together
for a common goal. Such cell types include digestive cells, tubular pore cells; and epidermal cells. Though the
different cell types create a large organized, multicellular structurethe visible spongethey are not organized into
true interconnected tissues. If a sponge is broken up by passing it through a sieve, the sponge will reform on the
other side. However, if the sponges cells are separated from each other, the individual cell types cannot survive
alone. Simpler colonial organisms, such as members of the genus Volvox, as shown in Figure 3.31, differ in that
their individual cells are free-living and can survive on their own if separated from the colony.
A tissue is a group of connected cells that have a similar function within an organism. More complex organisms
such as jellyfish, coral, and sea anemones have a tissue level of organization. For example, jellyfish have tissues that
have separate protective, digestive, and sensory functions. Though most animals have many different types of cells,
they only have four basic types of tissue: connective, muscle, nervous, and epithelial.
Even more complex organisms, such as the roundworm shown in Figure 3.32, while also having differentiated cells
and tissues, have an organ level of development. An organ is a group of tissues that has a specific function or group
of functions. Organs can be as primitive as the brain of a flatworm (a group of nerve cells), as large as the stem of a
sequoia (up to 90 meters, or 300 feet, in height), or as complex as a human liver.
The most complex organisms (such as mammals, trees, and flowers) have organ systems. An organ system is a
group of organs that act together to carry out complex related functions, with each organ focusing on a part of the
task. An example is the human digestive system in which the mouth ingests food, the stomach crushes and liquifies
it, the pancreas and gall bladder make and release digestive enzymes, and the intestines absorb nutrients into the
blood.
Vocabulary

biofilm: A colony of prokaryotes that is stuck to a surface, such as a rock or a hosts tissue.
colonial organism: Organism formed from a grouping of individuals of the same species living symbiotically
together; one of the first evolutionary steps towards multicellular organisms.
232

www.ck12.org

Chapter 3. Cell Biology - Advanced

FIGURE 3.32
This roundworm, a multicellular organism,
was stained to highlight the nuclei of all
the cells in its body (red dots).

Colonial Theory: Proposes that cooperation between many organisms of the same species led to the development of a multicellular organism.
colony: A group of individual organisms of the same species that live closely together.
multicellular organism: Organism made up of more than one type of cell; most have specialized cells that
are grouped together to carry out specialized functions.
organ: A structure composed of two or more tissues that work together for a common purpose.
organ system: A group of organs that act together to carry out complex interrelated functions, with each organ
focusing on a subset of the overall task.
tissue: An aggregation of similar cells that work together to carry out a specific function within the organism/body.
233

3.24. Organization of Cells - Advanced

www.ck12.org

Summary

Single-celled organisms are able to carry out all the processes of life without help from other cells.
Multicellular organisms carry out their life processes through division of labor. They have specialized cells
that do specific jobs.
The Colonial Theory proposes that cooperation among cells of the same species led to the development of a
multicellular organism.
Multicellular organisms, depending on their complexity, may be organized from cells to tissues, organs, and
organ systems.
Explore More

Use these resources to answer the questions that follow.


http://www.hippocampus.org/Biology Non-Majors Biology Search: Tissues
1. Why are multicellular organisms highly organized?
2. What is a tissue?
http://www.hippocampus.org/Biology Non-Majors Biology Search: Organs and Systems
1. What is the difference between an organ and an organ system?
2. How many organ systems do humans have?
Review

1. What is a cell feature that distinguishes a colonial organism from a multicellular organism?
2. What is the difference between a cell and a tissue?
3. Describe the levels of organization of an organism.

234

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.25 Cell Transport - Advanced


Describe the importance of cell transport.

What is cell transport?


It is the movement of substances across the cell membrane either into or out of the cell. Sometimes things just move
through the phospholipid bilayer. Other times, substances need the assistance of a protein, like a channel protein or
some other transmembrane protein, to cross the cell membrane.
Cell Transport

Cell transport refers to the movement of substances across the cell membrane. Probably the most important feature of
a cells phospholipid membranes is that they are selectively permeable. A membrane that is selectively permeable,
or semipermeable, has control over what molecules or ions can enter or leave the cell, as shown in Figure 3.33. This
feature allows a cell to control the transport of materials, as dictated by the cells function. The permeability of a
membrane is dependent on the organization and characteristics of the membrane lipids and proteins. In this way,
cell membranes help maintain a state of homeostasis within cells (and tissues, organs, and organ systems) so that an
organism can stay alive and healthy.
Transport Across Membranes

The molecular make-up of the phospholipid bilayer limits the types of molecules that can pass through it. For
example, hydrophobic (water-hating) molecules, such as carbon dioxide (CO2 ) and oxygen (O2 ), can easily pass
235

3.25. Cell Transport - Advanced

www.ck12.org

FIGURE 3.33
A selectively permeable, or semipermeable, membrane allows certain molecules
through, but not others.

through the lipid bilayer, but ions such as calcium (Ca2+ ) and polar molecules such as water (H2 O) cannot. The
hydrophobic interior of the phospholipid bilayer does not allow ions or polar molecules through because they are
hydrophilic, or water loving. In addition, large molecules such as sugars and proteins are too big to pass through
the phospholipid bilayer. Transport proteins within the membrane allow these molecules to cross the membrane into
or out of the cell. This way, polar molecules avoid contact with the nonpolar interior of the membrane, and large
molecules are moved through large pores.
Every cell is contained within a membrane punctuated with transport proteins that act as channels or pumps to let in
or force out certain molecules. The purpose of the transport proteins is to protect the cells internal environment and
to keep its balance of salts, nutrients, and proteins within a range that keeps the cell and the organism alive.
There are four main ways that molecules can pass through a phospholipid membrane. The first way requires no
energy input by the cell and is called simple diffusion. This type of transport includes passive diffusion and osmosis.
No assistance by a transport is necessary in simple diffusion. Facilitated diffusion, does involve the assistance of
transport proteins. The third way, called active transport, requires that the cell uses energy to pull in or pump out
certain molecules and ions. Active transport involves proteins known as pumps. The fourth way is through vesicle
transport, in which large molecules are moved across the membrane in bubble-like sacks that are made from pieces
of the membrane. Vesicular transport includes exocytosis and endocytosis.

Homeostasis and Cell Transport

Homeostasis refers to the balance, or equilibrium, within the cell or a body. It is an organisms ability to keep a constant internal environment. Keeping a stable internal environment requires constant adjustments as conditions change
inside and outside the cell. The adjusting of systems within a cell is referred to as homeostatic regulation. Because
the internal and external environments of a cell are constantly changing, adjustments must be made continuously to
stay at or near the normal proportions of all internal substances. This involves continual adjustments in transport of
substances across the cell membrane. Homeostasis is a dynamic equilibrium rather than an unchanging state. The
cellular processes discussed in the cell transport (passive and active transport) concepts all play an important role in
homeostatic regulation.
236

www.ck12.org

Chapter 3. Cell Biology - Advanced

Vocabulary

concentration gradient: Difference in the concentrations of a molecule across two distinct areas, such as a
cell membrane.
diffusion: The movement of molecules from an area of high concentration of the molecules to an area with a
lower concentration.
endocytosis: The cellular process of capturing a material/substance from outside the cell by vesicle formation.
exocytosis: The cellular process of secreting materials by vesicle fusion.
homeostasis: The process of maintaining a stable environment inside a cell or an entire organism.
passive transport: Transport of small molecules or ions across the cell membrane without an input of energy
by the cell.
selectively permeable: The ability to allow only certain molecules to cross the plasma membrane; semipermeable.
semipermeable: The feature of a cell membrane that allows only select molecules (ions and organic molecules)
to enter and/or leave the cell; the ability to allow only certain molecules to cross the plasma membrane;
selectively permeable.
Summary

The cell membrane is selectively permeable, allowing only certain substances to pass through.
Cell transport may require assistance by a protein/pump.
Cell transport may require energy.
Some transport involves vesicles.

Review

1. What is meant by cell transport? Why is cell transport important?


2. List types of cell transport.
3. Explain how cell transport helps an organism maintain homeostasis.

237

3.26. Diffusion - Advanced

www.ck12.org

3.26 Diffusion - Advanced


Define diffusion.

What will eventually happen to these dyes?


They will all blend together. The dyes will move through the water until an even distribution, or equilibrium, is
achieved. The process of moving from areas of high amounts of a substance to areas of low amounts of the same
substance is called diffusion.
Diffusion

Passive transport is a way that small molecules or ions move across the cell membrane without input of energy by
the cell. The three main kinds of passive transport are diffusion (or simple diffusion), osmosis, and facilitated diffusion. Simple diffusion and osmosis do not involve transport proteins. Facilitated diffusion requires the assistance of
proteins.
Diffusion is the movement of molecules from an area of high concentration of the molecules to an area with a lower
concentration. For cell transport, diffusion is the movement of small molecules across the cell membrane. The
difference in the concentrations of the molecules in the two areas is called the concentration gradient. The kinetic
energy of the molecules results in random motion, causing diffusion. In simple diffusion, this process proceeds
without the aid of a transport protein. it is the random motion of the molecules that causes them to move from an
area of high concentration to an area with a lower concentration.
Diffusion will continue until the concentration gradient has been eliminated. Since diffusion moves materials from
an area of higher concentration to the lower, it is described as moving solutes "down the concentration gradient."
The end result of diffusion is an equal concentration, or equilibrium, of molecules on both sides of the membrane.
At equilibrium, movement of molecules does not stop. At equilibrium, there is equal movement of materials in both
directions.
If a molecule can pass freely through a cell membrane, it will cross the membrane by diffusion ( Figure 3.34).
The inside of the plasma membrane is hydrophobic, so certain molecules cannot easily pass through the membrane.
238

www.ck12.org

Chapter 3. Cell Biology - Advanced

Recall the semipermeable nature of the lipid bilayer. Molecules that cannot easily pass through the bilayer include
ions and small hydrophilic molecules, such as glucose, and macromolecules, including proteins and RNA. Examples
of molecules that can easily diffuse across the plasma membrane include carbon dioxide and oxygen gas. These
molecules diffuse freely in and out of the cell, along their concentration gradient. Though water is a polar molecule,
it can also diffuse through the plasma membrane. The diffusion of water through the cell membrane is of such
importance to the cell that it is given a special name, osmosis.

FIGURE 3.34
Molecules move from an area of high
concentration to an area of lower concentration until an equilibrium is met. The
molecules continue to cross the membrane at equilibrium, but at equal rates in
both directions.

Vocabulary

concentration gradient: Difference in the concentrations of a molecule across two distinct areas, such as a
cell membrane.
diffusion: The movement of molecules from an area of high concentration of the molecules to an area with a
lower concentration.
equilibrium: State of equal concentration of a molecule, such as on both sides of the cell membrane.
passive transport: Transport of small molecules or ions across the cell membrane without an input of energy
by the cell.
Summary

The cell membrane is selectively permeable, allowing only certain substances to pass through.
Passive transport is a way that small molecules or ions move across the cell membrane without input of energy
by the cell. The three main kinds of passive transport are diffusion, osmosis, and facilitated diffusion.
Diffusion is the movement of molecules from an area of high concentration of the molecules to an area with a
lower concentration.
Review

1. What is diffusion? What is the main difference between simple diffusion and facilitated diffusion?
239

3.26. Diffusion - Advanced


2. What is a concentration gradient?
3. What happens at equilibrium?

240

www.ck12.org

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.27 Osmosis - Advanced


Define osmosis.
Distinguish between diffusion and osmosis.

Saltwater Fish vs. Freshwater Fish?


Fish cells, like all cells, have semi-permeable membranes. Eventually, the concentration of "stuff" on either side of
them will even out. A fish that lives in salt water will have somewhat salty water inside itself. Put it in the freshwater,
and the freshwater will, through osmosis, enter the fish, causing its cells to swell, and the fish will die. What will
happen to a freshwater fish in the ocean?
Osmosis

Imagine you have a cup that has 100ml water, and you add 15g of table sugar (sucrose, C12 H22 O11 ) to the water.
The sugar dissolves and the mixture that is now in the cup is made up of a solute (the sugar), that is dissolved in the
solvent (the water). The mixture of a solute in a solvent is called a solution.
241

3.27. Osmosis - Advanced

www.ck12.org

Imagine now that you have a second cup with 100ml of water, and you add 45 grams of sucrose to the water. Just
like the first cup, the sugar is the solute, and the water is the solvent. But now you have two mixtures of different
solute concentrations. In comparing two solutions of unequal solute concentration, the solution with the higher
solute concentration is hypertonic, and the solution with the lower concentration is hypotonic. Solutions of equal
solute concentration are isotonic. The first sugar solution is hypotonic to the second solution. The second sugar
solution is hypertonic to the first.
You now add the two solutions to a beaker that has been divided by a selectively permeable membrane. The pores
in the membrane are too small for the sugar molecules to pass through, but are big enough for the water molecules
to pass through. The hypertonic solution is on one side of the membrane and the hypotonic solution on the other.
The hypertonic solution has a lower water concentration than the hypotonic solution, so a concentration gradient of
water now exists across the membrane. Water molecules will move from the side of higher water concentration to
the side of lower concentration until both solutions are isotonic.

What if the two solutions being compared are on either side of a cell membrane? A hypertonic solution is one having
a larger concentration of a substance on the outside of a cell than is found within the cells themselves. A hypotonic
solution contains a lesser concentration of impermeable solutes outside the cell compared to within the cell.
Osmosis is the diffusion of water molecules across a selectively permeable membrane from an area of higher
concentration to an area of lower concentration. Water moves into and out of cells by osmosis. If a cell is in a
hypertonic solution, the solution has a lower water concentration than the cell cytosol does, and water moves out
of the cell until both solutions are isotonic. Cells placed in a hypotonic solution will take in water across their
membrane until both the external solution and the cytosol are isotonic.
A cell that does not have a rigid cell wall (such as a red blood cell), will swell and lyse (burst) when placed in a
hypotonic solution. Cells with a cell wall will swell when placed in a hypotonic solution, but once the cell is turgid
(firm), the tough cell wall prevents any more water from entering the cell. When placed in a hypertonic solution, a
cell without a cell wall will lose water to the environment, shrivel, and probably die. In a hypertonic solution, a cell
with a cell wall will lose water too. The plasma membrane pulls away from the cell wall as it shrivels, a process
called plasmolysis. Animal cells tend to do best in an isotonic environment, plant cells tend to do best in a hypotonic
environment. This is demonstrated in Figure 3.35.
Osmotic Pressure

When water moves into a cell by osmosis, osmotic pressure may build up inside the cell. If a cell has a cell wall, the
wall helps maintain the cells water balance. Osmotic pressure is the main cause of support in many plants. When a
plant cell is in a hypotonic environment, the osmotic entry of water raises the turgor pressure exerted against the cell
wall until the pressure prevents more water from coming into the cell. At this point the plant cell is turgid ( Figure
3.36). The effects of osmotic pressures on plant cells are shown in Figure 3.35.
Osmosis can be seen very effectively when potato slices are added to a high concentration of salt solution (hypertonic). The water from inside the potato moves out of the potato cells to the salt solution, which causes the potato
cells to lose turgor pressure. The more concentrated the salt solution, the greater the difference in the size and weight
of the potato slice after plasmolysis.
242

www.ck12.org

Chapter 3. Cell Biology - Advanced

FIGURE 3.35
Unless an animal cell (such as the red
blood cell in the top panel) has an adaptation that allows it to alter the osmotic
uptake of water, it will lose too much water
and shrivel up in a hypertonic environment. If placed in a hypotonic solution,
water molecules will enter the cell causing
it to swell and burst. Plant cells (bottom
panel) become plasmolyzed in a hypertonic solution, but tend to do best in a
hypotonic environment. Water is stored in
the central vacuole of the plant cell.

FIGURE 3.36
The central vacuoles of the plant cells in
this image are full of water, so the cells
are turgid.

The action of osmosis can be very harmful to organisms, especially ones without cell walls. For example, if a
saltwater fish (whose cells are isotonic with seawater), is placed in fresh water, its cells will take on excess water,
lyse, and the fish will die. Another example of a harmful osmotic effect is the use of table salt to kill slugs and snails.
Diffusion and osmosis are discussed at http://www.youtube.com/watch?v=aubZU0iWtgI (18:59).

243

3.27. Osmosis - Advanced

www.ck12.org

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/253

Controlling Osmosis

Organisms that live in a hypotonic environment such as freshwater, need a way to prevent their cells from taking
in too much water by osmosis. A contractile vacuole is a type of vacuole that removes excess water from a
cell. Freshwater protists, such as the paramecia shown in Figure 3.37, have a contractile vacuole. The vacuole is
surrounded by several canals, which absorb water by osmosis from the cytoplasm. After the canals fill with water,
the water is pumped into the vacuole. When the vacuole is full, it pushes the water out of the cell through a pore.
Other protists, such as members of the genus Amoeba, have contractile vacuoles that move to the surface of the cell
when full and release the water into the environment.

FIGURE 3.37
The contractile vacuole is the star-like
structure within the paramecia.

Vocabulary

contractile vacuole: An organelle found in freshwater protists involved in osmoregulation; pumps excess
water out of a cell.
hypotonic: In comparing two solutions of unequal solute concentration, the solution with the higher solute
concentration.
hypertonic: In comparing two solutions of unequal solute concentration, the solution with the lower solute
concentration.
isotonic: Solutions of equal solute concentration.
244

www.ck12.org

Chapter 3. Cell Biology - Advanced

osmosis: The diffusion of water molecules across a selectively permeable membrane.


osmotic pressure: Pressure exerted on a cell wall due to osmosis of water into a cell.
plasmolysis: The process where the cytoplasm pulls away from the cell wall due to the loss of water through
osmosis; occurs in plant cells.
solute: The substance that is dissolved in a solvent.
solution: Mixture that has the same composition throughout; mixture of a solute in a solvent.
solvent: A substance that dissolves another substance to form a solution.
Summary

Osmosis is the diffusion of water molecules across a semipermeable membrane and down a concentration
gradient. They can move into or out of a cell, depending on the concentration of the solute.
Review

1. How does osmosis differ from diffusion?


2. What would cause the central vacuole of a plant cell to shrunk and become smaller than normal? What is the
likely solute concentration of the cells environment which has caused this change?

245

3.28. Facilitated Diffusion - Advanced

www.ck12.org

3.28 Facilitated Diffusion - Advanced


Describe facilitated transport mechanisms.
Define ion channels.
Identify the role of ion channels in facilitated diffusion.

Can you help me move?


What is one of the questions no one likes to be asked? Sometimes the cell needs help moving things as well, or
facilitating the diffusion process. And this would be the job of a special type of protein.
246

www.ck12.org

Chapter 3. Cell Biology - Advanced

Facilitated Diffusion

Facilitated diffusion is the diffusion of solutes through integral membrane transport proteins. Facilitated diffusion
is a type of passive transport. Even though facilitated diffusion involves transport proteins (and is essentially a
transport process), it can still be considered passive transport because the solute is moving down the concentration
gradient, and no input of energy is required. Facilitated diffusion utilizes proteins known as uniporters. A uniporter
can be either a channel protein or a carrier protein.
As was mentioned earlier, small nonpolar molecules can easily diffuse across the cell membrane. However, due to
the hydrophobic nature of the phospholipids that make up cell membranes, polar molecules and ions cannot do so.
Instead, they diffuse across the membrane through transport proteins. A transport protein completely spans the
membrane, and allows certain molecules or ions to diffuse across the membrane. Channel proteins, gated channel
proteins, and carrier proteins are three types of transport proteins that are involved in facilitated diffusion.
A channel protein, a type of transport protein, acts like a pore in the membrane that lets water molecules or small
ions through quickly. Water channel proteins allow water to diffuse across the membrane at a very fast rate. Ion
channel proteins allow ions to diffuse across the membrane.
A gated channel protein is a transport protein that opens a "gate," allowing a molecule to pass through the
membrane. Gated channels have a binding site that is specific for a given molecule or ion. A stimulus causes
the "gate" to open or shut. The stimulus may be chemical or electrical signals, temperature, or mechanical force,
depending on the type of gated channel. For example, the sodium gated channels of a nerve cell are stimulated by
a chemical signal which causes them to open and allow sodium ions into the cell. Glucose molecules are too big to
diffuse through the plasma membrane easily, so they are moved across the membrane through gated channels. In
this way glucose diffuses very quickly across a cell membrane, which is important because many cells depend on
glucose for energy.
A carrier protein is a transport protein that is specific for an ion, molecule, or group of substances. Carrier proteins
"carry" the ion or molecule across the membrane by changing shape after the binding of the ion or molecule. Carrier
proteins are involved in passive and active transport. A model of a channel protein and carrier proteins is shown in
Figure 3.38.
FIGURE 3.38
Facilitated diffusion through the cell membrane. Channel proteins and carrier proteins are shown (but not a gated-channel
protein). Water molecules and ions move
through channel proteins. Other ions or
molecules are also carried across the cell
membrane by carrier proteins. The ion or
molecule binds to the active site of a carrier protein. The carrier protein changes
shape, and releases the ion or molecule
on the other side of the membrane. The
carrier protein then returns to its original
shape.

An animation depicting facilitated diffusion can be viewed at http://www.youtube.com/watch?v=OV4PgZDRTQw


(1:36).

247

3.28. Facilitated Diffusion - Advanced

www.ck12.org

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/254

Ion Channels

Ions such as sodium (Na+ ), potassium (K+ ), calcium (Ca2+ ), and chloride (Cl ), are important for many cell
functions. Because they are polar, these ions do not diffuse through the membrane. Instead they move through
ion channel proteins where they are protected from the hydrophobic interior of the membrane. Ion channels allow
the formation of a concentration gradient between the extracellular fluid and the cytosol. Ion channels are very
specific as they allow only certain ions through the cell membrane. Some ion channels are always open, others are
"gated" and can be opened or closed. Gated ion channels can open or close in response to different types of stimuli
such as electrical or chemical signals.
Vocabulary

carrier protein: A transport protein that is specific for an ion, molecule, or group of substances; carries the
ion or molecule across the membrane by changing shape after the binding of the ion or molecule.
channel protein: A transport protein that acts like a pore in the membrane that lets water molecules or small
ions through quickly.
facilitated diffusion: The diffusion of solutes through transport proteins in the plasma membrane.
gated channel protein: A transport protein that opens a "gate," allowing a molecule to flow through the
membrane.
ion channel: A channel protein that transports ions across the membrane by facilitated diffusion.
passive transport: Transport of small molecules or ions across the cell membrane without an input of energy
by the cell.
transport protein: A protein that completely spans the membrane, and allows certain molecules or ions to
diffuse across the membrane; channel proteins, gated channel proteins, and carrier proteins are three types of
transport proteins that are involved in facilitated diffusion.
uniporter: An integral membrane protein that is involved in facilitated diffusion; can be either a channel or a
carrier protein.
Summary

Facilitated diffusion is the diffusion of solutes through transport proteins in the plasma membrane. Channel
proteins, gated channel proteins, and carrier proteins are three types of transport proteins that are involved in
facilitated diffusion.
248

www.ck12.org

Chapter 3. Cell Biology - Advanced

Explore More

Membrane Channels at http://phet.colorado.edu/en/simulation/membrane-channels .

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/4736

Review

1. Compare and contrast simple diffusion and facilitated diffusion. For each type of diffusion, give an example
of a molecule that is transported.
2. Explain the three types of transport proteins involved in facilitated diffusion.

249

3.29. Active Transport - Advanced

www.ck12.org

3.29 Active Transport - Advanced


Compare passive and active transport.
Explain how different types of active transport occur.

Need to move something really heavy?


If you did, it would take a lot of energy. Sometimes, moving things into or out of the cell also takes energy. How
would the cell move something against a concentration gradient? It starts by using energy.

Active Transport

In contrast to facilitated diffusion which does not require energy and carries molecules or ions down a concentration
gradient, active transport pumps molecules and ions against a concentration gradient. Sometimes an organism needs
to transport something against a concentration gradient, such as specific ions, or glucose and amino acids. The
only way this can be done is through active transport which uses transport proteins and energy that is produced by
cellular respiration (ATP) or through an electrochemical gradient. In active transport, the particles move across
a cell membrane from a lower concentration to a higher concentration. Active transport is the energy-requiring
process of pumping molecules and ions across membranes "uphill" against a gradient. The active transport of
small molecules or ions across a cell membrane is generally carried out by transport proteins that are found in the
membrane. These transport proteins have receptor regions that bind to specific molecules and transport them into
the cell. Larger molecules such as starch can also be actively transported across the cell membrane by vesicular
transport processes.
During active transport, specialized integral membrane proteins recognize the substance and allows it access. Essentially this process is forcing a ion or molecule to cross the membrane when normally it would not. Moving a
substance against its concentration gradient is known as primary active transport, and the proteins involved in it
as "pumps". This process uses the energy of ATP. In secondary active transport, energy from an electrochemical
gradient is used to transport substances. This process involves pore-forming proteins that form channels through the
cell membrane.
250

www.ck12.org

Chapter 3. Cell Biology - Advanced

Primary Active Transport

Primary active transport involves an integral membrane protein and the energy from ATP to transport molecules
across a membrane. This type of transport is mainly done by ATPases. ATPases are a class of enzymes that catalyze
the dephosphorylation of adenosine triphosphate into adenosine diphosphate (ADP) and a free phosphate ion. This
reaction releases energy, which is used to drive other chemical reactions that would not otherwise occur.
One ATPase necessary to all life is the sodium-potassium pump, which helps to maintain the cell potential. This
pump will be discussed in the Active Transport: The Sodium-Potassium Pump (Advanced) concept. Other sources of
energy for primary active transport are redox energy and photon energy (light energy). Redox energy is used in the
mitochondrial electron transport chain during cellular respiration. In this transport, the reduction energy of NADH
is used to move protons across the inner mitochondrial membrane against their concentration gradient. An example
of primary active transport using photon energy occurs during photosynthesis. During photosynthesis, proteins use
the energy of photons to create a proton gradient across the chloroplast thylakoid membrane. That energy is used to
pump H+ ions into the thylakoid.
Secondary Active Transport

In secondary active transport, which is also known as cotransport, energy is used to transport molecules across
a membrane. However, in contrast to primary active transport, there is no direct coupling of ATP. Instead, the
electrochemical potential difference created by pumping ions out of the cell is used. The process is called cotransport
because one carrier protein mediates the transport of both substances. The two main forms of this are antiport and
symport.
Antiport and Symport

The difference between the two types of cotransport depends on the direction of transport of the molecules. A system
in which one substance moves in one direction while cotransporting another substance in the other direction is called
antiport. Symport is transport of two substrates in the same direction across the membrane. The protein involved
in this transport is a symporter. The protein involved in antiport is an antiporter.
The energy for these processes come from an electrochemical gradient. In such a gradient, one of the two substances
is transported in the direction of their concentration gradient,and the energy derived is used to transport the second
substance against its concentration gradient. Thus, energy stored in the electrochemical gradient of an ion is
used to drive the transport of another solute against a concentration or electrochemical gradient. In antiport,
one substance moves along its electrochemical gradient, allowing a different substance to move against its own
electrochemical gradient. This movement is in contrast to primary active transport, in which all solutes are moved
against their concentration gradients, fueled by ATP. In symport, one substance moves down the electrochemical
gradient, allowing the other molecule(s) to move against its concentration gradient. One substance moves by
facilitated diffusion, which is coupled with the active transport of the other substance.
Vocabulary

active transport: Transport of molecules and ions across membranes against a concentration gradient; requires energy.
antiport: The secondary active transport process of transporting two or more different molecules or ions
across a phospholipid membrane in opposite directions.
antiporter: An integral membrane protein involved in secondary active transport; transports two or more
different molecules or ions across a phospholipid membrane in opposite directions.
251

3.29. Active Transport - Advanced

www.ck12.org

ATPase: A class of enzymes that catalyze the decomposition of adenosine triphosphate (ATP) into adenosine
diphosphate (ADP) and a free phosphate ion.
cotransport: The simultaneous or sequential transport of more than one molecule or ion across biological
membranes; also known as secondary active transport.
electrochemical gradient: Difference across a membrane due to both a chemical force and an electrical force;
drives the movement of ions across the membrane.
primary active transport: Active transport in which solutes are moved against their concentration gradients;
fueled by ATP.
redox energy: Energy that is either stored or released by redox reactions.
secondary active transport: Active transport in which one substance moves along its electrochemical gradient, allowing a different substance to move against its own electrochemical gradient; also known as cotransport.
symport: The secondary active transport process of transporting two or more different molecules or ions
across a phospholipid membrane in the same direction.
symporter: An integral membrane protein involved in secondary active transport; transports two or more
different molecules or ions across a phospholipid membrane in the same direction.
Summary

Active transport moves molecules across a cell membrane from an area of lower concentration to an area of
higher concentration. Active transport requires the use of energy.
The active transport of small molecules or ions across a cell membrane is generally carried out by transport
proteins that are found in the membrane.
During antiport and symport two substances are cotransported.
Explore More

Diffusion, Osmosis and Active Transport at http://www.concord.org/activities/diffusion-osmosis-and-acti


ve-transport .
Active Transport

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/1781

252

www.ck12.org

Chapter 3. Cell Biology - Advanced

Review

1. What is active transport?


2. Describe the main difference between primary and secondary active transport.
3. Explain antiport and symport.

253

3.30. The Sodium-Potassium Pump - Advanced

www.ck12.org

3.30 The Sodium-Potassium Pump - Advanced


Explain how different types of active transport occur.
Describe the function of the sodium-potassium pump.

What is this incredible object?


Would it surprise you to learn that it is a human cell? The image represents an active human nerve cell. How nerve
cells function will be the focus of another concept. However, active transport processes play a significant role in the
function of these cells. Specifically, it is the sodium-potassium pump that is active in the axons of these nerve cells.
The Sodium-Potassium Pump

Carrier proteins can work with a concentration gradient (passive transport), but some carrier proteins can move
solutes against the concentration gradient (from low concentration to high concentration), with energy input from
ATP. As in other types of cellular activities, ATP supplies the energy for most active transport. One way ATP powers
active transport is by transferring a phosphate group directly to a carrier protein. This may cause the carrier protein
to change its conformation, which moves the molecule or ion to the other side of the membrane. An example of
this type of active transport system, as shown in Figure 3.39, is the sodium-potassium pump, or Na+ /K+ -ATPase,
a transmembrane ATPase, an integral membrane protein that exchanges sodium ions for potassium ions across the
plasma membrane of animal cells. The sodium-potassium pump is found in the plasma membrane of almost every
human cell and is common to all cellular life. It helps maintain resting potential, especially in neurons following a
nerve impulse, and regulates cellular volume.
The Mechanism

As is shown in Figure 3.39, the sodium-potassium pump transports Na+ ions and K+ ions in the following manner:
1. The sodium-potassium pump binds ATP and three intracellular Na+ ions.
254

www.ck12.org

Chapter 3. Cell Biology - Advanced

FIGURE 3.39
The sodium-potassium pump system
moves

sodium

and

potassium

ions

against large concentration gradients. It


moves two potassium ions into the cell
where potassium levels are high, and
pumps three sodium ions out of the cell
and into the extracellular fluid.

