Ty Jacobs Bio Study Guide

Table of contents

Cell and molecular

biology

Intro to biomolecules
Water
Carbohydrates
Lipids
Nucleic acids
Proteins
Eukaryotic cell structure
Prokaryotic cell structure
Prokaryotes vs Eukaryotes
Viruses and Prions
Diffusion and Osmosis
Substrate Transport
Cell signalling
Energy in the cell
Glycolysis
Pyruvate decarboxylation
Oxidative phosphorylation
Photosynthesis
Other sources of energy

1
3
8
13
17
22
34
44
49
50
53
56
58
64
70
75
80
86
93

Cell cycle and cancer

Mitosis and meiosis
Origins of life
Cell/Molecular biology lab

95
100
107
113

Genetics

115

Evolution and
ecology

Evolution
The biosphere
Behavior
Population ecology
Community ecology
Conservation biology

156
173
184
190
195
205

Diversity of life

Archaea and bacteria

Prokaryotes and Protists
Plant and fungal diversity

141
208
218

Developmental
biology

Anatomy and
physiology

Invertebrate diversity
Vertebrate diversity
Plant structure and function

229
245
252

Animal reproduction
Embryonic development

282
291

Body organization & tissues

Respiratory systems
Circulatory systems
Digestive systems
Excretory systems
Nervous systems
Immune systems
Muscular systems
Sensory systems
Skeletal systems
Integumentary systems
Endocrine systems

301
305
314
324
334
342
354
364
371
373
377
380

Life's molecular diversity is based on the properties of carbon

Why is carbon great?
Carbon is unparalleled in its ability to from large and complex molecules due to its
capacity to make 4 bonds.
Almost all of the molecules in the cell are composed of carbon. Carbon based molecules
are called organic compounds.
How can carbon molecules vary?
The chain of carbon atoms in an organic molecule is called a carbon skeleton.
Length: carbon skeletons vary in length
Branching: skeletons may be unbranched or branched
Double or triple bonds: skeletons may have double or triple bonds
Rings: skeletons may be arranged in rings (i.e. cyclohexane, benzene)
Compounds composed of only hydrogen and carbon atoms are called hydrocarbons.
Two molecules might have the same molecular formulas, but different three-dimensional
shapes due to the locations of certain bonds.
Compound with the same formula but different structural arrangements are called
isomers.
A few chemical groups are key to the functioning of biological molecules
Chemical groups that are important to reactivity and structure are called functional groups.
The table below shows the 6 most popular functional groups found in biomolecules.

Cells make a huge number of large molecules from a limited set of polymers
What are macromolecules?
Molecules of major classes (i.e. carbohydrates, proteins, lipids, nucleic acids) are called
macromolecules.
Cells make most of their macromolecules by joining together smaller molecules into
chains called polymers. The building blocks of polymers are called monomers.
Types of monomers:

2
Carbohydates: monosaccharides
Nucleic acids: nucleotides
Proteins: amino acids
Lipids: glycerol and fatty acids
Making polymers
Cells link monomers together to form polymers by a dehydration reaction, a reaction
that removes a molecule of water.
For each monomer added to a chain, a water molecule is released.
Dehydration reactions are the same regardless of the specific monomers and the type of
polymer the cell is producing.

Breaking polymers
Cells not only make macromolecules but also have to break them down. This digestion
process is called hydrolysis.
Essentially the reverse of a dehydration reaction, hydrolysis involves adding a water
molecule to break a bond.
One water molecule is used up every time a bond between two monomers is broken.

The diversity of polymers

Remarkably, a cell makes all its thousands of different macromolecules from a small list
of ingredientsabout 40 to 50 common components and a few others that are rare.
The key to the great diversity of polymers is arrangementvariation in the sequence in
which monomers are struck together.
The variety in polymers account for the uniqueness of each organism.

3
1. Weak Interactions in Aqueous Systems
a) Hydrogen bonding gives water its unusual properties
Each hydrogen atom of a water molecule shares an electron pair with the central oxygen
atom. The H-O-H bond angle is 104.5 degrees.
The oxygen nucleus attracts electrons more strongly than does the hydrogen nucleus;
that is, oxygen is more electronegative. The result of this unequal electron sharing is two
electric dipoles in the water molecule, one along each of the H-O bonds; each hydrogen
atom bears a partial positive charge and the oxygen atom bears a partial negative charge
equal in magnitude.

As a result, there is an electrostatic attraction between the oxygen atom of one water
molecule and the hydrogen of another, called a hydrogen bond. It is a weak bond, about
10% covalent and 90% electrostatic.
Hydrogen bonds in water have a very short lifetime, but they are constantly breaking
and forming. The sum of all the hydrogen bonds between water molecules confers great
internal cohesion on liquid water.
The nearly tetrahedral arrangement of the orbitals about the oxygen atom allows each
water molecule to form hydrogen bonds with as many as four neighboring water
molecules.
Hydrogen bonds account for a higher melting point because much thermal energy is
required to break a sufficient portion of hydrogen bonds to destabilize the crystal lattice
of ice.
During melting or evaporation, the entropy of the system increases as the water
molecules become less orderly.
b) Water forms hydrogen bonds with polar solutes
Hydrogen bonds form between an electronegative atom (the hydrogen acceptor, usually
oxygen or nitrogen) and a hydrogen atom covalently bonded to another electronegative
atom (the hydrogen donor) in the same or another molecule.
Hydrogen bonded to carbons do not participate in hydrogen bonding.
4 important hydrogen bonds in our body:
Between the hydroxyl group of an alcohol and water
Between the carbonyl group of a ketone and water
Between peptide groups in polypeptides
Between complementary bases of DNA

Hydrogen bonds are strongest when the bonded molecules are oriented to maximize
electrostatic reaction, which occurs when the hydrogen atom and the two atoms that
share it are in a straight linethat is, when the acceptor atom is in line with the covalent
bond between the donor atom and H.

c) Water interacts electrostatically with charged solutes

Compounds that dissolve easily in water are hydrophilic whereas nonpolar solvents that
does not dissolve easily in water are hydrophobic.
Water easily dissolves charged molecules; it destabilizes the charge by surrounding the
individual ions. Water has a very high dielectric constant, a physical property that
reflects the number of dipoles in a solvent. By this being high, it is effective in screening
electrostatic reactions between dissolved ions.

5
d) Water readily dissolves polar solutes
Because water is a polar molecule, it can readily dissolve other polar solutes (like
dissolves like).
e) Water is the solvent of life
Water readily dissolves ionic and polar solvents.
Many organic molecules are either ionic or polar (i.e. proteins, sugars, etc.)
As the solvent inside all cells, in blood, and in plant sap, water dissolves an enormous
variety of solutes necessary for life.
f) Nonpolar gasses are poorly soluble in water.
g) Nonpolar compounds force energetically unfavorable changes in the structure of water.
When water is mixed with a nonpolar compound, two phases form; neither liquid is
soluble in the other.
The nonpolar compounds interfere with the hydrogen bonding among water molecules.
Dissolving hydrophobic molecules in water produces a measurable decrease in entropy.
Water molecules in the immediate vicinity of a nonpolar solute are constrained in their
possible orientations as they form a highly ordered cage-like shell around each solute
molecule. The number of ordered water molecules, and therefore the magnitude of of
the entropy decrease, is proportional to the surface area of the hydrophobic solute
enclosed within the cage of water molecules.
Amphipathic compounds contain regions that are polar and regions that are nonpolar.
When an amphipathic compound is mixed with water, the polar, hydrophilic region
interacts favorably with water and tends to dissolve, but the nonpolar, hydrophobic
region tends to avoid contact with water. The nonpolar regions cluster together to
present the smallest hydrophobic area to the aqueous solvent, and the polar regions
are arranged to maximize their interaction with the solvent. These structures are
called micelles. The forces that hold the nonpolar regions of the molecules together
are called hydrophobic interactions.
2. Ionization of Water, Weak acids, and weak bases
a) Pure water is slightly ionized
When any acid is dissolved in water, they contribute H+ by ionizing; bases consume H+
by becoming protonated. The total hydrogen ion concentration from all sources is
measurable and is expressed as the pH of the solution.
Hydrogen ions formed in water are immediately hydrated to form hydronium ions
(H3O+). Hydrogen bonding between water molecules makes the hydration of
dissociating protons virtually instantaneous.
No individual proton moves very far through the solution, but a series of proton hops
between hydrogen-bonded water molecules causes the net movement of a proton over a
long distance in a remarkably short time.
As a result of the high ionic mobility of H+, the acid-base reactions in aqueous solutions
are exceptionally fast.
b) The pH and blood
When the pH of the blood often falls below the normal value of 7.4, this condition is
called acidosis. When the pH of the blood is higher than normal, the condition is called
alkalosis.
3. Cohesion vs Adhesion and Capillary Action
a) Cohesion
Cohesion water is attracted to other water molecules. Defined as the stickiness that
water molecules have for eachother.

6
Cohesion makes a water droplet a drop.
b) Adhesion
Adhesion water is attracted to other substances (namely polar ones).
c) Capillary action
Capillary action is the movement of water within the spaces of a porous material
against the flow of gravity. This is due to adhesion and cohesion.
4. Water's hydrogen bonds moderate temperature

a) Water's high specific heat

The ability of water to stabilize temperature stems from its relatively high specific heat.
The specific heat of a substance is defined as the amount of heat that must be absorbed
for 1g of that substance to change its temperature by 1 degree Celsius.
This means that water will change its temperature less than other liquids when it absorbs
or loses a given amount of heat.
The high specific heat of water can be due to its hydrogen bonding. Heat must be
absorbed to break hydrogen bonds. Since hydrogen bonds are strong, lots of heat is
required to make this happen.
5. Ice is less dense than liquid water
a) Water exists on Earth in the form of a gas (water vapor), liquid, or solid.
b) Unlike most substances, water is less dense as a solid than as a liquid. This is because of
hydrogen bonding.
As water freezes, each molecule forms stable hydrogen bond with their neighbors,
creating a three-dimensional crystal. This keeps water molecules relatively far apart
from one another, which causes a decrease in density.
In liquid form, water atoms constantly break and re-form hydrogen bonds. This disorder
causes water molecules to be packed tightly in a given space.

8
A. What are carbohydrates?
I. The name carbohydrate refers to a class of molecules ranging from the small sugar
molecules dissolved in soft drinks to large polysaccharides, such as the starch molecules we
consume in pasta and potatoes.
B. Monosaccharides and Disaccharides
I. Monosaccharides are the simplest carbohydrates
a. Carbohydrate monomers are monosaccharides. They generally have the moleuclar
formulas that are some multiple of CH2O (i.e. C6H12O6).
II. The two families of monosaccharides are aldoses and ketoses
a. The backbones of common monosaccharides are unbranched carbon chains in which all
the carbon atoms are linked by single bonds. In this form, one of the carbon atoms is
double-bonded to an oxygen atom to form a carbonyl groups; each of the other carbon
atoms has a hydroxyl group.
i. If the carbonyl group is at the end of a carbon chain, the monosaccharide is an
aldose (aldehyde).
ii. If the carbonyl group is at any other position, the monosaccharide is a ketose
(ketone).

III.

Monosaccharides have asymmetric centers

a. All of the monosaccharides contain one or more chiral carbon atoms.
b. D/L configuration is based on the chiral center most distant from the carbonyl carbon.
Those with the OH on the left is the L-stereoisomer and those with the OH on the right
is the D-stereoisomer. (The molecules shown above are both D-stereoisomers)
c. Two sugars that differ only in the configuration around one carbon atom are called
epimers. Note that the carbon that differs among the two molecules is NOT the
anomeric carbon.
IV. The common monosaccharides have cyclic structures
a. In aqueous solution, all monosaccharides with five or more carbon atoms in the
backbone occur predominantly as cyclic structures in which the carbonyl group has
formed a covalent bond with the oxygen of a hydroxyl group along the chain.
b. The formation of these ring compounds is the result of a general reaction between
alcohols and aldehydes or ketones to form derivatives called hemiacitals or hemiketals.
i. hemi meaning that the alcohol and the aldehyde or ketone are all in the same
molecule.
c. The reaction with the first molecule of alcohol creates an additional chiral center (the
carbonyl carbon). The alcohol can add in either one of two ways, attacking either the
front or the back of the carbonyl carbon, meaning that two stereoisomeric
configurations (denoted alpha and beta) can be produced. You don't need to distinguish
between alpha and beta; just know there are two different stereoisomers.

9
d. Isomeric forms of monosaccharides that differ only in their configuration about the
anomeric carbon are called anomers, and the carbonyl carbon is called the anomeric
carbon. In the picture below C1 in all 3 molecules is the anomeric carbon.

e. Six-membered ring compounds are called pyranoses (formed from aldohexoses) and 5membered ring compounds are called furanoses (formed from aldopentoses and
ketohexoses).