2. ATP is hydrolyzed resulting in adenosine diphosphate (ADP) and an inorganic phosphate. The free phosphate
phosphorylates the sodium-potassium pump.
3. A conformational change in the pump exposes the Na+ ions to the outside. The phosphorylated form of the
pump has a low affinity for Na+ ions, so they are released.
4. The pump binds two extracellular K+ ions. This causes the dephosphorylation of the pump, reverting it to its
previous conformational state, transporting the K+ ions into the cell.
5. The unphosphorylated form of the pump has a higher affinity for Na+ ions than K+ ions, so the two bound
K+ ions are released.
6. ATP binds, and the process starts again.
A more detailed look at the sodium-potassium pump is available at http://www.youtube.com/watch?v=C_H-ONQFj
pQ (13:53) and http://www.youtube.com/watch?v=ye3rTjLCvAU (6:48).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/208

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/500

Vocabulary

Na+ /K+ -ATPase: An active transport carrier protein/a transmembrane ATPase; moves sodium and potassium
ions against large concentration gradients; the sodium-potassium pump.
resting potential: The membrane potential of a cell/neuron at rest; the membrane potential of an unstimulated
neuron.
255

3.30. The Sodium-Potassium Pump - Advanced

www.ck12.org

sodium-potassium pump: An active transport carrier protein/a transmembrane ATPase; moves sodium and
potassium ions against large concentration gradients; the Na+ /K+ -ATPase.
Summary

The sodium-potassium pump is an example of an active transport membrane protein/transmembrane ATPase.


Using the energy from ATP, the sodium-potassium moves three sodium ions out of the cell and brings two
potassium ions into the cell.
Explore More

Use this resource to answer the questions that follow.


The Sodium Potassium Pump at http://hyperphysics.phy-astr.gsu.edu/hbase/biology/nakpump.html .
1.
2.
3.
4.
5.

Are there more sodium ions on the outside of cells or the inside?
Are there more potassium ions on the outside of cells or the inside?
What is the hydrolysis of ATP?
In what type of cells can a sodium-potassium pump be found?
What is the role of the sodium-potassium pump?

Review

1. What is the sodium-potassium pump?


2. Why is the pump called a transmembrane ATPase?
3. Outline how the sodium-potassium pump works.

256

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.31 The Electrochemical Gradient - Advanced


Describe the electrochemical gradient.

Do you really have electricity flowing through your body?


Yes you do. These electrical signals allow information to flow through the nervous system extremely rapidly. And it
all starts with the formation of an electrochemical gradient.
The Electrochemical Gradient

The active transport of ions across the cell membrane causes an electrical gradient to build up across this membrane.
The number of positively charged ions outside the cell is usually greater than the number of positively charged ions
in the cytosol. This results in a relatively negative charge on the inside of the membrane, and a positive charge on
the outside. This difference in charges causes a voltage to exist across the membrane. Voltage is electrical potential
energy that is caused by a separation of opposite charges, in this case across the membrane. The voltage across
a membrane is the membrane potential. Membrane potential is very important for the conduction of electrical
impulses along nerve cells. The membrane potential of a cell at rest is known as its resting potential, and is
discussed below. A non-excited nerve cell is an example of a cell at rest.
Because of the ion gradient, there are less positive ions inside the cell, the inside of the cell is negative compared
to outside the cell. This resulting membrane potential favors the movement of positively charged ions (cations) into
the cell, and the movement of negative ions (anions) out of the cell. So, there are two forces that drive the diffusion
of ions across the plasma membranea chemical force (the ions concentration gradient), and an electrical force
257

3.31. The Electrochemical Gradient - Advanced

www.ck12.org

(the effect of the membrane potential on the ions movement). These two forces working together are called an
electrochemical gradient.
The electrochemical gradient determines the direction an ion moves by diffusion or active transport across a membrane. In mitochondria and chloroplasts, proton gradients are used to generate a chemiosmotic potential that is
also known as a proton motive force, due to both the proton gradient and voltage gradient across the membrane.
This potential energy is used for the synthesis of ATP by oxidative phosphorylation.

The Resting Potential

In order to maintain the membrane potential, cells maintain a low concentration of sodium ions (Na+ ) and high
levels of potassium ions (K+ ) within the cell (intracellular). The sodium-potassium pump moves three Na+ ions out
of the cell and brings two K+ ions into the cell. This essentially removes one positive charge from the intracellular
space. The resulting membrane potential is known as the resting potential.

FIGURE 3.40
This diagram shows how ions maintain the membrane potential.

The

sodium-potassium pump is shown in the


membrane, transporting three Na+ ions
(green) out of the cell and bringing two K+
ions (blue) into the cell.

The Ion Gradient

The electrochemical potential across a membrane determines the tendency of an ion to cross the membrane. The
membrane may be that of a cell or organelle or other sub cellular compartment. The electrochemical potential arises
from three factors:
1. the difference in the concentration of the ions on either side of the membrane,
2. the charge of the ions (for example Na+ , Ca++ , Cl ), and
3. the difference in voltage between the two sides of the membrane (the transmembrane potential).
258

www.ck12.org

Chapter 3. Cell Biology - Advanced

Cotransport of ions by symporters and antiporter carriers is commonly used to actively move ions across biological
membranes. Transmembrane ATPases are often involved in maintaining ion gradients. The Na+/K+ ATPase uses
ATP to build and maintain a sodium ion gradient and a potassium ion gradient.

Proton Gradients and ATP synthase

One particular ion gradient with biological significance is the proton (H+ ) gradient. This type of gradient is
established through active transport involving proton pumps. The proton gradient is used during photosynthesis
and cellular respiration to generate a chemiosmotic potential, or proton motive force. This potential energy is used
for the synthesis of ATP by oxidative phosphorylation. The proton gradient can also be used to store energy for heat
production and flagellar rotation.
The energy held within the proton gradient can be used to synthesize ATP. ATP synthase is a transmembrane enzyme
that provides energy for the cell to use by producing ATP. The protein has two distinct regions, F0 and F1 . The F0
domain is embedded within the membrane, while the F1 domain is above the membrane, inside the matrix of the
mitochondria, or the stroma of the chloroplast. The F0 region is the proton pore, allowing hydrogen ions to diffuse
across the membrane. The F1 region of the protein has ATP synthesis activity, catalyzing the formation of ATP from
ADP and inorganic phosphate. Hence, ATP synthase is both an ion channel protein and enzyme. The synthesis
reaction is driven by the proton flow, which forces the rotation of a part of the enzyme; the ATP synthase is a rotary
mechanical motor. Bacteria may also have a version of this enzyme, where it, of course, is embedded in the cell
membrane.
During electron transport within the mitochondria (during cellular respiration) or chloroplast (during photosynthesis)
(discussed in the Concept Metabolism (Advanced) concept), a proton gradient is formed when protons are pumped
across the membrane by active transport. These hydrogen ions flow back across the membrane by facilitated
diffusion through ATP synthase, releasing energy which is then used to convert ADP to ATP (by phosphorylation).
Chemiosmosis is the diffusion of protons across the biological membrane through ATP synthase, due to a proton
gradient that forms across the membrane during electron transport.
Vocabulary

ATP synthase: Ion channel and enzyme complex; chemically bonds a phosphate group to ADP, producing
ATP as H+ ions flow through the ion channel.
chemiosmosis: Process in cellular respiration or photosynthesis which produces ATP; uses the energy of
hydrogen ions diffusing through ATP synthase.
chemiosmotic potential: A difference in concentration of hydrogen ions across a membrane within the
mitochondrion or chloroplast; established using energy from an electron transport chain; also known as a
chemiosmotic gradient.
electrochemical gradient: Difference across a membrane due to both a chemical force and an electrical force;
drives the movement of ions across the membrane.
membrane potential: The voltage difference across a membrane; the basis for the conduction of nerve
impulses along the cell membrane of neurons.
oxidative phosphorylation: A metabolic process that uses energy released by the oxidation of nutrients to
produce adenosine triphosphate (ATP).
259

3.31. The Electrochemical Gradient - Advanced

www.ck12.org

proton gradient: Gradient established from a higher concentration of protons on one side of a membrane
compared to the other side of the membrane.
proton motive force: The storing of energy due to a combination of a proton gradient and a voltage gradient
across a membrane.
resting potential: The membrane potential of a cell/neuron at rest; the membrane potential of an unstimulated
neuron.
voltage: The difference in electrical potential energy of two points/areas; electrical potential energy that is
caused by a separation of opposite charges.
Summary

The voltage across a membrane is the membrane potential and the membrane potential of a cell at rest is the
resting potential.
The electrochemical gradient is composed of a chemical force (the ions concentration gradient) and an
electrical force (the effect of the membrane potential on the ions movement).
Chemiosmosis is the diffusion of protons across the biological membrane through ATP synthase, due to a
proton gradient that forms across the membrane.
Explore More

Use this resource to answer the questions that follow. Gradients at http://www.youtube.com/watch?v=kQ_3mI0WY
i0

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139344

1. Why does an electrochemical gradient form across a cell membrane?


2. Why are positive ions attracted to the inside of a cell?
3. How do ions flow in and out of a cell?
Review

1. Define the electrochemical gradient.


2. Describe the role of ATP synthase.
3. What is chemiosmosis?

260

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.32 Exocytosis and Endocytosis - Advanced


Explain how different types of active transport occur.
Compare endocytosis and exocytosis.

What does a cell "eat"?


Is it possible for objects larger than a small molecule to be engulfed by a cell? Of course it is. This image
depicts a cancer cell being attacked by a cell of the immune system. Cells of the immune system consistently
destroy pathogens by essentially "eating" them. Just as cells can bring substances into the cell, they can also export
substances out of the cell.
Vesicles and Active Transport

Some molecules or particles are just too large to pass through the plasma membrane or to move through a transport
protein. So cells use two other active transport methods to move these macromolecules (large molecules) into or
out of the cell. Vesicles or other bodies in the cytoplasm move macromolecules or large particles across the plasma
membrane. There are two types of vesicle transport, endocytosis and exocytosis. These processes are active transport
mechanisms, therefore energy is required.
Endocytosis and Exocytosis

Endocytosis is the process of capturing a substance or particle from outside the cell by engulfing it with the cell
membrane. The membrane folds over the substance and it becomes completely enclosed by the membrane. At this
point a membrane-bound sac, or vesicle pinches off and moves the substance into the cytosol. There are two main
kinds of endocytosis:
261

3.32. Exocytosis and Endocytosis - Advanced

www.ck12.org

Phagocytosis or "cellular eating," occurs when the dissolved materials enter the cell. The plasma membrane
engulfs the solid material, forming a phagocytic vesicle.
Pinocytosis or "cellular drinking," occurs when the plasma membrane folds inward to form a channel allowing
dissolved substances to enter the cell, as shown in Figure 3.41. When the channel is closed, the liquid is
encircled within a pinocytic vesicle.

FIGURE 3.41
Transmission electron microscope image
of brain tissue that shows pinocytotic vesicles. Pinocytosis is a type of endocytosis.

Exocytosis describes the process of vesicles fusing with the plasma membrane and releasing their contents to the
outside of the cell, as shown in Figure 3.42. Exocytosis occurs when a cell produces substances for export, such as a
protein, or when the cell is getting rid of a waste product or a toxin. Newly made membrane proteins and membrane
lipids are moved to the plasma membrane by exocytosis.

FIGURE 3.42
Illustration of the two types of vesicle
transport, exocytosis and endocytosis.
Endocytosis and exocytosis are types of
vesicle transport that carry very large
molecules across the cell membrane.

262

www.ck12.org

Chapter 3. Cell Biology - Advanced

For a detailed animation on cellular secretion, see http://vcell.ndsu.edu/animations/constitutivesecretion/first.htm .

FIGURE 3.43
Illustration of an axon releasing dopamine
by exocytosis.

Receptor-Mediated Endocytosis

Some substances are internalized after binding to a membrane-bound receptor. This process is known as receptormediated endocytosis (RME). RME is a process by which cells internalize molecules by endocytosis. This occurs
by the inward budding of plasma membrane vesicles containing proteins with receptor sites specific to the molecules
being internalized. After the binding of a ligand to the plasma membrane-spanning receptors, a signal is sent through
the membrane, leading to membrane coating by the protein clathrin, and formation of a membrane invagination. The
receptor and its ligand are then internalized in clathrin-coated vesicles. RME is also known as clathrin-dependent
endocytosis, named after the clathrin protein that accumulates on the internal segment of membrane that will form
a vesicle.
Clathrin-mediated endocytosis is further discussed at http://www.youtube.com/watch?v=-ZFnO5RY1cU .

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139338

Homeostasis and Cell Function

Homeostasis refers to the balance, or equilibrium within the cell or a body. It is an organisms ability to keep a
constant internal environment. Keeping a stable internal environment requires constant adjustments as conditions
change inside and outside the cell. The adjusting of systems within a cell is called homeostatic regulation. Because
the internal and external environments of a cell are constantly changing, adjustments must be made continuously
to stay at or near the set point (the normal level or range). Homeostasis is a dynamic equilibrium rather than an
263

3.32. Exocytosis and Endocytosis - Advanced

www.ck12.org

unchanging state. The cellular processes discussed in this lesson all play an important role in homeostatic regulation.
More concerning homeostasis will be presented in additional concepts.
Vocabulary

clathrin: A protein that plays a major role in the formation of coated vesicles.
clathrin-dependent endocytosis: Endocytosis in which the inward budding of plasma membrane vesicles
containing proteins with receptor sites specific to the molecules being internalized; also known as receptormediated endocytosis.
endocytosis: The cellular process of capturing a material/substance from outside the cell by vesicle formation.
exocytosis: The cellular process of secreting materials by vesicle fusion.
homeostasis: The process of maintaining a stable environment inside a cell or an entire organism.
phagocytosis: The process of engulfing and breaking down pathogens and other unwanted substances.
pinocytosis: Type of vesicle transport that occurs when the plasma membrane folds inward to form a channel,
allowing dissolved substances to enter the cell.
receptor-mediated endocytosis (RME): Endocytosis in which the inward budding of plasma membrane
vesicles containing proteins with receptor sites specific to the molecules being internalized; also known as
clathrin-dependent endocytosis.
Summary

Endocytosis and exocytosis are active transport mechanisms in which large molecules enter and leave the cell
inside vesicles.
In endocytosis, a substance or particle from outside the cell is engulfed by the cell membrane. The membrane
folds over the substance and it becomes completely enclosed by the membrane. There are two main kinds of
endocytosis: pinocytosis and phagocytosis.
Review

1. What is the difference between endocytosis and exocytosis?


2. Why is pinocytosis a form of endocytosis?
3. Are vesicles involved in passive transport?

264

www.ck12.org

Chapter 3. Cell Biology - Advanced

3.33 Cell Communication - Advanced


Describe what is meant by cell communication.

What does adrenaline do?


Adrenaline, or epinephrine, is a hormone and a neurotransmitter. It increases heart rate, constricts blood vessels,
dilates air passages, and participates in the fight-or-flight response of the sympathetic nervous system. Adrenaline is
produced in the adrenal medulla of the adrenal gland. So how does it effect processes all over the body?

The Language of Cells

To survive and grow, cells need to be able to communicate with their neighboring cells and be able to detect change
in their environment. "Talking" with neighboring cells is even more important to a cell if it is part of a multicellular
organism. Cell communication, or cell signaling, is the basis of development, tissue repair, and immunity. It is
also necessary for normal tissue homeostasis. The trillions of cells that make up your body need to be able to
communicate with each other to allow your body to grow, and to keep you alive and healthy. The same is true for
any organism. Cell signaling is part of a complex system of communication that governs basic cellular activities and
coordinates cell actions. Cell signaling is a major area of research in biology today. Defects in cell signaling are
associated with diseases such as cancer, autoimmunity, and diabetes.
Recently scientists have discovered that many different cell types, from bacteria to plants, use similar types of
communication pathways, or cell-signaling mechanisms. This suggests that cell-signaling mechanisms evolved long
before the first multicellular organism did.
For cells to be able to signal to each other, a few things are needed:
265

3.33. Cell Communication - Advanced

www.ck12.org

a signal,
a cell receptor, which is a protein usually on the plasma membrane, but can be found inside the cell,
a response to the signal.
Cells that are communicating may be right next to each other or far apart. In juxtacrine signaling, also known
as contact-dependent signaling, two adjacent cells must make physical contact in order to communicate. Cell
communication may also occur over short distances, which is known as paracrine signaling, or over large distances,
which is known as endocrine signaling.
The type of chemical signal a cell will send differs depending on the distance the message needs to go. For example,
hormones, ions, and neurotransmitters are all types of signals that are sent depending on the distance the message
needs to go. Endocrine signals are hormones, produced by endocrine organs. These signals travel through the blood
stream to reach all parts of the body.
The target cell then needs to be able to recognize the signal. Chemical signals are received by the target cell on
receptor proteins. Most receptor proteins are found associated with the plasma membrane, but some are also found
inside the cell. Receptor proteins are very specific for only one particular signal molecule, much like a lock that
recognizes only one key. Therefore, a cell has lots of receptor proteins to recognize the large number of cell signal
molecules. There are three stages to sending and receiving a cell "message:" reception, transduction, and response.
1. Reception occurs when a ligand binds to its receptor.
2. Through transduction, the signal is then internalized. The ligand does not have to be internalized for this
process to occur.
3. The response may initiate a cascade of reactions including the activation/deactivation of enzymes and/or an
alternation in gene transcription.
Vocabulary

cell receptor: Specialized proteins that take part in communication between the cell and the extracellular
environment; often are integral membrane proteins.
cell signaling: Part of a complex communication system that governs basic cellular activities and coordinates
cell actions.
endocrine signaling: Cell communication over long distances.
hormone: A chemical messenger molecule.
juxtacrine signaling: Cell communication via direct contact.
neurotransmitter: Chemical messages which are released at the synapse; relay the message/signal onto the
next neuron or other type of cell.
paracrine signaling: Cell communication over short distances.
Summary

Cell communication or cell signaling describes how cells share information.


Cell communication usually begins when a molecule (a ligand) binds to its receptor.
Cell communication can be over short or long distances.
266

www.ck12.org

Chapter 3. Cell Biology - Advanced

Explore More

Use this resource to answer the questions that follow.


The Fight or Flight Response at http://learn.genetics.utah.edu/content/begin/cells/cellcom/ .
1.
2.
3.
4.

Describe the role of signaling molecules.


How do signaling molecules travel throughout the body?
Describe the results of a stress response.
Based on this video, what is your definition of cell communication?

Review

1. Define cell communication.


2. Compare juxtacrine, paracrine and endocrine signaling.
3. Describe the process of cell signaling.

267

3.34. Signal Receptors - Advanced

www.ck12.org

3.34 Signal Receptors - Advanced


Describe the types of signal receptors used in cell communication.

What pulls a signal in from vast distances?


Some sort of signal receptor. This receptor is usually a protein embedded in the cell membrane. Once the signal
binds to its receptor, some sort of outcome is initiated - the signal is transferred to the cell. This may be from an ion
channel opening or some other process.
Signal Receptors

A signal molecule must bind to its receptor to initiate a response. Receptors are proteins that bind to their signal
molecule either externally (cell-surface receptors) or internally (nuclear receptors) within the cytoplasm or nucleus.
This process is known as signal transduction, and the internal activator is the second messenger. Once a ligand
binds to its receptor, a series of reactions are initiated.
Cell-Surface Receptors

Cell-surface receptors are integral membrane proteinsthey reach right through the phospholipid bilayer, spanning
from the outside to the inside of the cell. These receptor proteins are specific for just one signal molecule. The
signaling molecule acts as a ligand when it binds to a receptor protein. A ligand is a small molecule that binds to a
268

www.ck12.org

Chapter 3. Cell Biology - Advanced

larger molecule. Signal molecule binding causes the receptor protein to undergo a conformational change (a change
in shape). At this point the receptor protein can interact with another molecule. The ligand (the signal molecule)
itself does not pass through the plasma membrane.
In eukaryotic cells, most of the intracellular proteins that are activated by a ligand binding to a receptor protein are
enzymes. Receptor proteins are named after the type of enzyme that they interact with inside the cell. These enzymes
include G proteins and protein kinases, likewise there are G-protein-linked receptors and tyrosine kinase receptors.
A kinase is a protein involved in phosphorylation. Tyrosine kinase receptors bind many polypeptide growth factors,
cytokines, and hormones. Once the ligand is bound, these receptors specifically phosphorylate tyrosine amino acids,
activating the signal transduction process inside the cell.
A G-protein linked receptor is a receptor that works with the help of a protein called a G-protein. A G-protein gets
its name from the molecule to which it is attached, guanosine triphosphate (GTP), or guanosine diphosphate (GDP).
The GTP molecule is similar to ATP.
Second Messengers

Once G proteins or protein kinase enzymes are activated by a receptor protein - after the ligand binds to its receptor they create molecules called second messengers. A second messenger is a small molecule that starts a change inside
a cell in response to the binding of a specific signal to a receptor protein. Some second messenger molecules include
small molecules called cyclic nucleotides, such as cyclic adenosine monophosphate (cAMP) and cyclic guanosine
monophosphate (cGMP). Calcium ions (Ca2+ ) also act as secondary messengers. Secondary messengers are a part
of signal transduction pathways.
Nuclear Receptors

Some receptors bind the ligand internally. In this case, the ligand must be able to enter the cell. These receptors
usually interact with steroid and thyroid hormones. Once the ligand binds to the receptor, the receptor becomes
activated, and the whole complex enters the nucleus, hence these receptors are known as nuclear receptors. In the
nucleus, the activated receptor acts as a transcription factor, where it interacts with other proteins to regulate the
expression of specific genes, thereby controlling the development, homeostasis, and metabolism of the organism.
Vocabulary

cell-surface receptor: Specialized integral membrane protein that take part in communication between the
cell and the extracellular environment.
cyclic adenosine monophosphate (cAMP, cyclic AMP): A second messenger important in many biological
processes; used for intracellular signal transduction, such as transferring into cells the effects of hormones.
G protein (guanine nucleotide-binding protein): Guanine nucleotide-binding proteins; a family of proteins
involved in transmitting chemical signals outside the cell, causing changes inside the cell.
G-protein linked receptor: A large protein family of transmembrane receptors that bind molecules outside
the cell and activate signal transduction pathways inside the cell; also known as G protein coupled receptors
and seven-transmembrane domain receptors.
kinase: A type of enzyme that transfers phosphate groups from high-energy donor molecules, such as ATP, to
specific substrates, a process known as phosphorylation.
269

3.34. Signal Receptors - Advanced

www.ck12.org

FIGURE 3.44
Two-component signal transduction system. This process begins with the stimulus binding to its receptor. Shown here
is a cell-surface receptor. The signal in
then transduced to the inside of the cell.

ligand: A small molecule that binds to a larger molecule.


nuclear receptor: A class of proteins found within cells that are responsible for binding steroid and thyroid
hormones; may act as a transcription factor.
second messenger: A molecule that relays a signal from a receptor on the cell surface to target molecules
inside the cell.
signal transduction: The process that occurs when an extracellular signaling molecule activates a cell surface
receptor, which then alters intracellular molecules creating a response.
transcription factor: A protein involved in regulating gene expression; usually bound to a cis-regulatory
element on the DNA; also known as a regulatory protein or a trans-acting factor.
tyrosine kinase receptor: Family of cell surface receptors for many polypeptide growth factors, cytokines,
and hormones; specifically phosphorylate tyrosine amino acids; also known as receptor tyrosine kinases.
270

www.ck12.org

Chapter 3. Cell Biology - Advanced

Summary

Signal transduction begins with a ligand binding to its receptor.


Cell-surface receptors bind a ligand outside of the cell and internalize the signal, acting through a second
messenger.
Nuclear receptors bind a ligand inside the cell and change transcription of genes by acting as a transcription
factor.
Explore More

Use this resource to answer the questions that follow.


G-Protein Coupled Hormone Signal Transduction at http://www.youtube.com/watch?v=A3AUhMCE9n0

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139340

1.
2.
3.
4.
5.
6.
7.

What is a peptide hormone?


How does the message from a peptide hormone enter the cell?
Describe the structure of a G-protein.
Describe the function of an activated G-protein.
What is the function of an active phospholipase C?
What are the two second messengers discussed in this process?
What is the role of an active protein kinase C?

Review

1. Compare and contrast cell-surface and nuclear receptors.


2. What is a second messenger?
3. What are nuclear receptors functions?

271

3.35. Signal Transduction - Advanced

www.ck12.org

3.35 Signal Transduction - Advanced


Outline the process of signal transduction.

How is information transduced from the outside of the cell?


It starts with the ligand binding its receptor. Once the signal is internalized, the second messenger then begins a
cascade of reactions that can greatly change the behavior of the cell.

Signal Transduction

A signal-transduction pathway is the signaling mechanism by which a cell changes a signal on its surface into a
specific response inside the cell. This process begins when a ligand binds to its receptor. The receptor may either be
a cell-surface receptor in the cell membrane or a nuclear receptor in the cytoplasm of the cell. See DNA responds
to signals from outside the cell at http://www.dnaftb.org/35/animation.html to see James Darnall speak about signal
transduction.
Signal transduction most often involves an ordered sequence of chemical reactions inside the cell which is carried out
by enzymes and other molecules. In many signal transduction processes, the number of proteins and other molecules
participating in these events increases as the process progresses from the binding of the signal. A "signal cascade"
begins. Think of a signal cascade as a chemical domino-effect inside the cell, in which one domino knocks over two
dominoes, which in turn knock over four dominoes, and so on. The advantage of this type of signaling to the cell is
that the message from one little signal molecule can be greatly amplified and have a dramatic effect.
272

www.ck12.org

Chapter 3. Cell Biology - Advanced

FIGURE 3.45
How a G-protein linked receptor works
with the help of a G-protein.

G Proteins

G proteins (guanine nucleotide-binding proteins) are a family of GTPases involved in transmitting chemical
signals outside the cell, and causing changes inside the cell. When a ligand binds to a G protein coupled receptor,
an intracellular domain of the receptor activates a G protein. The G protein then activates additional intracellular
pathways, resulting in an altered intracellular environment. G proteins function as molecular switches. When they
bind guanosine triphosphate (GTP), they are on, and, when they bind guanosine diphosphate (GDP), they are off.

G Protein Coupled Receptors and Cyclic AMP

G protein linked receptors are only found in higher eukaryotes, including yeast, plants, and animals. Your senses
of sight and smell are dependent on G-protein linked receptors. The ligands that bind to these receptors include
light-sensitive compounds, odors, hormones, and neurotransmitters. The ligands for G-protein linked receptors
come in different sizes, from small molecules to large proteins. When a ligand binds to the receptor, it causes a
conformational change in the receptor, which allows it to act as a guanine nucleotide exchange factor. The receptor
can then activate an associated G-protein by exchanging its bound GDP for a GTP. The G-proteins subunit,
together with the bound GTP, can then dissociate from the and subunits to further affect intracellular signaling
proteins.
Many times the activated G-protein-linked receptor will then activate cyclic AMP (cAMP), which acts as the second
messenger in initiating a cascade of reactions.
The process of how a G-protein linked receptor works is outlined in Figure 3.46.

273

3.35. Signal Transduction - Advanced

www.ck12.org

FIGURE 3.46
How a G-protein linked receptor works
with the help of a G-protein.

In panel

C, the second messenger cAMP can be


seen moving away from the enzyme.

G-Protein Linked Receptors

A. A ligand such as a hormone (small, purple molecule) binds to the G protein-linked receptor (red molecule).
Before ligand binding, the inactive G-protein (yellow molecule) has GDP bound to it.
B. The receptor changes shape and activates the G-protein and a molecule of GTP replaces the GDP.
C. The G-protein moves across the membrane then binds to and activates the enzyme (green molecule). This then
triggers the next step in the pathway to the cells response. After activating the enzyme, the G-protein returns
to its original position. The second messenger of this signal transduction is cAMP, as shown in C.

The sensing of the external and internal environments at the cellular level relies on signal transduction. Defects
in signal transduction pathways can contribute or lead to many diseases, including cancer and heart disease. This
highlights the importance of signal transductions to biology and medicine.
274

www.ck12.org

Chapter 3. Cell Biology - Advanced

G-protein linked receptors are also involved in the phosphatidylinositol (PI) signal pathway. In this pathway, PI
can be phosphorylated to form phosphatidylinositol phosphate (PIP), phosphatidylinositol bisphosphate (PIP2 ) and
phosphatidylinositol trisphosphate (PIP3 ), which are collectively called phosphoinositides. These molecules play
important roles in lipid signaling, cell signaling and membrane trafficking.
Signal Response

In response to a signal, a cell may change activities in the cytoplasm or in the nucleus that include the switching on
or off of genes. Changes in metabolism, continued growth, movement, or death are some of the cellular responses
to signals that require signal transduction.
Gene activation leads to other effects, since the protein products of many of the responding genes include enzymes
and factors that increase gene expression. Gene expression factors produced as a result of a cascade can turn on
even more genes. Therefore one stimulus can trigger the expression of many genes, and this in turn can lead to the
activation of many complex events. In a multicellular organism these events include the increased uptake of glucose
from the blood stream (stimulated by insulin), and the movement of neutrophils to sites of infection (stimulated by
bacterial products). The set of genes and the order in which they are activated in response to stimuli are often called
a genetic program.
FIGURE 3.47
Signal transduction pathways. Ras (upper middle section) activates a number of
pathways but an especially important one
seems to be the mitogen-activated protein
kinases (MAPK). MAPK transmit signals
downstream to other protein kinases and
gene regulatory proteins. Note that many
of these pathways are initiated when a
signal binds to its receptor outside the
cell. Most pathways end with altered gene
regulation and cell proliferation. The p53
tumor suppressor protein is shown at the
lower section of the figure stimulating p21.
The complexity of the pathways demonstrate the significant role these play in the
cell.

Vocabulary

cyclic adenosine monophosphate (cAMP, cyclic AMP): A second messenger important in many biological
processes; used for intracellular signal transduction, such as transferring into cells the effects of hormones.
G protein (guanine nucleotide-binding protein): Guanine nucleotide-binding proteins; a family of proteins
involved in transmitting chemical signals outside the cell, causing changes inside the cell.
G protein-linked receptor: A large protein family of transmembrane receptors that bind molecules outside
275

3.35. Signal Transduction - Advanced

www.ck12.org

the cell and activate signal transduction pathways inside the cell; also known as G protein coupled receptors
and seven-transmembrane domain receptors.
GTPase: A large family of hydrolase enzymes that can bind and hydrolyze guanosine triphosphate (GTP) to
guanosine diphosphate (GDP).
second messenger: A molecule that relays a signal from a receptor on the cell surface to target molecules
inside the cell.
signal-transduction: The process that occurs when an extracellular signaling molecule activates a cell surface
receptor, which then alters intracellular molecules creating a response.
Summary

Signal transduction occurs when a ligand binds its receptor and alters intracellular conditions.
Often the signal is transducer from the outside of the cell to the inside.
This process usually involves G-protein linked receptors and cyclic AMP.
Explore More

Use this resource to answer the questions that follow.


Signal Transduction Pathways at http://www.youtube.com/watch?v=qOVkedxDqQo

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139339

1.
2.
3.
4.
5.