V. Disaccharides contain a glycosidic bond

a. Disaccharides consist of two monosaccharides joined covalently by an O-glycosidic
bond, which is formed when a hydroxyl group of one sugar molecule reacts with the
anomeric carbon of the other. Water is removed as a byproduct.
b. A glycosidic linkage is named after the anomers of monosaccharides (alpha or beta
units) involved in the linkage. The numbering of a glycosidc linkage refers to the
carbons from each monomer that are involved in the bond.

c. (picture) Alpha 1--> 4 linkage: both monomers are alpha anomers and the glycosidic
linkage takes place between C-1 of one anomer and C-4 of the second anomer.

10
C. Polysaccharides
I. Introduction
a. Polysaccharides, also called glycans, differ from each other in the identity of their
recurring monosaccharide units, in length of their chains, in the types of bonds linking
the units, and in the degree of branching.
i. Homopolysaccharides contain only a single monomeric species.
ii. Heteropolysaccharides contain two or more different kinds.
b. Polysaccharides do not have defining molecular weights.
II. Some homopolysaccharides are stored forms of fuel
a. Starch in plant cells and glycogen in animal cells are the most important storage
polysaccharides.
i. They are both heavily hydrated, because they have many exposed OH groups
available to hydrogen-bond with water.
b. Starch contains two types of glucose polymer, amylose and amylopectin.
i. Amylose consists of long, unbranched chains of D-glucose residues connected by
alpha14 linkages.
ii. Amylopectin consists of highly branched chains (branch points occurring every 24
to 30 residues). The glucose residues are connected by alpha14 linkages and the
branch points are connected by alpha16 linkages.

c. Glycogen is the main storage polysaccharide of animal cells. Glycogen is a polymer of

alpha14 linked subunits of glucose, with alpha16 linked branches, but glycogen is
more extensively branched (every 8-12 residues) and more compact than starch.
i. When glycogen is used as an energy source, glucose units are removed one at a time.
ii. Reacts positively with iodine to turn purple.

11
III. Some homopolysaccharides serve structural roles
a. Cellulose is a fibrous, tough, water-insoluble substance, found in the cell walls of
plants.
i. It is a linear, unbranched homopolysaccharide. All the glucose residues have a beta
configuration.
ii. Each monomer is turned 180 degrees around the glycosidic bond; this gives the
polymer a linear, extended chain.
iii. Cellulose contains many intrachain and interchain hydrogen bonds, but no interchain
covalent bonds.
iv. The supermoleuclar structure has high tensile strength and low water content (no
place for water hydrogen bonds)

b. Chitin is a lnear homopolysaccharide composed of N-acetylglucosamine residues in a

(beta14) linkage.
i. The only chemical difference from cellulose is the replacement of the hydroxyl
group C-2 with an acetylated amino group.
ii. It is the principal component of the hard exoskeletons of arthropods.

IV.Bacterial and algal cell walls contain structural heteropolysaccharides

a. The rigid component of bacterial cell walls, peptidoglycan, is a heteropolymer of
alternating beta14 linked N-acetylglucosamine and N-acetylmuramic acid residues.
i. The linear polymers lie side by side in the cell wall, cross-linked by short peptides,
the exact structure depends on species.
ii. Penicillin and related antibiotics kill bacteria by preventing synthesis of the cross
links, leaving the cell wall to weak to resist osmotic lysis.

12
V. Glycosaminoglycans are heteropolysaccharides of the extracellular matrix
a. The extracellular space in the tissues of multicellular animals is filled with a gel-like
material, the extracellular matrix (ECM), which holds cells together and provides a
porous pathway for the diffusion of nutrients and oxygen to individual cells.
i. The ECM is composed of an interlocking network of heteropolysaccharides and
fibrous proteins. These heteropolysaccharides are called glycosaminoglycans
(GAG); they are unique to animals and are not found in plants.
D. Glycoconjugates: Proteoglycans, Glycoproteins, and Glycophingolipids
I. Types of glycoconjugates
a. A glycoconjugate is a carbohydrate covalently joined to a protein or a lipid (these
molecules are biologically active).
b. Proteoglycans are macromolecules of the cell surface or ECM where one or more
sulfated GAG chains are joined covalently to a membrane protein or a secreted protein.
i. They bind to ECM proteins through electrostatic interactions (GAGs are very
negative).
c. Glycoproteins have one or more several oligosaccharides of varying complexity joined
covalently to a protein. They are usually found on the outer face of the plasma
membrane.
d. Glycosphingolipids are plasma membrane components in which the hydrophilic head
groups are oligosaccharides.
II. Proteoglycans are glycoasminoglcyancontaining macromoleucles of the cell surface and
ECM
a. Some proteoglycans can form proteoglycan aggregates, enormous supramolecular
assemblies of many core proteins bound to a single molecule of hyaluronan.

13
A. Storage Lipids
I. Fatty Acids are Hydrocarbon Derivatives
a. Fatty acids are hydrocarbon derivatives. They are carboxylic acids with hydrocarbon
chains ranging from 4 to 36 carbons long.
i. In some fatty acids, this chain is unbranched and fully saturated (contains no double
bonds); in others, the chain contains one or more double bonds (unsaturated).

b. The most commonly occurring fatty acids have even number of carbon atoms in an
unbranched chain of 12 to 24 carbons.
i. The even number of carbons are a result of bio synthesis from acetate (2 carbon unit)
c. In most monounsaturated (one double bond) fatty acids, the double bond is between C9 and C-10 and the other double bonds of polyunsaturated (multiple double bonds)
fatty acids are usually at C-12 and C-15.
d. Polyunsaturated fatty acid double bonds are separated by a methylene group meaning,
--CH=CH--CH2--CH=CH-e. The physical properties of the fatty acids, and the compounds that contain them, are
largely determined by the length and degree of unsaturation of the hydrocarbon chain.
f. The nonpolar hydrocarbon chain accounts for the poor solubility of fatty acids in water.
i. The longer the fatty acyl chain and the fewer the double bonds, the lower is the
solubility in water. The carboxylic acid group is polar (and ionized at neutral pH)
and accounts for the slight solubility of short-chain fatty acids in water.
g. At room temperature, saturated fatty acids are waxy and unsaturated fatty acids are oily.
h. Melting points are also strongly influenced by the length and degree of unsaturation of
the hydrocabon chain.
i. In the fully saturated compounds, free rotation around each carbon-carbon bond
gives the hydrocarbon chain great flexibility; the most stable conformation is the
fully extended form, in which the steric hindrance of neighboring atoms is
minimized. In water, these molecules can pack together tightly in nearly crystalline
arrays.
ii. In unsaturated fatty acids, a cis double bond forces a kink in the hydrocabon chain.
Fatty acids with these kinks cannot pack together as tightly as saturated fatty acids,
and their interactions with each other are therefore weaker. As a result, unsaturated
fatty acids have way lower melting points.

14
II. Triacylglycerols
a. The simplest lipids constructed from fatty acids are the triacylglycerols, which are
composed of three fatty acids each in ester linkage with a single glycerol.
b. Most triacylglycerols are are mixed; they contain two or three different fatty acids.
c. Because the polar hydroxyls of glycerol and the polar carboxylates of the fatty acids are
bound in ester linkages, triacylglycerols are nonpolar, hydrophobic molecules,
essentially insoluble in water.

III.

Triacylglycerols provide stored energy and insulation

a. There are two significant advantages to using tryacylglycerols as stored fuels, rather
than carbohydrates.
i. First, the carbon atoms of fatty acids are more reduced than those of sugars, and
oxidation of tryacylglycerols yields 2x more energy, as the oxidation of
carbohydrates.
ii. Second, because triacylglycerols are hydrophobic and therefore unhydrated, the
organism that carries fat as fuel does not have to carry the extra weight of water of
hydration that is associated with sugars.
B. Structural lipids in membranes
I. Phospholipids
a. Phospholipids are the main building block of plasma membranes. Phospholipids are
amphipathic, meaning that they contain hydrophobic sections and hydrophilic sections.
i. The hydrophobic section are 2 fatty acid chains connected to glycerol. The
hydrophillic section is the phosphate group attached to the glycerol.
ii. In a typical plasma membrane, the hydrophilic head points toward the surface, where
it will interact with the polar, aqueous media in the ECM whereas the hydrophobic
tails point toward the inside to prevent interactions with polar molecules.

15
b. Phospholipids and sphingolipids are degraded in lysosomes
i. Phospholipases degrade phospholipids and into lysophospholipid.
ii. Depending on the type of phospholipase, different products are generated
II. Sterols have four fused carbon rings
a. Sterols are structural lipids present in the membranes of most eukaryotic cells.
b. Structure is defined by the steroid nucleus (4 fused rings), three with 6 carbons and
one with 5.
i. The steroid nucleus is almost planar and relatively rigid; the fused rings do not allow
rotation around C-C bonds.

c. Cholesterol, the most major sterol in animal tissues, is amphipathic, with a polar head
group (the hydroxyl group at C-3) and a nonpolar hydrocarbon body (the steroid nucleus
and the hydrocarbon side chain at C-17).
d. Bacteria cannot synthesize sterols.
e. Bile acids are polar derivatives of cholesterol that act as detergents in the intestine,
emulsifying dietary fats to make them more readily accessible to digestive lipases.
III. Eicosanoids carry messages to nearby cells
a. Eicosanoids are paracrine hormones, substances that act only on the cells near the point
of hormone synthesis instead of being transported in the blood to act on cells in other
tissues or organs.
b. All eicosanoids are derived from arachidonic acid, the 20-carbon polyunsaturated fatty
acid.
c. Three classes:
i. Prostaglandins (PG) contains a 5-carbon ring originating from the chain of
arachidonic acid.
ii. Thromboxanes have a 6-membered ring also containing an ether. They are
produced by platelets and act in the formation of blood clots and the reduction of
blood flow to the site of a clot.
iii. Leukotrienes contain three conjugated double bonds, open form, no cyclic
structure. They are powerful biological signals. Overproduction of lenukotrienes
causes asthmatic attacks.
C. Waxes, Cartoenoids, Porphyrins, and adipose cells
I. Waxes are esters of fatty acids and monodhydroxylic alcohols. Used as protective coating or
exoskeleton.
a. Lanolin is a waxy secretion of wool bearing animals.
II. Carotenoids are fatty acid carbon chains with conjugated double bonds and 6 carbon rings
at each end. They are pigmented molecules in animals and plants.
III. Porphyrins are 4 fused pyrrole rings usually in a complex with a metal heme. Examples
would be chlorophyll and hemoglobin.
IV.Adipose cells are fat storing cells. Two types:
a. White fat cells have a large lipid droplet composed of triacylglycerides with a small

16
layer of cytoplasm.
b. Brown fat cells have lots of cytoplasm, scattered lipid droplets, and lots of
mitochondria.
D. Working with lipids
I. Adsorption chromatography separates lipids of different polarity
a. Lipids can be fractionated by chromatographic procedures based on different polarities
of each class of lipid.
b. In adsorption chromatography, an insoluble, polar material, such as silica gel is
packed into a glass column, and the lipid mixture is applied to the top of the column.
c. The polar lipids bind tightly to the polar silicic acid, but the neutral lipids pass directly
through the column and emerge in the first chloroform wash.
d. The polar lipids are then eluted, in order of increasing polarity, by washing the column
with solvents of progressively higher polarity.
II. Thin-layer chromatography
a. Thin-layer chromatogrpahy on silicic acid employs the same principle as adsorption
chromatography.
b. A thin layer of silica gel is spread onto a glass plate, to which it adheres.
c. A small sample of lipids dissolved in chloroform is applied to near one edge of the plate,
which is dipped in a shallow container of an organic solvent or solvent mixture; the
entire setup is enclosed in a chamber saturated the solvent vapor.
d. As the solvent rises on the plate by capillary action, it carries lipids with it.
e. The less polar lipids move farthest, as they have less tendency to bind to the silicic acid.
f. The separated lipids can be detected by spraying the plate with a dye or by exposing the
plate to iodine fumes. Lipids containing unsaturated fatty acids develop a yellow or
brown color when exposed to iodine.
III. Gas-liquid chromatography resolves mixtures of volatile lipid derivatives
a. Gas-liquid chromatography separates volatile components of a mixture according to
their relative tendencies to dissolve in the inert material packed in the chromatography
column or to volatilize and move through the column, carried by a current of an inert
gas such as helium.
IV.Mass spectrometry reveals complete lipid structure
a. Mass spectrometric analysis of lipids establishes the length of a hydrocarbon chain or
the position of double bonds.