Describe a general signal transduction pathway.


What is meant by a phosphorylation cascade?
How is adenyl cyclase activated? What is the role of adenyl cyclase?
Describe the role of cAMP.
How is protein kinase activated? What is the role of protein kinase?

Review

1. Define G-protein.
2. Describe the process of signal transduction, focusing on the roles of G-protein linked receptors and cyclic
AMP.

Summary
The cell is the smallest unit of structure and function of all living organisms. Cell Biology focuses on significant
aspects of the cell from its structure to its division. Some organisms contain just one cell, and others contain
276

www.ck12.org

Chapter 3. Cell Biology - Advanced

trillions. Some have a nucleus with DNA, others do not. Some have many organelles, others do not. But all cells
are surrounded by a cell membrane. And it is this semipermeable membrane that determines what can enter and
leave the cell. All cells need energy, and for many organisms, this energy comes from photosynthesis and cellular
respiration. All cells come from preexisting cells through the process of cell division, which can produce a new
prokaryotic organism. The cell cycle, which includes mitosis, defines the life of an eukaryotic cell.

277

3.36. References

www.ck12.org

3.36 References
1.
2.
3.
4.

5.
6.
7.

8.

9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.

20.
21.

22.
278

Robert Hooke, Micrographia, 1665. Suber cells and mimosa leaves. . Public Domain
J. Verkolje. http://commons.wikimedia.org/wiki/File:Antoni_van_Leeuwenhoek.png . Public Domain
Damin H. Zanette. http://commons.wikimedia.org/wiki/File:Bdelloidea1_w.jpg . Public Domain
(A) Robert Hooke; (B) Evan Bench (Flickr: austinevan). (A) http://commons.wikimedia.org/wiki/File:Hooke
-microscope.png; (B) http://www.flickr.com/photos/austinevan/3368430443/ . (A) Public Domain; (B) CC
BY 2.0
Dartmouth Electron Microscope Facility. http://commons.wikimedia.org/wiki/File:Chlamydomonas_TEM_07.jpg . Public Domain
Niamh Gray-Wilson. CK-12 Foundation . CC BY-NC 3.0
(A) Lenore Edman (Flickr:1lenore); (B) National Science Foundation. (A) http://www.flickr.com/photos/len
ore-m/6123190318/; (B) http://commons.wikimedia.org/wiki/File:Mouse_embryonic_stem_cells.jpg . (A)
CC BY 2.0; (B) Public Domain
Nerve cell: WA Lee et al.; Blood cell: Courtesy of National Institute of Health; Bacteria: TJ Kirn, MJ Lafferty,
CMP Sandoe, and RK Taylor; Algae: EF Smith and PA Lefebvre; Pollen: L Howard and C Daghlian. Nerv
e cell: http://en.wikipedia.org/wiki/File:GFPneuron.png; Blood cell: http://commons.wikimedia.org/wiki/F
ile:Redbloodcells.jpg; Bacteria: http://remf.dartmouth.edu/images/bacteriaSEM/source/1.html; Algae: http
://remf.dartmouth.edu/images/algaeSEM/source/1.html; Pollen: http://remf.dartmouth.edu/images/botanicalP
ollenSEM/source/10.html . Nerve cell: CC-BY 2.5; Blood cell: Public Domain; Bacteria: Public Domain;
Algae: Public Domain; Pollen: Public Domain
Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/Fi
le:Average_prokaryote_cell-_en.svg . Public Domain
Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/Fi
le:Animal_cell_structure_en.svg . Public Domain
Science Primer (National Centre for Biotechnology Information). http://commons.wikimedia.org/wiki/File:C
elltypes.svg . Public Domain
User:TimVickers/Wikipedia and User:Fvasconcellos/Wikimedia Commons. http://commons.wikimedia.org
/wiki/File:Relative_scale.svg . Public Domain
Laura Guerin. CK-12 Foundation . CC BY-NC 3.0
Image copyright udaix, 2014. Animal Cell . Used under license from Shutterstock.com
Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/Fi
le:Cell_membrane_detailed_diagram_en.svg . Public Domain
(a) Courtesy of the US Government; (b) Weerapong Prasongchean. (a) http://commons.wikimedia.org/wiki/Fi
le:FluorescentCells.jpg; (b) http://commons.wikimedia.org/wiki/File:E7_amnion_cells.png . Public Domain
Courtesy of CDC/Dr. William A. Clark. http://commons.wikimedia.org/wiki/File:BacillusCereus.jpg . Public
Domain
Left: Charles Daghlian; Right: Louisa Howard, Michael Binder. Left: http://commons.wikimedia.org/wiki/
File:Bronchiolar_epithelium_3_-_SEM.jpg; Right: http://commons.wikimedia.org/wiki/File:Bronchiolar_area_cilia_cross-sections_2.jpg . Public Domain
Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/Fi
le:Diagram_human_cell_nucleus.svg . Public Domain
(a) Courtesy of the National Institutes of Health; (b) Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia
Commons). (a) http://en.wikipedia.org/wiki/File:Mitochondrion_186.jpg; (b) http://commons.wikimedia.or
g/wiki/File:Animal_mitochondrion_diagram_en.svg . Public Domain
User:Magnus Manske/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Nucleus_ER_golgi.jpg

www.ck12.org

23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
34.
35.

36.
37.
38.
39.
40.
41.
42.
43.
44.
45.
46.
47.

Chapter 3. Cell Biology - Advanced

. Public Domain
Laura Guerin. CK-12 Foundation . CC BY-NC 3.0
Image copyright somersault1824, 2014. Animal Cell . Used under license from Shutterstock.com
Mariana Ruiz Villarreal (LadyofHats), modified for CK-12 Foundation. http://commons.wikimedia.org/wik
i/File:Endomembrane_system_diagram_en.svg . Public Domain
User:Magnus Manske/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Nucleus_ER_golgi.jpg
. Public Domain
User:Kelvinsong/Wikimedia Commons, modified by Laura Guerin. Structure of the centrioles . CC BY 3.0
Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/File:P
lant_cell_structure_svg.svg . Public Domain
User:HermannSchachner/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Plagiomnium_affin
e_%28f,_144553-474756%29_8099.JPG . Public Domain
User:ItsJustMe/Wikipedia. http://commons.wikimedia.org/wiki/File:Chloroplast-new.jpg . Public Domain
Dr. Ralf Wagner. Colonial algae of the genus Volvox . CC BY 3.0
(2005) The Evolution of Self-Fertile Hermaphroditism: The Fog Is Clearing. PLoS Biol 3(1): e30. doi:10.1371/journal.pbio
Wild-type Caenorhabditis elegans . CC BY 2.5
User:Pidalka44/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Semipermeable_membrane.pn
g . Public Domain
Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/File:S
cheme_simple_diffusion_in_cell_membrane-en.svg . Public Domain
Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/Fi
le:Osmotic_pressure_on_blood_cells_diagram.svg; http://commons.wikimedia.org/wiki/File:Turgor_pressure_on_plant_cells_diagram.svg . Public Domain
Flickr:fickleandfreckled. http://www.flickr.com/photos/fickleandfreckled/7980692858/ . CC BY 2.0
Image copyright Lebendkulturen.de, 2014. A photo that shows the contractile vacuole within paramecia .
Used under license from Shutterstock.com
Hana Zavadska, based on image by Mariana Ruiz Villarreal (http://commons.wikimedia.org/wiki/File:Scheme_facilitated_diffusion_in_cell_membrane-en.svg). CK-12 Foundation . CC BY-NC 3.0
Mariana Ruiz Villarreal (User:LadyofHats). http://commons.wikimedia.org/wiki/File:Scheme_sodium-potassi
um_pump-en.svg . Public Domain
Image copyright Alila Medical Media, 2014. Ionic basis of resting membrane potential . Used under license
from Shutterstock.com
Louisa Howard, Miguel Marin-Padilla. http://commons.wikimedia.org/wiki/File:Junctional_complex_and_pi
nocytotic_vesicles_-_embryonic_brain-TEM.jpg . Public Domain
Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Image copyright Andrea Danti, 2014. Axon signaling using exocytosis . Used under license from Shutterstock.com
Laura Guerin. CK-12 Foundation . CC BY-NC 3.0
Image copyright Alila Medical Media, 2014. http://www.shutterstock.com . Used under license from
Shutterstock.com
User:Bensaccount/Wikipedia. http://commons.wikimedia.org/wiki/File:GPCR_mechanism.png . Public Domain
User:Boghog2/Wikipedia. http://commons.wikimedia.org/wiki/File:Signal_transduction_pathways.png . Public Domain

279

www.ck12.org

C HAPTER

Biochemistry - Advanced

Chapter Outline
4.1

B IOCHEMICAL E NERGY - A DVANCED

4.2

S TATES OF M ATTER IN B IOLOGICAL S YSTEMS - A DVANCED

4.3

C HEMICAL R EACTIONS - A DVANCED

4.4

C HEMICAL R EACTIONS AND E NERGY - A DVANCED

4.5

E NZYMES AND ACTIVATION E NERGY - A DVANCED

4.6

E NZYMES AND B IOCHEMICAL R EACTIONS - A DVANCED

4.7

R EFERENCES

Introduction

What do you get when you cross biology and chemistry?


Hummingbirds, with their tiny bodies and high levels of activity, have the highest metabolic rates of any animals
roughly a dozen times that of a pigeon and a hundred times that of an elephant. The metabolic rate, or rate of
metabolism, has to do with the amount of energy the organism uses. And that energy is used to drive the chemical
reactions in cells or the biochemical reactions. And, of course, it is all the biochemical reactions that allow the
cells function properly, and maintain life.

280

www.ck12.org

Chapter 4. Biochemistry - Advanced

4.1 Biochemical Energy - Advanced


Define energy, and describe how energy can be changed from one form to another.

What is energy? Where does your energy come from? Can energy be recycled?
This team of ants is breaking down a dead tree. A classic example of teamwork. And all that work takes energy. In
fact, each chemical reaction - the chemical reactions that allow the cells in those ants to do the work - needs energy
to get started. And all that energy comes from the food the ants eat. Whatever eats the ants gets their energy from
the ants. Energy passes through an ecosystem in one direction only.
Matter and Energy

All living things are made of matter. In fact, matter is the stuff of which all organisms are made. Anything
that occupies space and has mass is known as matter. Matter, in turn, consists of chemical substances. It is the
carbons, hydrogens, oxygens and other elements that combine to form molecules, compounds, organelles, cells and
eventually tissues, organs and organisms. In addition to being made of matter, all living organisms also need energy
to survive.
Energy is a property of matter that is defined as the ability to do work. The concept of energy is useful for explaining
and predicting most natural phenomena, and it is the foundation for an understanding of biology. All living organisms
need energy to grow and reproduce. However, energy can never be created nor destroyed. Energy can only be
transformed. That is, energy is always conserved. This is called the law of conservation of energy. Therefore,
organisms cannot create the energy they need. Instead, they must obtain energy from the environment. Organisms
also cannot destroy or use up the energy they obtain. They can only change it from one form to another. Organisms
will either use their energy (for metabolism) or release it to the environment as heat.
281

4.1. Biochemical Energy - Advanced

www.ck12.org

In biology, energy is required for ecosystems to survive, as all living organisms need energy. Within an organism,
energy is needed for growth and development of a biological cell or an organelle within that cell. Energy is also
needed for all biochemical reactions within that cell. Therefore, energy is stored within cells in the chemical bonds
of substances such as carbohydrates (including sugars), lipids, and proteins. This energy is released during aerobic
respiration.
The energy for most living organisms initially originates from the sun. This energy is absorbed by producers,
usually photosynthetic organisms such as plants. Plants convert this energy into chemical energy, in the form of
carbohydrates, such as glucose. Energy can be stored in this state, or converted into a usable form of energy,
adenosine triphosphate (ATP). This occurs in both the plant, as well as the organisms that eat the plant, or eat the
organism that ate the plant.
Forms of Energy

Energy can take several different forms. Common forms of energy include light, chemical, and heat energy. Other
common forms are kinetic and potential energy.
How Organisms Change Energy

In organisms, energy is always changing from one form to another. For example, plants obtain light energy from
sunlight and change it to chemical energy in food molecules, such as glucose. Chemical energy is energy stored in
bonds between atoms within food molecules. When other organisms eat and digest the food, they break the chemical
bonds and release the chemical energy. Organisms do not use energy very efficiently. About 90 percent of the energy
they obtain from food is converted to heat energy that is given off to the environment.
Kinetic and Potential Energy

Energy also constantly changes back and forth between kinetic and potential energy. Kinetic energy is the energy
of movement. For example, a ball falling through the air has kinetic energy because it is moving ( Figure 4.1). The
random motion of molecules is due to kinetic energy, and the driving force behind diffusion.
Potential energy is the energy stored in an object due to its position. A bouncing ball at the top of a bounce, just
before it starts to fall, has potential energy. For that instant, the ball is not moving, but it has the potential to move
because gravity is pulling on it. Once the ball starts to fall, the potential energy changes to kinetic energy. When the
ball hits the ground, it gains potential energy from the impact. The potential energy changes to kinetic energy when
the ball bounces back up into the air. As the ball gains height, it regains potential energy because of gravity.
Like the ball, every time you move you have kinetic energy whether you jump or run or just blink your eyes.
Can you think of situations in which you have potential energy? Obvious examples might include when you are
standing on a diving board or at the top of a ski slope or bungee jump. What gives you potential energy in all of
these situations? The answer is gravity.
Vocabulary

adenosine triphosphate (ATP): Energy-carrying molecule that cells use to power their metabolic processes;
energy-currency of the cell.
energy: Property of matter that is defined as the ability to do work.
kinetic energy: Form of energy that an object has when it is moving.
282

www.ck12.org

Chapter 4. Biochemistry - Advanced

FIGURE 4.1
Energy in a bouncing ball is transformed
from potential energy to kinetic energy
and then back to potential energy. This
cycle of energy changes keeps repeating
as long as the ball continues to bounce.
The ball rises less on each successive
bounce because some energy is used to
resist air molecules.

law of conservation of energy: Law of physics that states that energy may neither be created nor destroyed;
the sum of all the energies in a system remains constant over time.
matter: All the substances of which things are made.
potential energy: Form of energy that is stored in an object due to its position.
Summary

Energy is a property of matter. It cannot be created or destroyed. Organisms obtain light energy from sunlight
or chemical energy from food and change the energy into different forms, including heat energy.
Explore More

Use this resource to answer the questions that follow.


http://www.hippocampus.org/Biology Non-Majors Biology Search: Energy
1.
2.
3.
4.

What is energy?
Why do living organisms need energy?
What is the main difference between potential and kinetic energy?
What is the original source of most energy used by living organisms on Earth?

Review

1. What is energy?
2. Describe two ways that energy changes form in the following sequence of events: A plant grows in the sun.
A rabbit eats the plant.
3. Describe a real-life situation in which the energy of an object or person changes back and forth between kinetic
energy and potential energy. Identify each time energy changes form.

283

4.2. States of Matter in Biological Systems - Advanced

www.ck12.org

4.2 States of Matter in Biological Systems Advanced


Identify three states of matter and explain how they differ.

Solid, liquid or gas?


The state of matter is a physical property of that matter. H2 O can exist in three different states of matter. This glacier
is obviously a solid state of H2 O, floating in the liquid state. Why does the ice float on water? Which has a greater
density, solid H2 O or liquid H2 O?
States of Matter

The amount of energy in molecules of matter determines the state of matter. Matter can exist in one of several
different states, including a gas, liquid, or solid state. These different states of matter have different properties,
which are illustrated in Figure 4.2. Gasses have the most energy, and solids have the least energy.
A gas is a state of matter in which atoms or molecules have enough energy to move freely. The molecules
come into contact with one another only when they randomly collide. Forces between atoms or molecules are
not strong enough to hold them together, allowing the molecules to move independently of one another.
284

www.ck12.org

Chapter 4. Biochemistry - Advanced

A liquid is a state of matter in which atoms or molecules are constantly in contact but have enough energy
to keep changing positions relative to one another. Forces between atoms or molecules are strong enough to
keep the molecules together but not strong enough to prevent them from moving. The particles of a liquid
have enough energy to allow them to slide past one another, but not enough energy to allow them to move
freely.
A solid is a state of matter in which atoms or molecules do not have enough energy to move. They are
constantly in contact and in fixed positions relative to one another. Forces between atoms or molecules are
strong enough to keep the molecules together and to prevent them from moving. The particles of a solid only
have enough energy to vibrate in place.

FIGURE 4.2
States of Matter.

All three containers contain a substance with the same mass, but the substances are in different states. In the lefthand container, the substance is a gas, which has spread to fill its container. It takes both the shape and volume of the
container. In the middle container, the substance is a liquid, which has spread to take the shape of its container but
not the volume. In the right-hand container, the substance is a solid, which takes neither the shape nor the volume
of its container.
What Determines a Substances State?

A substances state depends partly on temperature and air pressure. For example, at the air pressure found at sea
level, water exists as a liquid at temperatures between 0C and 100C. Above 100C, water exists as a gas (water
vapor). Below 0C, water exists as a solid (ice). Different substances have a different range of temperatures at which
they exist in each state. For example, oxygen is gas above -183C, but iron is a gas only above 2861C. These
differences explain why some substances are always solids at normal Earth temperatures, whereas others are always
gases or liquids.
Changing States

Matter constantly goes through cycles that involve changing states. Water and all the elements important to organisms, including carbon and nitrogen, are constantly recycled on Earth (see Principles of Ecology). As matter moves
through its cycles, it changes state repeatedly. For example, in the water cycle, water repeatedly changes from a gas
to a liquid or solid and back to a gas again. How does this happen?
Adding energy to matter gives its atoms or molecules the ability to resist some of the forces holding them together.
For example, heating ice to its melting point (0C) gives its molecules enough energy to move. The ice melts and
becomes liquid water. Similarly, heating liquid water to its boiling point (100C) gives its molecules enough energy
to pull apart from one another so they no longer have contact. The liquid water vaporizes and becomes water vapor.
In biological systems, matter is continuously changing states as well. For example, carbon in the form of the gas
carbon dioxide is changed into glucose, a solid. This change, of course, occurs during photosynthesis. During
cellular respiration, carbons from the glucose molecule are changed back into the carbon dioxide gas.
285

4.2. States of Matter in Biological Systems - Advanced

www.ck12.org

Conservation of Matter

Though matter can change states, and it often does, matter cannot be created or destroyed. Similar to the law of
the conservation of energy, the law of conservation of mass states that the mass (or matter) of an isolated system
will remain constant over time. This means that mass or matter cannot be created or destroyed, although it may
be rearranged and changed into different types of substances. Hence, matter is continuously recycled, resulting in
the so called "circle of life." The carbon and other elements of organisms are recycled to be used by other living
organisms. This law also states that in a chemical reaction, or a biochemical reaction, as mass cannot be created or
destroyed, the mass of the reactants must equal the mass of the products. In other words, the atoms in the starting
materials must be equivalent to the atoms in the ending materials.
Vocabulary

biochemical reaction: Chemical reaction within a cell or organism; usually controlled by an enzyme.
boiling point: The temperature at which a liquid changes state into a gas.
gas: State of matter in which atoms or molecules have enough energy to move freely.
law of conservation of mass: Law that states that the mass of an isolated system will remain constant over
time.
liquid: State of matter in which atoms or molecules are constantly in contact but have enough energy to keep
changing positions relative to one another.
melting point: The temperature at which a solid changes state into a liquid.
solid: State of matter in which atoms or molecules do not have enough energy to move.
state of matter: Condition that matter is in, depending on how much energy its atoms or molecules have.
Summary

Matter can exist in one of several different states, including a gas, liquid, or solid state. States of matter differ
in the amount of energy their molecules have. When matter recycles, it changes state by gaining or losing
energy.
Explore More

Use this resource to answer the questions that follow.


States of Matter at http://www.youtube.com/watch?v=HAPc6JH85pM

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139422

286

www.ck12.org

Chapter 4. Biochemistry - Advanced

1. What state of matter is glass?


2. How and why does the glass in the video change states?
Review

1.
2.
3.
4.
5.

Compare and contrast the three common states of matter?


What determines a substances state?
At what temperatures does the state of water change?
Explain what happens to molecules of matter when matter changes state from a liquid to a gas.
What is the law of conservation of mass?

287

4.3. Chemical Reactions - Advanced

www.ck12.org

4.3 Chemical Reactions - Advanced


Describe what happens in a chemical reaction, and identify types of chemical reactions.

Understanding chemistry is essential to fully understand biology. Why?


A general understanding of chemistry is necessary to understand biology. Essentially, our cells are just thousands
of chemicals made of elements like carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur in just the right
combinations. And these chemicals combine through chemical reactions.
What are Chemical Reactions?

A chemical compound may be very different from the substances that combine to form it. For example, the element
chlorine (Cl) is a poisonous gas, but when it combines with sodium (Na) to form sodium chloride (NaCl), it is no
longer toxic. You may even eat it on your food. Sodium chloride is just table salt. What process changes a toxic
chemical like chlorine into a much different substance like table salt?
A chemical reaction is a process that changes some chemical substances into other chemical substances. The
substances that start a chemical reaction are called reactants. The substances that form as a result of a chemical
reaction are called products. During the reaction, the reactants are used up to create the products. For example,
when methane burns in oxygen, it releases carbon dioxide and water. In this reaction, the reactants are methane
(CH4 ) and oxygen (O2 ), and the products are carbon dioxide (CO2 ) and water (H2 O).
Chemical Equations

A chemical reaction can be represented by a chemical equation. Using the same example, the burning of methane
gas can be represented by the equation:
288

www.ck12.org

Chapter 4. Biochemistry - Advanced

CH4 + 2 O2 CO2 + 2 H2 O.
The arrow in a chemical equation separates the reactants from the products and shows the direction in which the
reaction occurs. If the reaction could also occur in the opposite direction, then two arrows, one pointing in each
direction, or one arrow pointing in both directions, would be used. On each side of the arrow, a mixture of chemicals
is indicated by the chemical symbols joined by a plus sign (+). The numbers preceding some of the chemical symbols
(such as 2 O2 ) indicate how many molecules of the chemicals are involved in the reaction. (If there is no number in
front of a chemical symbol, it means that just one molecule is involved.)
In a chemical reaction, the quantity of each element does not change. There is the same amount of each element at
the end of the reaction as there was at the beginning. This is reflected in the chemical equation for the reaction. The
equation should be balanced. In a balanced equation, the same number of atoms of a given element appear on each
side of the arrow. For example, in the equation above, there are four hydrogen atoms on each side of the arrow.
Types of Chemical Reactions

In general, a chemical reaction involves the breaking and forming of chemical bonds. In the methane reaction above,
bonds are broken in methane and oxygen, and bonds are formed in carbon dioxide and water. A reaction like this, in
which a compound or element burns in oxygen, is called a combustion reaction. This is just one of many possible
types of chemical reactions. Other types of chemical reactions include synthesis, decomposition, and substitution
reactions.
A synthesis reaction occurs when two or more chemical elements or compounds unite to form a more complex
product. For example, nitrogen (N2 ) and hydrogen (H2 ) unite to form ammonia (NH3 ):
N2 + 3 H2 2 NH3 .
A decomposition reaction occurs when a compound is broken down into smaller compounds or elements.
For example, water (H2 O) breaks down into hydrogen (H2 ) and oxygen (O2 ):
2 H2 O 2 H2 + O2 .
A substitution reaction occurs when one element replaces another element in a compound. For example,
sodium (Na+ ) replaces hydrogen (H) in hydrochloric acid (HCl), producing sodium chloride (NaCl) and
hydrogen gas (H2 ):
2 Na+ + 2 HCl 2 NaCl + H2 .
Redox Rections

Reduction-oxidation reactions, or redox reactions include all chemical reactions in which atoms have their oxidation
state changed. This can be either a simple redox process, such as the oxidation of carbon into carbon dioxide or the
reduction of carbon by hydrogen into methane, or a complex process such as the oxidation of glucose through a
series of complex electron transfer processes during cellular respiration. Oxidation is the loss of electrons or an
increase in oxidation state by a molecule, atom, or ion. Reduction is the gain of electrons or a decrease in oxidation
state by a molecule, atom, or ion.
Redox Reactions in Biology

Many important biological processes involve redox reactions, which frequently store and release energy. For
example, photosynthesis involves the reduction of carbon dioxide into glucose and the oxidation of water into
289

4.3. Chemical Reactions - Advanced

www.ck12.org

oxygen. This process stores the energy of sunlight in the bonds of sugars. The reverse reaction, cellular respiration,
converts the energy in glucose into ATP. Cellular respiration involves the oxidation of glucose to carbon dioxide and
the reduction of oxygen gas to water. This process depends on the reduction of NAD+ to the electron carrier NADH,
and the reverse oxidation of NADH to NAD+ . The reduction of NAD+ leads to the formation of a proton (H+ )
gradient, which drives the synthesis of ATP. NADH (nicotinamide adenine dinucleotide) and NADPH (Nicotinamide
adenine dinucleotide phosphate) are electron carriers in biological systems. The term redox state is often used to
describe the balance between NAD+ /NADH and NADP+ /NADPH (Nicotinamide adenine dinucleotide phosphate).
Vocabulary

chemical reaction: A process that changes some chemical substances into other chemical substances.
combustion reaction: Type of chemical reaction in which a compound or element burns in oxygen.
decomposition reaction: Type of chemical reaction in which a compound is broken down into smaller
compounds or elements.
oxidation: The loss of electrons or an increase in oxidation state by a molecule, atom, or ion.
product: Substance that forms as a result of a chemical reaction.
reactant: Substance involved in a chemical reaction that is present at the beginning of the reaction.
redox reaction: A chemical reaction in which atom(s) have their oxidation state changed.
redox state: Describes the balance between NAD+ /NADH and NADP+ /NADPH.
reduction: The gain of electrons or a decrease in oxidation state by a molecule, atom, or ion.
substitution reaction: Type of chemical reaction in which one element replaces another element in a compound.
synthesis reaction: Type of chemical reaction in which elements or compounds unite to form a more complex
product.
Summary

A chemical reaction is a process that changes some chemical substances into others. It involves breaking
and forming chemical bonds. Types of chemical reactions include synthesis reactions and decomposition
reactions.
Review

1.
2.
3.
4.

290

Identify the roles of reactants and products in a chemical reaction.


Describe each type of chemical reaction.
What is wrong with the following chemical equation? How could you fix it? CH4 + O2 CO2 + 2H2 O
What type of reaction is represented by the following chemical equation? Explain your answer. 2Na + 2HCl
2NaCl + H2

www.ck12.org

Chapter 4. Biochemistry - Advanced

4.4 Chemical Reactions and Energy - Advanced


Explain the role of energy in chemical reactions, and define activation energy.

How do you change one thing into another?


The bonds between the atoms need to be rearranged. That is the definition of a chemical reaction. And all chemical
sections need energy to get started.
Chemical Reactions and Energy

All chemical reactions involve energy. Some chemical reactions consume energy, whereas other chemical reactions
release energy. Chemical reactions can be either spontaneous, which do not require an input of energy, or nonspontaneous, which does require an input of some type of energy. Energy may be in the form of heat, light or
electricity. Each of the energy changes that occur during a reaction are graphed in Figure 4.3. In the reaction on the
left, energy is released. In the reaction on the right, energy is consumed.
Bill Nye discusses chemical reactions at http://www.youtube.com/watch?v=66kuhJkQCVM (2:05).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/201

Thermodynamics

Chemical reactions follow the laws of thermodynamics. The First Law of Thermodynamics states that energy can
be changed from one form to another, but it cannot be created or destroyed. This law is also known as the Law of
Conservation of Energy. The Second Law of Thermodynamics states the energy available after a chemical reaction
291

4.4. Chemical Reactions and Energy - Advanced

www.ck12.org

FIGURE 4.3
The exothermic reaction on the left releases energy. The endothermic reaction
on the right consumes energy.

is always less than that at the beginning of a reaction. This is also commonly referred to as entropy. Entropy can
be described as the degree of disorder in a system. That is, as energy is transferred from one form to another, some
of the energy is lost as heat, and the amount of available energy decreases. As the energy decreases, the disorder in
the system increases, and, by definition, the entropy increases. Ice melting provides an example in which entropy
increases. Entropy essentially is a measure of the tendency of a process, such as a chemical reaction, to proceed in a
particular direction.
Reactions can proceed by themselves if they are exergonic or exothermic, that is if they release energy. The
associated free energy of the reaction is composed of two different thermodynamic quantities, enthalpy and entropy.
Enthalpy is a measure of the total energy of a thermodynamic system. The change in enthalpy is positive in
endothermic reactions, and negative in exothermic processes.
Exothermic Reactions

Chemical reactions that release energy are called exothermic reactions. An example is the combustion of methane
described at the beginning of this lesson. In organisms, exothermic reactions are called catabolic reactions.
Catabolic reactions break down molecules into smaller units. An example is a decomposition reaction, such as
the breakdown of glucose molecules for energy. Exothermic reactions can be represented by the general chemical
equation:
Reactants Products + Heat.
Endothermic Reactions

Chemical reactions that consume energy are called endothermic reactions. Energy is usually absorbed from
the surroundings as heat. An example is the synthesis of ammonia, described above. In organisms, endothermic
reactions are called anabolic reactions. Anabolic reactions construct molecules from smaller units. An example
is the synthesis of proteins from amino acids. Endothermic reactions can be represented by the general chemical
equation:
Reactants + Heat Products.
Endothermic Organisms

In biological systems, the term endothermic is a metabolic term related to maintenance of body temperature. An
endothermic animals is an organism that produces heat through internal means, a process known as endothermy.
Animals may do this through muscle shivering or increasing metabolism. These animals do to absorb heat from
their surroundings, so the term endothermic has distinct uses related to chemical reactions or maintenance of body
temperature. The opposite of endothermy is ectothermy. Ectothermic animals (cold-blooded) do absorb heat from
their surroundings.
292

www.ck12.org

Chapter 4. Biochemistry - Advanced

FIGURE 4.4
This pack gets cold due to an endothermic reaction.

Vocabulary

anabolic reaction: Endothermic reaction that occurs in organisms; chemical reaction that builds new molecules
and/or stores energy.
catabolic reaction: Chemical reaction that breaks down more complex organic molecules into simpler substances; usually releases energy.
decomposition reaction: Type of chemical reaction in which a compound is broken down into smaller
compounds or elements.
endothermic reaction: Any chemical reaction that consumes energy.
enthalpy: A measure of the total energy of a thermodynamic system.
entropy: A measure of the tendency of a process, such as a chemical reaction, to proceed in a particular
direction.
exothermic reaction: Any chemical reaction that releases energy.
Summary

Chemical reactions follow the laws of thermodynamics.


Some chemical reactions are exothermic, which means they release energy. Other chemical reactions are
endothermic, which means they consume energy.
Catabolic and anabolic reactions occur in cells/organisms.
Explore More

Use this resource to answer the questions that follow. Assignment Discovery: Chemical Reactions at http://www.d
iscovery.com/tv-shows/other-shows/videos/assignment-discovery-shorts-chemical-reactions.htm

293

4.4. Chemical Reactions and Energy - Advanced

www.ck12.org

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139421

1.
2.
3.
4.
5.
6.
7.