17
A. Some basics
I. Introduction
a. A segment of DNA that contains the information required for the synthesis of a
functional biological product, whether protein or RNA, is referred to as a gene.
b. RNAs have a broader range of functions, and several types are found in cells:
i. Ribosomal RNAs are components of ribosomes, the complexes that carry out the
synthesis of proteins.
ii. Messenger RNAs are intermediaries, carrying genetic information from one or a
few genes to a ribosome, where the corresponding proteins are synthesized.
iii. Transfer RNAs are adapter molecules that faithfully translate the information in
mRNA into a specific sequence of amino acids.
c. Transcriptome vs. Genome
i. Genome is the collection of all the genes in an organism.
ii. Transcriptome is the collection of all the RNA transcripts in a cell, tissue, or
organism.

II. Nucleotides and nucleic acids have characteristic bases and pentoses
a. Nucleotides have three characteristic components: (1) a nitrogenous base, (2) a pentose,
and (3) one or more phosphates.
i. The molecule without a phosphate group is called a nucleoside.
ii. The nitrogenous bases are derivatives of two parent compounds, pyrimidine and
purine.
b. The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines)
in an N-B-glycosyl bond to the 1' carbon of the pentose, and the phosphate is esterified
to the 5' carbon.
i. N-B-glycosyl bond is formed by the removal of the elements of water (OH from the
pentose and the H from the base).

18
c. Both DNA and RNA contain two major purine bases, adenine and guanine, and two
major pyrimidines. In both DNA and RNA one of the pyrimidines is cytosine, but the
second common pyrimidine is not the same in both: it is thymine in DNA and uracil in
RNA.

d. Nucleic acids have two kinds of pentoses.

i. DNA contains 2'-deoxy-D-ribose and RNA contains D-ribose. Both types of
pentoses are in their B-furanose (closed five-membered ring) form.
ii. The pentose ring is not planar but occurs in one of a variety of conformations
generally described as puckered.
e. Deoxyribonucleotides are the structural units of DNA (base + phosphate +
deoxyribose) and ribonucleotides are the structural units of RNA (base + phosphate +
ribose).

III. Phosphodiester bonds link successive nucleotides in nucleic acids

a. Nucleotides in both DNA and RNA are covalently linked together through phosphategroup bridges, in which the 5'-phosphate group of one nucleotide unit is joined to the
3'-hydroxyl group of the next nucleotide, creating a phosphodiester linkage.
i. Thus, backbones of nucleic acids consist of alternating phosphate and pentose
residues. The backbones of both DNA and RNA are hydrophilic.
b. All phosphodiester linkages have the same orientation giving the nucleic acid a specific
directionality which goes from a 5' to a 3' direction (refers to the end of the strand).

19
i. The 5' end lacks a nucleotide at the 5' position and the 3' end lacks a nucleotide at
the 3' position.

IV.The properties of nucleotide bases affect the 3D structure of nucleic acids

a. Pyrimidines and purines are weakly basic compound and are thus called bases.
b. Electron delocalization among atoms in the ring gives most of the bonds partial doublebond character.
i. One result of this is that pyrimidines and purines are nearly to very planar.
c. All nucleotide bases absorb UV light, and nucleic acids are characterized by a strong
absorption at wavelengths near 260 nm.
d. Purine and pyrimidine bases are hydrophobic and relatively insoluble in water at nearneutral pH of the cell.
e. Hyrophobic stacking interactions in which two or more bases are positioned with the
planes of their rings parallel (like a stack of coins) helps create the 3D structure.
i. The stacking provides a combination of van der Waals and dipole-dipole interactions
and helps minimize contact of the bases with water.
f. The bases hydrogen bond with one another: this is the most important mode of
interaction between two complementary strands of nucleic acid.
i. A bonds to T = 2 hydrogen bonds
ii. G bonds to C = 3 hydrogen bonds
B. Nucleic acid structure
I. DNA is a double helix that stores genetic information
a. Chargaff's rules
i. The base composition of DNA generally varies from one species to another.
ii. DNA specimens isolated from different tissues of the same species have the same
base composition.
iii. The base composition of DNA in a given species does not change with an organism's
age, nutritional state, or changing environment.
iv. A = T
G=C
A+G=T+C
b. Two helical DNA chains are wound around the same axis to form a right-handed double
helix.
c. The hydrophilic backbones are on the outside of the double helix, facing the surrounding
water. These strands are antiparallel to one another (one in 5' to 3' direction and the
other is in 3' to 5' direction).
d. The pairing of the two strands creates a major groove and minor groove on the surface
of a duplex.

20
e. 10.5 base pairs per helical turn when in aqueous solution.
f. The sequence of DNA from each strand is complementary to each other (wherever
adenine occurs in one chain, thymine is found in the other).

II. DNA can occur in different 3D forms

a. Structural variation in DNA reflects 3 things: (1) different possible conformations of the
deoxyribose, (2) rotation about the contiguous bonds that make up the
phosphodeoxyribose backbone, and (3) free rotation about the C-1'-N glycosyl bond.
b. The b-form DNA is the most stable structure for DNA molecule under physiological
conditions.
c. A-form DNA is favored in solutions that are devoid of water. It is a right-handed
double helix, but the helix is wider and their number of base pairs per helical turn is 11.
d. Z-form DNA has 12 base pairs per helical turn and the structure appears more slender
and elongated. The backbone takes on a zigzag appearance. Z-DNA is a left-handed
helix and there is barely a minor groove. Z-DNA have been found in bacteria and
eukaryotes. It may play a role in regulating the expression of some genes.

III. Certain DNA sequences adopt unusual structures

a. A common type of DNA sequence is a palindrome: the sequence is spelled identically
when read either forward or backward. Palindromes are repeats in opposite strands.
They create special structures:

21
i. When only a single DNA (or RNA) strand is involved, the structure is called a
hairpin.
ii. When both strands of duplex DNA are involved, it is called a cruciform.
b. When an inverted repeat occurs within each individual strand of the DNA (on the same
strand), the sequence is called a mirror repeat.

IV.Many RNAs have more complex 3D structures

a. The product of transcription of DNA is always single-stranded RNA.
b. The single strand tends to assume a right-handed helical conformation dominated by
base-stacking interactions.
c. RNA can base-pair with complementary regions of either DNA or RNA.
d. Double stranded RNA is usually found in the A-form. (B-form is not observed, Z-form
has been synthesized in the lab)
e. The 3D structure of RNA is very complex. Weak interactions, especially base-stacking
interactions help stabilize RNA structures.
V. Nucleic acids from different species can form hybrids
a. Hybrid duplexes are which segments of one species DNA strand form base-paired
regions with segments of another species DNA strand.
i. It reflects a common evolutionary heritage; the closer the evolutionary relationship
between two species, the more extensively their DNAs will hybridize.
C. Other functions of nucleotides
I. Nucleotides carry chemical energy in cells
a. The phosphate group covalently linked at the 5' hydroxyl of a ribonucleotide may have
one or two additional phosphates attached.
i. The resulting molecules are referred to as nucleoside mono-, di-, and triphosphates.
ii. Hydrolysis of the nucleoside phosphates provides the chemical energy to drive many
cellular reactions.
II. Some nucleotides are regulatory molecules
a. Second messengers tend to be nucleotides.
i. One of the most common is cyclic AMP or cAMP, formed from ATP in a reaction
catalyzed by adenylyl cyclase.
ii. Another regulatory nucleotide, ppGpp, is produced in bacteria in response to a
slowdown in protein synthesis during amino acid starvation. It inhibits the synthesis
of rRNA and tRNA molecules needed for protein synthesis, preventing the uncessary
production of nucleic acids.

22
1. Amino acids
a) Amino acids share common structural features
All 20 of the common amino acids are alpha-amino acids. They have a carboxyl group
and an amino group bonded to the same carbon atom (the alpha carbon).
They differ from each other in their side chains, or R groups, which influence the
solubility of the amino acids in water.

For all amino acids except glycine, the alpha carbon is bonded to four different
groups. This means that the alpha-carbon is a chiral center and thus, amino acids
have two possible stereoisomers. The two forms are enantiomers and the
stereoisomers are optically activethat is, they rotate plane-polarized light.
The absolute configurations of simple sugars and amino acids are specified by the D,
L system.
L-amino acids are those with an alpha-amino group on the left whereas D-amino
acids have the alpha-amino group on the right.

b) Major type of proteins in the body

The amino acid residues in proteins are L stereoisomers The amino acid residues in
protein molecules are exclusively L stereoisomers.
c) Amino acids can be classified by R group
Amino acids can be simplified by grouping the amino acids into 5 main classes based on
the properties of their R groups, particularly their polarity, or tendency to interact with
water at biological pH.
Nonpolar, Alipathic R Groups
Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine
The R groups in this class of amino acids are nonpolar and hydrophobic.
These proteins tend to stabilize protein structure by means of hydrophobic
interactions.
Aromatic R groups
Phenylalanine, Tyrosine, Tryptophan
All of the aromatic amino acids are relatively nonpolar and can participate in
hydrophobic interactions.
Can absorb UV light.
Polar, Uncharged R Groups
Serine, Threonine, Cysteine, Proline, Asparagine, Glutamine

23

These amino acids contain functional groups that form hydrogen bonds with water.
Cysteine is readily oxidized to form a covalently linked dimeric amino acid called
cystine, in which two cysteine molecules or residues are joined by a disulfide bond.
The S-S bond is strongly hydrophobic. These bonds play a special roles of many
proteins by forming covalent links between parts of a polypeptide molecule or
between two polypeptide chains.
Positively charged (basic) R groups
Lysine, Arginine, Histidine
Histidine has an ionizable side chain with a pKa near neutrality, histidine may be
positively charged or uncharged at 7.0
Negatively charged (acidic) R groups
Aspartate + glutamate
Random important information
Most flexible amino acid = glycine
Most constrained amino acid = proline
d) Amino acids can act as acids or bases
When an amino acid lacking an ionizable R group is dissolved in water at neutral pH, it
exists in solution as the dipolar ion, or zwitterion, which can act as either an acid or
base. Amino acids are thus amphoteric.

e) Titration curves predict the electric charge of amino acids

An important piece of information derived from the titration curve of an amino acid is
the relationship between its net charge and the pH of the solution.
The characteristic pH at which the net electric charge is zero is called the isoelectric
point or isoelectric pH, designated pI. pI = 0.5(pKa1 + pKa2)
pH > pI, molecule will have a negative charge (amino acid will act like acid and
donate H+ into the more basic solution)
pH < pI, molecule will have a more positive charge (amino acid will act like base
and accept H+ from the more acidic solution)
At its isoelectric point, the Amino acid is least soluble in water and does not migrate in
an electric field.
The the farther the pH of the solution is from the isoelectric point, the greater the net
electric charge of the amino acid.
2. Peptides and proteins
a) Peptides are chains of amino acids
A peptide is two or more amino acid molecules covalently linked together.
The amino acids are held together by a peptide bond.
In a peptide, the amino acid residue at the end with a free alpha-amino group is the
amino-terminal (or N-terminal) residue; the residue at the other end, which has a free
carboxyl group, is the carboxyl terminal (C-terminal) residue.

24

b) Biologically active peptides and polypeptides occur in a vast range of sizes and
compositions
Some proteins consist of a single polypeptide chain, but others, called multisubunit
proteins, have two or more polypeptides associated noncovalently.
If at least two polypeptide chains are identical, then the protein is said to be
oligomeric, and the identical units are referred to as protomers.
3. Working with proteins
a) Proteins can be separated and purified
It is important to purify proteins before the protein's properties and activities can be
determined.
The first step in purification is to break open the cells, releasing the proteins into a
solution called a crude extract.
The extract is subjected to treatments that separate the proteins into different fractions
based on a property such as size or charge, a process referred to as fractionization.
A solution containing the protein of interest usually must further be altered before
subsequent purification steps are possible.
Dialysis is a procedure that separates proteins from small solutes by taking
advantage of the proteins' larger size. The purified extract is placed in a bag or tube
made up of some semipermeable membrane. When this is suspended in a much
larger volume of buffered solution, the membrane allows the exchange of salt but
not proteins.
Column chromatography takes advantage of differences in protein charge, size,
binding affinity, and other properties. A porous solid material with the appropriate
chemical properties (the stationary phase) is held in a column, and a buffered
solution (the mobile phase) migrates through it. The protein, dissolved in the same

25
buffered solution that was used to establish the mobile phase, is layered on top of the
column. The protein then percolates through the solid matrix. Individual proteins
migrate faster or more slowly through the column depending on their properties.
Ion-exchange chromatographyexploits differences in the sign and magnitude
of the net electric charge of proteins at a given pH. The column matrix is a
synthetic polymer (resin) containing bound charged groups; those bound with
anionic groups are called cation exchangers, and those with bound cationic
groups are called anion exchangers. The affinity of each protein for the charged
groups on the column is affected by the pH (which determines the ionization
state of the molecule) and the concentration of completing free salt ions in the
surrounding solution. Separation can be optimized n band in the mobile phase
(the protein solution) is caused both by separation of proteins with different
properties and by diffusional spreading. As the length of the column increases,
the resolution of two types of proteins with different net charges generally
improves.
In cation-exchanged chromatography, the solid matrix has negatively
charged groups. In the mobile phase, proteins with a net positive charge
migrate through the matrix more slowly than those with a net negative
charge, because the migration of the former is retarded more by interaction
with the stationary phase. The expansion of the protein band in the mobile
phase is caused by both separation of proteins with different properties and
by diffusional spreading.
Size-exclusion crhomatography separates proteins according to size. Large
proteins emerge fro the column sooner than small ones. The solid phase consists of
cross-linked cavities of a particular size. Large proteins cannot enter the cavities and
so take a shorter path through the column. Small proteins enter the cavities and are
slowed by their more labyrinthine path through the column.
Affinity chromatography is based on binding affinity. The beads in the column
have a covalently attached chemical group called a liganda group or molecule that
binds to a macromolecule such as a protein. When a protein mixture is added to the
column, any protein with affinity to the ligand binds to the beads, and its migration
through the matrix is retarded.
b) Proteins can be separated and characterized by electrophoresis
Electrophoresis helps separate proteins based on the migration of charged proteins in an
electric field.
Proteins can be visualized meaning a researcher can quickly estimate the number of
different proteins in a mixture or the degree of purity of a particular protein preparation.
Can be also sued to determine isoelectric point and molecular weight.
Carried out in a gel that helps slow the migration of proteins approximately in
proportion to their charge-to-mass ratio.
An electrophoretic method commonly employed for estimation of purity and molecular
weight makes use of sodium dodecyl sulfate (SDS).
A protein will bind about 1.4 times its weight of SDS. SDS bound contributes a large
net negative charge, rendering the overall charge from the protein insignificant and
conferring on each protein a similar charge-to-mass ratio.
Electrophoresis in the presence of SDS therefore separates proteins almost
exclusively
After electrophoresis, the proteins are visualized by adding a blue color dye.

26
Position on the band is used to determine molecular weight.
Isoelectric focusing is a procedure used to determine the isoelectric point (pI) of a
protein. A pH gradient is established by allowing a mixture of low molecular weight
organic acids and bases to distribute themselves in an electric field across the gel. When
a protein mixture is applied, each protein migrates until it reaches the pH that matches
its pI so proteins will be at different points on the gel.
Two-dimensional electrophoresis is combining isoelectric focusing and SDS
electrophoresis sequentially. Proteins are first separated by isoelectric focusing in a thin
strip gel. The gel is then laid horizontally on a second gel, and the proteins are separated
by SDS gel electrophoresis. Horizontal separation reflects differences in pI; vertical
separation reflects differences in molecular weight.
c) Protein chemistry is enriched by methods derived from classical polypeptide sequencing
The Edman degradation procedure labels and removes the only amino-terminal residue
from a peptide, leaving all other peptide bonds intact.
d) Mass spectrometry offers an alternative method to determine amino acid sequences
Mass spectrometry can provide a highly accurate measure of the molecular weight of a
protein.
4. Overview of Protein Structure
a) Introduction
The spatial arrangement of atoms in a protein or any part of a protein is called its
conformation.
The possible conformations a protein include any structural state it can achieve
without breaking covalent bonds.
Proteins must have multiple stable conformationsthis reflects the changes that
must take place in most proteins as they bind to other molecules or catalyze
reactions.
The most stable conformation is the one that is the most thermodynamically stable,
also known as having the lowest Gibbs free energy.
Proteins in any of their functional, folded conformations are called native proteins.
b) A protein's conformation is stabilized largely by weak interactions
Stability is defined as the tendency to maintain a native conformation.
The chemical interactions that stabilize the native conformation include disulfide bonds
and weak interactions.
Disulfide bonds are typically found in extracellular proteins because the
environment is more oxidizing (inside the cell it is more reducing).
Disulfide bridges are NOT broken down during allosteric interactions.
Weak interactions that predominate as a stabilizing force in a protein structure because
there are so many.
In general, the protein conformation with the lowest free energy (the most stable
conformation) is the one with the maximum number of weak interactions.
On carefully examining the contribution of weak interactions to protein stability, we find
that hydrophobic interactions generally predominate.
When water surrounds a hydrophobic molecule, the optimal arrangement of the
hydrogen bonds results in a highly structured shell, or solvation layer, of water
around the molecule. This creates an unfavorable decrease in entropy. When
nonpolar groups cluster together, the extent of the solvation layer decreases, because
each group no longer presents its entire surface to the solution. This results an a
favorable increase in entropy.

27

Hydrophobic amino acid side chains therefore tend to cluster in a protein's interior,
away from water. Amino acid sequences of most proteins contain a significant
content of hydrophobic amino acid side chains.
It is also important that any polar or charged groups in the protein interior have suitable
partners for hydrogen bonding or ionic interactions. The presence of hydrogen-bonding
groups without partners in the hydrophobic core of a protein can be destabilizing.
Most of the structural patterns reflect two simple rules: (1) hydrophobic residues are
largely buried in the protein interior, away from water, and (2) the number of hydrogen
bonds and ionic interactions within the protein is maximized, thus reducing the number
of hydrogen-bonding and ionic groups that are not paired with a suitable partner.
5. Protein secondary structure
a) Introduction
Secondary structure is the chosen segment of a polypeptide chain and describes the
local spatial arrangement of its main-chain atoms, without regard to positioning of its
side chains or its relationship to other segments.
A regular secondary structure occurs when each dihedral angle, phi and psi, remains the
same or nearly the same throughout the segment.
Where a regular pattern is not found, the secondary structure is sometimes referred to as
undefined or a random coil.
b) The alpha helix is a common protein secondary structure
In the alpha helix, the polypeptide backbone is wound around an imaginary axis drawn
longitudinally through the middle of the helix, and the R groups of the amino acid
residues protrude outward from the helical backbone.
Each helical turn includes 3.6 amino acid residues.
Why does the alpha helix form more readily than many other possible conformations?
The structure is stabilized by a hydrogen bond between the hydrogen atom attached
to the electronegative nitrogen atom of a peptide linkage and the electronegative

28
nitrogen atom of a peptide linkage.
Within the alpha helix, every peptide bond participates in such hydrogen bonding.
c) Amino acid sequence affects stability of the alpha helix
Each amino acid residue in a polypeptide has an intrinsic propensity to form an alpha
helix (some are more likely to form an alpha helix, some less likely).
Alanine shows the greatest tendency to form alpha helices.
The position of an amino acid residue relative to its neighbors is also important. The
order of the amino acid side chains can stabilize or destabilize the alpha-helical
structure.
The twist of an alpha helix ensures that the critical interactions occur between an amino
acid side chain and the side chain three to four residues away on either side of it.
Positively charged amino acids are often found three residues away from negatively
charged amino acids, permitting the formation of an ion pair.
A final factor affecting the stability of an alpha helix is the identity of the amino acid
residues near the ends of the alpha-helical segment of the polypeptide.
A small electric dipole exists in each peptide bond. These dipoles are aligned
through the hydrogen bonds of the helix, resulting in a net dipole across the helical
axis that increases with helix length.
For this reason, negatively charged amino acids are often found near the amino
terminus of the helical segment, where they have a stabilizing interaction with the
positive charge of the helix dipole; a positively charged amino acid at the aminoterminal end is destabilizing.
The opposite is true at the carboxyl-terminal end of the helical segment.

29
d) The beta conformation organizes polypeptide chains into sheets
The beta conformation is defined by backbone of a polypeptide chain extending into a
zigzag rather than a helical structure. Hydrogen bonds form between adjacent segments
of the polypeptide within the sheet.
The arrangement of several segments side by side, all of which are in the beta
conformation, is called a beta sheet.
The individual segments that form a beta sheet are usually nearby on the polypeptide
chain but can also be quite distant from each other in the linear sequence of the
polypeptide; they may be in different polypeptide chains.
The adjacent polypeptide chains in a Beta sheet can be either parallel or antiparallel.
Hydrogen bonds are linear in the antiparallel conformations

6. Protein tertiary and quaternary structures

a) Introduction
The overall three-dimensional arrangement of all atoms in a protein is referred to as the
protein's tertiary structure.
Amino acids that are far apart in the polypeptide sequence and are in different types of
secondary structure may interact within the completely folded structure of a protein.
The location of bends in the polypeptide chain and the direction and angle of these

30
bends are determined by the number and location of specific bend-producing residues,
such as Pro, Thr, Ser, and Gly.

Some proteins contain multiple subunits. The arrangement of these protein subunits in
three-dimensional complexes constitutes quaternary structure.
There are two major groups in which many proteins are classified: fibrous proteins,
with polypeptide chains arranged in long strands or sheets, and globular proteins, with
polypeptide chains folded into a spherical or globular shape.

31

32
b) Fibrous proteins are adapted for a structural function.
Fibrous proteins share properties that give strength and/or flexibility to the structures in
which they occur.
They are all insoluble in water.
Alpha-keratin
Alpha-keratin is found only in mammals (make up hair, nails, etc.). The alphakeratin helix is a right-handed alpha helix. Two strands of alpha-keratin, oriented in
parallel (with the same amino termini at the same end, are wrapped about each other
to form a supertwisted coiled coil. The supertwists are left-handed, opposite in the
sense to the alpha helix. The surfaces where the two alpha helices touch are made up
of hydrophobic amino acids, which permits close packing.
The strength of fibrous proteins is enhanced by covalent cross-links between
polypeptide chains and between adjacent chains in a supramolecular assembly.
These cross-links are disulfide bonds.
Collagen
Collagen helix is a unique secondary structure (like an alpha helix with key
differences). It is left-handed and has three amino acid residues per turn.
Three separate polypeptides, called alpha chains, are supertwisted about each other.
The twisting is right-handed. The tight wrapping provides a lot of strength.
c) Methods for determining 3-D structure of a protein
X-ray diffraction
The spacing of atoms in a crystal lattice can be determined by measuring the
intensities and locations of spots produced on photographic film by a beam of x rays
of given wavelength, after the beam has been diffracted by the electrons of the
atoms.
The physical environment in a crystal is not like in a living cell, so the protein can
look different.
X-ray diffraction is done best in tandem with NMR.
Nuclear magnetic resonance
Advantages: NMR is carried out on macromolecules in solution and it can illustrate
the dynamic side of protein structure.
Only certain atoms have the kind of nuclear spin that gives rise to an NMR signal.
d) Protein Quaternary Structures range from simple dimers to large complexes
Many proteins have multiple polypeptide subunits. A multisubunit protein is referred to
as a multimer. A multimer with just a few subunits is often called an oligomer.
Most multimers have identical subunits in symmetrical arrangements.
The repeating structural unit in a multimeric protein is called a protomer.
e) Some proteins or protein segments are intrinsically disordered
Intrinsically disordered proteins have properties that are distinct from classical
structured proteins. They lack a hydrophobic core, and instead are characterized by high
densities of charged amino acid residues. Pro residues are also prominent, as they tend
to disrupt ordered structures.
7. How do proteins fold into its native 3D conformation?
a) Protein folding is the physical process by which a protein chain acquires its native 3dimensional structure, a conformation that is usually biologically functional.
b) Each protein exists as an unfolded polypeptide or random coil when translated from a
sequence of mRNA to a linear chain of amino acids.

33
c) Proteins are folded and held together by several forms of molecular interactions (weak
interactions, disulfide bonds, etc.). The biggest factor in a protein's ability to fold is the
thermodynamics of the structure.
d) If the protein is not in the lowest energy conformation it will continue to move and adjust
until it finds its most stable state.
e) Chaperonins are proteins that provide favorable conditions for the correct folding of other
proteins.
Chaperonins prevent protein unfolding, misfolding, and aggregation.

8. Post-translational modification of proteins

a) Within the last few decades, scientists have discovered that the human proteome (collection
of all the proteins in a cell) is vastly more complex than the human genome. The human
genome comprises between 20,000 to 25,000 genes but the human proteome is estimated at
over 1 million. How is this possible?
b) Protein post-translational modification (PTM) increases the functional diversity of the
proteome by the covalent addition of functional groups or proteins, cleavage of subunits, or
degradation of entire proteins.
Most of the modifications take place in the golgi complex, although some occurs in the
rough endoplasmic reticulum lumen (specifically proper folding and formation of
disulfide bonds)
5 principal modification: formation of disulfide bonds, proper folding, addition and
processing of carbohydrates, specific proteolytic cleavages, assembly into multimeric
proteins

34

Why are cells so small?