What is the chemical reaction definition used in this video?


How does a chemical reaction form new substances?
What is a balanced equation? Give an example.
Define a single replacement reaction.
Give an example of a double replacement reaction.
What is a redox reaction?
Define oxidation and reduction.

Review

1. Compare and contrast each of the following:


a.
b.
c.
d.

294

The first and seconds laws of thermodynamics.


Entropy and enthalpy.
Endothermic and exothermic reactions.
Anabolic and catabolic reactions.

www.ck12.org

Chapter 4. Biochemistry - Advanced

4.5 Enzymes and Activation Energy - Advanced


Explain the importance of enzymes in organisms, and describe how enzymes work.
State factors that affect the rate of chemical reactions.

What is the energy needed for biochemical reactions?


Is it light or heat? It could be either. But whatever form energy takes, every single biochemical reaction in your body
- and there are trillions of these reactions (or more) every split second, needs energy to start or activate. And that is
known as activation energy.
Activation Energy

Regardless of whether reactions are exothermic reactions or endothermic reactions, they all need energy to get
started. This energy is called activation energy. Activation energy is like the push you need to start moving down
a slide. The push gives you enough energy to start moving. Once you start, you keep moving without being pushed
again. Activation energy is defined as the energy that must be overcome in order for a chemical reaction to occur, or
the minimum energy required to start a chemical reaction. The concept of activation energy is illustrated in Figure
4.5.
An overview of activation energy can be viewed at http://www.youtube.com/watch?v=VbIaK6PLrRM (1:16).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/202

295

4.5. Enzymes and Activation Energy - Advanced

www.ck12.org

FIGURE 4.5
To start this reaction, a certain amount of
energy is required, called the activation
energy. How much activation energy is
required depends on the nature of the reaction and the conditions under which the
reaction takes place. Activation energy
can be thought of as the height of the
energy barrier between the reactants and
the products.

Why do reactions need energy to get started? In order for reactions to occur, three things must happen, and they all
require energy:
Reactant molecules must collide. To collide, they must move, so they need kinetic energy.
Unless reactant molecules are positioned correctly, intermolecular forces may push them apart. To overcome
these forces and move together requires more energy.
If reactant molecules collide and move together, there must be enough energy left for them to react.
Rates of Chemical Reactions

The rates at which chemical reactions take place in organisms are very important. Chemical reactions in organisms
are involved in processes ranging from the contraction of muscles to the digestion of food. For example, when you
wave goodbye, it requires repeated contractions of muscles in your arm over a period of a couple of seconds. A huge
number of reactions must take place in that time, so each reaction cannot take longer than a few milliseconds. If the
reactions took much longer, you might not finish waving until sometime next year.
Factors that help reactant molecules collide and react speed up chemical reactions. These factors include the
concentration of reactants and the temperature at which the reactions occur.
Reactions are usually faster at higher concentrations of reactants. The more reactant molecules there are in a
given space, the more likely they are to collide and react.
Reactions are usually faster at higher temperatures. Reactant molecules at higher temperatures have more
energy to move, collide, and react.
Vocabulary

activation energy: Energy needed for a chemical reaction to get started.


endothermic reaction: Any chemical reaction that consumes energy.
exothermic reaction: Any chemical reaction that releases energy.
296

www.ck12.org

Chapter 4. Biochemistry - Advanced

product: Substance that forms as a result of a chemical reaction.


reactant: Substance involved in a chemical reaction that is present at the beginning of the reaction.
Summary

All chemical reactions require activation energy, which is the energy needed to get a reaction started.
Rates of chemical reactions depend on factors such as the concentration of reactants and the temperature at
which reactions occur. Both factors affect the ability of reactant molecules to react.
Explore More

Use this resource to answer the questions that follow.


Activation Energy at http://www.sophia.org/activation-energy--2/activation-energy5-tutorial?pathway=the
rmochemistry
1.
2.
3.
4.
5.

In this video, what does A + B represent?


In this video, what does P + Q represent?
What is the activation energy?
Why is one activation energy lower than the other?
What is the main difference between an endothermic and exothermic reaction?

Review

1. What is activation energy?


2. Why do all chemical reactions require activation energy?

297

4.6. Enzymes and Biochemical Reactions - Advanced

www.ck12.org

4.6 Enzymes and Biochemical Reactions - Advanced


Explain the importance of enzymes in organisms, and describe how enzymes work.

What is a biological catalyst?


This super fast train can obviously reach great speeds. And theres a lot of technology that helps this train go fast.
Speaking of helping things go fast brings us to enzymes. Life could not exist without enzymes. Essentially, enzymes
are biological catalysts that speed up biochemical reactions.
Enzymes and Biochemical Reactions

Most chemical reactions within organisms would be impossible under the normal conditions within cell. For
example, the body temperature of most organisms is too low for reactions to occur quickly enough to carry out
life processes. Reactants may also be present in such low concentrations that it is unlikely they will meet and
collide. Therefore, the rate of most biochemical reactions must be increased by a catalyst. A catalyst is a chemical
that speeds up chemical reactions. In organisms, catalysts are called enzymes.
Like other catalysts, enzymes are not reactants in the reactions they control. They help the reactants interact but
are not used up in the reactions. Instead, they may be used over and over again. Unlike other catalysts, enzymes
are usually highly specific for a particular chemical reaction. They generally catalyze only one or a few types of
reactions.
Enzymes are extremely efficient in speeding up biochemical reactions. They can catalyze up to several million
reactions per second. As a result, the difference in rates of biochemical reactions with and without enzymes may be
enormous. A typical biochemical reaction might take hours or even days to occur under normal cellular conditions
without an enzyme, but less than a second with the enzyme.
An overview of enzymes can be viewed at http://www.youtube.com/watch?v=E90D4BmaVJM (9:43).

298

www.ck12.org

Chapter 4. Biochemistry - Advanced

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/203

How Enzymes Work

How do enzymes speed up biochemical reactions so dramatically? Like all catalysts, enzymes work by lowering the
activation energy of chemical reactions. This is illustrated in Figure 4.6. The biochemical reaction shown in the
figure requires about three times as much activation energy without the enzyme as it does with the enzyme.
An animation of how enzymes work can be seen at http://www.youtube.com/watch?v=CZD5xsOKres (2:02).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/204

FIGURE 4.6
The reaction represented by this graph
is a combustion reaction involving the reactants glucose (C6 H12 O6 ) and oxygen
(O2 ). The products of the reaction are
carbon dioxide (CO2 ) and water (H2 O).
Energy is also released during the reaction. The enzyme speeds up the reaction
by lowering the activation energy needed
for the reaction to start.

Compare the

activation energy with and without the enzyme.

Enzymes generally lower activation energy by reducing the energy needed for reactants to come together and react.
For example:
Enzymes bring reactants together so they dont have to expend energy moving about until they collide at
random. Enzymes bind both reactant molecules (called substrates), tightly and specifically, at a site on the
enzyme molecule called the active site ( Figure 4.7). This forms an enzyme-substrate complex.
299

4.6. Enzymes and Biochemical Reactions - Advanced

www.ck12.org

By binding reactants at the active site, enzymes also position reactants correctly, so they do not have to
overcome intermolecular forces that would otherwise push them apart. This allows the molecules to interact
with less energy.
Enzymes may also allow reactions to occur by different pathways that have lower activation energy.
FIGURE 4.7
This enzyme molecule binds reactant
moleculescalled substrateat its active
site, forming an enzyme-substrate complex. This brings the reactants together
and positions them correctly so the reaction can occur. After the reaction, the
products are released from the enzymes
active site. This frees up the enzyme so it
can catalyze additional reactions.

The activities of enzymes also depend on the temperature, ionic conditions, and the pH of the surroundings. Some
enzymes work best at acidic pHs, while others work best in neutral environments.
Digestive enzymes secreted in the acidic environment (low pH) of the stomach help break down proteins into
smaller molecules. The main digestive enzyme in the stomach is pepsin, which works best at a pH of about
1.5). These enzymes would not work optimally at other pHs. Trypsin is another enzyme in the digestive
system which break protein chains in the food into smaller parts. Trypsin works in the small intestine, which
is not an acidic environment. Trypsins optimum pH is about 8.
Biochemical reactions are optimal at physiological temperatures. For example, most biochemical reactions
work best at the normal body temperature of 98.6F (37C). Many enzymes lose function at lower and higher
temperatures. At higher temperatures, an enzymes shape deteriorates, and only when the temperature comes
back to normal does the enzyme regain its shape and normal activity.
Importance of Enzymes

Enzymes are involved in most of the chemical reactions that take place in organisms. About 4,000 such reactions are
known to be catalyzed by enzymes, but the number may be even higher. In animals, an important function of enzymes
is to help digest food. Digestive enzymes speed up reactions that break down large molecules of carbohydrates,
proteins, and fats into smaller molecules the body can use. Without digestive enzymes, animals would not be able to
break down food molecules quickly enough to provide the energy and nutrients they need to survive.
Vocabulary

active site: Site on the enzyme where the reaction occurs.


biochemical reaction: Chemical reaction within a cell or organism; usually controlled by an enzyme.
enzyme: Chemical, usually a protein, that speeds up chemical reactions in organisms; a biological catalyst.
pepsin: The main digestive enzyme in the stomach; degrades food proteins into peptides.
300

www.ck12.org

Chapter 4. Biochemistry - Advanced

reactant: Substance involved in a chemical reaction that is present at the beginning of the reaction.
substrates: The reactants in an enzyme catalyzed reaction.
trypsin: Digestive enzyme which break protein chains in food into smaller peptide fragments; a serine
protease, cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine, except
when either is followed by proline.
Summary

Enzymes are needed to speed up chemical reactions in organisms. They work by lowering the activation
energy of reactions.
Enzymes position substrates into active sites.
Various conditions affect enzyme function. Pepsin and trypsin are two digestive enzymes that work in
contrasting environments.
Review

1.
2.
3.
4.
5.

In general, how do enzymes speed up chemical reactions?


How do enzymes bring reactants together? How is it beneficial?
Explain why organisms need enzymes to survive.
What are the conditions necessary for enzymes to perform optimally?
What are pepsin and trypsin?

301

4.7. References

4.7 References
1.
2.
3.
4.
5.
6.
7.

302

Laura Guerin. CK-12 Foundation . CC BY-NC 3.0


Christopher Auyeung. CK-12 Foundation . CC BY-NC 3.0
CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Julie Magro. Ice Pack . CC BY 2.0
CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Hana Zavadska. Enzyme Action . CC BY-NC 3.0
Laura Guerin. CK-12 Foundation . CC BY-NC 3.0

www.ck12.org

www.ck12.org

Chapter 5. Metabolism - Advanced

C HAPTER

Metabolism - Advanced

Chapter Outline
5.1

P HOTOSYNTHESIS - A DVANCED

5.2

AUTOTROPHS VS . H ETEROTROPHS - A DVANCED

5.3

E NERGY C ARRYING M OLECULES - A DVANCED

5.4

T HE P HOTOSYNTHESIS R EACTION - A DVANCED

5.5

T HE C HLOROPLAST - A DVANCED

5.6

T HE L IGHT R EACTIONS - A DVANCED

5.7

T HE C ALVIN C YCLE - A DVANCED

5.8

C HEMOSYNTHESIS - A DVANCED

5.9

C ELLULAR R ESPIRATION - A DVANCED

5.10

C ELLULAR R ESPIRATION OVERVIEW - A DVANCED

5.11

G LYCOLYSIS - A DVANCED

5.12

T HE M ITOCHONDRIA IN C ELLULAR R ESPIRATION - A DVANCED

5.13

T HE K REBS C YCLE - A DVANCED

5.14

T HE E LECTRON T RANSPORT C HAIN - A DVANCED

5.15

A NAEROBIC R ESPIRATION - A DVANCED

5.16

L ACTIC ACID F ERMENTATION - A DVANCED

5.17

A LCOHOLIC F ERMENTATION - A DVANCED

5.18

A EROBIC VS . A NAEROBIC R ESPIRATION - A DVANCED

5.19

R EFERENCES

303

www.ck12.org

Introduction

This caterpillar is busily munching its way through leaf after leaf. In fact, caterpillars do little more than eat, day and
night. Like all living things, they need food to provide their cells with energy. The caterpillar will soon go through
an amazing transformation to become a beautiful butterfly. These changes require a lot of energy.
Like this caterpillar and all other living things, you need energy to power everything you do. Whether its running
a race or blinking an eye, it takes energy. In fact, every cell of your body constantly needs energy to carry out life
processes. You probably know that you get energy from the food you eat, but where does food come from? How
does it come to contain energy, and how do your cells get the energy from food? When you read this chapter, you
will learn the answers to these questions.

304

www.ck12.org

Chapter 5. Metabolism - Advanced

5.1 Photosynthesis - Advanced


Identify the kind of energy which powers life.
Contrast the behavior of energy to that of materials in living systems.

When youre hungry, what do you do?


Well, a plant cannot eat. So it has to make its own food. How does it do this? Photosynthesis. And it all starts with
sunlight.
Photosynthesis

All living things require an ongoing source of energy to do the work of life. You often see energy in action on a
large scale: a whale breaches, apple blossoms swell and burst, a firefly glows, or an inky cap mushrooms overnight.
However, energy works constantly to maintain life on a very small scale as well. Inside each cell of every organism,
energy assembles chains of information and constructs cellular architecture. It moves tiny charged particles and
305

5.1. Photosynthesis - Advanced

www.ck12.org

giant protein molecules. Moreover, it builds and powers cell systems for awareness, response, and reproduction. All
lifes work requires energy.
Physics tells us that organized systems, such as living organisms, tend to disorder without a constant input of energy.
You have direct, everyday experience with this law of nature: after a week of living in your room, you must spend
energy in order to return it to its previous, ordered state. Tides and rain erode your sandcastles, so you must work to
rebuild them. And your body, after a long hike or big game, must have more fuel to keep going. Living things show
amazing complexity and intricate beauty, but if their source of energy fails, they suffer injury, illness, and eventually
death.
Physics also tells us that, although energy can be captured or transformed, it inevitably degrades, becoming heat, a
less useful form of energy. This is why organisms require a constant input of energy; the work they must do uses up
the energy they take in. Energy, unlike materials, cannot be recycled. The story of life is a story of energy flow its
capture, transformation, use for work, and loss as heat.
Energy, the ability to do work, can take many forms: heat, nuclear, electrical, magnetic, light, and chemical energy.
Life runs on chemical energy - the energy stored in covalent bonds between atoms in a molecule. Where do
organisms get their chemical energy? That depends. Most organisms get their energy from the food they make, eat
or absorb. Plants, for example, make their own "food" through the process of photosynthesis. When we eat a plant,
such as lettuce or a tomato, we acquire energy. This energy is in the form of glucose, a simple sugar. Or the energy
may be in the form of a starch, which we eat and then our body breaks down into glucose. This glucose then must be
converted into usable chemical energy. Chemical energy in our cells is ATP. Glucose is converted into ATP during
cellular respiration.

FIGURE 5.1
This diagram depicts photosynthesis.
CO2 and H2 O enter the plant leaf cell,
and in the presence of solar energy, these
reactants are converted into the products
O2 and glucose.

An overview of photosynthesis is available at http://www.youtube.com/watch?v=-rsYk4eCKnA (13:37).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/256

306

www.ck12.org

Chapter 5. Metabolism - Advanced

Photosynthesis and Cellular Respiration

What is the relationship between photosynthesis and cellular respiration? Does photosynthesis have to occur prior to
cellular respiration? No. Though it is true that the products of photosynthesis are the reactants of cellular respiration,
the two can occur simultaneously in the plant cell. The light reactions of photosynthesis also obviously occur during
daylight hours, while the light-independent reactions of photosynthesis and the reactions of cellular respiration can
occur whenever reactants are available.

FIGURE 5.2
This diagram compares and contrasts
photosynthesis (in the chloroplast) and
cellular respiration (in the mitochondria).
It also shows how the two processes are
related.

Vocabulary

ATP ( adenosine triphosphate): Energy-carrying molecule that cells use to power their metabolic processes;
energy-currency of the cell.
cellular respiration: Metabolic process which transfers chemical energy from glucose (a deliverable fuel
molecule) to ATP (a usable energy-rich molecule); most efficient in the presence of oxygen (aerobic).
energy: Property of matter that is defined as the ability to do work
glucose: The carbohydrate product of photosynthesis; serves as the universal fuel for life; C6 H12 O6 .
photosynthesis: The process by which carbon dioxide and water are converted to glucose and oxygen, using
sunlight for energy.
307

5.1. Photosynthesis - Advanced

www.ck12.org

Summary

All organisms require a constant input of energy to do the work of life; life runs on chemical energy.
Energy cannot be recycled; energy must be constantly captured by organisms in an ecosystem, transformed
and passed to other organisms.
Most energy is lost to the environment as heat.
Explore More

Use this resource to answer the questions that follow.


Photosynthesis at http://biology.clc.uc.edu/courses/bio104/photosyn.htm
1.
2.
3.
4.

Define photosynthesis.
In what part of the plant does photosynthesis occur?
What chemical reaction makes one glucose molecule in photosynthesis?
What are the two parts of photosynthesis? Briefly explain what occurs in each part.

Review

1.
2.
3.
4.

308

Compare the behavior of energy to the behavior of matter in living systems.


Describe the forms of energy in living organisms.
What happens to most of an ecosystems energy?
Do photosynthesis and cellular respiration occur dependent of each other? Does photosynthesis have to occur
prior to cellular respiration?

www.ck12.org

Chapter 5. Metabolism - Advanced

5.2 Autotrophs vs. Heterotrophs - Advanced


Analyze the way in which autotrophs obtain energy and evaluate the importance of autotrophs to energy for
all life.
Explain the relationship between autotrophs and heterotrophs.

Name one major difference between a plant and an animal.


There are many differences, but in terms of energy, it all starts with sunlight. Plants absorb the energy from the sun
and turn it into food. You can sit in the sun for hours and hours. You will feel warm, but youre not going to absorb
any energy. You have to eat to obtain your energy. You, of course, can go to the kitchen and cook something to eat.
Other animals can also eat, but a plant cannot.
How Do Organisms Get Energy? Autotrophs vs. Heterotrophs

Living organisms obtain chemical energy in one of two ways.


Autotrophs, shown in the Figure 5.3, store chemical energy in carbohydrate food molecules they produce themselves. Food is chemical energy stored in organic molecules. Food provides both the energy to do work and the
carbon to build the organic structures from cells to organisms. Because most autotrophs transform sunlight to make
or synthesize food, we call the process they use photosynthesis. The food produced via this process is glucose. Only
three groups of organisms - plants, algae, and some bacteria - are capable of this life-giving energy transformation.
Autotrophs make food for their own use, but they make enough to support other life as well. Almost all other
organisms depend absolutely on these three groups for the food they produce. The producers, as autotrophs are also
known, begin food chains which feed all life. Food chains will be discussed in the Ecology concepts.
Heterotrophs cannot make their own food, so they must eat or absorb it. For this reason, heterotrophs are also
known as consumers. Consumers include all animals and fungi and many protists and bacteria. They consume
309

5.2. Autotrophs vs. Heterotrophs - Advanced

www.ck12.org

FIGURE 5.3
Photosynthetic autotrophs, which make
food for more than 99% of the organisms
on earth, include only three groups of organisms: plants such as the redwood tree
(a), algae such as kelp (b), and certain
bacteria like this Anabaena (c).

either autotrophs or other heterotrophs. Heterotrophs show great diversity and may appear far more fascinating than
producers. But heterotrophs are limited by their utter dependence on those autotrophs which originally made the
food. If plants, algae, and autotrophic bacteria vanished from Earth, animals, fungi, and other heterotrophs would
soon disappear as well. All life requires a constant input of energy. Only autotrophs can transform that ultimate,
solar source into the chemical energy in food which powers life, as shown in Figure 5.4.

FIGURE 5.4
Food chains carry energy from producers (autotrophs) to consumers (heterotrophs). 99% of energy for life comes
from the sun via photosynthesis. Note
that only nutrients recycle. Energy must
continue to flow into the system. Though
this food chains "ends" with decomposers, do decomposers, in fact, digest
matter from each level of the food chain?
(See the Energy Transfer: Decomposers
(Advanced) concept).

Photosynthesis provides over 99% of the energy supply for life on Earth. A much smaller group of autotrophs mostly bacteria in dark or low-oxygen environments - produce food using the chemical energy stored in inorganic
molecules such as hydrogen sulfide, ammonia, or methane. While photosynthesis transforms light energy to chemical energy, this alternate method of making food transfers chemical energy from inorganic to organic molecules. It
is therefore called chemosynthesis, and is characteristic of the tubeworms shown in Figure 5.5. Some of the most
recently discovered chemosynthetic bacteria inhabit deep ocean hot water vents or black smokers. There, they use
the energy in gases from the Earths interior to produce food for a variety of unique heterotrophs: giant tube worms,
blind shrimp, giant white crabs, and armored snails. Some scientists think that chemosynthesis may support life
below the surface of Mars, Jupiters moon, Europa, and other planets as well. Ecosystems based on chemosynthesis
may seem rare and exotic, but they too illustrate the absolute dependence of heterotrophs on autotrophs for food.
310

www.ck12.org

Chapter 5. Metabolism - Advanced

FIGURE 5.5
Tubeworms deep in the Gulf of Mexico get
their energy from chemosynthetic bacteria living within their tissues. No digestive
systems needed!

Phototrophs are organisms that capture light energy and convert it to chemical energy inside their cell. Most
phototrophs are the autotrophs that perform photosynthesis, which are also known as photoautotrophs. These organisms have the ability to fix carbon from carbon dioxide into organic compounds, such as glucose. Chemotrophs,
on the other hand, do not get their energy from carbon. These are organisms that break down either organic or
inorganic molecules to supply energy for the cell through chemosynthesis. Chemotrophs can be either autotrophic
(chemoautotrophs) or heterotrophic (chemoheterotrophs). Chemoautotrophs derive their energy from chemical
reactions, and synthesize all necessary organic compounds from carbon dioxide. Chemoheterotrophs are unable to
fix carbon to form their own organic compounds. The various types of metabolisms are discussed in the Prokaryotes:
Nutrition and Metabolism (Advanced) concept.
Vocabulary

autotroph: Organism that produces organic compounds from energy and simple inorganic molecules; also
known as a producer.
chemosynthesis: The process by which carbon dioxide molecules are converted to carbohydrates; uses energy
from the oxidation of inorganic compounds.
chemotroph: An organism that breaks down either organic or inorganic molecules to supply energy for the
cell.
consumer: A heterotrophic organism; must eat or absorb organic food molecules.
food: Organic (carbon-containing) molecules which store energy in the chemical bonds between their atoms.
311

5.2. Autotrophs vs. Heterotrophs - Advanced

www.ck12.org

FIGURE 5.6
This flowchart helps to determine if a
species is an autotroph or a heterotroph,
a phototroph or a chemotroph. For example, Carbon obtained from elsewhere?
asks if the source of carbon is another
organism.

If the answer is yes, the

organism is heterotrophic. If the answer


is no, the organisms is autotrophic.

food chain: A pathway which traces energy flow through an ecosystem.


heterotroph: Organisms which must consume organic molecules; also known as a consumer.
inorganic molecule: Molecule which does not contain carbon (with a few exceptions such as carbon dioxide);
a molecule not necessarily made by living organisms.
organic molecule: A molecule which contains carbon, made by living organisms; examples include carbohydrates, lipids, proteins and nucleic acids.
photosynthesis: The process by which carbon dioxide and water are converted to glucose and oxygen, using
sunlight for energy.
phototroph: An organism that captures light energy from the sun and converts it into chemical energy inside
their cell.
producer: Organism that produces organic compounds from energy and simple inorganic molecules; an
autotroph.
Summary

Food is chemical energy stored in organic molecules.


Food provides both the energy to do lifes work and the carbon to build lifes bodies.
Autotrophs make their own carbohydrate foods, transforming sunlight in photosynthesis or transferring chemical energy from inorganic molecules in chemosynthesis.
Heterotrophs consume organic molecules originally made by autotrophs.
All life depends absolutely upon autotrophs to make food molecules.
312

www.ck12.org

Chapter 5. Metabolism - Advanced

Review

1. Water and carbon dioxide molecules are reactants in the process of photosynthesis. Does this mean they are
food for plants, algae, and blue-green bacteria? Use the definition of food to answer this question.
2. Compare autotrophs to heterotrophs, and describe the relationship between these two groups of organisms.
3. Name and describe the two types of food making found among autotrophs, and give an example of each.
Which is quantitatively more important to life on earth?
4. Define chemosynthesis.
5. Trace the flow of energy through a typical food chain (describing "what eats what"), including the original
source of that energy and its ultimate form after use. Underline each form of energy or energy-storing
molecule, and boldface each process which transfers or transforms energy.

313

5.3. Energy Carrying Molecules - Advanced

www.ck12.org

5.3 Energy Carrying Molecules - Advanced


Discuss the importance of glucose to all life on earth.
Compare the energy-carrying role of ATP to that of glucose.
Explain the roles of chlorophyll and NADPH as sources of energy for life.

When do you need lots of energy?


To run a marathon, probably. Where does this extra energy come from? Remember that energy from the sun
is transformed into the carbohydrate glucose. Carbohydrate loading is a strategy used by endurance athletes to
maximize the storage of energy, in the form of glycogen, in the muscles. Glycogen forms an energy reserve that
can be quickly mobilized to meet a sudden need for glucose, which is then turned into ATP through the process of
cellular respiration.

Food and Other Energy-Carrying Molecules

You know that the chicken you had for lunch contained protein molecules. But do you know that the atoms in those
proteins could easily have formed the color in a dragonflys eye, the heart of a water flea, and the whiplike tail of
a Euglena before they hit your plate as sleek fish muscle? Food consists of organic (carbon-containing) molecules
which store energy in the chemical bonds between their atoms. Organisms use the atoms of food molecules to build
larger organic molecules including proteins, DNA, and fats, and use the energy in food to power life processes.
By breaking the bonds in food molecules, cells release energy to build new compounds. Although some energy
dissipates as heat at each energy transfer, much of it is stored in the newly made molecules. Chemical bonds in
organic molecules are a reservoir of the energy used to make them. Fueled by the energy from food molecules, cells
can combine and recombine the elements of life to form thousands of different molecules. Both the energy (despite
some loss) and the materials (despite being reorganized) pass from producer to consumer perhaps from algal tails,
to water flea hearts, to dragonfly eye colors, to fish muscle, to you!
314

www.ck12.org

Chapter 5. Metabolism - Advanced

The process of photosynthesis, which usually begins the flow of energy through life, uses many different kinds of
energy-carrying molecules to transform sunlight energy into chemical energy and build food.

Chlorophyll and NADPH

Some carrier molecules hold energy briefly, quickly shifting it like a hot potato to other molecules. This strategy
allows energy to be released in small, controlled amounts. An example is chlorophyll, the green pigment present
in most plants which absorbs solar energy and helps convert that energy into chemical energy. When a chlorophyll
molecule absorbs light energy, electrons are excited and jump to a higher energy level. The excited electrons then
bounce to a series of carrier molecules, losing a small amount of energy at each step. Most of the lost energy
powers some small cellular task, such as moving ions across a membrane or building up another molecule. Another
short-term energy carrier important to photosynthesis, NADPH, holds chemical energy a bit longer but soon that
energy is used to help to build sugar. NADPH is the reduced form of NADP+ , Nicotinamide adenine dinucleotide
phosphate. NADP+ accepts an electron at the end of the light reactions electron transport chain of photosynthesis.
Two related short term energy carriers, NADH (nicotinamide adenine dinucleotide) and FADH2 (flavin adenine
dinucleotide) are used during cellular respiration.

Glucose and ATP

Two of the most important energy-carrying molecules are glucose and ATP ( adenosine triphosphate). These are
nearly universal fuels throughout the living world and both are also key players in photosynthesis.
A molecule of glucose, which has the chemical formula C6 H12 O6 , carries a packet of chemical energy just the right
size for transport and uptake by cells. In your body, glucose is the deliverable form of energy, carried in your
blood through capillaries to each of your roughly 100 trillion cells. Glucose is also the carbohydrate produced by
photosynthesis, and as such is the near-universal food for life.
ATP molecules store smaller quantities of energy, but each releases just the right amount to actually do work within
a cell. Muscle cell proteins, for example, pull each other with the energy released when bonds in ATP break open
(discussed below). The process of photosynthesis also makes and uses ATP - for energy to build glucose. ATP, then,
is the useable form of energy for your cells.
Why do we need both glucose and ATP? Why dont plants just make ATP and be done with it? If energy were money,
ATP would be a quarter. Enough money to operate a parking meter or washing machine. Glucose would be a dollar
bill (or $10) much easier to carry around in your wallet, but too large to do the actual work of paying for parking or
washing. Just as we find several denominations of money useful, organisms need several denominations of energy
a smaller quantity for work within cells, and a larger quantity for stable storage, transport, and delivery to cells.
Lets take a closer look at a molecule of ATP. Although it carries less energy than glucose, its structure is more
complex. A in ATP refers to the majority of the molecule adenosine a combination of a nitrogenous base and a
five-carbon sugar. T and P indicate the three phosphates, linked by bonds which hold the energy actually used
by cells. Usually, only the outermost bond breaks to release or spend energy for cellular work.
An ATP molecule, shown in the Figure 5.8, is like a rechargeable battery: its energy can be used by the cell when
it breaks apart into ADP (adenosine diphosphate) and phosphate, and then the worn-out battery ADP can be
recharged using new energy to attach a new phosphate and rebuild ATP. The materials are recyclable, but recall that
energy is not! ADP can be further reduced to AMP (adenosine monophosphate and phosphate, releasing additional
energy. As with ADT "recharged" to ATP, AMP can be recharged to ADP.
How much energy does it cost to do your bodys work? A single cell uses about 10 million ATP molecules per
second, and recycles all of its ATP molecules about every 20-30 seconds.
Keep these energy-carrying molecules in mind as we look more carefully at the process which originally captures
the energy to build them: photosynthesis. Recall that it provides nearly all of the food (energy and materials) for
315

5.3. Energy Carrying Molecules - Advanced

www.ck12.org

FIGURE 5.7
Glucose, C6 H12 O6 , is the energy-rich
product of photosynthesis, a universal
food for life.

It is also a six-carbon

monosaccharide, or simple sugar. Glucose is the primary form in which your


bloodstream delivers energy to every cell
in your body, where it is converted into
ATP. The six carbons are numbered.