The answer lies in the surface area-to-volume ratio.
Cells must constantly interact with their surrounding environment to survive.
Molecules must be absorbed while other molecules must be eliminated. For most cells,
the passage of all materials must occur through the plasma membrane.
As a cell gets larger, the surface area to volume ratio gets smaller. This means that the
relative amount of surface area available to pass materials to a unit volume of the cell
steadily decreases.
Thus, if a cell grows beyond a certain limit, not enough material will be able to cross the
membrane fast enough to accommodate the increased cellular volume.
Cellular membranes
Introduction
Fluid mosaic model of membranes because it is a patchwork of different types of
molecules and these molecules move rapidly within the lipid bilayer
Cell membranes are permeable for non-polar compounds, but not for polar compounds.
Cell membranes are made up of sterols, sphingolipids, and glycerophospholipids
non-polar elements face each other internally and polar head groups face outward
Hydrophobic interactions in water
Glycerophospholipids and sphingolipids spontaneously form bilayers when placed in a
polar solution like water. This is done to minimize the surface area of contact between
the nonpolar areas of the molecule and the polar liquid.
In a bilayer, polar head groups are on the outside, whereas the hydrophobic tales on are
on the inside, pointing down to one another. The tails on the end of the bilayer are
exposed to water, so they form a (liposome) vescile.
It can be thought that cells and organelles are big vesicles

Membrane fluidity
Membrane fluidity depends on temperature
At low temperatures, the lipids solidify into a paracrystal
At higher temperatures, lipids adopt a fluid state
Most stable state is called liquid ordered state (this is at intermediate temps).
If the membrane becomes too hot, it turns into the liquid disordered state (not as

35

stable). If the membrane becomes too cold, it solidifies into a paracrystal.

Sterols broaden the transition range between paracrystal and liquid disordered state.
Sterols increase ordering of unsaturated fatty acids and decrease ordering of
saturated fatty acids
If the membrane has more unsaturated fatty acids, the transition temperature is
lowered.
Lipids in the plasma membrane are free to move around across.
Membrane proteins
Channel proteins: provide passageway through membrane for hydrophilic substances.
Recognition proteins (glycoproteins) are peripheral proteins on the extracellular side of
the plasmamembrane that helps other cells distinguish it from foreign cells. The
oligosaccharide chain attached to the protein serves as this recognition tag.
Ion channels help move ions across the membrane. Two different types:
Voltage gated ion channels respond to differences in membrane potential
Ligand gated ion channels require a chemical to bind to a receptor site, which will
cause the channel to open.
Mechanically-gated ion channels respond to environmental stimuli such as
pressure, vibration, temperature, etc.
Porins allow passage of certain ions and small polar molecules through the membrane.
Tend to not be specific, they are just large passages. If you can fit you can go through
Aquaporin increase rate of H2O passing.
Carrier proteins bind to specific molecules, change shape, then allow the passage of
certain molecules through.
Transport proteins help move molecules (ions, large molecules, polar molecules) move
through the passive membrane. Can be done passively, or actively by coupling
movement with the hydrolysis of ATP. It is a very broad category of proteins.
Adhesion proteins attach cells to neighboring cells, providing anchors for internal
filaments and tubules (stability)
Receptor proteins are the binding sites for hormones and other trigger molecules.
Cell Wall
Cell Wall found in plants, fungi, protists, and bacteria.
Made up of cellulose in plants; chitin in fungi; peptidoglycans in bacteria;
polysaccharides in archaea.
Cell walls are not found in animal cells.
Provides support to the cell. Sometimes, a secondary structure develops beneath the primary
one.
Glycocalyx: a carbohydrate coat that covers the outer face of cell wall of some bacteria and
outer face of plasma membrane of some animal cells. Consists of glycolipids (attached to
plasma membranes) and glycoproteins (such as recognition proteins). May provide adhesive
capabilities, a barrier to infection, or markers for cell-cell recognition.

36

Extracellular matrix
Found in animals: areas between adjacent cells occupied by fibrous structural proteins,
adhesion proteins, and polysaccharides secreted by cells.
Common structures: collagen (most common), integrin + fibronectin, laminin
Provides mechanical support and helps bind adjacent cells.
Cells adhere to the ECM in two ways:
focal adhesions connection of the ECM to actin filaments in the cell
hemidesmosomes connection of ECM to intermediate filaments
Cytoskeleton
Cytoskeleton is a network of specialized proteins that provides a framework for
maintenance of cell shape. Involved in cell movement and movement of organelles.
Protein filaments are the basic units for maintenance of cell's shape. Three types:
microfilaments: made up two intertwined strands of actin. Thinnest of the three types.
Involved in muscle contraction, and cell motility.
Microtubules: made up of the protein tubulin, provide support and motility for cellular
activities. Thickest of the three types. Spindle fibers for mitosis and meiosis are made up
of microtubules.
Colchinine inhibits microtubule activity, and will interfere with mitosis.
If a person is born with a genetic defect that produces abnormal microtubules, sperm
cells, cells of the larynx, and trachea would be greatly effected.
Intermediate filaments: provide support for maintaining cell shape (keratin)

Locomotion
Microtubule organizing enters (MTOCs) Structures from which microtubules emerge.
Include centrioles and basal bodies (are at the base of each flagellum and cillium and
organize their development). Are in a 9x3 array. Plants, although they lack centrioles, do
have MTOCs.
Some types of cell motility involve the cytoskeleton. Cell motility generally requires
interaction of the cytoskeleton with motor proteins.
Flagella and cilia are microtubule-containing extensions that project from some cells.
Both are in a 9+2 array; 9 pairs + 2 singlets in center
Microtubule assembly of cilium or flagellum is anchored in the cell by a basal body.
Fagella are usually limited to just one or a few per cell, and are longer than cillia.
Dyenin is a protein associated with a flagellum. Converts chemical energy from ATP
into mechanical energy of movement.
Motile cillia usually occur in large numbers on the cell surface.
Intracellular circulation
Brownian movement: particles spread out randomly throughout cytoplasm due to
kinetic energy.
Cytoplasmic streaming refers to the circular motion of cytosol and organelles around

37

larg fungal and plant cells through the mediation of actin filaments in the cytoskeleton.
This movement aids in the delivery of organelles, nutrients, and genetic information,
and other mateirals to all parts of the cell.
Endoplasmic reticulum provides a direct, continuous passageway from the plasma
membrane to the nuclear membrane.
Extracellular circulation
Molecules from the external environment can diffuse into cells.
In more complex animals, molecules travel through a circulatory system to move from
one cell to another one that is far away.
Cell Junctions
Plant cell walls are perforated with plasmodesmata: channels that connect plant cells.
These connections unify most of the plant into one living continuum.
There are three main types of cell juntions in animal cells:
Tight junctions: Plasma membranes of the neighboring cells are tightly pressed against
each other, bound together by specific proteins.
Desmosomes (adhesion junction): function like rivets, fastening cells together into
strong sheets.
Gap Junctions: provide direct connection between cytoplasm of one cell and cytoplasm
of neighboring cell via channels called connexins.

Endomembrane system
The endomembrane system is composed of the different membranes that are suspended in
the cytoplasm within a eukaryotic cells.
These membranes divide the cell into functional and structural compartments, or
organelles.
In eukaryotes, organelles of the endomembrane system include: the nuclear membrane, the
endoplasmic retriculum, the golgi apparatus, lysosomes, vesicles, and the cell membrane.
Nucleus
The nucleus contains the DNA, the genetic material of the cell.
The nuclear envelope surrounds the nucleus with a double membrane with multiple pores.
Separates the contents of the nucleus from the cytoplasm.
Regulate the passage of macromolecules (proteins, RNA), but permit free passage of
water, ions, ATP, and other small molecules.
Inside the nuclear envelope is the chromatin, which consists of DNA tightly twisted around
proteins. They form long strands called chromosomes.
When a cell is not dividing, chromatin appears as a diffuse mass and you can't determine

38
one chromosome from another. As the cell prepares to divide, the chromosomes move
farther away to the point where they can be distinguished from one another.
The nucleolus is the central portion of the cell nucleus and is composed of chromosomal
RNA, proteins, and DNA. The nucleolus accomplishes the manufacture of ribosomes.
The nuclear side of the envelope is lined by the nuclear lamina. This is the dense fiber
network of most cells. Composed of intermediate filaments and membrane associated
proteins. Provides mechanical support and regulates cellular events such as DNA replication
and cell division. Participates in chromatin organization.
There is much evidence for a nuclear matrix, a framework of protein fibers extending
throughout the nuclear interior.

Cytosol vs Cytoplasm
Cytoplasm is the streaming movement within a cell. It includes everything suspended
between the cell wall and the nucleus. Cytoplasm = veggie-stew. Cytosol + organelles +
everything else that is suspended.
Cytosol is the aqueous substance that everything is suspended in. IT JUST DESCRIBES
THE FLUID. Cytosol = broth.
Ribosomes
Ribosomes are complexes made up of ribosomes RNA and protein. They carry out protein
synthesis.
Cells that have high rates of protein synthesis have large numbers of ribosomes.
Ribosomes build proteins in to cytoplasmic locations:
free ribosomes are suspended in the cytosol. Proteins made from these types of
ribosomes function within the cytosol.
bound ribosomes are attached to the outside of the endoplasmic reticulum or the
nuclear envelope. Proteins made from these types of ribosomes are usually destined for
insertion into membranes or for export from the cell.
Endoplasmic Reticulum
The Endoplasmic reticulum (ER) is an extensive network of membrane tubules and sacs
called cisternae. Internal compartment of the ER surrounded by the membranes is called the
ER lumen. ER runs adjacent to the nucleus.

39
Two distinct types of ER:
The smooth ER outer surface lacks ribosomes. Functions of the smooth ER include:
lipid and sterol synthesis, detoxification of drugs and poisons, and storage of calcium
ions.
The rough ER outer surface is studded with ribosomes. The rough ER is continuous
with the outer nuclear membrane. The main function of the rough ER is to generate
proteins and package them for secretion. Many of these secretory proteins are
glycoproteins. Another function of the rough ER is to build parts that add to the plasma
membrane.

Golgi Apparatus
Many transport vesicles travel to the Golgi apparatus after leaving the ER. The golgi
apparatus is like a warehouse for receiving, sorting, and shipping, and some modifications
of the vesicles. The vast majority of protein post-translational modifications happen here.
Consists of flattened membranous sacscisternae. The membrane of each cisterna in a
stack separates its internal space from the cytosol.
The two sides of a Golgi stack are referred to as the cis and trans face; these act,
respectively, as the receiving and the shipping departments of the Golgi apparatus.
Vesicles adds its comments to the Golgi apparatus on the cis side and the vesicles leave
the Golgi apparatus on the trans side.

40

Lysosomes
A lysosome is a membranous sac of hydrolitic enzymes that many eukaryotic cells use to
digest marocmolecules and damaged organelles.
Lysosomes are found in animal cells; NOT in most plant cells.
Glycosidases, aryl sulfatases, and phosphatases are found in lysosomes.
Lysosomes internal evironment is acidic because its enzymes function best in those pH
levels.
Functions in phagocytosis. When a cell engulfs good, the lysosome fuses with the food
vacoule and then catalyzes digestion.
Functions in autophagy. A damaged organelle becomes surrounded by a double membrane,
and the lysosome fusees with the vesicle, catalyzing digestion.

Vacuoules
Vacuoules are large vesicles derived from the ER or Golgi apparatus. Perform a variety of
functions in different kinds of cells.
Food vacuoules are formed by phagocytosis.
Vacuoules are mostly found in plant cells, not animal cells.
Many unicellular eukaryotes in living in fresh water have contractile vacuoules that pump
out excess water out of the cell, thereby maintaining the appropriate internal osmolarity.

41

Mature plant cells generally contain a large central vacuoule, which develops by the
coalescence of smaller vacuoules. Solution inside the central vacuoule is called cell sap, and
it is the main repository of inorganic ions.
Peroxisomes
The peroxisome is a specialized metabolic compartment bounded by a single membrane.
They contain enzymes that remove hydrogen atoms from various substrates and transfer
them to oxygen, producing hydrogen peroxide as a by-product.
In plant cells, peroxisomes modify by-products of photorespiration.
Specialized peroxisomes called glyoxysomes are found in fat-storing tissues of plant seeds.
Contain enzymes that initiate the conversion of fatty acids to sugar, which seedlings use as
source of energy.
Mitochondria
Exceptions to the universality of the genetic code is seen with mitochondria. This is
discussed in the genetics unit (see mitochondrial inheritance)
Structure and function of the mitochondria is discussed in the chapter on the citric acid
cycle.
Plastids
Found in plant cells
Chloroplast: structure of chloroplasts are discussed in the photosynthesis chapter.
Lecuoplasts can specialize to store starch/lipids/proteins or serve biosynthetic functions
Chromoplasts store carotenoids
Ribosomes
Structure and function of chloroplasts are discussed in the genetics unit.