FIGURE 5.8
An arrow shows the bond between two
phosphate groups in an ATP molecule.
When this bond breaks, its chemical energy can do cellular work. The resulting
ADP molecule is recycled when new energy attaches another phosphate, rebuilding ATP.

life. Actually, as you will see, we are indebted to photosynthesis for even more than just the energy and building
blocks for life.
A explanation of ATP as biological energy is found in ATP: Adenosine Triphosphate at http://www.youtube.com/w
316

www.ck12.org

Chapter 5. Metabolism - Advanced

atch?v=YQfWiDlFEcA (13:35).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/263

Vocabulary

ATP ( adenosine triphosphate): Energy-carrying molecule that cells use to power their metabolic processes;
energy-currency of the cell.
cellular respiration: Metabolic process which transfers chemical energy from glucose (a deliverable fuel
molecule) to ATP (a usable energy-rich molecule); respiration is most efficient in the presence of oxygen
(aerobic).
chlorophyll: The primary pigment of photosynthesis; found in the thylakoid membranes of chloroplasts.
FADH2 : Flavin adenine dinucleotide; an energy carrier molecule produced during the Krebs cycle of aerobic
cellular respiration.
glucose: The carbohydrate product of photosynthesis; it serves as the universal fuel for life: C6 H12 O6 .
NADH: Short-term energy carrier; temporarily stores energy during cellular respiration; nicotinamide adenine
dinucleotide.
NADP+ (NADPH): Nicotinamide adenine dinucleotide phosphate; an energy carrier molecule produced in
the light reactions of photosynthesis; NADPH is the reduced form of NADP+ .
photosynthesis: The process by which carbon dioxide and water are converted to glucose and oxygen, using
sunlight for energy.
Summary

All organisms use similar energy-carrying molecules for food and to carry out life processes.
Glucose (C6 H12 O6 ,) is a nearly universal fuel delivered to cells, and the primary product of photosynthesis.
ATP molecules store smaller amounts of energy and are used within cells to do work.
Chlorophyll and NADPH molecules hold energy temporarily during the process of photosynthesis.

Review

1. The fact that all organisms use similar energy-carrying molecules shows one aspect of the grand "Unity of
Life." Name two universal energy-carrying molecules, and explain why most organisms need both carriers
rather than just one.
2. A single cell may use millions of ATP molecules each second. Explain how cells use the energy and recycle
the materials in ATP.
3. How many ATP molecules does a single cell use per second?
4. Describe NADPH, NADH, and FADH2 .
317

5.4. The Photosynthesis Reaction - Advanced

www.ck12.org

5.4 The Photosynthesis Reaction - Advanced


Summarize the process of photosynthesis and write out the overall chemical equation for photosynthesis.
Identify reactants, necessary conditions, and products in the chemical equation for photosynthesis.
Understand that hundreds of years of scientific exploration have contributed to our understanding of photosynthesis.

What is the most common biochemical reaction ever?


Well, it may or may not be this one. Every split second that sunlight strikes a plants leaf, the process of photosynthesis begins. Thats on every leaf, on every plant, including all the blades of grass. All over the world.
Photosynthesis: The Most Important Chemical Reaction for Life on Earth

What do pizza, campfires, dolphins, automobiles, and glaciers have in common? In the following section, youll
learn that all five rely on photosynthesis, some in more ways than one. Photosynthesis is often considered the most
318

www.ck12.org

Chapter 5. Metabolism - Advanced

important chemical reaction for life on earth. Lets delve into how this process works and why we are so indebted to
it.
The Photosynthesis Song can be heard at http://www.youtube.com/watch?v=C1_uez5WX1o (1:52).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/257

Photosynthesis involves a complex series of chemical reactions, each of which convert one substance to another.
These reactions taken as a whole can be summarized in a single symbolic representation as shown in the chemical
equation below.

We can substitute words for the chemical symbols. Then the equation appears as below.

Like all chemical equations, this equation for photosynthesis shows reactants connected by plus signs on the left
and products, also connected by plus signs, on the right. An arrow indicating the process or chemical change leads
from the reactants to the products, and conditions necessary for the chemical reaction are written above the arrow.
Note that the same kinds of atoms, and number of atoms, are found on both sides of the equation, but the kinds of
compounds they form change.
You use chemical reactions every time you cook or bake. You add together ingredients (the reactants), place them in
specific conditions (often heat), and enjoy the results (the products). A recipe for chocolate chip cookies written in
chemical equation form is shown below.

Compare this familiar recipe to photosynthesis below.

319

5.4. The Photosynthesis Reaction - Advanced

www.ck12.org

The equation shows that the ingredients for photosynthesis are carbon dioxide, water, and light energy. Plants,
algae, and photosynthetic bacteria take in light from the sun, molecules of carbon dioxide from the air, and water
molecules from their environment and combine these reactants to produce food (glucose).
Of course, light, carbon dioxide, and water mix in the air even without plants. But they do not chemically change to
make food without very specific necessary conditions which are found only in the cells of photosynthetic organisms.
Necessary conditions include:
1. enzymes - proteins which speed up chemical reactions
2. chlorophyll - a pigment within plant cells which absorbs light
3. chloroplasts - organelles whose membranes embed chlorophyll, accessory pigments, and enzymes in patterns
which maximize photosynthesis
Within plant cells or algal cells, chloroplasts organize the enzymes, chlorophyll, and accessory pigment molecules
necessary for photosynthesis.

FIGURE 5.9
Within plant cells or algal cells, chloroplasts organize the enzymes, chlorophyll,
and accessory pigment molecules necessary for photosynthesis.

When the reactants meet inside chloroplasts, or the very similar cells of blue-green bacteria, chemical reactions
combine them to form two products: energy-rich glucose molecules and molecules of oxygen gas. Photosynthetic
organisms store the glucose (usually as starch) and release the oxygen gas into the atmosphere as waste.
Lets review the chemical equation for photosynthesis once more, this time at the level of atoms as in the equation
below.

Look closely at its primary purpose: storing energy in the chemical bonds of food molecules. The source of energy
for food is sunlight energy. The source of carbon atoms for the food molecules is carbon dioxide from the air, and
the source of hydrogen atoms is water. Inside the cells of plants, algae, and photosynthetic bacteria, chlorophyll, and
enzymes use the light energy to rearrange the atoms of the reactants to form the products, molecules of glucose and
oxygen gas. Light energy is thus transformed into chemical energy, stored in the bonds which bind six atoms each
of carbon and oxygen to twelve atoms of hydrogen forming a molecule of glucose. This energy rich carbohydrate
320

www.ck12.org

Chapter 5. Metabolism - Advanced

molecule becomes food for the plants, algae, and bacteria themselves as well as for the heterotrophs which feed on
them.
One last detail: why do 6s precede the CO2 , H2 O, and O2 ? Look carefully, and you will see that this balances
the equation: the numbers of each kind of atom on each side of the arrow are equal. Six molecules each of CO2 and
H2 O make 1 molecule of glucose and 6 molecules of oxygen gas.

FIGURE 5.10
The two stages of photosynthesis are the
light reactions and the Calvin cycle. Do
you see how the two stages are related?

Historical Perspective

Life requires photosynthesis for fuel and for the oxygen to burn that fuel. Since the Industrial Revolution (late 18th
and early 19th centuries), we humans have relied on products of ancient photosynthesis for enormous quantities of
fossil fuel energy. And, knowingly or not, we have also benefited from photosynthesis to remove the carbon dioxide
produced when we burn those fuels. So it may not surprise you that biologists have studied this critical process in
great detail.
Although photosynthesis may seem straightforward in this form, such simplicity is deceiving for two reasons.
First, the photosynthesis equation summarizes dozens of individual chemical reactions involving many intermediate
compounds. And second, just discovering major players like CO2 and O2 was challenging, because our ordinary
senses cannot detect these molecules in thin air!
How do we know that the chemical reaction in photosynthesis really happens? Two famous historical experiments
help us begin to understand this process. In the 17th century, people who thought about it at all assumed that plants
get their food from the soil. Many people, encouraged by sellers of plant food, still do. In 1638, Jan Baptist Van
Helmont planted a 5 pound willow tree, like the one shown in the Figure 5.11, in a 200 pound tub of soil. After 5
years of watering the plant, he weighed both again. The willow had gained over 160 pounds, but the soil had lost
321

5.4. The Photosynthesis Reaction - Advanced

www.ck12.org

only 2 ounces. Van Helmont concluded that plants do not get their materials from soil, and inferred that they grow
using materials from water (which he did not measure). As you know now, he was half right. Although soil provides
important nutrients to plants, it supplies neither the energy nor the vast majority of the materials to build the plant.
We must excuse him, because no one in the 17th century knew that carbon atoms form the basis of life, or that they
float around in air in the form of carbon dioxide.

FIGURE 5.11
In the 17th century, Jan Van Helmont, a Flemish chemist, physiologist,
and physician, weighed and potted a willow tree, showing that plants do
not get food from the soil.

In the late 1770s, minister and natural philosopher Joseph Priestley burned a candle in a jar of air and observed that
the candle burned out long before it ran out of wax. A similar experiment with a mouse resulted in the mouses
death. Priestley suggested that animals, like candles, injure the air. Adding a mint plant, as shown in Figure 5.12,
however, restored the air which had been injured by the mouse or the candle. Only later, after many chemistry
experiments, did Priestley publish his discovery of dephlogisticated air. But in his studies of mice, plants, and
candles, he had shown that plants produce, and animals consume, oxygen gas.

FIGURE 5.12
Joseph Priestlys bell jar experiment.

During the 20th century, scientists learned that photosynthesis involves much more than just the three reactants, the
three necessary conditions, and the two products shown in the equation. Using powerful microscopes, scientists
narrowed the process to one type of organelle within the plant the chloroplast.
322

www.ck12.org

Chapter 5. Metabolism - Advanced

For a detailed animation of the complete photosynthesis process, see http://vcell.ndsu.edu/animations/photosynthe


sis/first.htm .
Vocabulary

chlorophyll: The primary pigment of photosynthesis; found in the thylakoid membranes of chloroplasts.
chloroplast: The organelle of photosynthesis; site of photosynthesis.
enzyme: Chemical, usually a protein, that speeds up chemical reactions in organisms; a biological catalyst.
Summary

The photosynthesis chemical equation states that the reactants (carbon dioxide, water and sunlight), yield two
products, glucose and oxygen gas.
The single chemical equation represents the overall process of photosynthesis. It also summarizes many
individual chemical reactions that were understood only after hundreds of years of scientific exploration.
Chloroplasts are the organelles within plant and algal cells that organize enzymes and pigments so that the
chemical reactions proceed efficiently.
Chlorophyll is a pigment that absorbs sunlight energy.
Explore More

Use this resource to answer the questions that follow.


What is Photosynthesis at http://www.youtube.com/watch?v=eJQxHoqIPIM

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/139371

1.
2.
3.
4.

What are the "raw materials" of photosynthesis? Where do these materials come from?
What are the products of photosynthesis? How are these products made?
Where does photosynthesis occur?
What happens to the glucose molecules?

Review

1. Using symbols, write the overall chemical equation for photosynthesis, labeling the reactants, necessary
conditions, and products.
2. Summarize Jan Van Helmonts willow tree experiment. State his conclusion and the inference he made after
his experiment, and explain how his data supports each. Finally, relate his findings to what we know today
about the overall process of photosynthesis.
3. Using the overall equation for photosynthesis, explain which components relate to J.B. Priestleys observation
that Plants restore the air that animals injure.

323

5.5. The Chloroplast - Advanced

www.ck12.org

5.5 The Chloroplast - Advanced


Describe the structure and function of chloroplasts, thylakoids, and pigments.
Explain how electron carrier molecules form electron transport chains.

What do pancakes and chloroplasts have in common?


The chloroplast is the site of photosynthesis. Part of the photosynthesis reactions occur in an internal membrane
within the organelle. Many of the pigments and other molecules necessary for photosynthesis are embedded within
these internal membranes, The chloroplast contains many of these internal membranes, allowing numerous photosynthetic reactions to occur simultaneously, and making photosynthesis very efficient. These internal membranes
stack on top of each other, just like a stack of pancakes.
Chloroplasts: Theaters for Photosynthesis

If you examine a single leaf of the aquatic plant Elodea, shown in Figure 5.13, under a microscope, you will see
within each cell dozens of small green ovals. These are chloroplasts, the organelles which conduct photosynthesis
in plants and algae. Chloroplasts closely resemble cyanobacteria, containing their own circular DNA and ribosomes.
In fact, the Theory of Endosymbiosis holds that chloroplasts were once independently living bacteria (prokaryotes).
So when we say that photosynthesis occurs within chloroplasts, we speak not only of the organelles within plants
and algae, but also of some bacteria in other words, virtually all photosynthetic autotrophs.
Both chloroplasts and photosynthetic bacteria contain grana, neat stacks of flattened sac-shaped membrane compartments called thylakoids. Thylakoids can be considered a sub-organelle within the chloroplast. Between the
chloroplast membrane and the grana is an aqueous fluid known as stroma. Thylakoids, especially the thylakoid
membrane, organize patterns of proteins and other molecules which conduct photosynthesis, as shown in Figure
5.14. In addition to enzymes, two basic types of molecules - pigments and electron carriers are significant in this
process. You can take a video tour of a chloroplast at Encyclopedia Britannica: Chloroplast: http://www.britannic
a.com/EBchecked/media/16440/Chloroplasts-circulate-within-plant-cells .
324

www.ck12.org

Chapter 5. Metabolism - Advanced

FIGURE 5.13
Elodea (above), like all plants and algae,
consists of cells which contain organelles
called chloroplasts (small green ovals). If
you look carefully at living cells through a
microscope, you may see the chloroplasts
moving slowly around the cell edges. The
plant itself may not move, but this cyclosis
hints at all the action within plant cells.
Remember that chloroplasts are one of
the main differences between plant and
animal cells; animal cells do not contain
chloroplasts.

Pigments and Electron Carriers

Pigment molecules, often arranged together with proteins in large, complex photosystems within the thylakoid
membrane, absorb specific wavelengths of light energy and reflect others; therefore, they appear colored. The most
common photosynthetic pigment is chlorophyll, which absorbs blue-violet and red wavelengths of light, and reflects
green. Various types of chlorophyll exist, including chlorophyll a and chlorophyll b. Accessory pigments absorb
other colors of light and then transfer the energy to chlorophyll. These include xanthophylls (yellow) and carotenoids
(orange).
Electron carrier molecules are usually arranged in electron transport chains (ETCs), also within the thylakoid
membrane. These accept and pass along energy-carrying electrons in small steps ( Figure 5.15). In this way, they
produce ATP and NADPH, which temporarily store chemical energy. Electrons in transport chains behave much
like a ball bouncing down a set of stairs a little energy is lost with each bounce. However, the energy lost at each
step in an electron transport chain accomplishes a little bit of work, including the active transport of H+ ions from
the stroma into the thylakoid, which eventually results in the synthesis of ATP. Chlorophyll a is the primary electron
donor in the electron transport chain.
Now that youve met some of the key players and explored the chloroplast, lets put them together to see how the
photosynthetic process unfolds. We will divide the process into two basic sets of reactions, known as the light
reactions, which of course uses sunlight, and the Calvin cycle, which uses carbon dioxide. As you study the details,
refer frequently to the chemical equation of photosynthesis. In the first stage, youll discover how chloroplasts
transform light energy, and why we owe our ability to breathe to plants!
325

5.5. The Chloroplast - Advanced

www.ck12.org

FIGURE 5.14
The structure of a chloroplast shows how membrane and molecular architecture helps life processes.

chloroplast consists of thylakoid membranes surrounded by stroma. The thylakoids stack on top of each other, like
a stack of pancakes. The thylakoid stacks arrange chlorophyll, accessory pigment molecules, and photosynthetic
proteins to capture sunlight and allow a concentration of ions within the sacs. You can see the green color of the
chlorophyll. You cannot see the electron carriers, sequenced within the sac membranes, but their arrangement
helps harvest small amounts of energy from excited electrons. The thylakoid membranes contain molecules of
the green pigment chlorophyll.

FIGURE 5.15
This figure shows the light reactions of
photosynthesis.

This stage of photo-

synthesis begins with photosystem II (so


named because it was discovered after
photosystem I). Find the two electrons (2
e ) in photosystem II, and then follow
them through the electron transport chain
(also called the electron transfer chain) to
the formation of NADPH. Where do the
hydrogen ions (H+ ) come from that help
make ATP?

Vocabulary

chlorophyll: The primary pigment of photosynthesis; found in the thylakoid membranes of chloroplasts.
chloroplast: The organelle of photosynthesis; site of photosynthesis.
326

www.ck12.org

Chapter 5. Metabolism - Advanced

electron carrier: Molecules that accept and temporarily hold high-energy electrons.
electron transport chain: Series of electron-transport molecules that pass high-energy electrons from molecule
to molecule and capture their energy.
grana (singular: granum): Structure within the chloroplast; consists of stacks of sac-like thylakoid membranes.
photosystems: Group of molecules, including chlorophyll, in the thylakoid membrane of a chloroplast;
captures light energy.
pigment molecules: Molecules that absorb specific wavelengths (colors) of light.
stroma: Space outside the thylakoid membranes of a chloroplast; site of the Calvin cycle of photosynthesis.
Theory of Endosymbiosis: Theory that proposes that eukaryotic organelles, such as mitochondria, evolved
from ancient, free-living prokaryotes that invaded other prokaryotic cells.
thylakoid: Sub-organelle within the chloroplast; site of the light reactions of photosynthesis.
Summary

Chloroplasts are the organelles where the process of photosynthesis takes place in plants and algae.
Chloroplasts have stacks of internal membranes called thylakoids; these membranes sequence pigments and
electron carrier molecules for efficient photosynthesis.
Thylakoids create compartments, which allow concentration gradients to store energy.
Pigment molecules absorb specific wavelengths (colors) of light; chlorophyll is the primary pigment in photosynthesis.
Electron carrier molecules form electron transport chains, which transfer energy in small steps so that the
energy can be stored or used for work.
Explore More

Use this resource to answer the questions that follow.


http://www.hippocampus.org/Biology Non-Majors Biology Search: Photosynthetic Structures
1.
2.
3.
4.
5.

What are the functions of a plants leaves?


Where do the photosynthetic reactions occur?
What is a stomata?
Describe the internal structure of a chloroplast.
What reactions occur in the thylakoid membranes?

Review

1. Explain the structure of the chloroplast, and how the structure of a chloroplast makes the chemical reactions
of photosynthesis more efficient.
2. What structure specifically absorbs specific wavelengths and therefore appears colored?
327

5.5. The Chloroplast - Advanced

www.ck12.org

3. What is a pigment molecule? What is the major pigment of photosynthesis? What are the pigments of
xanthophylls and carotenids?
4. Describe electron carriers and the electron transport chain.
5. Name the two stages (sets of reactions) which make up the process of photosynthesis.

328

www.ck12.org

Chapter 5. Metabolism - Advanced

5.6 The Light Reactions - Advanced


Trace the flow of energy and materials through the Light Reactions, including chemiosmosis.

Oxygen has been described as a "waste product." How is this possible?


You could argue that oxygen is one of the most important, if not THE most important molecule necessary for life.
However, oxygen is essentially just a waste product of the light reactions of photosynthesis. It is a "leftover" from
a necessary part of the process. All the oxygen that is necessary to maintain most forms of life just happens to be
released from the plant during this process.

Photosynthesis Stage I: The Light Reactions: in which Chloroplasts Capture Sunlight Chemical
Energy. . .

Every second, the sun fuses over 600 million tons of hydrogen into 596 tons of helium, converting over 4 tons
of helium (4.3 billion kg) into light and heat energy. Countless tiny packets of that light energy travel 93 million
miles (150 million km) through space, and about 1% of the light which reaches the Earths surface participates in
photosynthesis. Sunlight is the source of energy for photosynthesis, and the first set of reactions which begin the
329

5.6. The Light Reactions - Advanced

www.ck12.org

FIGURE 5.16
The pigment molecule, chlorophyll, shown here, appears green because
its electrons absorb blue-violet and red light and reflect green, orange, and
yellow light. This diagram shows that there are actually several different
kinds of chlorophyll (a,b, and d shown here) in plants.

FIGURE 5.17
Each kind of pigment absorbs specific
wavelengths (colors) of light (dashed
lines). Sunlight contains many different
wavelengths, which you see when they
separate into a rainbow. Not all colors
of light are used in photosynthesis (solid
line).

Most plants, algae, and photo-

synthetic bacteria appear green because


they reflect green wavelengths. Their pigments have absorbed the violet-blue and
red wavelengths. The amount of photosynthesis depends on the wavelength of
light available. Beta-carotene is another
type of pigment that absorbs sunlight.

330

www.ck12.org

Chapter 5. Metabolism - Advanced

process requires light thus the name, "Light Reactions", or Light-dependent Reactions. This light is absorbed by
chlorophyll in the thylakoid membrane of chloroplasts in the plant cell.
The pigment molecule chlorophyll of leaf cells appears green because its electrons absorb blue-violet and red light
and reflect green, orange, and yellow light. There are actually several different kinds of chlorophyll (a,b, and d)
in plants. Each kind of pigment absorbs specific wavelengths (colors) of light. Sunlight contains many different
wavelengths, which you see when they separate into a rainbow. Not all colors of light are used in photosynthesis.
Most plants, algae, and photosynthetic bacteria appear green because they reflect green wavelengths. Their pigments
have absorbed the violet-blue and red wavelengths. The amount of photosynthesis depends on the wavelength of
light available. Cartenoids are also pigments that absorb sunlight.
When light strikes chlorophyll (or an accessory pigment) within the chloroplast, the energy is absorbed and transferred to electrons in the chlorophyll. Essentially, sunlight energizes or "excites," electrons within the chlorophyll
molecule. Photosystem II is also known as P680, with P standing for pigment and 680 referring to the absorption
maximum in the red part of the visible spectrum (680 nm). The primary electron donor in P680 receives excitation
energy by absorbing a photon of light. These excited electrons jump up to higher energy levels and enter the
electron transport chain; they have absorbed or captured, and now carry, that energy. These high energy electrons
are holding the energy that will be be transferred to glucose. In essence, these high energy electrons are holding the
energy needed to support life.

...And Change the Rules of Chemistry for Life!

The excited electrons leave chlorophyll to participate in further reactions, leaving the chlorophyll at a loss;
eventually they must be replaced. That replacement process also requires light, working with an enzyme complex to
split water molecules. In this process of photolysis (splitting by light), H2 O molecules are broken into hydrogen
ions, electrons, and oxygen atoms. The electrons replace those originally lost from chlorophyll. Hydrogen ions and
the high-energy electrons from chlorophyll will carry on the energy transformation drama after the Light Reactions
are over.
The oxygen atoms, however, form oxygen gas, which is a waste product of photosynthesis ( Figure 5.18). The
oxygen given off supplies most of the oxygen in our atmosphere. Before photosynthesis evolved, Earths atmosphere
lacked oxygen altogether, and this highly reactive gas was toxic to the many organisms living at the time. Something
had to change! Most contemporary organisms rely on oxygen for efficient respiration. So plants dont just restore
the air, as Joseph Priestley suggested. They also had a major role in creating it!

FIGURE 5.18
Photosynthesis has made the Earths atmosphere today very different from what
it was 2-3 billion years ago, by giving
off oxygen gas as waste. The table to
the right shows the composition of todays
atmosphere. On the left is an Apollo 17
photograph of Earth.

To summarize, chloroplasts capture sunlight energy in two ways. Light excites electrons in pigment molecules,
and light provides the energy to split water molecules, providing more electrons as well as hydrogen ions.
331

5.6. The Light Reactions - Advanced

www.ck12.org

Now lets follow those excited electrons. . .

How Do Chloroplasts Convert Light Energy to Chemical Energy?

Excited electrons which have absorbed light energy are unstable. However, the highly organized electron carrier
molecules embedded in chloroplast membranes order the flow of these electrons, directing them through electron
transport chains (ETCs). At each transfer, small amounts of energy released by the electrons are captured and put to
work or stored. Some is also lost as heat with each transfer, but overall the light reactions are extremely efficient at
capturing light energy and transforming it to chemical energy.
Two sequential transport chains harvest the energy of excited electrons, as shown in Figure 5.19.
1. First, starting with photosystem II, electrons pass down an ETC which captures their energy and uses it to
pump hydrogen ions by active transport into the thylakoids. These concentrated ions store potential energy
by forming a chemiosmotic gradient or electrochemical gradient a higher concentration of both positive
charge and hydrogen inside the thylakoid than outside. The gradient formed by the H+ ions is known
as a chemiosmotic gradient. Picture this energy buildup of H+ as a dam holding back a waterfall. Like
water flowing through a hole in the dam, hydrogen ions slide down their concentration gradient through a
membrane protein which acts as both ion channel and enzyme. As they flow, the ion channel/enzyme ATP
synthase uses their energy to chemically bond a phosphate group to ADP, making ATP.
2. Light re-energizes the electrons in photosystem I, and they travel down a second electron transport chain
(ETC), eventually bonding hydrogen ions to NADP+ to form a more stable energy storage molecule, NADPH.
NADPH is sometimes called hot hydrogen, and its energy and hydrogen atoms will be used to help build
sugar in the second stage of photosynthesis. Whereas photosystem II has an absorption maximum at 680nm,
photosystem I has an absorption maximum at 700nm, and is known as P700.

FIGURE 5.19
Membrane

architecture:

The

large

colored carrier molecules form electron


transport

chains

that

capture

small

amounts of energy from excited electrons


in order to store it in ATP and NADPH.
Follow the energy pathways:

light

electrons NADPH (blue line) and light

electrons concentrated H+ ATP


(red line). Note the intricate organization
of the chloroplast.

NADPH and ATP molecules now store the energy from excited electrons energy which was originally sunlight in
chemical bonds. Thus chloroplasts, with their orderly arrangement of pigments, enzymes, and electron transport
chains, transform light energy into chemical energy. The first stage of photosynthesis light-dependent reactions
or simply light reactions is complete.
For a detailed discussion of photosynthesis, see http://www.youtube.com/watch?v=GR2GA7chA_c (20:16) and http
://www.youtube.com/watch?v=yfR36PMWegg (18:51).

332

www.ck12.org

Chapter 5. Metabolism - Advanced

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/258

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/504

Vocabulary

ATP synthase: Ion channel and enzyme complex; chemically bonds a phosphate group to ADP, producing
ATP as H+ ions flow through the ion channel.
chemiosmotic gradient: H+ difference across a membrane; established by the active transport of hydrogen
ions by an electron transport chain.
electrochemical gradient: Difference across a membrane due to both a chemical force and an electrical force;
drives the movement of ions across the membrane.
electron carrier: Molecules that accept and temporarily hold high-energy electrons.
electron transport chain: Series of electron-transport molecules that pass high-energy electrons from molecule
to molecule and capture their energy.
light-dependent reactions: First stage of photosynthesis in which light energy from the sun is captured and
transformed into chemical energy; also known as the light reactions.
photolysis: The splitting of a water molecule to replace electrons used during the light reactions; splitting by
light.

Summary

Light Reactions transform energy from sunlight into chemical energy, and produce and release oxygen gas.
Light also provides energy to split water molecules into electrons, hydrogen ions, and oxygen gas.
The oxygen gas is released as waste, but it is the source of the oxygen in Earths atmosphere.
The captured energy is stored in the bonds of molecules, NADPH and ATP.
Hydrogen ions are pumped into the thylakoids, forming an electrochemical gradient whose energy builds ATP
molecules.
333

5.6. The Light Reactions - Advanced

www.ck12.org

Review

1. Summarize the events of the light reactions of photosynthesis.


2. What is photolysis and describe the importance of photolysis.
3. Explain the role of the first electron transport chain in the formation of ATP during the light reactions of
photosynthesis.
4. Explain chemiosmosis.
5. What are the final products of the light reaction?

334

www.ck12.org

Chapter 5. Metabolism - Advanced

5.7 The Calvin Cycle - Advanced


Trace the flow of energy and materials through the Calvin cycle.

Other than being green, what do all these fruits and vegetables have in common?
They are full of energy. Energy in the form of glucose. Fruit and vegetable plants, like all plants, are autotrophs and
producers, producing energy from sunlight. The energy from sunlight is briefly held in NADPH and ATP, which is
needed to drive the formation of sugars such as glucose. And this all happens in the Calvin Cycle.
Photosynthesis Stage II: The Calvin Cycle - Making Food From Thin Air

During the light-dependent stage of photosynthesis, two of the three reactants (water and light) were used to produce
oxygen gas, one of the products (and essentially a waste product of this process). All three necessary conditions are
required the chloroplast with chlorophyll pigments, and enzyme catalysts. The first stage transforms light energy
into chemical energy, stored to this point in molecules of ATP and NADPH. Look again at the overall equation
below. What is left?

Waiting in the atmosphere is one more reactant, carbon dioxide, and yet to come is the product which is food for
all life glucose. These key players perform in the second stage of the photosynthesis, in which food is made from
thin air. The second stage of photosynthesis can proceed without light, so its steps are sometimes called lightindependent or dark reactions. Many biologists honor the scientist, Melvin Calvin, who won a 1961 Nobel Prize
for working out this complex set of chemical reactions, naming it the Calvin Cycle. The Calvin Cycle has two parts.
335

5.7. The Calvin Cycle - Advanced

www.ck12.org

First carbon dioxide is "fixed." Then ATP and NADPH from the Light Reactions provide energy to combine the
fixed carbons to make sugar.
The Calvin Cycle is discussed at http://www.youtube.com/watch?v=slm6D2VEXYs (13:28).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/259

Carbon Dioxide is Fixed

Why does carbon dioxide need to be fixed? Was it ever broken? Life on Earth is carbon-based. Organisms need not
only energy but also carbon atoms for building bodies. For nearly all life, the ultimate source of carbon is carbon
dioxide (CO2 ), an inorganic molecule pulled into the producer from the atmosphere. CO2 , as you saw in Figure
5.20, makes up .038% of the Earths atmosphere.
Animals and most other heterotrophs cannot take in CO2 directly. They must eat other organisms or absorb organic
molecules to get carbon. Only autotrophs can build low-energy inorganic CO2 into high-energy organic molecules
like glucose. This process is carbon fixation.

FIGURE 5.20
Stomata on the underside of leaves take in CO2 and release water and O2 .
Guard cells close the stomata when water is scarce. Leaf cross-section
(above) and stoma (below).

Plants have evolved three pathways for carbon fixation. The most common pathway combines one molecule of CO2
with a 5-carbon sugar called ribulose biphosphate (RuBP). The enzyme which catalyzes this reaction, ribulose-1,5bisphosphate carboxylase oxygenase (nicknamed RuBisCo), is the most abundant enzyme on earth! The resulting
6-carbon molecule is unstable, so it immediately splits into two much more stable 3-carbon phosphoglycerate
molecules. The 3 carbons in the first stable molecule of this pathway give this largest group of plants the name
C-3.
Dry air, hot temperatures, and bright sunlight slow the C-3 pathway for carbon fixation. This is because the stomata,
tiny openings under the leaf which normally allow CO2 to enter and O2 to leave, must close to prevent loss of water
vapor ( Figure 5.20) by transpiration. Closed stomata lead to a shortage of CO2 . Two alternative pathways for
carbon fixation demonstrate biochemical adaptations to differing environments. All three carbon fixation pathways
lead to the Calvin Cycle to build sugar.
336

www.ck12.org

Chapter 5. Metabolism - Advanced

See CAM Plants at http://www.youtube.com/watch?v=xp6Zj24h8uA (8:37) for further information.

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/261

FIGURE 5.21
Even chemical reactions adapt to specific
environments. Carbon fixation pathways
vary among three groups.