42

43

44

Cell wall
Prokaryotic cell walls give structural integrity and shape and serve to anchor flagellae.
Cell walls are typically made up of peptidoglycan in eubacteria and polysaccharides in
archaebacteria.
Peptidoglycan is a polymer composed of modified sugars cross-linked by short
polypeptides.
Two main types:
Gram positive bacteria have a thick peptidoglycan wall. Contain teichoic acid chains.
Gram negative bacteria have a thin peptidoglycan wall and are structurally more
complex, with an outer membrane that contains lipopolysaccharides. Outer membranepeptidoglycan layer-plasma membrane.

Cell wall of many prokaryotes is surrounded by a sticky layer of polysaccharide or protein.

Called a capsule if it is dense and well-defined or a slime layer if it is not well
organized.
Both structures help prokaryotes to adhere to their substrate or to other individuals.
Certain bacteria have developed resistant cells called endospores to withstand hard
conditions.
The original cell produces a copy of its chromosome and surrounds that copy with a
tough, mulitlayered structure, forming the endospore.
Endospore can live in harsh conditions. When conditions get better, it turns back into a
normal cell.

45

Some prokaryotes stick to their substrate or to one another by hairlike appendages called
fimbriae.
Fimbriae are usually shorter than more numerous than pili.

Motility
About half of all prokaryotes are capable of taxis, a directed movement toward or away
from a stimulus.
Chemotaxis means changing movement in response to chemicals.
Organization of DNA
genome of prokaryote usually has considerably less DNA.
1 chromosome that is circular, whereas eukaryotes have linear chromosomes.
Chromosomes of prokaryotes are associated with many fewer proteins than are the
chromosomes of eukaryotes.
Chromosome is located in the nucleoid, a region of the cytoplasm that is not enclosed by a
membrane.
A typical prokaryotic cell have much smaller rings of independently replicating DNA
molecules called plasmids, most carrying only a few genes.
Prokaryotic ribosomes are slightly smaller than eukaryotic ribosomes.
restriction endonuclease is a bacterial protein that cleaves foreign DNA at specific sites
Reproduction
Reproduce by binary fission, a process very similar to, but slightly different than mitosis.
They are small and have short generation times. Binary fission is a type of asexual
reproduction.
Differences between binary fission and mitosis:
Binary fission occurs among prokaryotes (cells that do not have a nucleus) whereas
Mitosis occurs among eukaryotes (cells that do have a nucleus)
binary fission does not include spindle formation and sister chromatids in its process
making it faster means of cell division than mitosis

46

Binary fission does not have the 4 distinct cellular phases that are seen in mitosis
Transformation, transduction, conjugation = how to introduce variation in prokaryotes
In transformation, the genotype and possible phenotype of a prokaryotic cell are altered by
the uptake of foreign DNA from its surroundings.

In transduction, phages carry prokaryotic genes from one host cell to another. This results
from accidents that occur during the phage replication cycle. When the phage replicate its

47
own DNA in a host cell and then packages new phages, some phages may have accidentally
uptook non-viral DNA or DNA that is partially viral or partially host. When that virus
injects the DNA into a new host, the DNA cannot replicate but now is injected into the
prokaryote.
In conjugation, DNA is transferred between two prokaryotic cells. Ability to do this results
from a piece of DNA on the plasmid called the F factor. (F- cell, Hfr cell, F+ cell). (Look at
picture for more information)

48

Prokaryotes are diverse in metabolism

Obligate aerobes must use oxygen for cellular respiration and cannot grow without it.
Appear in top of test tube.
Obligate anaerobes cannot use O2, they are poisoned by it. Appear at very bottom of test
tube.
Facultative anaerobes use O2 if it is present but also can carry out fermentation or
anaerobic respiration if it is an anaerobic environment. Appear mostly at top because
aerobic respiration is better.
Microaerophiles need oxygen because they cannot ferment or respire anaerobically but are
poisoned at very high O2 concentrations. Appear in upper part of test tube but not very top.
Aerotolerant organisms do not require oxygen because they metabolize energy
anaerobically. Can be found spread evenly throughout the test tube.

49

DNA replication
Prokaryotes
Only one origin of replication per DNA molecule
Occurs inside the cytoplasm
Eukaryotes
Multiple origin of replication sites per DNA molecule
Occurs inside nucleus
Transcription/Translation
Prokaryotes
Transcription and translation occur simultaneously
Eukaryotes
Transcription occurs in nucleus, translation occurs in cytoplasm
Cellular respiration
Prokaryotes
Occurs on plasma membrane
Eukaryotes
Occurs in mitochonrida

Cell theory (5 parts)

all living things are composed of cells
the cell is the basic functional unit of life
the chemical reactions of life take place inside the cell
cells only arise from pre-existing cells
cells carry genetic information in the form of DNA (passed from parent cell to daughter
cell)

50

Viruses introduction
Viruses are infectious particles consisting of little more than genes packed in a protein coat.
Viruses are nonliving because they cannot reproduce on their own.
Structure of viruses
Virus genomes can be double stranded DNA, single stranded DNA, double stranded RNA,
or single stranded RNA.
The genome is usually organized as a single linear or circular molecule of nucleic acid.
The protein shell enclosing the viral genome is called a capsid. Could be rod-shaped,
polyhedral, or more complex in shape.
Capsids are built from a large number of protein subunits called capsomeres.
Viral envelopes are membranes surrounding viruses that contain host cell phospholipids
and glycoproteins. This aids the virus in entering the host cell.
Viruses that infect bacteria are called bacteriophages. These viruses usually bind to
teichoic acid chains of gram-positive bacteria as means to cell attachment.
Viruses only replicate in host cells. The number of species a particular virus can infect is
called the host range of the virus.
Phages that can reproduce by lytic and lysogenic cycle are called temperate phages.

Lytic cycle
A phage that replicates only by the lytic cycle is called a virulent phage.
Stage 1: Virus attaches to the host cell.
Stage 2: Virus injects DNA into host cell. Host cell's DNA is hydrolyzed.
Stage 3: Viral DNA directs production of viral proteins and copies of the viral genome by
host and viral enzymes.

51
Step 4: New viruses are put together.
Step 5: Virus directs production of an enzyme that damages the cell wall, allowing to fluid
and enter. The cell swells and bursts, releasing new virus particles.

Lysogenic cycle
A prophage is a virus who has injected its DNA into the host cell and the DNA
incorporated itself into the host chromosome.
Phage injects DNA into the host cell. The host cell incorporates itself into the host DNA and
lays dormant. Bacterium reproduces normally, copying the prophage DNA long with it.
Certain stress factors activates the prophage DNA to begin the lytic cycle. When this
happens, the phage DNA will begin creating itself and will follow the lytic cycle from hereon out, until it re-enters the lysogenic cycle.

52

RNA viruses
RNA viruses are called retroviruses.
These viruses are equipped with an enzyme called reverse transcriptase, which transcribes
an RNA template into DNA.

Prions
Prions are proteins that are unique in their ability to reproduce on their own and become
infectious. They are misfolded versions of proteins in the brain that cause normal proteins to
misfold too.

53

Facilitated diffusion
Diffusion is the spontaneous movement of particles from an area of high concentration to
low concentration.
Diffusion can also occur if there is a difference in charge (electrical potential difference)
between two different areasthis is called a membrane potential.
If a concentration gradient (difference in concentration between two sides of a
membrane) and a membrane potential exists between two sides of a membrane, there is
said to be an electrochemical gradient. Diffusion will occur down the electrochemical
gradient.
Facilitated diffusion is the process of moving polar, large, and ionic molecules through the
plasma membrane via protein channels.
Can be done without the input of energy passive diffusion. Molecules can only move
in the direction of the concentration gradient.
Can be done with input of energy (coupled with ATP hydrolysis) active diffusion.
Molecules can move against the concentration gradient.

Cotransport
A cotransport protein can couple the downhill diffusion of a solute to the uphill
transport of a second substance against its own concentration gradient.
Osmosis
Osmosis is the spontaneous movement of water from areas of low osmolarity to high
osmolarity.
Osmolarity is defined as the total amount of solutes in moles divided by liters of solution.
Tonicity is the ability of a surrounding solution to cause a cell to gain or lose water.
Depends on solute concentration and membrane permeability.
In an isotonic environment, the external osmolarity is equal to the internal osmolarity of
the cell. There will be no net movement of water across the plasma membrane. Volume of
the cell is stable.
In a hypertonic environment, the external osmolarity is greater than the internal osmolarity
of the cell. There will be a net movement of water out of the cell. The cell may shrivel up
and die.
In a hypotonic environment, the external osmolarity is lower than the internal osmolarity

54
of the cell. There will be a net movement of water into the cell. The shell may get too big
and lyse.
Plant cells have a cell wall, so that changes how the cell responds to changes in osmolarity.
When in a hypotonic solution, the cell becomes turgid (normal state).
When in an isotonic solution, the cell becomes flaccid.
When in a hypertonic solution, the cell becomes plasmolyzed.

Water potential
Water potential is a measurement that combines the effects of solute concentration and
pressure. It determines the direction of movement of water. Water moves from regions of
higher water potential to regions of lower water potential.
Potential refers to water's capacity to perform work.
Water potential is abbreviated as and is measured in units of megapascal (Mpa)
= 0 Mpa for pure water at sea level and at room temperature
Both pressure and solute concentration affect water potential. This is expressed by the water
potential equation: = s + p
The solute potential (s) of a solution is directly proportional to its molarity. Also
called osmotic potential.
Pressure potential (p) is the physical pressure on a solution
Turgor pressure is the pressure exerted by the plasma membrane against the cell wall, and
the cell wall against the protoplast.
The protoplast is the living part of the cell, which also includes the plasma membrane
Consider a U-shaped tube where the two arms are separated by a membrane permeable only
to water. Water moves in the direction from higher water potential to lower water potential
(picture on next page).

55

Types of transport molecules

Uniport transports one solute at a time.
Co-transport involves moving two different molecules.
Symport transports the solute and another molecule in the same direction at the same time
Antiport transports the solute and another molecule in different directions at the same time.

56

Endocytosis
In endocytosis, the cell enguls some of its extracellular fluid including material dissolved or
suspended in it. A portion of the plasma membrane is invaginated and pinched off forming a
membrane-bounded vesicle called an endosome.
Clathrin participates in endocytosis by forming a polyhedral lattice around coated pits.
Three types: phagocytosis, pintocytosis, and receptor mediated endocytosis
Receptor mediated endocytosis
Receptor mediated endocytosis is an endocytotic mechanism in which specific molecules
are ingested into the cell. The specificity results from a receptor-ligand interaction.
Receptors on the plasma membrane of the target tissue will specifically bind to ligands on
the outside of the cell. An endocytotic process occurs and the ligand is ingested.
Phagocytosis
Phagocytosis results in the ingestion of living matter (i.e. bacteria) from the extracellular
fluid. The endosome is called a phagosome.
Occurs in certain specialized cells such as neutrophils, macrophages, amoeba, etc.
Happens sporadically.
Pintocytosis
Pintocytosis, cell drinking, is a mode of endocytosis in which small particles are brought
into the cell, forming an invagination, and then suspended within small vesicles.
Primarily used for absorption of extracellular fluids.

Exocytosis
Exocytosis is the energy-consuming process by which a cell directs the contents of
secretory vesicles out of the cell membrane and into the extracellular space.

57

Autophagy
Autophagy is a normal physiological process in the body that deals with destruction of cells
in the body.
It maintains homeostasis or normal functioning by protein degradation and turnover of the
destroyed cell organelles for new cell formation.
During cellular stress the process of Autophagy is upscaled and increased. Cellular stress is
caused when there is deprivation of nutrients and/or growth factors.
Thus Autophagy may provide an alternate source of intracellular building blocks and
substrates that may generate energy to enable continuous cell survival.

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5 common features of signal transducing systems

Specificity: signal molecule fits binding site on its own complementary receptor; other
signals do not fit. Particular receptor in a cell may listen to one signal but not the other. In
addition, the receptor may not be present in every cell so a cell may not be able to listen to
a certain signal. A signal will not be heard in each and every cell type.
Amplification: when enzymes activate systems, the number of affected molecules increases
geometrically in an enzyme cascade. A single signaling molecule can activate a large
number of target molecules.
Modularity: proteins with multivalent affinities from diverse signaling complex form
interchangeable parts. Phosphorylation provides reversible proteins of interaction.
Adaptation/desensitization: Receptor activation triggers a feedback circuit that shuts off
the receptor or moves it from the cell surface.
Integration: when two signals have opposite effects on a metabolic characteristic, the
regulatory outcomes results from the integrated input of both receptors. Integrated means at
some point, both receptor pathways will converge on the same molecule and will cause a
common response.
Signal transduction generalizations
Signal transduction pathways have unique features:
differ between cell types, even closely related ones
they change with cellular and environmental conditions
Gated ion channels
generally found in excitable cells
Usually move ions by facilitated diffusion very quickly (these channels cannot be saturated)
Gated ion channels are one of two signaling systems which actually move molecules
through the membrane
The membrane has a very asymmetric ion distribution (creates membrane potential)
Sodium-potassium pump
energy source: ATP hydrolysis
3 Na+ leaves, 2 K+ comes in (moves one positive charge to the outside)
Generates a membrane potential (electrochemical gradient)

59

Changes in membrane potential

polarization: a difference in charge across a membrane, results in a positive or negative Vm
depolarization: a decrease in the absolute value of Vm (membrane potential moves closer to
0)
hyperpolarization: an increase in absolute value of Vm (membrane potential moves farther
from 0)
Three types of cell signals
Paracrine signals: A secreting cell acts on nearby target cells by secreting molecules of a
local regulator.
Synaptic signaling: A nerve cell releases neurotransmitter molecules into a synapse,
stimulating the target cell.
Endocrine (hormonal) signaling: specialized endocrine cells secretes hormones into body
fluids. Hormones reach virtually all body cells.
G protein-coupled receptors
A G protein-coupled receptor is a cell-surface trans membrane receptor that works with
the help of a G protein, a protein that binds the energy-rich molecule GTP. When GDP is
bound to the protein, the protein is inactive. When GTP is bound to the protein, the protein
becomes active.
Step 1: When the appropriate signaling molecule binds to the extracellular side of the
receptor, the receptor is activated and changes shape. Its cytoplasmic side binds an
inactive G protein, causing a GTP to displace the GDP. This activates the G protein.
Step 2: The activated G protein dissociates from the receptor, diffuses along the
membrane, and then binds to the enzyme, altering the enzyme's conformation. Once
activated, the enzyme can trigger the next step leading to a cellular response. (Binding is
reversible).
Step 3: The changes in the enzyme and G protein are only temporary because the G
protein also functions as a GTPase enzymeit then hydrolyzes GTP to GDP and Pi. It
now is available for reuse.

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Receptor tyrosine kinases

Receptor tyrosine kinases catalyzes the transfer of phosphate groups from ATP to the
amino acid tyrosine on a substrate proteins.
Step 1: before the signaling molecule binds, the receptors exist as individual units refer
to as monomers.
Step 2: the binding of a signaling molecule causes two receptor monomers to associate
closely with each other, forming a complex known as a dimer.
Step 3: Dimerization activates the tyrosine kinase region of each monomer; each
tyrosine adds a phosphate from an ATP molecule to a tyrosine on the tail of the other
monomer.
Step 4: Now that the receptor is fully activated, it is recognized by specific relay
proteins inside the cell. Each protein binds to a specific phosphorylated tyrosine, thus
activating the protein. Each activated protein triggers a transduction pathway, leading to
a cellular response.

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Ligand-gated ion channel

Ligand-gated ion channel is a type of membrane receptor containing a region that can act
as gate when the receptor changes shape.
Step 1: Ligand-gated ion channel receptor remains closed until a ligand binds to the
receptor.
Step 2: when the ligand binds to the receptor and the gate opens, specific ions flow
through the channel and rapidly change the electrochemical gradient of the cell.
Step 3: when the ligand dissociates from the receptor, the gate closes and ions no longer
enter the cell.

Steroid hormones
Steroid hormones are nonpolar: they can diffuse through the plasma membrane without a
problem. They have a different pathway than other ligands:
Step 1: hormone diffuses into the cell through the plasma membrane
Step 2: hormone binds to an intracellular receptor in the cytoplasm or nucleus. This
binding activates the protein.
Step 3: the bound protein acts as a transcription factor, stimulating the transcription of
the gene into mRNA

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cyclic AMP and second messengers

Second messengers are small, non-protein, water-soluble molecules that act in a signal
transduction pathway.
Binding of epinephrine to the plasma membrane elevates the cytosolic concentration of
cyclic AMP (cAMP).
A membrane-bound enzyme called adenylyl cyclase, converts ATP to cAMP in response to
an extracellular-signal.
Phosphodiesterase is the enzyme that breaks down cAMP.
The effect of increased cAMP levels is the activation of protein kinase A.
IP3 and Ca2+ pathway
Step 1: signaling molecule binds to a receptor, leading to activation of phospholipase C
Step 2: Phospholipase C cleaves a plasma membrane phospholipid called PIP2 into DAG
(diacylglycerol) and IP3 (inositol triphoshoate). /DAG functions as a 2nd messenger in other
pathways.
Step 3: IP3 quickly diffuses through the cytosol and binds to an IP3-gated calcium-ion
channel in the ER membrane, causing it to open.
Step 4: Calcium flows out of the ER (down the concentration gradient), raising cytosolic
Ca2+ levels.
Step 5: The calcium ions activate the next protein in one or more signaling pathways.

63

64

Forms of energy
Energy is defined as the capacity to change or to perform work.
Two basic forms of energy:
kinetic energy: the energy of motion
Heat, or thermal energy, is a type of kinetic energy associated with the random movement of
atoms or molecules.
Light, a type of kinetic energy, can be harnessed to power photosynthesis
potential energy: energy that matter possesses as a result of its location or structure
Molecules possess potential energy because of the arrangement of electrons in the bonds
between their atoms.
Chemical energy is the potential energy available for a chemical reaction. It is the most
important type of energy for living organisms; it is the energy that can be transformed to
power the work of the cell.
Energy transformations
Thermodynamics is the study of energy transformations that occur in a collection of matter.
System refers to the matter under study and refer to the rest of the universe (everything outside
of the system) as the surroundings.
An organism is an open system; that is, it exchanges both energy and matter with its
surroundings.
The first law of thermodynamics (law of energy conservation) states that energy in the universe is
constant. Energy can be transferred and transformed, bu tit cannot be created or destroyed.
If energy cannot be destroyed, then why can't organisms simply recycle their energy? It turns out
that during every transformation, some energy becomes unusable, unavailable to do work.
In most energy transformations, some energy is converted to heat, a disordered form of
energy.
Scientists use a quantity called entropy as a measure of disorder, or randomness.
The more randomly arranged a collection of matter is, the greater its entropy.
According to the second law of thermodynamics, energy conversions increase the entropy
(disorder) of the universe.

Chemical reactions either release or store energy

An exergonic reaction is a chemical reaction that releases energy.

65
An exergonic reaction begins with reactants whose covalent bonds contain more energy than
those in the products. The reaction releases to the surroundings an amount of energy equal to the
difference in potential energy between the reactants and the products
Cellular respiration is exergonic; cells release energy from fuel molecules.
Endergonic reactions yield products that are rich in potential energy.
They start out with reactant molecules that contain relatively little potential energy. Energy is
absorbed from the surroundings as the reaction occurs, so the products of an endergonic reaction
contain more chemical energy than the reactants did.

The amount of additional energy stored in the products

equals the difference in potential energy between the reactants and the products. Photosynthesis, the
process by which plant cells make sugar using the energy from ATP, is an example of an endergonic
process. Every working cell in an organism carries out thousands of endergonic and exergonic
reactions. The total of an organism's chemical reactions is called metabolism.
A metabolic pathway is a series of chemical reactions that either builds a complex molecules or
breaks down a complex molecule into simpler compounds.
Catabolism refers to chemical reactions that result the breakdown of more complex organic
molecules into simpler substances.
Anabolism refers to chemical reactions in which simpler substances are combined to form more
complex molecules. Anabolic reactions usually require energy.
The energy of catabolic reactions is used to drive anabolic reactions. The energy for chemical
reactions is stored in ATP.
ATP drives cellular work by coupling exergonic and endergonic reactions

ATP, or adenosine triphosphate, powers nearly all forms of cellular

work. The structure of ATP is shown below. The adenosine part of
ATP consists of adenine (a nitrogenous base that's found in DNA)
and ribose, a 5-carbon sugar. The triphosphate part is a chain of
three phosphate groups. Each phosphate group is negatively
charged. These like charges are crowded together, making the
bonds connecting the phosphate groups unstable. ATP can readily
be broken down by hydrolysis, the addition of water. Notice below
when the bond to the third group breaks, a phosphate group leaves
ATP, becomes ADP (adenosine diphosphate), and energy is
released.
Thus, the hydrolysis of ATP is exergonic, it releases energy.

66
How does the cell couple the hydrolysis of ATP (exergonic) with an endergonic reaction?
It usually does so by transferring a phosphate group from ATP to some other molecule by a
process called phosphorylation.
Most cellular work depends on ATP energizing molecules by phosphorylating them.
There are three types of cellular work:
Chemical work phosphorylation of reactants provide energy to drive the endergonic of
synthesis of products
Mechanical work. (i.e. transfer of phosphate group to special motor proteins in the muscle cell
causes the proteins to change shape and pull on protein filaments, in turn causing the cell to
contract)
Transport work. (i.e. transfer of a phosphate group to a membrane protein allowing through the
passage of a large, polar solute).

Work can be sustained because ATP is a renewable energy source that cells regenerate. Energy from
exergonic reactions drives the conversion of ADP + Pi (inorganic phosphate) into ATP. The energy
released from hydrolysis of ATP back into ADP and Pi drives endergonic reactions.

How do enzymes work?

In every chemical reaction, there is an energy barrier that must be overcome before the reaction itself
can proceed. This energy barrier is known as activation energy (EA).
We can think of activation energy as the amount of energy needed for reactant molecules to
move uphill to a higher-energy, unstable transition state, so that the downhill part of a
reaction can begin.
Activation energy protects the highly ordered molecules of your cells from spontaneously breaking

67
down but life depends on countless chemical reactions that must occur quickly and precisely for a
cell to survive. How can the specific reactions that a cell requires get over that energy barrier?
The answer to the dilemma lies in enzymes, molecules that function as biological catalysts,
increasing the rate of a reaction without being consumed by the reaction. An enzyme speeds up a
reaction by lowering the activation energy needed for a reaction to begin.

With the aid of an enzyme, the bonds in a reactant are contorted into the higher-energy, unstable
transition state from which the reaction can proceed. Without an enzyme, the activation energy
might never be reached.
An enzyme is very selective in the reaction it catalyzes. Because an enzyme is a protein, an
enzyme has a unique 3D shape, and that shape determines the enzyme's specificity.
The specific reactant that an enzyme acts on is called the enzyme's substrate. A substrate fits
into the region of an enzyme called an active site.
Enzymes are specific because their active site fit only specific substrate molecules.
The catalytic cycle of an enzyme
Follow the picture of an enzyme sucrase catalyzing the hydrolysis of sucrose into fructose and
glucose.

Step 1: The enzyme starts with an empty active site

Step 2: A substrate (sucrose in this example) enters the active site, attaching through intermolecular
attractive forces (hydrogen bond, dipole-dipole interactions, etc.).
The active site changes shape slightly, embracing the substrate more snugly. This induced fit
may contort substrate bonds or place chemical groups of the amino acids making up the active
site in position to catalyze the reaction.
Step 3: The strained bond of the substrate reacts, and the substrate is converted to the products.

68

Step 4: The enzyme releases the products and emerges unchanged from the reaction. Its active site is
now available for another substrate molecule, and another round of cycle can begin.
Optimal conditions for enzymes
As with all protein's, an enzymes shape is central to its function, and this 3D shape is affected by the
environment.
For every enzyme, there are optimal conditions under which it is most effective.
Deviations from these conditions (i.e. change temperature, pH, salinity) can cause the enzyme to
denature, altering its specific shape and destroying its function.
Most human enzymes work best close to body temperature at 35-40 degrees Celsius.
The optimal pH for most enzymes is near neutrality, in the range of 6-8. There are exceptions
(i.e. pepsin in your stomach works best at pH = 2).
Cofactors vs. prosthetic groups
Many enzymes require nonprotein helpers called cofactors, which loosely bind to the active site and
function in catalysis.
The cofactors of some enzymes are inorganic (i.e. iron).
If the cofactor is an organic molecule, it is called a coenzyme.
A prosthetic group is a tightly bound, specific non-polypeptide unit required for the biological
function of some proteins. (i.e. heme group, vitamins)
Enzyme inhibitors
A chemical that interferes with an enzyme's activity is called an inhibitor.
A competitive inhibitor reduces an enzyme's productivity by blocking substrate molecules from
entering the active site.
Competitive inhibition can be overcome by increasing the concentration of the substrate, making
it more likely that a substrate molecule rather than an inhibitor will be nearby when an active site
becomes vacant.
A noncompetitive inhibitor does not enter the active site; instead, it binds to the enzyme
somewhere else, a place called an allosteric site, and its binding changes the shape of the enzyme so
that the active site no longer fits the substrate.