Temperate

species (maple tree, left) use the C-3


pathway. C-4 species (corn, center) concentrate CO2 in a separate compartment
to lessen water loss in hot bright climates.
Desert plants (jade plant, right) fix CO2 by
CAM photosynthesis only at night, closing
stomata in the daytime to conserve water.

C-4 Plants

Plants such as corn solve the problem by using a separate compartment to fix CO2 . C-4 plants utilize a specific leaf
anatomy. These plants have both bundle-sheath cells, which are photosynthetic cells arranged into tightly packed
coverings or sheaths around the veins of a leaf, and loosely arranged mesophyll cells, which lie between the bundle
sheath cells and the leaf surface. The bundle-sheath cells form a protective covering on leaf veins. The Calvin Cycle
is confined to the chloroplasts of these bundle sheath cells in C-4 plants. Instead of direct fixation to RuBisCO in
the Calvin Cycle, CO2 is incorporated into a 4-carbon organic acid, which has the ability to regenerate CO2 in the
chloroplasts of the bundle sheath cells. Bundle sheath cells can then utilize this CO2 to generate carbohydrates by
the conventional C-3 pathway.
In these C-4 plants, fixation of CO2 occurs in mesophyll cells when it combines with a 3-carbon molecule, phosphoenolpyruvate (PEP), resulting in a 4-carbon oxaoloacetate molecule. This reaction is catalyzed by the enzyme PEP
carboxylase. Because the first stable organic molecule has four carbons (oxaoloacetate), this adaptation has the name
C-4. This 4-carbon molecule is converted into another 4-carbon molecule, malate, which is shuttled unto the bundlesheath cells, where it is broken down into CO2 and a 3-carbon pyruvate. When enough CO2 accumulates, RuBisCo
fixes it a second time, this time as part of the Calvin Cycle. The pyruvate is transported back to the mesophyll
cell where it is converted into phosphoenolpyruvate, allowing the process to continue. Compartmentalization allows
efficient use of low concentrations of carbon dioxide in these specialized plants.
See C-4 Photosynthesis at http://www.youtube.com/watch?v=7ynX_F-SwNY (16:58) for further information.

337

5.7. The Calvin Cycle - Advanced

www.ck12.org

FIGURE 5.22
In this diagram of the cross section of a
leaf, bundle sheath cells can be seen in
pink around a leaf vein, and mesophyll
cells can be seen in green surrounding
the bundle sheath cells and the outer
layers of the leaf. Also noticeable is a cutaway of two guard cells (purple) surrounding a stomata.

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/260

CAM Photosynthesis

Cacti and succulents such as the jade plant avoid water loss by fixing CO2 only at night. These plants close their
stomata during the day (by closing their guard cells) and open them only in the cooler and more humid nighttime
hours. Leaf structure differs slightly from that of C-4 plants, but the fixation pathways are similar. The family of
plants in which this pathway was discovered gives the pathway its name, Crassulacean Acid Metabolism, or CAM
( Figure 5.21). CAM photosynthesis is an adaptation to arid conditions in some plants. CAM photosynthesis is a
two-step process: part occurs during the day and part at night.
At night, when the stomata are open, CO2 can enter the leaf cell, but the light reactions of photosynthesis cannot
take place, so ATP and NADPH cant be made. The carbon dioxide is fixed in the cytoplasm of mesophyll cells by
a PEP reaction similar to that of C-4 pathway, PEP carboxylase combines CO2 and PEP, making oxalacetate, which
is subsequently transformed into malate. But, unlike the C-4 plant, the resulting malate is not immediately passed
on to the Calvin Cycle but are stored in vacuoles for later use. The next day, after the sun comes out and the light
reactions restart making ATP and NADPH, malate is released from the vacuoles of the mesophyll cells and enters
the stroma of the chloroplasts where an enzyme releases the CO2 , which then enters into the Calvin Cycle.
338

www.ck12.org

Chapter 5. Metabolism - Advanced

How Does the Calvin Cycle Store Energy in Sugar?

As Melvin Calvin discovered, carbon fixation is the first step of a cycle. Like an electron transport chain, the Calvin
Cycle, shown in Figure 5.23, transfers energy in small, controlled steps. Each step pushes molecules uphill in terms
of energy content. Recall that in the electron transfer chain, excited electrons lose energy to NADPH and ATP. In
the Calvin Cycle, NADPH and ATP formed in the light reactions lose their stored chemical energy to build glucose.
Use the diagram below to identify the major aspects of the process:
the general cycle pattern
the major reactants
the products

FIGURE 5.23
Overview of the Calvin Cycle Pathway.

First, notice where carbon is fixed by the enzyme Rubisco. In C-3, C-4, and CAM plants, CO2 enters the cycle by
joining with 5-carbon ribulose bisphosphate to form a 6-carbon intermediate, which splits (so quickly that it isnt
even shown) into two 3-carbon 3-phosphoglycerate molecules. Now look for the points at which ATP and NADPH
(made in the light reactions) add chemical energy (Reduction in the diagram) to the 3-carbon molecules. The
resulting glyceraldehyde-3-phosphate half-sugars can enter several different metabolic pathways. One recreates
the original 5-carbon precursor, completing the cycle. A second combines two of the 3-carbon molecules to form
glucose, the universal fuel for life. The cycle begins and ends with the same 5-carbon RuBP molecule, but the
process combines carbon and energy to build carbohydrates food for life.
So how does photosynthesis store energy in sugar? Six turns of the Calvin Cycle use chemical energy from ATP
to combine six carbon atoms from six CO2 molecules with 12 hydrogens from NADPH. The result is one molecule
of glucose, C6 H12 O6 .
Vocabulary

bundle-sheath cells: Photosynthetic cells arranged into tightly packed sheaths around the veins of a leaf.
339

5.7. The Calvin Cycle - Advanced

www.ck12.org

Calvin Cycle: The second stage of photosynthesis; results in the formation of a sugar.
CAM photosynthesis: A photosynthetic adaptation to arid conditions in some plants; allows stomata to be
closed during the day.
carbon fixation: The process which converts carbon dioxide in the air to organic molecules, as in photosynthesis.
mesophyll cells: Photosynthetic parenchyma cells that lie between the upper and lower epidermis layers of a
leaf.
RuBisCo: The enzyme that combines one molecule of CO2 with a 5-carbon sugar called ribulose biphosphate
(RuBP); the most abundant enzyme on earth.
stomata (singular, stoma): Openings on the underside of a leaf which allow gas exchange and transpiration.
transpiration: A process by which plants lose water; occurs when stomata in leaves open to take in carbon
dioxide for photosynthesis and lose water to the atmosphere in the process.
Summary

The Calvin Cycle uses the NADPH and ATP from the Light Reactions to fix carbon and produce glucose.
Carbon dioxide enters the Calvin Cycle when Rubisco attaches it to a 5-carbon sugar.
Most plants fix CO2 directly with the Calvin Cycle, so they are called C-3 plants.
Some plants have evolved preliminary fixation pathways, which help them conserve water in hot, dry habitats.
C-4 plants use a 3-carbon carrier to compartmentalize initial carbon fixation in order to concentrate CO2 before
sending it on to Rubisco.
CAM plants open their stomata for preliminary CO2 fixation only at night.
In the Calvin Cycle, the fixed CO2 moves through a series of chemical reactions, gaining a small amount of
energy from ATP or NADPH at each step.
Six turns of the cycle process 6 molecules of carbon dioxide and 12 hydrogens to produce a single molecule
of glucose.

Review

1. Match the major events with the stage of photosynthesis (Light Reactions or Calvin Cycle) in which they
occur.
a.
b.
c.
d.
e.
f.
g.

Carbon dioxide is fixed.


Electrons in chlorophyll jump to higher energy levels.
Glucose is produced.
NADPH and ATP are produced.
NADPH and ATP are used.
Oxygen gas is released.
Water is split.

2. Explain the value of cycles of chemical reactions, such as the Calvin Cycle.
3. Define carbon fixation.
4. Explain how their various methods of carbon fixation adapt C-3, C-4, and CAM plants to different habitats.

340

www.ck12.org

Chapter 5. Metabolism - Advanced

5.8 Chemosynthesis - Advanced


Define chemosynthesis and describe chemosynthetic organisms.

Is it possible to live in temperatures over 175F?


It is if youre a Pompeii worm. The Pompeii worm, the most heat-tolerant animal on Earth, lives in the deep ocean
at super-heated hydrothermal vents. Covering this deep-sea worms back is a fleece of bacteria. These microbes
contain all the genes necessary for life in extreme environments.
Chemosynthesis

Why do bacteria that live deep below the oceans surface rely on chemical compounds instead of sunlight for energy
to make food?
Most autotrophs make food by photosynthesis, but this isnt the only way that autotrophs produce food. Some
bacteria make food by another process, which uses chemical energy instead of light energy. This process is called
chemosynthesis. In chemosynthesis, one or more carbon molecules (usually carbon dioxide or methane, CH4 )
and nutrients is converted into organic matter, using the oxidation of inorganic molecules, such as hydrogen gas,
hydrogen sulfide (H2 S) or ammonia (NH3 ) or methane as a source of energy, rather than sunlight. In hydrogen
sulfide chemosynthesis, in the presence of carbon dioxide and oxygen, carbohydrates (CH2 O) can be produced:
CO2 + O2 + 4H2 S CH2 O + 4S + 3H2 O
Many organisms that use chemosynthesis are extremophile members of the kingdom Archaea. These prokaryotes
live in harsh conditions such as in the absence of sunlight, and in a wide range of water temperatures, some
341

5.8. Chemosynthesis - Advanced

www.ck12.org

approaching the boiling point. Some chemosynthetic bacteria live around deep-ocean vents known as black
smokers. Compounds, including hydrogen sulfide, which flow out of the vents from Earths interior, are used by
the bacteria for energy to make food. Consumers that depend on these bacteria to produce food for them include
giant tubeworms, like those pictured in Figure 5.24. These organisms are known as chemoautotrophs. Many
chemosynthetic microorganisms are consumed by other organisms in the ocean, and symbiotic associations between
these organisms and respiring heterotrophs are quite common.
FIGURE 5.24
Tubeworms deep in the Galapagos Rift
get their energy from chemosynthetic
bacteria.

Tubeworms have no mouth,

eyes, or stomach. Their survival depends


on a symbiotic relationship with the billions of bacteria that live inside them.
These bacteria convert the chemicals that
shoot out of the hydrothermal vents into
food for the worm.

Vocabulary

chemoautotrophs: Organisms that use the energy stored in chemical compounds to make organic molecules
by chemosynthesis.
chemosynthesis: The process by which carbon dioxide molecules are converted to carbohydrates; uses energy
from the oxidation of inorganic compounds.
extremophile: Any organism that thrives in extreme conditions of temperature, pressure, salinity, or concentrations of hostile chemicals; these are characteristics of the Kingdom Archaea.
Summary

Chemosynthesis is a process in which some organisms use chemical energy instead of light energy to produce
"food."
Review

1. What is chemosynthesis?
2. What is the chemical process of hydrogen sulfide chemosynthesis?
3. Why do bacteria that live deep below the oceans surface rely on chemical compounds instead of sunlight for
energy to make food?
4. What are chemoautotrophs? Give an example.

342

www.ck12.org

Chapter 5. Metabolism - Advanced

5.9 Cellular Respiration - Advanced


Clarify the relationship between breathing and cellular respiration.

In the presence of oxygen. Why?


Oxygen is made by trees and other plants during photosynthesis. We know that we need oxygen to live. But why?
This oxygen is an essential component for the optimal production of usable energy - which occurs through cellular
respiration.
Cellular Respiration

You know that humans deprived of oxygen for more than a few minutes will quickly become unconscious and die.
Breathing, also known as respiration, is essential for human life, because the body cannot store oxygen for later
use as it does food. The mammalian respiratory system, shown in Figure 5.25 features a diaphragm, trachea, and
a thin membrane whose surface area is equivalent to the size of a handball court - all for efficient oxygen intake.
Other forms of life employ different types of respiratory organs: fish and aquatic amphibians and insects flaunt gills,
spiders and scorpions develop "book lungs," and terrestrial insects use an elaborate network of tubes called tracheae,
which open via spiracles, as shown in Figure 5.25. A constant supply of oxygen gas is clearly important to life.
However, do you know why you need oxygen?
Many people would answer that oxygen is needed to make carbon dioxide, the gas exhaled or released by each of
the respiratory systems listed above. However, CO2 is a waste product. But a waste product of what?
There must be more to this story than just gas exchange with the environment. To begin to appreciate the role of
oxygen inside your body, think about when your breathing rate increases: climbing a steep slope, running a race,
or skating a shift in a hockey game. Respiration rate correlates with energy use, and that correlation reflects the
link between oxygen and energy metabolism. For this reason, the chemical process inside your cells that consume
oxygen to produce usable energy is known as cellular respiration. During this process, energy is converted from
glucose, in the presence of oxygen, into numerous ATP molecules. The glucose, of course, comes from the food
343

5.9. Cellular Respiration - Advanced

www.ck12.org

FIGURE 5.25
(left) The human respiratory system is only part of the story of respiration. Diaphragm, lungs, and trachea take
air deep into the body and provide oxygen gas to the bloodstream. The fate of that oxygen is the story of cellular
respiration. (center) Spiracles in this Cluentius Sphinx (Neococytius cluentius) caterpillar connect to a system of
internal tubes (tracheae), which carry oxygen throughout the animals body. (right) Gills in this alpine newt larva,
Ichthyosaura alpestris, bring blood close to an extensive surface area so that the newt can absorb dissolved
oxygen gas from its watery habitat.

you eat. In biological terms, you do not eat because you are hungry, you eat to get energy. Other heterotrophic
organisms also acquire glucose from other organisms, whereas autotrophic organisms make their own glucose,
mostly through photosynthesis.
Though cellular respiration can occur anaerobically without oxygen, the process is much more efficient under
aerobic conditions, in the presence of oxygen. And what exactly is the role of oxygen? Oxygen is the final electron
acceptor of the electron transport chain in the final step of cellular respiration. Oxygen combines with electrons and
hydrogen ions to produce water.
An introduction to cellular respiration can be viewed at http://www.youtube.com/watch?v=2f7YwCtHcgk (14:19).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/262

Vocabulary

aerobic: With oxygen, or living or occurring only in the presence of oxygen.


anaerobic: Without oxygen; living or occurring in the absence of oxygen.
ATP ( adenosine triphosphate): Energy-carrying molecule that cells use to power their metabolic processes;
energy-currency of the cell.
autotroph: Organism that produces organic compounds from energy and simple inorganic molecules; also
known as a producer.
344

www.ck12.org

Chapter 5. Metabolism - Advanced

cellular respiration: Metabolic process which transfers chemical energy from glucose (a deliverable fuel
molecule) to ATP (a usable energy-rich molecule); most efficient in the presence of oxygen (aerobic).
glucose: The carbohydrate product of photosynthesis; serves as the universal fuel for life; C6 H12 O6 .
heterotroph: Organisms which must consume organic molecules; also known as a consumer.
respiration: Exchange of gases between the body and the outside air.
respiration rate: The rate of respiration; the rate of gas exchange between the body and the outside air.
Summary

Respiration is the exchange of gases between the body and the outside air.
Cellular respiration is the cellular process which transfers chemical energy from glucose to ATP.
Oxygen is essential to have efficient cellular respiration; most organisms need oxygen for a single purpose: to
release energy from food for use by cells.
Explore More

Use this resource to answer the questions that follow.


Cellular Respiration at http://hyperphysics.phy-astr.gsu.edu/hbase/biology/celres.html
1.
2.
3.
4.

Define the term cellular respiration.


What is a main difference between cellular respiration in prokaryotes and eukaryotes?
What is ATP?
Give an overview of aerobic cellular respiration.

Review

1.
2.
3.
4.

Why do nearly all organisms die without a constant supply of oxygen?


Describe the difference between respiration and cellular respiration.
What is the role of oxygen in cellular respiration?
Which is most efficient, aerobic respiration or anaerobic respiration?

345

5.10. Cellular Respiration Overview - Advanced

www.ck12.org

5.10 Cellular Respiration Overview - Advanced

Trace the flow of energy from food molecules through ATP to its use in cellular work.
Compare cellular respiration to burning.
Analyze the chemical equation for cellular respiration.
Briefly describe the role of mitochondria in producing ATP.
Compare cellular respiration to photosynthesis.

Why eat?
Because were hungry. Not necessarily. Biologically speaking, we eat to get energy. The food we eat is broken
down, the glucose extracted, and that energy is converted into ATP. And this happens most efficiently in the presence
of oxygen.
346

www.ck12.org

Chapter 5. Metabolism - Advanced

An Overview of Cellular Respiration

Another way to think about the role of oxygen in your body - and a good starting point for understanding the whole
process of cellular respiration - is to recall (or imagine) the last time you sat by a campfire (see Figure 5.26) and
noticed that it was "dying." Often people will blow on a campfire to keep it from "dying out." How does blowing
help? What happens in a campfire?

FIGURE 5.26
Analyzing what happens when wood
burns in a campfire is a good way to begin
to understand cellular respiration.

You know that a fire produces light and heat energy. However, it cannot create energy (remember that energy cannot
be created or destroyed). Fire merely transforms the energy stored in its fuel chemical energy into light and heat.
Another way to describe this energy transformation is to say that burning releases the energy stored in fuel. As
energy is transformed, so are the compounds that make up the fuel. In other words, burning is a chemical reaction.
We could write our understanding of this energy-releasing chemical reaction up to this point as:

Now return to what happens when you blow on a fire. The fire was "dying out," so you blew on it to get it going
again. Was it movement or something in the air that promoted the chemical reaction? If you have ever "smothered" a
fire, you know that a fire needs something in the air to keep burning. That something turns out to be oxygen. Oxygen
gas is a reactant in the burning process. At this point, our equation is:

To complete this equation, we need to know what happens to matter, to the atoms of oxygen, and to the atoms of
the fuel during the burning. If you collect the gas rising above a piece of burning wood in an inverted test tube,
you will notice condensation - droplets appearing on the sides of the tube. To identify the products, the experiment
shown below can be performed. Cobalt chloride paper will change from blue to pink, confirming that these droplets
are water. If you add bromothymol blue (BTB) to a second tube of collected gases, the blue solution will change
347

5.10. Cellular Respiration Overview - Advanced

www.ck12.org

to green or yellow ( Figure 5.27), indicating the presence of carbon dioxide. Thus, carbon dioxide and water are
products of burning wood fuel. The oxygen atoms have been incorporated into carbon dioxide and water.

FIGURE 5.27
Bromothymol blue (BTB) changes from
blue to green to yellow as carbon dioxide
is added. Thus, it is a good indicator for
this product of burning or cellular respiration.

The oxygen atoms have been incorporated into carbon dioxide and water, but what is the sources of the carbon atoms
in the CO2 and of the hydrogen atoms in the water. These atoms make up the wood fuel and nearly all fuels we burn,
from coal to propane to candle wax to gasoline. Overall, burning is the combining of oxygen with hydrogen and
carbon atoms in a fuel (combustion or oxidation) to release the stored chemical energy as heat and light. Products of
combustion are CO2 (oxidized carbon) and H2 O (oxidized hydrogen). The equation can be modified to:

Cellular Respiration

Recall that breathing rate and oxygen intake is related to energy use. Burning consumes oxygen as it releases stored
chemical energy, transforming it into light and heat. Cellular respiration is actually a slow burn. Your cells absorb
the oxygen carried by your blood from your lungs, and use the O2 to release stored chemical energy so that you can
use it.
Stages of Cellular Respiration

Cellular respiration involves many chemical reactions. As you saw earlier, the reactions can be summed up in this
equation:
348

www.ck12.org

Chapter 5. Metabolism - Advanced

C6 H12 O6 + 6O2 6CO2 + 6H2 O + Chemical Energy (in ATP)


The reactions of cellular respiration can be grouped into three stages: glycolysis, the Krebs cycle (also called the
citric acid cycle), and electron transport. Figure 5.28 gives an overview of these three stages, which are also
described below.

FIGURE 5.28
Cellular respiration takes place in the
stages shown here. The process begins
with a molecule of glucose, which has six
carbon atoms. What happens to each of
these atoms of carbon?

ATP

However, releasing energy within cells does not produce light or intense heat. Cells run on chemical energy
specifically, the small amount temporarily stored in ATP molecules. Cellular respiration transfers chemical energy
from a "deliverable" fuel molecule glucose to many "usable" molecules of ATP. Like oxygen, glucose is delivered
by your blood to your cells. If ATP were delivered to cells, more than 60,221,417,930,000,000,000,000,000 of these
large molecules (which contain relatively small amounts of energy) would clog your capillaries each day. Pumping
them across cell membranes would "cost" a great deal of energy. A molecule of glucose contains a larger amount
of chemical energy in a smaller package. Therefore, glucose is much more convenient for bloodstream delivery, but
too "powerful" to work within the cell. The process of cellular respiration uses oxygen to help transfer the chemical
energy from glucose to ATP, which can be used to do work in the cell. This chemical equation expresses what we
have worked out:

As with burning, we must trace what happens to atoms during cellular respiration. You can readily see that when
the carbon atoms in glucose are combined with oxygen, they again form carbon dioxide. And when the hydrogen
atoms in glucose are oxidized, they form water, as in burning. You can detect these products of cellular respiration
349

5.10. Cellular Respiration Overview - Advanced

www.ck12.org

in your breath on a cold day (as water condensation) and in the lab (BTB turns yellow when you blow into it through
a straw).

This equation accounts for the energy transfer and the carbon, hydrogen, and oxygen atoms, but it does not show the
"raw materials" or reactants which build ATP. Recall that the energy temporarily stored in ATP is released for use
when the bond between the second and third phosphates is broken. The resulting ADP can be recycled within the
cell by recombining it with inorganic phosphate (Pi ).
FIGURE 5.29
Like recharging batteries, cells recycle
ATP and ADP (and AMP) molecules
by combining them with inorganic phosphate. When the high-energy bond between phosphate groups in ATP breaks,
its chemical energy can do cellular work.
The bonds between phosphate groups
can be broken and reformed, recycling
this cellular energy.

The source of energy for re-attaching the phosphate and making ATP is the chemical energy in glucose. Materials
cycle and recycle, but energy gets used up and must be replaced. That is the key to understanding cellular respiration:
it is a "recharging of the batteries" - ATP molecules which power cellular work. How many ATP can be made by
harnessing the energy in a single glucose molecule? Although this number varies under certain conditions, most
cells can capture enough energy from one molecule of glucose to build 38 molecules of ATP. Our equation becomes:

Mitochondria

This equation for cellular respiration is not quite complete, however, because we can easily mix air and glucose
sugar (even adding ADP and Pi ) and nothing will happen. For the campfire, we indicated above the arrow that
a necessary condition was a spark or match to start the reaction. A spark or match would damage or destroy
living tissue. What necessary condition initiates the slow burn that is cellular respiration? Recall that enzymes
are highly specific proteins which "speed up" or catalyze chemical reactions in living cells. More than 20 different
enzymes are necessary to carry out cellular respiration. Recall also that membranes within organelles often sequence
enzymes for efficiency, as in chloroplasts for photosynthesis, you will not be surprised that a specific organelle, the
mitochondrion ( Figure 5.30), is also a necessary condition of cellular respiration - at least in eukaryotes.
Within each eukaryotic cell, the membranes of a few to a few thousand mitochondria sequence enzymes and
electron carriers and compartmentalize ions so that cellular respiration proceeds efficiently. Mitochondria, like
chloroplasts, contain their own DNA and ribosomes and resemble certain bacteria. The Theory of Endosymbiosis
350

www.ck12.org

Chapter 5. Metabolism - Advanced

FIGURE 5.30
Mitochondria, shown here as the green
ovals in this animal cell, are membranous organelles which sequence enzyme
and electron carrier molecules to make
cellular respiration highly efficient. Mitochondria have both an inner and outer
membrane, with a matrix inside the inner membrane.

The inner membrane

has many internal folds, increasing the


surface area for proteins and molecules
involved in cellular respiration.

holds that mitochondria, like chloroplasts, were once independently living prokaryotes. Larger prokaryotes engulfed
(or enslaved) these smaller aerobic cells, forming eukaryotic cells. Many prokaryotes today can perform cellular
respiration; perhaps they and mitochondria have common ancestors. Their expertise in generating ATP made
mitochondria highly valued symbionts.
Including these necessary conditions and balancing numbers of atoms on both sides of the arrow, our final equation
for the overall process of cellular respiration is:

In words, cellular respiration uses oxygen gas to break apart the carbon-hydrogen bonds in glucose and release their
energy to build 38 molecules of ATP. Most of this process occurs within the mitochondria of the cell. Carbon dioxide
and water are waste products. This is similar to burning, in which oxygen breaks the carbon-hydrogen bonds in a
fuel and releases their chemical energy as heat and light. Again, carbon dioxide and water are waste.

Cellular Respiration and Photosynthesis

Comparing this process to that of photosynthesis, the similarity between the two processes is striking. Both are
processes within the cell which make chemical energy available for life. Photosynthesis transforms light energy into
chemical energy stored in glucose, and cellular respiration releases the energy from glucose to build ATP, which
does the work of life. Moreover, photosynthesis reactants CO2 and H2 O are products of cellular respiration. And the
reactants of respiration, C6 H12 O6 and O2 , are the products of photosynthesis. This interdependence is the basis of the
carbon-oxygen cycle ( Figure 5.31), which connects producers to consumers and their environment. At first glance,
351

5.10. Cellular Respiration Overview - Advanced

www.ck12.org

the cycle merely seems to show mitochondria undoing what chloroplasts do; but the cycles energy transformations
power all the diversity, beauty, and mystery of life.

FIGURE 5.31
Photosynthesis in the chloroplast and
cellular respiration in the mitochondrion
show the interdependence of producers
and consumers, the flow of energy from
sunlight to heat, and the cycling of carbon
and oxygen between living world and environment.

A explanation of ATP as biological energy is found at http://www.youtube.com/watch?v=YQfWiDlFEcA (13:35).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/263

Vocabulary

ATP: ( adenosine triphosphate): Energy-carrying molecule that cells use to power their metabolic processes;
energy-currency of the cell.
carbon-oxygen cycle: The movement of carbon and oxygen between the ground, atmosphere, oceans, and
living organisms.
cellular respiration: Metabolic process which transfers chemical energy from glucose (a deliverable fuel
molecule) to ATP (a usable energy-rich molecule); most efficient in the presence of oxygen (aerobic).
352

www.ck12.org

Chapter 5. Metabolism - Advanced

enzyme: Chemical, usually a protein, that speeds up chemical reactions in organisms; a biological catalyst.
glucose: The carbohydrate product of photosynthesis; serves as the universal fuel for life; C6 H12 O6 .
hydrocarbon: An organic compound consisting entirely of hydrogen and carbon.
mitochondria: (singular, mitochondrion): Membrane-enclosed organelles that are found in most eukaryotic
cells; called the "power plants" of the cell because they use energy from organic compounds to make ATP.
product: Substance that forms as a result of a chemical reaction.
reactant: Substance involved in a chemical reaction that is present at the beginning of the reaction.
symbiont: An organism in a symbiotic relationship.
Theory of Endosymbiosis: Theory that proposes that eukaryotic organelles, such as mitochondria, evolved
from ancient, free-living prokaryotes that invaded other prokaryotic cells.
Summary

Cellular respiration is a series of chemical reactions which transfer energy from glucose (deliverable or fuel
energy) to ATP (usable energy).
Analyzing a campfire can clarify your understanding of cellular respiration. A campfire breaks chemical bonds
in wood, releasing stored energy as light and heat; respiration breaks chemical bonds in glucose, releasing
stored energy and transferring some to 38 ATP; some energy is lost as heat.
This equation summarizes the process of cellular respiration:

In eukaryotic cells, mitochondria organize enzymes and electron carriers and compartmentalize ions so that
cellular respiration proceeds efficiently.
Cellular respiration, in many ways the opposite of photosynthesis, shows the interdependence of producers
and consumers. Combined, the two equations demonstrate how energy flows and the carbon and oxygen cycle
between organisms and environment.
Explore More I

Use this resource to answer the questions that follow.


http://www.hippocampus.org/Biology Non-Majors Biology* Search: Cellular Respiration
1.
2.
3.
4.

What is the goal of cellular respiration?


What are the two stages of cellular respiration?
Which organisms are able to perform glycolysis?
What is the main product of glycolysis? What happens to this product?
353

5.10. Cellular Respiration Overview - Advanced

www.ck12.org

Explore More II

Cellular Respiration at http://www.concord.org/activities/cellular-respiration .


Review

1. What source of energy do cells use to build ATP by cellular respiration?


2. Compare the purpose and energy content of glucose to the function and energy content of ATP; in other words,
why do organisms need both kinds of energy-rich molecules?
3. Compare the process of burning gasoline in your automobiles engine to the process of cellular respiration in
terms of reactants, products, and necessary conditions.
4. Write out the chemical reaction which summarizes the overall process of cellular respiration, first in symbols
as a chemical equation, and then in words in a complete sentence.
5. In what eukaryote organelle does cellular respiration take place? Does this mean that prokaryotes cannot carry
out the entire process of cellular respiration? Explain.
6. Compare and contrast cellular respiration and photosynthesis.

354

www.ck12.org

Chapter 5. Metabolism - Advanced

5.11 Glycolysis - Advanced


Recognize that glycolysis is the first and most universal of three stages in cellular respiration.
Explain why biologists consider glycolysis to be one of the oldest energy production pathways.
Describe how some of the energy in glucose is transferred to ATP in the cytoplasm, without oxygen.

How do you slice a molecule of glucose in half?


With sharp knives? Not really. But you lyse it with enzymes during a process named glycolysis. Glucose is sliced
right in half from a 6-carbon molecule to two 3-carbon molecules. This is the first step and an extremely important
part of cellular respiration. It happens all the time, both with and without oxygen. And in the process, transfers some
energy to ATP.
Glycolysis: A Universal and Ancient Pathway for Making ATP

When was the last time you enjoyed yogurt on your breakfast cereal, or had a tetanus shot? These experiences may
appear unconnected, but both relate to bacteria which do not use oxygen to make ATP. In fact, tetanus bacteria cannot
355

5.11. Glycolysis - Advanced

www.ck12.org

survive if oxygen is present. However, Lactobacillus acidophilus (bacteria which make yogurt) and Clostridium
tetani (bacteria which cause tetanus or lockjaw) share with nearly all organisms the first stage of cellular respiration,
glycolysis ( Figure 5.32). Because glycolysis is universal, whereas aerobic (oxygen-requiring) cellular respiration
is not, most biologists consider it to be the most fundamental and primitive pathway for making ATP.

FIGURE 5.32
Clostridium tetani bacteria are obligate
anaerobes, which cannot grow in the
presence of oxygen and use a variation
of glycolysis to make ATP. Because they
can grow in deep puncture wounds and
secrete a toxin, which can cause muscle
spasms, seizures, and death, most people receive tetanus vaccinations at least
every ten years throughout life.

Return to the overall equation for cellular respiration:

Like photosynthesis, the process represented by this equation is actually many small, individual chemical reactions.
We grouped the reactions of photosynthesis into two stages, the light reactions and the Calvin Cycle. We will divide
the reactions of cellular respiration into three stages: glycolysis, the Krebs Cycle, and the electron transport chain
( Figure 5.33). In this concept, Stage 1, glycolysis, the oldest and most widespread pathway for making ATP, is
discussed. Before diving into the details, we must note that this first stage of cellular respiration is unique among
the three stages: it does not require oxygen, and it does not take place in the mitochondrion. The chemical reactions
of glycolysis occur without oxygen in the cytosol of the cell ( Figure 5.34).
The name for Stage 1 clearly indicates what happens during that stage: glyco- refers to glucose, and -lysis means
"splitting." In glycolysis, within the cytosol of the cell, a minimum of eight different enzymes break apart glucose
into two 3-carbon molecules. The energy released in breaking those bonds is transferred to carrier molecules, ATP
and NADH. NADH temporarily holds small amounts of energy which can be used later to build ATP. The 3-carbon
product of glycolysis is pyruvate, or pyruvic acid ( Figure 5.36). (The difference between them is actually a sole
hydrogen atom. Pyruvic acid: CH3 COCOOH, pyruvate: CH3 COCOO .) Overall, glycolysis can be represented as:
C6 H12 O6 + 2NAD+ + 2Pi + 2ADP 2 pyruvate + 2NADH + 2ATP
However, even this equation is deceiving. Just the splitting of glucose requires many steps, each transferring or
capturing small amounts of energy. Individual steps appear in Figure below. Studying the pathway in detail reveals
that cells must "spend" or "invest" two ATP in order to begin the process of breaking glucose apart. Note that
the phosphates produced by breaking apart ATP join with glucose, making it unstable and more likely to break
apart. Later steps harness the energy released when glucose splits, and use it to build "hot hydrogens" (NAD+ is
reduced to NADH) and ATP (ADP + Pi ATP). If you count the ATP produced, you will find a net yield of two
ATP per glucose (4 produced 2 spent). Remember to double the second set of reactions to account for the two
356

www.ck12.org

Chapter 5. Metabolism - Advanced

FIGURE 5.33
The many steps in the process of aerobic
cellular respiration can be divided into
three stages. The first stage, glycolysis,
produces ATP without oxygen. Because
this part of the cellular respiration pathway is universal, biologists consider it the
oldest segment. Note that glycogen and
fats can also enter the glycolysis pathway.
The second stage is the Krebs Cycle, and
the third stage is the electron transport
chain.

It is during the third stage that

chemiosmosis produces numerous ATP


molecules.

3-carbon molecules which follow that pathway! The "hot hydrogens" can power other metabolic pathways, or in
many organisms, provide energy for further ATP synthesis.
357

5.11. Glycolysis - Advanced

www.ck12.org

FIGURE 5.34
Glycolysis, unlike the latter two stages of
cellular respiration, takes place without
oxygen in the cytosol (blue) of the cell.
For many organisms, aerobic respiration
continues with the Krebs cycle and the
electron transport chain in the mitochondria (green). To enter the mitochondria,
glucose must first be lysed into smaller
molecules.

To summarize: In the cytosol of the cell, glycolysis transfers some of the chemical energy stored in one molecule
of glucose to two molecules of ATP and two NADH. This makes (some of) the energy in glucose, a universal fuel
molecule for cells, available to use in cellular work - moving organelles, transporting molecules across membranes,
or building large organic molecules.
358

www.ck12.org

Chapter 5. Metabolism - Advanced

FIGURE 5.35
In glycolysis, glucose (C6) is split into two
3-carbon (C3) pyruvate molecules. This
releases energy, which is transferred to
ATP. How many ATP molecules are made
during this stage of cellular respiration?

FIGURE 5.36
Glycolysis breaks the 6-carbon molecule
glucose into two 3-carbon pyruvate
molecules, releasing some of the chemical energy which had been stored in glucose.

Although glycolysis is universal, pathways leading away from glycolysis vary among species depending on the availability of oxygen. If oxygen is unavailable, pyruvate may be converted to lactic acid or ethanol and carbon dioxide
in order to regenerate NAD+ , ending anaerobic respiration. Anaerobic respiration is also called fermentation,
which will be discussed in another concept.
If oxygen is present, pyruvate enters the mitochondria for further breakdown, releasing far more energy and producing many additional molecules of ATP in the latter two stages of aerobic respiration - the Krebs cycle and electron
359

5.11. Glycolysis - Advanced

www.ck12.org

transport chain. We will explore these, too, in a later section.


A summary of glycolysis can be viewed at http://www.youtube.com/watch?v=FE2jfTXAJHg (13:30).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/264

Vocabulary

aerobic respiration: Cellular respiration in the presence of oxygen; produces 36-38 ATP molecules/glucose.
anaerobic respiration: Cellular respiration in the absence of oxygen; produces 2 ATP molecules/glucose;
fermentation.
electron transport chain: Series of electron-transport molecules that pass high-energy electrons from molecule
to molecule and capture their energy.
fermentation: Type of anaerobic respiration that includes glycolysis followed by the conversion of pyruvic
acid to one or more other compounds and the formation of NAD+ ; the process of producing ATP in the
absence of oxygen through glycolysis.
glycogen: A carbohydrate used for long-term energy storage in animal cells; human muscle and liver cells
store energy in this form.
glycolysis: The process of splitting glucose; stage 1 of aerobic cellular respiration and also the basis of
anaerobic respiration; splits glucose into two 3-carbon pyruvate molecules, producing 2 (net) ATP.
Krebs Cycle: Stage 2 of aerobic cellular respiration; a series of chemical reactions which completes the
breakdown of glucose begun in stage 1, releasing more chemical energy and producing carbon dioxide; also
called the Citric Acid Cycle.
NADH: Short-term energy carrier; temporarily stores energy during cellular respiration; nicotinamide adenine
dinucleotide.
pyruvate: The 3-carbon product of glycolysis; also known as pyruvic acid.
Summary

The process of cellular respiration is actually many separate reactions, which can be divided into three stages:
glycolysis, the Krebs Cycle, and the electron transport chain.
During glycolysis, glucose is split into two 3-carbon pyruvate molecules, using 2 ATP but generating 4 ATP,
for a net gain of 2 ATP.
During glycolysis, 2 NADH are also produced.
360

www.ck12.org

Chapter 5. Metabolism - Advanced

Explore More

Glycolysis at http://johnkyrk.com/glycolysis.html .
Review

1. List the three stages of cellular respiration, and contrast the first stage with the other two in terms of distribution
throughout the living world, location within the cell, and use of oxygen.
2. Summarize the overall process of glycolysis, following both the path of carbon atoms and chemical energy.
3. What molecules can enter the glycolysis pathway, besides glucose?

361

5.12. The Mitochondria in Cellular Respiration - Advanced

www.ck12.org

5.12 The Mitochondria in Cellular Respiration Advanced


Describe the structure of the mitochondrion, and identify the site of Krebs Cycle reactions.

Why does this organelle have such a distinct internal structure?


It is the many internal folds of the inner membrane that allow mitochondria to be efficient at producing ATP. And
in the presence of oxygen, the organelle is highly efficient. Even though, cells that needs lots of energy may have
thousands of these organelles.
Structure of the Mitochondrion: Key to Aerobic Respiration

The aerobic phases of cellular respiration in eukaryotes occur within organelles called mitochondria. These aerobic
phases are the Krebs Cycle and the electron transport chain. A detailed look at the structure of the mitochondrion
( Figure 5.37) helps to explain its role in the last stage of respiration, the electron transport chain. Mitochondria are
sometimes referred to as the "power plants" of the cell, as these are the organelles that generate most of the cells
supply of ATP.
Two separate membranes form the mitochondrion. The inner membrane folds into cristae which divide the organelle
into three compartments: the intermembrane space (between outer and inner membranes), cristae space (formed by
infoldings of the inner membrane), and the matrix (within the inner membrane). The Krebs Cycle takes place
within the matrix. The compartments are critical for the electron transport chain structure and function. Glycolysis
occurs in the cytoplasm of the cell, with the products of glycolysis entering the mitochondria to continue cellular
respiration.
Mitochondrial Compartments

The double membrane nature of the mitochondria results in five distinct compartments, each with an important role
in cellular respiration. These compartments are:
362

www.ck12.org

Chapter 5. Metabolism - Advanced


FIGURE 5.37
Mitochondria, organelles specialized to
carry out aerobic respiration, contain an
inner membrane folded into cristae, which
form two separate compartments:

the

inner membrane space and the matrix.


The Krebs Cycle takes place in the matrix.
The electron transport chain is embedded
in the inner membrane and uses both
compartments to make ATP by chemios-

mosis.

Mitochondria have their own

DNA and ribosomes, resembling those of


prokaryotic organisms.

1.
2.
3.
4.
5.

the outer mitochondrial membrane,


the intermembrane space (the space between the outer and inner membranes),
the inner mitochondrial membrane,
the cristae (formed by infoldings of the inner membrane), and
the matrix (space within the inner membrane).

The roles of these compartments in cellular respiration include:


1.
2.
3.
4.

the outer mitochondrial membrane: allows for the establishment of the inter membrane space,
the intermembrane space: holds protons that are pumped out of the matrix during electron transport,
the inner mitochondrial membrane: organizes the electron transport chain and holds ATP synthase,
the cristae: expand the surface area of the inner mitochondrial membrane, enhancing its ability to produce
ATP, and
5. the matrix: site of ATP synthesis and the location of the Krebs cycle.

Vocabulary

ATP synthase: Ion channel and enzyme complex; chemically bonds a phosphate group to ADP, producing
ATP as H+ ions flow through the ion channel.
chemiosmosis: Process in cellular respiration or photosynthesis which produces ATP; uses the energy of
hydrogen ions diffusing through ATP synthase.
cristae: Inner membrane folds of the mitochondrion.
electron transport chain: Series of electron-transport molecules that pass high-energy electrons from molecule
to molecule and capture their energy.
Krebs cycle: Stage 2 of aerobic cellular respiration; a series of chemical reactions which completes the
breakdown of glucose begun in stage 1, releasing more chemical energy and producing carbon dioxide; also
called the Citric Acid Cycle.
363

5.12. The Mitochondria in Cellular Respiration - Advanced

www.ck12.org

matrix: Fluid-filled inside of the mitochondrion; space inside of the inner membrane.
mitochondria: (singular, mitochondrion): Membrane-enclosed organelles that are found in most eukaryotic
cells; called the "power plants" of the cell because they use energy from organic compounds to make ATP.
Summary

Mitochondria are organelles whose membranes are specialized for aerobic respiration.
The matrix of the mitochondria is the site of Krebs Cycle reactions.
The electron transport chain and most ATP synthesis rely on the compartments created by the inner membrane
of the mitochondria.
Explore More

Use this resource to answer the questions that follow.


Mitochondria at http://biology.about.com/od/cellanatomy/ss/mitochondria.htm
1.
2.
3.
4.

Why are the mitochondria referred to as the "power houses" of a eukaryotic cell?
What cellular processes involve mitochondria?
Describe the distinguishing characteristics of mitochondria?
What is the importance of the matrix?

Review

1. List and describe the five compartments of the mitochondrion.


2. Identify the sites of the Krebs cycle and the electron transport chain.

364

www.ck12.org

Chapter 5. Metabolism - Advanced

5.13 The Krebs Cycle - Advanced


Relate the history of oxygen in the atmosphere to the evolution of photosynthesis, aerobic respiration, mitochondria, and life on earth.
Describe the fate in eukaryotic cells of the pyruvate molecules produced by glycolysis if oxygen is present.
Recognize that for most organisms, if oxygen is present, the products of glycolysis enter the mitochondria for
stage 2 of cellular respiration - the Krebs Cycle.
Trace carbon and hydrogen atoms through the Krebs Cycle.
Analyze the importance of the Krebs Cycle to cellular respiration by following the pathway taken by chemical
energy.

What type of acid do these fruits contain?


Citric acid. Citric acid is also the first product formed in the Krebs cycle, and therefore this acid occurs in the
metabolism of virtually all living things.
Aerobic Respiration

Enticing clues - volcanic gases, vast iron ore sediments, and bubbles of ancient air trapped in amber suggest
dramatic changes during the history of earths atmosphere. Correlating these clues with the fossil record leads to
two major conclusions: that early life evolved in the absence of oxygen, and that oxygen first appeared between
2 and 3 billion years ago ( Figure 5.38) because of photosynthesis by the blue green bacteria, cyanobacteria. The
chemistry of cellular respiration reflects this history. Its first stage, glycolysis, is universal and does not use oxygen.
Absolutely dependent on oxygen gas, we find it difficult to imagine that its appearance must have been disastrous
for the anaerobic organisms that evolved in its absence. But oxygen is highly reactive, and at first, its effect on
evolution was so negative that some have named this period the oxygen catastrophe. However, as oxygen gradually
formed a protective ozone layer, life rebounded. After the first organisms evolved to use oxygen to their advantage,
the diversity of aerobic organisms exploded. According to the Theory of Endosymbiosis, engulfing of some of
these aerobic bacteria led to eukaryotic cells with mitochondria, and multicellularity, the evolution of multicellular
eukaryotic organisms, followed. Today, we live in an atmosphere which is 21% oxygen, and most of life follows
glycolysis with the last two, aerobic stages of cellular respiration.
365

5.13. The Krebs Cycle - Advanced

www.ck12.org

FIGURE 5.38
Oxygen has increased in the atmosphere
throughout the history of the earth. Note
the logarithmic scale, which indicates
great increases after first photosynthesis
(in bacteria) and then land plants evolved.
Related geological events: A = no oxidized iron; B = oxidized iron bands in
seabed rock - evidence for O2 in the
oceans; C = oxidized iron bands on land
and ozone layer formation- evidence for
O2 in the atmosphere.

Recall the purpose of cellular respiration: to release energy from glucose to make ATP, the universal molecule
of energy for cellular work. The following equation describes the overall process, although it summarizes many
individual chemical reactions.

Once again, the first stage of this process, glycolysis, is ancient, universal, and anaerobic. In the cytoplasm of most
cells, glycolysis breaks each 6-carbon molecule of glucose into two 3-carbon molecules of pyruvate. Chemical
energy, which had been stored in the now broken bonds, is transferred to 2 ATP and 2 NADH molecules.
The fate of pyruvate depends on the species and the presence or absence of oxygen. If oxygen is present to drive
subsequent reactions, pruvate enters the mitochondrion, where the Krebs Cycle (Stage 2) and electron transport
chain (Stage 3) break it down and oxidize it completely to CO2 and H2 O. The energy released builds many more
ATP molecules, though of course some is lost as heat. Lets explore the details of how mitochondria use oxygen to
make more ATP from glucose by aerobic respiration.
The Krebs Cycle: Capturing Energy from Pyruvate

Aerobic respiration begins with the entry of the product of glycolysis, pyruvate, into the mitochondria. For each
initial glucose molecules, two pyruvate molecules will enter the mitochondria. Pyruvate, however, is not the
molecule that enters the Krebs cycle. Prior to entry into this cycle, pyruvate must be converted into a 2-carbon
acetyl-CoenzymeA (acetyl-CoA) unit. The conversion of pyruvate into acetyl-CoA is referred to as the pyruvate
dehydrogenase reaction. It is catalyzed by the pyruvate dehydrogenase complex. This process produces one NADH
electron carrier while releasing a CO2 molecule. This step is also known as the link reaction or transition step, as
it links glycolysis and the Krebs cycle. Of course, as two pyruvates result from glycolysis, two acetyl-CoAs are
produced as are 2 NADH molecules.
1. Within the mitochondria, each pyruvate is broken apart and combined with a coenzyme known as CoA to form
a 2-carbon molecule, Acetyl-CoA, which can enter the Krebs Cycle. A single atom of carbon (per pyruvate)
366

www.ck12.org

Chapter 5. Metabolism - Advanced


FIGURE 5.39
After glycolysis, two 3-carbon pyruvates
enter the mitochondrion, where they
are converted to two 2-carbon acetylCoenzymeA (CoA) molecules.

Acetyl-

CoA then enters the Krebs Cycle. Note


that the carbons removed become carbon
dioxide, accounting for two of the six such
end products of glucose oxidation. The
energy released by this breakdown is carried by NADH.

is lost as carbon dioxide. The energy released in this breakdown is captured in two NADH molecules.
See Figure 5.39. Fatty acids can also break down into Acetyl-CoA. By this means, lipids, like fats, can be
burned to make ATP using the Krebs Cycle.
2. The Krebs Cycle ( Figure 5.40) begins by combining each Acetyl-CoA with a four-carbon carrier molecule to
make a 6-carbon molecule of citric acid (or citrate, its ionized form). For this reason, the Krebs Cycle, named
for a scientist who worked out its details, is also called the Citric Acid Cycle.
3. The cycle carries citric acid through a series of chemical reactions which gradually release energy and capture
it in several carrier molecules. For each Acetyl-CoA which enters the cycle, 3 NAD+ are reduced to NADH,
one molecule of FAD (another temporary energy carrier) is reduced to FADH2 , and one molecule of ATP
(actually a precursor, GTP, guanine triphosphate) is produced. Study Figure 5.40 to locate each of these
energy-capturing events.
4. Note what happens to carbon atoms (black dots in Figure 5.40). For each 2-carbon Acetyl-CoA which enters
the cycle, two molecules of carbon dioxide are released, completing the breakdown of the original 6-carbon
glucose molecule. The final step regenerates the original 4-carbon molecule which began the cycle, so that
another Acetyl-CoA can enter the cycle.

In summary, the Krebs Cycle completes the breakdown of glucose which began with glycolysis. Its chemical
reactions oxidize all six of the original carbon atoms to CO2 , and capture the energy released in 2 ATP, 6 NADH,
and 2 FADH2 . These energy carriers join the 2 ATP and 2 NADH produced in glycolysis and the 2 NADH produced
in the conversion of 2 pyruvates to 2 Acetyl-CoA molecules.
At the conclusion of the Krebs Cycle, glucose is completely broken down, yet only four ATP have been produced.
Moreover, although oxygen is required to drive the Krebs Cycle, the cycles chemical reactions do not themselves
consume O2 . The conclusion of cellular respiration, stage 3, produces the majority of the ATP.
The Krebs cycle is reviewed at http://www.youtube.com/watch?v=juM2ROSLWfw (17:47).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/265

367

5.13. The Krebs Cycle - Advanced

www.ck12.org

FIGURE 5.40
The Krebs cycle completes the breakdown of glucose begun in glycolysis. If oxygen is present, pyruvate
enters the mitochondria and is converted to AcetylCoA. AcetylCoA enters the cycle by combining with 4-carbon
oxaloacetate. Study the diagram to confirm that each turn of the cycle (two for each glucose) stores energy in 3
NADH+H+ , one FADH2 , and one ATP (from GTP), and releases 2 CO2 . The Krebs cycle is also known as the
Citric Acid Cycle or the tricarboxylic acid cycle (TCA cycle).

368

www.ck12.org

Chapter 5. Metabolism - Advanced

Vocabulary

Citric Acid Cycle: Stage 2 of aerobic cellular respiration; a series of chemical reactions which completes the
breakdown of glucose begun in stage 1, releasing more chemical energy and producing carbon dioxide; also
called the Krebs cycle.
electron transport chain: Series of electron-transport molecules that pass high-energy electrons from molecule
to molecule and capture their energy.
FADH2 : Flavin adenine dinucleotide; an energy carrier molecule produced during the Krebs cycle of aerobic
cellular respiration.
glycolysis: The process of splitting glucose; stage 1 of aerobic cellular respiration and also the basis of
anaerobic respiration; splits glucose into two 3-carbon pyruvate molecules, producing 2 (net) ATP.
Krebs cycle: Stage 2 of aerobic cellular respiration; a series of chemical reactions which completes the
breakdown of glucose begun in stage 1, releasing more chemical energy and producing carbon dioxide; also
called the Citric Acid Cycle.
multicellularity: Refers to organisms that consist of more than one cell, in contrast to single-cell organisms;
this is characteristic of most eukaryotes.
ozone layer: A layer in Earths atmosphere containing relatively high concentrations of ozone; absorbs a high
percentage of the Suns medium-frequency ultraviolet light.
pyruvate: The 3-carbon product of glycolysis; also known as pyruvic acid.
Theory of Endosymbiosis: Theory that proposes that eukaryotic organelles, such as mitochondria, evolved
from ancient, free-living prokaryotes that invaded other prokaryotic cells.
Summary

Oxygen produced by the first photosynthetic organisms was probably toxic to early anaerobic life forms, but
later organisms evolved a way to harness the power of oxygen to make ATP.
In eukaryotic cells, if oxygen is present, the pyruvate molecules produced by glycolysis in the cytoplasm enter
the mitochondria for further breakdown and energy release. The Krebs Cycle harnesses the energy which
remains in pyruvate after glycolysis.
The Krebs Cycle removes energy from citric acid in small steps, storing it in diverse energy carrier molecules:
ATP, NADH and FADH2 .
The Krebs Cycle produces two molecules of CO2 per Acetyl-CoA, completing the breakdown of glucose.
Explore More I

Use these resources to answer the questions that follow.


The Citric Acid Cycle at http://virtuallabs.stanford.edu/other/biochem/TCA.swf .
1. Where does the Krebs cycle occur in the cell?
2. What is the first product of this cycle?
3. How many reactions does it take to complete the cycle?
369

5.13. The Krebs Cycle - Advanced

www.ck12.org

Explore More II

Krebs Cycle at http://johnkyrk.com/krebs.html .


Review

1. Explain why the appearance of oxygen in the atmosphere between two and three billions of years ago was
both good news and bad news for life on Earth.
2. In eukaryotic cells when oxygen is present, what is the fate of the pyruvate produced in glycolysis?
3. Define the Krebs cycle.
4. Trace the six carbon atoms originally from acetyl-CoA through the Krebs Cycle. Trace the flow of energy
from the pyruvates produced in glycolysis through the Krebs Cycle.
5. How many energy carriers are produced during the Krebs cycle per acetyl-CoA?

370

www.ck12.org

Chapter 5. Metabolism - Advanced

5.14 The Electron Transport Chain - Advanced


Recognize that electron transport chain is the third and final stage of aerobic cellular respiration.
Describe how chemiosmotic gradients in mitochondria store energy to produce ATP.
Identify the role of oxygen in making stored chemical-bond energy available to cells.

Train, truck, boat or plane?


What do these have in common? They are ways to transport. And they all use a lot of energy. To make ATP, energy
must be "transported" - first from glucose to NADH, and then somehow passed to ATP. How is this done? With an
electron transport chain, the third stage of aerobic respiration. This third stage uses energy to make energy.
The Electron Transport Chain: ATP for Life in the Fast Lane

At the end of the Krebs Cycle, energy from the chemical bonds of glucose is stored in diverse energy carrier
molecules: four ATPs, but also two FADH2 and ten NADH molecules. The primary task of the last stage of
cellular respiration, the electron transport chain, is to transfer energy from the electron carriers to even more
ATP molecules, the batteries which power work within the cell.
Pathways for making ATP in stage 3 of aerobic respiration closely resemble the electron transport chains used
in photosynthesis. In both electron transport chains, energy carrier molecules are arranged in sequence within a
371

5.14. The Electron Transport Chain - Advanced

www.ck12.org

membrane so that energy-carrying electrons cascade from one to another, losing a little energy in each step. In both
photosynthesis and aerobic respiration, the energy lost is harnessed to pump hydrogen ions into a compartment,
creating an electrochemical gradient or chemiosmotic gradient across the enclosing membrane. And in both
processes, the energy stored in the chemiosmotic gradient is used with ATP synthase to build ATP.
For aerobic respiration, the electron transport chain or respiratory chain is embedded in the inner membrane of
the mitochondria ( Figure 5.41). The FADH2 and NADH molecules produced in glycolysis and the Krebs Cycle,
donate high-energy electrons to energy carrier molecules within the membrane. As they pass from one carrier to
another, the energy they lose is used to pump hydrogen ions into the mitochondrial intermembrane space, creating
an electrochemical gradient. Hydrogen ions flow down the gradient from outer to inner compartment through
the ion channel/enzyme ATP synthase, which transfers their energy to ATP. Note the paradox that it requires energy
to create and maintain a concentration gradient of hydrogen ions that are then used by ATP synthase to create stored
energy (ATP). In broad terms, it takes energy to make energy. Coupling the electron transport chain to ATP synthesis
with a hydrogen ion gradient is chemiosmosis, first described by Nobel laureate Peter D. Mitchell. This process, the
use of energy to phosphorylate ADP and produce ATP is also known as oxidative phosphorylation.
FIGURE 5.41
The third stage of cellular respiration
uses the energy stored during the earlier stages in NADH and FADH2 to make
ATP. Electron transport chains embedded in the mitochondrial inner membrane
capture high-energy electrons from the
carrier molecules and use them to concentrate hydrogen ions in the intermembrane space. Hydrogen ions flow down
their electrochemical gradient back into
the matrix through ATP synthase channels which capture their energy to convert
ADP to ATP. Notice that the process regenerated NAD+ , supplying the electron
acceptor molecule needed in glycolysis.

After passing through the electron transport chain, low-energy electrons and low-energy hydrogen ions combine
with oxygen to form water. Thus, oxygens role is to drive the entire set of ATP-producing reactions within the
mitochondrion by accepting spent hydrogens. Oxygen is the final electron acceptor; no part of the process - from
the Krebs Cycle through electron transport chain can happen without oxygen.
The electron transport chain can convert the energy from one glucose molecules worth of FADH2 and NADH + H+
into as many as 34 ATP. When the four ATP produced in glycolysis and the Krebs Cycle are added, the total 0f 38
ATP fits the overall equation for aerobic cellular respiration:

A summary of the electron transport chain can be viewed at http://www.youtube.com/watch?v=mfgCcFXUZRk


(17:16).

372

www.ck12.org

Chapter 5. Metabolism - Advanced

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/266

Aerobic respiration is complete. If oxygen is available, cellular respiration transfers the energy from one molecule
of glucose to 38 molecules of ATP, releasing carbon dioxide and water as waste. Deliverable food energy has
become energy which can be used for work within the cell transport within the cell, pumping ions and molecules
across membranes, and building large organic molecules. Can you see how this could lead to life in the fast lane
compared to anaerobic respiration (glycolysis alone)?
An overall summary of this process can be seen at http://www.youtube.com/watch?v=W_Q17tqw_7A (4:59).

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/267

Vocabulary

ATP synthase: Ion channel and enzyme complex; chemically bonds a phosphate group to ADP, producing
ATP as H+ ions flow through the ion channel.
chemiosmosis: Process in cellular respiration or photosynthesis which produces ATP; uses the energy of
hydrogen ions diffusing through ATP synthase.
chemiosmotic gradient: H+ difference across a membrane; established by the active transport of hydrogen
ions by an electron transport chain.
electrochemical gradient: Difference across a membrane due to both a chemical force and an electrical force;
drives the movement of ions across the membrane.
electron transport chain: Series of electron-transport molecules that pass high-energy electrons from molecule
to molecule and capture their energy.
oxidative phosphorylation: A metabolic process that uses energy released by the oxidation of nutrients to
produce adenosine triphosphate (ATP).
Summary

The third and final stage of aerobic cellular respiration, the electron transport chain, accounts for most of the
ATP.
Stage 3 transfers the energy from NADH and FADH2 to make ATP.
During electron transport, energy is used to pump hydrogen ions across the mitochondrial inner membrane,
from the matrix into the intermembrane space.
373

5.14. The Electron Transport Chain - Advanced

www.ck12.org

A chemiosmotic gradient causes hydrogen ions to flow back across the mitochondrial membrane into the
matrix, through ATP synthase, producing ATP.
When ATP from glycolysis and the Krebs Cycle are added, a total of 38 ATP result from aerobic respiration
of one molecule of glucose.
Explore More

Mitochondria at http://johnkyrk.com/mitochondrion.html .
Review

1. Summarize the overall task of Stage 3 of aerobic respiration.


2. Explain the principle of chemiosmosis.
3. Name the three stages of aerobic cellular respiration. Then write the overall equation, and identify which
stage:
a. Uses each reactant.
b. Requires each necessary condition.
c. Produces each product.

374

www.ck12.org

Chapter 5. Metabolism - Advanced

5.15 Anaerobic Respiration - Advanced


Distinguish between obligate aerobes, obligate anaerobes, and facultative anaerobes.
Explain that, in the absence of oxygen fermentation reactions must regenerate NAD+ in order for glycolysis
to continue making ATP.
Discuss how your muscles continue to work for you even when your respiratory and cardiovascular system
can no longer keep up a continuous supply of oxygen.

Why does a bakery smell so good?


When bread bakes, yeast releases carbon dioxide gas, forming the small holes in bread. The gas was produced by
alcoholic fermentation carried out by yeast.
Anaerobic Respiration

After the photosynthetic oxygen catastrophe challenged life between 2.5 and 3 billion years ago, evolution rebounded with biochemical pathways to harness and protect against oxygens power. Today, most organisms use
O2 in aerobic respiration to produce ATP. Almost all animals, most fungi, and some bacteria are obligate aerobes,
which require oxygen. Some plants and fungi and many bacteria retain the ability to make ATP without oxygen.
Recall that O2 is the final electron acceptor at the end of the electron transport chain during aerobic respiration.
Oxygen is required for oxidative phosphorylation to produce ATP. But in the absence of O2 . ATP must still be made.
The facultative anaerobes use ancient anaerobic pathways when oxygen is limited. A few bacteria remain as
obligate anaerobes, which die in the presence of oxygen and depend on only the first (anaerobic) stage of cellular
respiration. Aerobic and anaerobic pathways diverge after glycolysis splits glucose into two molecules of pyruvate:
C6 H12 O6 + 2NAD+ + 2Pi + 2ADP 2NADH + 2ATP
Pyruvate still contains a great deal of chemical energy. In fact, two pyruvate molecules contain most of the chemical
energy from the original glucose molecule. If oxygen is present, pyruvate enters the mitochondria for complete
breakdown by the Krebs Cycle and electron transport chain. If oxygen is not present, cells must transform pyruvate
to regenerate NAD+ in order to continue making ATP. Keep in mind that glycolysis produces a net total of 2 ATP.
375

5.15. Anaerobic Respiration - Advanced

www.ck12.org

FIGURE 5.42
Anaerobic and aerobic respiration share
the glycolysis pathway. If oxygen is not
present, fermentation may take place,
producing lactic acid or ethyl alcohol and
carbon dioxide. Products of fermentation
still contain chemical energy and are used
widely to make foods and fuels.

Two different pathways accomplish the regeneration of NAD+ with rather famous products: lactic acid (C3 H6 O3 )
and ethyl alcohol (C2 H6 O) ( Figure 5.42). Making ATP in the absence of oxygen by glycolysis alone is known
as fermentation. Therefore, these two pathways are called lactic acid fermentation and alcoholic fermentation.
If you lack interest in organisms, such as yeast and bacteria, which have stuck with the anaerobic tradition, the
products of these chemical reactions may still intrigue you. Fermentation makes bread, yogurt, beer, wine, and
some new biofuels. In addition, some of your bodys cells are facultative anaerobes, retaining one of these ancient
pathways for short-term, emergency use.
Gut Fermentation

Behind each release of gas is an army of gut bacteria undergoing some crazy biochemistry. These bacteria break
down the remains of digested food through fermentation, creating gas in the process. Learn what these bacteria have
in common with beer brewing at http://youtu.be/R1kxajH629A?list=PLzMhsCgGKd1hoofiKuifwy6qRXZs7NG6a
.

MEDIA
Click image to the left or use the URL below.
URL: http://www.ck12.org/flx/render/embeddedobject/143958

Vocabulary

alcoholic fermentation: The process for making ATP in the absence of oxygen; converts glucose to ethanol
and carbon dioxide.
facultative anaerobe: An organism which can respire aerobically when oxygen is present, but is also capable
of fermentation when oxygen levels are low.
fermentation: Type of anaerobic respiration that includes glycolysis followed by the conversion of pyruvic
acid to one or more other compounds and the formation of NAD+ ; the process of producing ATP in the
absence of oxygen through glycolysis.
376

www.ck12.org

Chapter 5. Metabolism - Advanced

lactic acid fermentation: The process for making ATP in the absence of oxygen; converts glucose to lactic
acid.
obligate aerobe: An organism which requires oxygen for cellular respiration.
obligate anaerobe: An organism which uses anaerobic respiration, and dies in the presence of oxygen.
Summary

In the two to three billion years since photosynthesis added oxygen to earths atmosphere, life has become
mostly aerobic. Some organisms and types of cells retain the older, anaerobic pathways for making ATP;
these pathways comprise anaerobic respiration or fermentation.
Obligate aerobes require oxygen to make ATP. Facultative anaerobes make ATP with oxygen, but if oxygen
levels become low, they can use fermentation.
Review

1. Define fermentation.
2. What are the two paths of fermentation and how do they differentiate?
3. Describe obligate aerobes, obligate anaerobes, or facultative anaerobes, and give examples.

377

5.16. Lactic Acid Fermentation - Advanced

www.ck12.org

5.16 Lactic Acid Fermentation - Advanced


Describe lactic acid fermentation.
Describe how bacteria, including those we employ to make yogurt, make ATP in the absence of oxygen.
Discuss how your muscles continue to work for you even when your respiratory and cardiovascular system
can no longer keep up a continuous supply of oxygen.

Is there enough ATP?


Yes. But not to keep this effort up for a long time. Short spurts of sprinting are sustained by fermentation in muscle
cells. This produces just enough ATP to allow these short bursts of increased activity.
Lactic Acid Fermentation: Muscle Cells and Yogurt

For chicken or turkey dinners, do you prefer light meat or dark? Do you consider yourself a sprinter or a long
distance runner? What is the biological difference between light meat or dark meat? Or between the two types of
runners? Would you believe it has something to do with muscle color?

FIGURE 5.43
Light meat or dark?

Sprinting or en-

durance? Muscle cells know two ways


of making ATP aerobic and anaerobic
respiration.

378

www.ck12.org

Chapter 5. Metabolism - Advanced

Are Drumsticks and Athletic Prowess Related?

Muscle color reflects its specialization for aerobic or anaerobic metabolism. Although humans are obligate aerobes,
our muscle cells have not given up on ancient pathways which allow them to keep producing ATP quickly when
oxygen runs low. The difference is more pronounced in chickens and grouse ( Figure 5.44), which stand around all
day on their legs. For long periods of time, they carry out aerobic respiration in their specialized-for-endurance
red muscles. If you are familiar with grouse, you know that these birds flush with great speed over short distances.
Such sprinting flight depends on anaerobic respiration in the white cells of breast and wing muscle, allowing rapid
production of ATP in low oxygen situations.
No human muscle is all red or all white, but chances are, if you excel at sprinting short distances or at a sport such
as weight lifting, you have more white glycolytic fibers in your leg muscles, allowing anaerobic respiration. If you
run marathons, you probably have more red oxidative fibers, performing aerobic respiration.

FIGURE 5.44
Ruffed grouse use anaerobic respiration
(lactic acid fermentation) in wing and
breast muscles for quick bursts of speed
to escape from predators.

Lactic Acid Fermentation

You may have not been aware that your muscle cells can ferment. Fermentation is the process of producing ATP in
the absence of oxygen, through glycolysis alone. Recall that glycolysis breaks a glucose molecule into two pyruvate
molecules, producing a net gain of two ATP and two NADH molecules. Lactic acid fermentation is the type of
anaerobic respiration carried out by yogurt bacteria (Lactobacillus and others) and by your own muscle cells when
you work them hard and fast.
Lactic acid fermentation converts the 3-carbon pyruvate to the 3-carbon lactic acid (C3 H6 O3 ) (see Figure 5.45)
and regenerates NAD+ in the process, allowing glycolysis to continue to make ATP in low-oxygen conditions. Since
there is a limited supply of NAD+ available in any given cell, this electron acceptor must be regenerated to allow ATP
production to continue. To achieve this, NADH donates its extra electrons to the pyruvate molecules, regenerating
NAD+ . Lactic acid is formed by the reduction of pyruvate.
Lactic acid fermentation converts pyruvate to lactic acid, and regenerates NAD+ from NADH:
C3 H3 O3 (pyruvate) + NADH C3 H6 O3 (lactic acid) + NAD+
For Lactobacillus bacteria, the acid resulting from fermentation kills bacterial competitors in buttermilk, yogurt, and
some cottage cheese. The benefits extend to humans who enjoy these foods, as well ( Figure 5.47).
You may have noticed this type of fermentation in your own muscles, because muscle fatigue and pain are associated
379

5.16. Lactic Acid Fermentation - Advanced

www.ck12.org

FIGURE 5.45
Lactic acid, C3 H6 O3 .

FIGURE 5.46
Lactic acid fermentation makes ATP in the
absence of oxygen by converting glucose
to lactic acid (through a pyruvate intermediate). Making lactic acid from pyruvate
oxidizes NADH, regenerating NAD+ so
that glycolysis can continue to make more
ATP rapidly.

Each circle represents a

carbon atom.

FIGURE 5.47
Lactobacillus bacteria use the same type
of anaerobic respiration as our muscle
cells.

Lactic acid reduces competition

from other bacteria and flavors yogurt.

380

www.ck12.org

Chapter 5. Metabolism - Advanced

with lactic acid. Lactic acid accumulates in your muscle cells as fermentation proceeds during times of strenuous
exercise. During these times, your respiratory and cardiovascular system cannot transport oxygen to your muscle
cells, especially those in your legs, fast enough to maintain aerobic respiration. To allow the continuous production
of some ATP, your muscle cells use lactic acid fermentation.
Vocabulary

fermentation: Type of anaerobic respiration that includes glycolysis followed by the conversion of pyruvic
acid to one or more other compounds and the formation of NAD+ ; the process of producing ATP in the
absence of oxygen through glycolysis.
lactic acid fermentation: The process for making ATP in the absence of oxygen by converting glucose to
lactic acid.
obligate aerobe: An organism which requires oxygen for cellular respiration.
Summary

Some bacteria, including those we employ to make yogurt, make ATP using lactic acid fermentation.
Muscle cells can continue to produce ATP when oxygen runs low using lactic acid fermentation, but muscle
fatigue and pain may result.
Explore More

Use the resources below to answer the questions that follow.


Fermentation at http://www.tempeh.info/fermentation/fermentation.php
1. What is fermentation?
2. What are the fermentation end products of the following:
a. Lactobacillus.
b. Saccharomyces (yeast).
Lactic Acid Fermentation at http://www.tempeh.info/fermentation/lactic-acid-fermentation.php
1. What is the most important lactic acid producing bacteria?
2. List 5 foods produced by lactic acid fermentation.
3. Describe the fermentation process in yogurt production.
Review

1. Define lactic acid fermentation.


2. Identify yourself as a sprinter or an endurance runner and predict the type of muscle fiber (red or white)
which predominates in your body. Explain your reasoning.
3. What is the chemical equation of lactic acid fermentation?

381

5.17. Alcoholic Fermentation - Advanced

www.ck12.org

5.17 Alcoholic Fermentation - Advanced


Describe alcoholic fermentation.
Outline the process used to produce fuel from corn.
Explain how we employ anaerobic organisms to make bread, beer, and wine.

When you combine grapes and yeast, what have you begun to make?
Wine. It may be slightly more complicated than that, but you need to start with grapes and yeast, and allow a natural
fermentation process to occur. Essentially, this is respiration without oxygen.
Alcoholic Fermentation: A New Source of Energy?

Have you fueled your car with corn? You have, if you bought gas within the city of Portland, Oregon. Portland was
the first city to require that all gasoline sold within the city limits contain at least 10% ethanol. By mid-2006, nearly
6 million flex-fuel vehicles which can use gasoline blends up to 85% ethanol (E85 Figure 5.48) were traveling
US roads. This new industry employs an old crew of yeast and bacteria to make ethanol by an even older
biochemical pathway alcoholic fermentation. Alcoholic fermentation is a biochemical process in which sugars
such as glucose, fructose, and sucrose are converted into small amounts of ATP, producing ethanol and carbon
dioxide during the process.
Many people consider renewable biofuels such as ethanol a partial solution to the declining availability of nonrenewable fossil fuels. Although controversy still surrounds the true efficiency of producing fuel from corn, ethanol is
creeping into the world fuel resource picture ( Figure 5.49).
You are probably most familiar with the term fermentation in terms of alcoholic beverages. You may not have
considered that the process is actually a chemical reaction certain bacteria and yeasts use to make ATP. Like lactic
acid fermentation, alcoholic fermentation, which is also referred to ethanol fermentation, processes pyruvate
382

www.ck12.org

Chapter 5. Metabolism - Advanced

FIGURE 5.48
Ethanol provides up to 85% of the energy
needs of new flex-fuel cars. Although
its energy efficiency is still controversial,
ethanol from corn or cellulose appears to
be more renewable than fossil fuels.

FIGURE 5.49
One of the newest kids on the block,
ethanol from corn or cellulose is produced
by yeasts through alcoholic fermentation
an anaerobic type of respiration.

one step further in order to regenerate NAD+ so that glycolysis can continue to make ATP, even in low oxygen
environments. In this form of anaerobic respiration, pyruvate is broken down into ethyl alcohol (C2 H6 O) and carbon
dioxide.
C3 H3 O3 (pyruvate) + NADH C2 H5 OH (ethyl alcohol) + CO2 + NAD+

FIGURE 5.50
Alcoholic fermentation produces ethanol
and NAD+ . The NAD+ allows glycolysis
to continue making ATP.

Fermentation by Yeast

We have domesticated yeast ( Figure 5.51 and Figure 5.52) to carry out this type of anaerobic respiration for many
commercial purposes. Some yeasts, such as the bakers yeast Saccharomyces cerevisiae, actually prefer fermentation
over aerobic respiration. These yeasts will produce ethanol even under aerobic conditions. When you make bread,
you employ the yeast to make the bread rise by producing bubbles of carbon dioxide gas. Ethanol is also produced.
383

5.17. Alcoholic Fermentation - Advanced

www.ck12.org

Why do you suppose that eating bread does not intoxicate you?
Bread is not intoxicating because the bread fermentation process takes a short amount of time, only allowing for
a small amount of alcohol to be produced, most of which will evaporate during the baking process. A study was
reported to the American Chemical Society suggesting that after collecting samples from bakeries and housewives
ovens, they found that the alcohol content varied from 0.04% to 1.9%. The alcohol content of bread varies with the
kind of yeast used, the time it sets, and the temperature of baking. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC
1709087/?page=1
FIGURE 5.51
Yeasts (A) are facultative anaerobes,
which means that in the absence of oxygen, they use alcoholic fermentation to
produce ethyl alcohol and carbon dioxide. Both products are important commercially. Recall that yeasts are singlecelled eukaryotic organisms that reproduce asexually (B).

FIGURE 5.52
We employ yeasts to use their anaerobic talents to help bread rise (via bubbles of CO2 ) and grapes ferment (adding
ethanol).

Brewers of beer and wine use yeast to add alcohol to beverages. Traditional varieties of yeast not only make but
also limit the quantity of alcohol in these beverages, because above 18% by volume, alcohol becomes toxic to the
yeast itself. Wine is produced by fermentation of the natural sugars present in grapes and other kinds of fruit. Beer,
whiskey, and vodka are produced by fermentation of grain starches that have been converted to sugar by the enzyme
amylase, and rum is produced by fermentation of sugarcane. In each of these fermentations, sugars are converted
into small amounts of ATP, using and regenerating NAD+ in the process, and producing ethanol and carbon dioxide.
Scientists have recently developed new strains of yeast which can tolerate up to 25% alcohol by volume. These are
used primarily in the production of ethanol fuel.
Human use of alcoholic fermentation depends on the chemical energy remaining in pyruvate after glycolysis.
Transforming pyruvate does not add ATP to that produced in glycolysis, and for anaerobic organisms, this is the
end of the ATP-producing line. All types of anaerobic respiration yield only 2 ATP per glucose.
384

www.ck12.org

Chapter 5. Metabolism - Advanced

Vocabulary

alcoholic fermentation: The process for making ATP in the absence of oxygen; converts glucose to ethanol
and carbon dioxide.
ethanol fermentation: The process for making ATP in the absence of oxygen; converts glucose to ethanol
and carbon dioxide.
fermentation: Type of anaerobic respiration that includes glycolysis followed by the conversion of pyruvic
acid to one or more other compounds and the formation of NAD+ ; the process of producing ATP in the
absence of oxygen through glycolysis.
yeast: Eukaryotic single-celled microorganisms classified in the kingdom Fungi.
Summary

Both alcoholic and lactic acid fermentation pathways change pyruvate in order to continue producing ATP by
glycolysis.
Alcoholic fermentation is a type of anaerobic respiration that includes glycolysis followed by the conversion
of pyruvic acid to ethanol and carbon dioxide and the regeneration of NAD+ from NADH.
Explore More

Use this resource to answer the questions that follow.


Alcoholic Fermentation at http://www.tempeh.info/fermentation/alcohol-fermentation.php
1.
2.
3.
4.

What is alcoholic fermentation?


What is the fate of pyruvate during this process?
What is this process used for?
Briefly describe how bread rises and how alcohol is produced?

Review

1. Human cells cannot carry out alcoholic fermentation, yet we use it for many purposes. Analyze its importance
to human life.
2. Indicate the maximum alcohol content of wine and beer, and explain the reason for this limit.
3. Outline the process used to produce fuel from corn and explain why some consider this fuel renewable and
preferable to fossil fuels. Research the pros and cons of this fuel.
4. Explain how fermentation is used to make bread.
5. Explain why both alcoholic and lactic acid fermentation must change pyruvic acid, even though no energy is
gained in this conversion.

385

5.18. Aerobic vs. Anaerobic Respiration - Advanced

www.ck12.org

5.18 Aerobic vs. Anaerobic Respiration - Advanced


Compare the energy efficiency of aerobic cellular respiration to that of fermentation.
List the advantages of anaerobic over aerobic respiration.
Explain why vertebrate muscles use both aerobic and anaerobic pathways to make ATP.

Why oxygen?
Anaerobic vs. aerobic. Which is more efficient? It does depend on oxygen. Why do ALL your cells need oxygen?
Oxygen is the final electron acceptor at the end of the electron transport chain of aerobic respiration. In the absence
of oxygen, only a few ATP are produced from glucose. In the presence of oxygen, many more ATP are made.
Aerobic vs. Anaerobic Respiration: A Comparison

As aerobes in a world of aerobic organisms, we tend to consider aerobic respiration better than fermentation.
In some ways, it is. However, anaerobic respiration has persisted far longer on this planet, through major changes
in atmosphere and life. There must be value in this alternative way of making ATP.
A major argument in favor of aerobic over anaerobic respiration is overall energy production. Without oxygen,
organisms can only break a 6-carbon glucose into two 3-carbon pyruvate molecules. As we saw earlier, glycolysis
releases only enough energy to produce two (net) ATPs per molecule of glucose. In anaerobic respiration, this
is where ATP production stops. There is a final total of only two ATPs produced per molecule of glucose. This
anaerobic process does occur very quickly though. For example, it lets your muscles get the energy they need for
short bursts of intense activity.
Aerobic respiration, on the other hand, produces ATP more slowly. It does, however, break glucose all the way down
to CO2 , producing up to 38 ATPs. Membrane transport (active transport) costs can slightly reduce this theoretical
386

www.ck12.org

Chapter 5. Metabolism - Advanced

FIGURE 5.53
E. coli bacteria are anaerobic bacteria
that live in the human digestive tract.

FIGURE 5.54
The muscles of these hurdlers need to
use anaerobic respiration for energy. It
gives them the energy they need for the
short-term, intense activity of this sport.

yield, but aerobic respiration consistently produces at least 15 times as much ATP as anaerobic respiration. This vast
increase in energy production probably explains why aerobic organisms have come to dominate life on earth. It may
also explain how organisms were able to increase in size, adding multicellularity and great diversity.
However, anaerobic pathways do persist, and obligate anaerobes have survived over 2 billion years beyond the
evolution of aerobic respiration. So there must be advantages to fermentation. What are these advantages?
One advantage is available to organisms occupying the few anoxic (lacking oxygen) niches remaining on earth.
Oxygen remains the highly reactive, toxic gas which caused the Oxygen Catastrophe. Aerobic organisms have
evolved a few necessary materials, namely enzymes and antioxidants, to protect themselves. Organisms living in
anoxic niches do not run the risk of oxygen exposure, so they do not need to spend energy to build these elaborate
chemicals.
Individual cells which experience anoxic conditions face greater challenges. As demonstrated by lactic acid fermentation, muscle cells still remember anaerobic respiration, using this fermentation to make ATP in low-oxygen
conditions, regenerating NAD+ during this process. However, other cells, like brain cells do not remember
387

5.18. Aerobic vs. Anaerobic Respiration - Advanced

www.ck12.org

anaerobic respiration, and consequently cannot make any ATP without oxygen. This explains why death follows
for most humans who endure more than four minutes without oxygen.
Variation in muscle cells gives further insight into some benefits of anaerobic respiration. In vertebrate muscles,
lactic acid fermentation allows muscles to produce ATP quickly during short bursts of strenuous activity. Muscle
cells specialized for this type of activity show differences in structure as well as chemistry. Red muscle fibers are
dark because they have a rich blood supply for a steady supply of oxygen, and a protein, myoglobin, which holds
extra oxygen. They also contain more mitochondria, the organelle in which the Krebs cycle and electron transport
chain conclude aerobic respiration. This is endurance muscle. White muscle cells are light because they lack the
rich blood supply, have fewer mitochondria, and store the carbohydrate glycogen rather than oxygen. This is muscle
built for sprinting.
Each type of muscle fiber has advantages and disadvantages, which reflect their differing biochemical pathways.
Aerobic respiration in red muscles full of mitochondria, produces a great deal of ATP from far less glucose - but
slowly, over a long time. Anaerobic respiration in white muscle cells full of carbohydrates, produces ATP rapidly
for quick bursts of speed, but a predator who continues pursuit may eventually catch a white-muscled prey.
Summary

In summary, aerobic and anaerobic respiration each have advantages under specific conditions. Aerobic respiration
produces far more ATP, but risks exposure to oxygen toxicity. Anaerobic respiration is less energy-efficient, but
allows survival in habitats which lack oxygen. Within the human body, both are important to muscle function.
Muscle cells specialized for aerobic respiration provide endurance, and those specialized for lactic acid fermentation
support short but intense energy expenditures. Both ways of making ATP play critical roles in life on earth.
Vocabulary

aerobic respiration: Cellular respiration in the presence of oxygen; produces 36-38 ATP molecules/glucose.
anaerobic respiration: Cellular respiration in the absence of oxygen; produces 2 ATP molecules/glucose;
fermentation.
antioxidant: A molecule that inhibits the oxidation of other molecules.
fermentation: Type of anaerobic respiration that includes glycolysis followed by the conversion of pyruvic
acid to one or more other compounds and the formation of NAD+ ; the process of producing ATP in the
absence of oxygen through glycolysis.
glycogen: A carbohydrate used for long-term energy storage in animal cells; human muscle and liver cells
store energy in this form.
lactic acid fermentation: The process for making ATP in the absence of oxygen; converts glucose to lactic
acid.
obligate anaerobe: An organism which uses anaerobic respiration, and dies in the presence of oxygen.
Summary

Aerobic respiration is far more energy-efficient than anaerobic respiration.


Aerobic processes produce up to 38 ATP per glucose. Anaerobic processes yield only 2 ATP per glucose.
388

www.ck12.org

Chapter 5. Metabolism - Advanced

Review

1. What is the main advantage of aerobic respiration? Of anaerobic respiration?


2. Tanya is on the high school track team and runs the 100-meter sprint. Marissa is on the cross-country team
and runs 5-kilometer races. Explain which type of respiration the muscle cells in each runners legs use.
3. Construct a chart which compares aerobic to anaerobic fermentation in the following qualities; definition, cells
that use it, amount of energy released, reactants, products, stages and site of reactions.

389

5.19. References

www.ck12.org

5.19 References
1. Laura Guerin. Photosynthesis . CC BY-NC 3.0
2. Mariana Ruiz Villarreal (LadyofHats) for CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
3. (a) Courtesy of National Park Service; (b) Courtesy of Shane Anderson, National Oceanic and Atmospheric
Administration; (c) Courtesy of US Environmental Protection Agency. (a) http://commons.wikimedia.org/wik
i/File:Riesenmammutbaum.jpg; (b) http://commons.wikimedia.org/wiki/File:Kelp_300.jpg; (c) http://commons
.wikimedia.org/wiki/File:Anabaenaflosaquae_EPA.jpg . Public Domain
4. Mariana Ruiz Villarreal (LadyofHats) for CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
5. Charles Fisher. http://commons.wikimedia.org/wiki/File:Lamellibrachia_luymesi1.png . CC BY 2.5
6. Laura Guerin. CK-12 Foundation . CC BY-NC 3.0
7. User:NEUROtiker/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Alpha-D-Glucopyranose
.svg . Public Domain
8. Laura Guerin, using structure by User:Mysid/Wikimedia Commons. CK-12 Foundation (structure available
at http://commons.wikimedia.org/wiki/File:ATP_structure.svg) . CC BY-NC 3.0 (structure released into the
public domain)
9. CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
10. Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
11. CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
12. CK-12 Foundation. Joseph Priestlys bell jar experiment . CC BY-NC 3.0
13. Top: Gernot A. Molitor (Flickr:Nuuuuuuuuuuul); Bottom: that one doood. Top: http://www.flickr.com/photo
s/tonreg/5853761429/; Bottom: http://commons.wikimedia.org/wiki/File:Wet_Elodea.jpg . CC BY 2.0
14. Left: User:ItsJustMe/Wikipedia; Right: CK-12 Foundation. Left: http://commons.wikimedia.org/wiki/File
:Chloroplast-new.jpg; Right: CK-12 Foundation . Left: Public Domain; Right: CC BY-NC 3.0
15. Mariana Ruiz Villarreal (LadyofHats) for CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
16. User:Andreas 06/Wikimedia Commons. http://en.wikipedia.org/wiki/Image:Chlorophyll_structure.png . Public Domain
17. User:Lanzi/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Lichtabsorbtion_eines_buchenb
lattes.svg . Public Domain
18. Photograph of Earth: NASA/Apollo 17 crew. http://commons.wikimedia.org/wiki/File:The_Earth_seen_fr
om_Apollo_17.jpg . Public Domain
19. User:Tameeria/Wikipedia. http://commons.wikimedia.org/wiki/File:Thylakoid_membrane.png . Public Domain
20. Top: User:Maksim/Wikimedia Commons; Bottom: Alex Costa. Top: http://commons.wikimedia.org/wiki/F
ile:Leaf_anatomy.jpg; Bottom: http://commons.wikimedia.org/wiki/File:Plant_stoma_guard_cells.png . Top:
Public Domain; Bottom: CC BY 2.5
21. Left to right: John Talbot (Flickr:jbctalbot); Flickr:lobo235; Jill Robidoux (Flickr:jylcat). Left to right: http:
//www.flickr.com/photos/laserstars/503948601/; http://www.flickr.com/photos/lobo235/76154752/; http://ww
w.flickr.com/photos/jylcat/562393266/ . CC BY 2.0
22. Laura Guerin. CK-12 Foundation . CC BY-NC 3.0
23. Zachary Wilson. CK-12 Foundation . CC BY-NC 3.0
24. Courtesy of the NOAA Okeanos Explorer Program, Galapagos Rift Expedition 2011. http://www.flickr.co
m/photos/noaaphotolib/9664056402/ . CC BY 2.0
25. Left: User:BruceBlaus/Wikimedia Commons; Center: Geoff Gallice; Right: Piet Spaans. Left: http://com
mons.wikimedia.org/wiki/File:Blausen_0770_RespiratorySystem_02.png; Center: http://www.flickr.com/ph
otos/dejeuxx/6407247699/; Right: http://commons.wikimedia.org/wiki/File:MesotritonAlpestrisLarva1.JPG
. Left: CC BY 3.0; Center: CC BY 2.0; Right: CC BY 2.5
390

www.ck12.org
26.
27.
28.
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.

43.
44.
45.
46.
47.
48.
49.
50.
51.
52.

53.
54.

Chapter 5. Metabolism - Advanced

Erik Halfacre. http://www.flickr.com/photos/erikhalfacre/8730193007/ . CC BY 2.0


Brandon Fesser. http://commons.wikimedia.org/wiki/Image:Bromothymol_blue_colors.jpg . Public Domain
Hana Zavadska. CK-12 Foundation . CC BY-NC 3.0
User:NEUROtiker/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Adenosintriphosphat_proto
niert.svg . Public Domain
Image copyright somersault1824, 2014. Illustration of an animal cell in cross section . Used under license
from Shutterstock.com
Mariana Ruiz Villarreal (LadyofHats) for CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Courtesy of the Centers for Disease Control and Prevention. http://commons.wikimedia.org/wiki/File:Clost
ridium_tetani_01.png . Public Domain
User:Mikm/Wikipedia. http://commons.wikimedia.org/wiki/File:Cellular_respiration_flowchart_%28en%29.s
vg . Public Domain
Image copyright somersault1824, 2014. Illustration of an animal cell in cross section . Used under license
from Shutterstock.com
Hana Zavadska. CK-12 Foundation . CC BY-NC 3.0
Laura Guerin. CK-12 Foundation . CC BY-NC 3.0
Mariana Ruiz Villarreal (User:LadyofHats/Wikimedia Commons). http://commons.wikimedia.org/wiki/Fi
le:Animal_mitochondrion_diagram_en.svg . Public Domain
User:Tameeria/Wikipedia. http://commons.wikimedia.org/wiki/File:Oxygen_atmosphere.png . Public Domain
Joy Sheng. CK-12 Foundation . CC BY-NC 3.0
Laura Guerin. CK-12 Foundation . CC BY-NC 3.0
Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Bread: Flickr:PhotoDawg; Ethanol gas: Flickr:diaper; Red wine: George Hodan; Yogurt: Flickr:Mom the
Barbarian; Body builder: Lin Mei. Bread:http://commons.wikimedia.org/wiki/File:Mixed_bread_loaves.jpg;
Ethanol gas: http://www.flickr.com/photos/diaper/3799581840/; Red wine: http://www.publicdomainpictures
.net/view-image.php?image=35183&picture=glass-of-red-wine; Yogurt: http://www.flickr.com/photos/momt
hebarbarian/2441500/; Body builder: http://www.flickr.com/photos/leomei/2651904068/ . Bread, Ethanol
gas, Yogurt, Muscle builder: CC BY 2.0; Red wine: Public Domain
Left: Bonnie Bogle; Right: Flickr:davidd. Left: http://www.flickr.com/photos/bonniebogle/2064488794/;
Right: http://www.flickr.com/photos/puuikibeach/7721993052/ . CC BY 2.0
Flickr:Seabamirum. http://www.flickr.com/photos/seabamirum/3447982213/ . CC BY 2.0
CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
Hana Zavadska. CK-12 Foundation . CC BY-NC 3.0
Flickr:Mom the Barbarian. http://www.flickr.com/photos/momthebarbarian/2441500/ . CC BY 2.0
Car: Jeff Egnaczyk; Gas pump: Flickr:diaper. Car: http://www.flickr.com/photos/post406/252879466/; Gas
pump: http://www.flickr.com/photos/diaper/3799581840/ . CC BY 2.0
User:Delphi234/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Total_World_Energy_Consum
ption_by_Source_2011.png . Public Domain
Hana Zavadska. CK-12 Foundation . CC BY-NC 3.0
(A) User:Masur/Wikimedia Commons; (B) Laura Guerin. (A) http://commons.wikimedia.org/wiki/File:S_cer
evisiae_under_DIC_microscopy.jpg; (B) CK-12 Foundation . (A) Public Domain; (B) CC BY-NC 3.0
Bread: Flickr:FotoDawg; Red wine: Red wine: George Hodan. Bread: http://commons.wikimedia.org/wiki
/File:Mixed_bread_loaves.jpg; Red wine: http://www.publicdomainpictures.net/view-image.php?image=351
83&picture=glass-of-red-wine . Bread: CC BY 2.0; Red wine: Public Domain
User:Mattosaurus/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Diverse_e_Coli.png . Public Domain
Image copyright bikeriderlondon, 2014. http://www.shutterstock.com . Used under license from Shutterstock.com

391

www.ck12.org

C HAPTER

6
Cell Division - Advanced

Chapter Outline

392

6.1

C ELL D IVISION - A DVANCED

6.2

P ROKARYOTIC C ELL D IVISION - A DVANCED

6.3

E UKARYOTIC C ELL D IVISION - A DVANCED

6.4

C HROMOSOMAL D IVISION - A DVANCED

6.5

C ELL C YCLE - A DVANCED

6.6

M ITOSIS - A DVANCED

6.7

C ELL C YCLE R EGULATION - A DVANCED

6.8

G ENE R EGULATION AND C ANCER - A DVANCED

6.9

A SEXUAL R EPRODUCTION - A DVANCED

6.10

S EXUAL R EPRODUCTION - A DVANCED

6.11

M EIOSIS - A DVANCED

6.12

G ENETIC VARIATION - A DVANCED

6.13

G AMETOGENESIS - A DVANCED

6.14

S EXUAL L IFE C YCLES - A DVANCED

6.15

R EFERENCES

www.ck12.org

Chapter 6. Cell Division - Advanced

Introduction

What do you think this colorful picture shows? If you guessed that its a picture of a cell undergoing cell division,
you are right. In fact, the picture is an image of a lung cell stained with fluorescent dyes undergoing mitosis,
specifically during early anaphase. You will read about mitosis, a type of cell division, in these concepts. The
separating chromosomes and the spindles are visible in this photo.
Cell division is just one of the stages that all cells go through during their life. This includes cells that are harmful,
such as cancer cells. Cancer cells divide more often than normal cells, and grow out of control. In fact, this is how
cancer cells cause illness. In these concepts, you will read about how cells divide, what other stages cells go through,
and what causes cancer cells to divide out of control and harm the body.

393

6.1. Cell Division - Advanced

www.ck12.org

6.1 Cell Division - Advanced


Define cell division.

Where do cells come from?


No matter what the cell, all cells come from preexisting cells through the process of cell division. This is one of the