Cells use inhibitors as important regulators of cellular metabolism. Many of a cell's chemical
reactions are arranged in metabolic pathways. If a cell is producing more of a product than it needs,

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the product may act as an inhibitor of one of the enzymes in an earlier pathway. This is called
feedback inhibition.
Overview of cellular respiration
Cells need to generate energy to fuel anabolic pathways and other cellular processes. The main way
cells achieve this is by breaking down glucose into energy.
Glucose is broken down by being oxidized. Oxidation refers to the loss of electrons. Therefore,
electrons are stripped away from glucose in chemical reactions.
The freed up electrons are picked up by electron transport proteins (i.e. FAD, NAD) and then are
transported to the mitochondria and are given to the electron transport chain.
The energy of the electrons is used to generate ATP. Oxygen accepts the low energy electrons to
complete the process.
Steps:
(1) Glycolysis
takes place in the cytoplasm
glucose is oxidized into 2 molecules of pyruvate. Freed up electrons are picked up by
electron transport proteins.
2 molecules of ATP are produced by a process called substrate-level phosphorylation. In
this process, an enzyme transfers a phosphate group fro ma substrate molecule directly to
ADP, forming ATP.
(2) Pyruvate decarboxylation
takes place in the mytochondrial matrix
The molecules of pyruvate are oxidized into acetyl-CoA so they can be shunted into the citric
acid cycle. Freed up electrons are picked up by electron transport proteins.
(3) Citric acid cycle
actetyl-CoA is fully oxidized. Freed up electrons are picked up by electron transport proteins.
1 molecule of ATP is produced by substrate-level phosphorylation.
(4) Oxidative phosphorylation
Electron transport proteins that previously picked up electrons in steps 1-3 drop off electrons
at the electron transport chain (ETC).
Energy from the electrons are used to pump hydrogen ions (H+) from the mitochondrial
matrix out to the intermembrane space. The active transport of H+ creates an electrochemical
gradient between the intermembrane space and the mitochondrial matrix.
An electrochemical gradient refers to an electrical potential and a difference in
concentration across a membrane.
The electrochemical gradient becomes large enough to the point where the hydrogen ions
will begin moving down their electrochemical gradient (from the intermembrane space back
into the mitohcondrial matrix) through FoF1 ATPase (the enzyme that catalyzes the reaction of
ADP + Pi ATP), also known as chemiosmosis.
The movement of ions across a selectively permeable membrane down their
electrochemical gradient is known as chemiosmosis.
Movement of H+ ions through FoF1 ATPase provides a proton-motive force that drives
the synthesis of ATP.

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- Metabolic pathways in eukaryotic cells occur in specific compartments
reason behind this is that different metabolites can operate in different locations and in different
pathways
in eukaryotic cells (memorize this):
mitochondrion: citric acid cycle, electron transport oxidative phosphorylation, fatty acid
oxidation, amino acid breakdown
cytosol: glycolysis, pentose phosphate pathway, fatty acid biosynthesis, gluconeogenesis
rough ER: protein synthesis
smooth ER: lipid and steroid biosynthesis
central importance of glucose
glucose is an excellent fuel
yields good amount of energy upon oxidation (energy then is used to perform cellular
processes and synthesize biomolecules)
can be sufficiently stored in polymeric form (starch, glycogen)
many organisms and tissues can meet their energy needs on glucose only
glucose is a versatile biochemical precursor
Four major pathways of glucose utilization
(1) storage
can be stored in the polymeric form (starch, glycogen)
when there is plenty of excess energy
(2) glycolysis
generates energy via oxidation of glucose
short-term energy needs
(3) pentose phosphate pathway
generates NDAPH via oxidation of glucose
for detoxification and the bio synthesis of lipids and nucleotides
(4) synthesis of structural polysaccharides

Glycolysis: overview in the evolution of life

glycolysis probably was one of the earliest energy-yielding pathways
it was developed before photosynthesis, when the atmosphere was still anaerobic.
It is the anaerobic conversion of glucose into pyruvate by a sequence of enzyme-catalyzed

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reactions
pyruvate can be further aerobically oxidized
pyruvate can be used as a precursor in biosynthesis
STEP 1: Phosphorylation of Glucose
Glucose + ATP Glucose-6-phosphate + ADP
nucleophilic oxygen at C-6 of glucose attacks the last (gamma) phosphate of ATP
uses up the energy of ATP
catalyzed by hexokinase in eukaryotes, and glucokinase in prokaryotes
hexokinase = induced fit (binding of glucose and Mg*ATP induces a large conformational
change which brings the active site residues together)
Rationale:
traps glucose inside the cell (adding phosphate gives molecule negative charge)
lowers intracellular glucose concentration to allow further uptake of glucose
ATP-bound Mg2+ facilitates this process by shielding the negative charges on ATP
highly thermodynamically favorable/irreversible (regulated by substrate inhibition)
STEP 2: phosphohexose isomerization
Glucose-6-phosphate Fructose-6-phosphate
catalyzed by phosphohexose isomerase
Rationale:
C-1 of fructose is easier to phosphorylate by PFK-1
Allows for symmetrical cleavage by aldolase
Converts the aldose glucose into the ketose fructose
Slightly thermodynamically unfavorable/reversible
product concentration kept low to drive forward
STEP 3: 2nd priming phosphorylation
Fructose 6-phosphate + ATP Fructose 1,6-biphosphate
catalyzed by phosphofructokinase-1 (PFK-1)
Rationale:
further activation of glucose
allows for 1 phosphate/3-carbon sugar after step 4
First committed step of glycolysis
fructose 1,6-biphosphate is committed to become pyruvate and yield energy
this process uses the energy of ATP
highly thermodynamically favorable/irreversible
phosphofructokinase-1 is highly regulated because this is a committed step
STEP 4: Aldol Cleavage of F-1,6-bP
Fructose 1,6-biphosphate dihydorxyacetone phosphate (DHAP)+ glyceraldehyde 3phosphate (GAP)
catalyzed by aldolase
Rationale:
cleavage of a six-carbon sugar into two three-carbon sugars
high-energy phosphate sugars are three-carbon sugars
cleave of Frc 1,6-bisP is highly unfavorable under standard conditions, but only slightly under
physiological conditions
GAP (glyceraldehyde 3-phosphate) concentration is kept low to pull reaction forward

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STEP 5: triose phosphate interconversion

dihydroxyacetone phosphate glyceraldehyde 3-phosphate
catalyzed by: triose phosphate isomerase
rationale:
allows glycolysis to proceed by one pathway
GAP is the substrate for the next enzyme, so DHAP must be converted to GAP
thermodynaically unfavorable/reversible
GAP concentration kept low to pull reaction forward
****NOTE steps 6-10 happen twice since 2 GAP molecules are generated*********
STEP 6: Oxidation of GAP
glyceraldehyde 3-phosphate + Pi + NAD+ 1,3-bisphosphoglycerate + NADH + H+
catalyzed by: glyceraldehyde 3-phosphate dehydrogenase (GAPDH)
rationale:
generation of a high-energy phosphate compound
incorporates Pi which allows for net production of ATP via glycolysis
first energy-yielding step in glycolysis (forms NADH)
thermodynamically unfavorable/reversible
coupled to next reaction to pull forward
STEP 7: 1st production of ATP
1,3-bisphosphoglycerate + ADP ATP + 3-phosphoglycerate
catalyzed by phosphoglycerate kinase
Rationale: substrate-level phosphorylation to make ATP
catalyzed by phosphoglycerate kinase (PGK)
kinases transfer phosphate groups from ATP to various substrates)
1,3-bisphosphoglycerate is a high energy compound. It can donate the phosphate group to ADP
to make ATP
Highly thermodnamically favorable/reversible
Is reversible because of coupling to GAPDH reaction
STEP 8: Migration of the phosphate
3-phosphoglycerate 2-phosphoglycerate
catalyzed by phosphoglycerate mutase (mutases catalyze migration of functional groups)
rationale: be able to form high-energy phosphate compound
thermodynamically unfavorable/reversible
reactant concentration kept high by PGK to push forward
STEP 9: dehydration of 2-PG to PEP
2-phosphoglycerate phosphoenolpyruvate + H2O
catalyzed by enolase
rationale: generate a high-energy phosphate compound
2-phosphoaglycerate is not a good enough phosphate donor this is why step 8 happens
slightly thermodynamically unfavorable/reversible
product concentration kept low to pull forward
STEP 10: phosphotransfer from PEP
phosphoenolpyruvate + ADP pyruvate + ATP
catalyzed by pyruvate kinase (requires divalent metals for activity)
second substrate level phosphorylation: generates another ATP molecule

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rationale:
substrate-level phosphorylation to make ATP
produces 2 ATP
Loss of phosphate from PEP yields an enol that tautomerizes into ketone
Tautomerization:
effectively lowers the concentration of the reaction product
drives the reaction toward ATP formation
highly thermodynamically favorable/irreversible
Balanced equation of glycolysis
C6H12O6 + 2 ADP + 2 Pi + 2NAD+ 2 pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O
Pyruvate has 3 fates:
1) TCA cycle (oxygen is present)
2) lactic acid fermentation (no oxygen is present) occurs in humans (muscles) and other
organisms
pyruvate + NADH + H+ l-lactate + NAD+
rationale: NAD+ is regenerated by transferring e- to pyruvate and reducing it to lactate. By
regenerating NAD+, it can be re-used in glycolysis.
lactate builds up in muscle during strenuous exercise the acidification of muscle prevents
its continuous strenuous work
the lactate can be transported to the liver and converted back to glucose (cori cycle)

3) ethanol fermentation (no oxygen is present) Done in yeast only

rationale: NAD+ is regenerated by transferring e- to acetaldehyde and reducing it to ethanol.
By regenerating NAD+, it can be re-used in glycolysis.
Pyruvate acetyldehyde + CO2
catalyzed by pyruvate decarboxylase
Acetaldehyde + NADH + H+ ethanol + NAD+
catalyzed by alcohol dehydrodgenase
two-step reduction of pyruvate to ethanol, irreversible
Note that acetaldehyde is the final electron acceptor
humans do not have pyruvate dehydrogenase for ethanol metabolism

74
CO2 is responsible for carbonation in beer, rising in bread

75

In eukaryotes, citric acid cycle occurs in mitochondria

glycolysis occurs in cytoplasm
citric acid cycle occurs in the mitochondrial matrix. The goal of the citric acid cycle is to
fully oxidize the pyruvate molecule so the energy from the freed up electrons can be used to
make ATP.
oxidative phosphorylation occurs in the inner membrane
Memorize the parts of the mitochondria in the picture below.

(Pyruvate decarboxylation) conversion of pyruvate to acetyl-CoA

net reaction: oxidative decarboxylation of pyruvate
Rationale: acetyl-CoA can enter the citric acid cycle and yield energy. Acetyl-CoA can
also be used to synthesize storage lipids.
Pyruvate + CoA-SH + NAD+ ----> Acetyl-CoA + NADH + CO2
enzyme: pyruvate dehydrogenase complex (PDC) (E1 + E2 + E3)
PDC is a large multi-enzyme complex
short distance between catalytic sites all channeling of substrates from one catalytic
site of another. This minimizes side reactions.
TPP, lipoyllysine and FAD are prosthetic groups
structure of Coenzyme A
recall that coenzymes or co-substrates are not a permanent part of the enzyme's
structure; they associate, fulfill a function, and dissociate
the function of CoA is to accept and carry acetyl groups
Step 1: Condensation
Acetyl-CoA + Oxaloacetate + H2O ----> CoA-SH + Citrate
enzyme: citrate synthase (induced fit = wont be active until all substrates bind to it)
rate-limiting step of citric acid cycle
activity largely depends on concentration of oxaloacetate
highly thermodynamically favorable/irreversible
regulated by substrate availability and product inhibition

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Step 2: transformation of 6 carbon unit to isocitrate

citrate ----> cis-Aconitate + H2O
enzyme = aconitase
cis-aconiate +H2O ----> Isocitrate
enzyme: aconitase
citrate, a tertiary alcohol, is a poor substrate for oxidation. However, isocitrate is a
secondary alcohol and is a good substrate for oxidation.
Addition of H2O to cis-aconitate is stereospecific
thermodynamically unfavorable/reversible
product concentration kept low to pull forward
step 3: decarboylation #2 and formation of NADH
Isocitrate + NADP+ ----> alpha-ketoglutarate + NADPH + H+ + CO2
NADPH + NAD+ ---> NADH + NADP+
enzyme: isocitrate dehydrogenase
oxidative decarboxylation: lose a carbon as co2 and generate NADH
oxidation of the alcohol to a ketone: transfers a hydride to NAD
cytosolic isozyme uses NADP+ as a cofactor
highly thermodynamically favorable/irreversible
regulated by product inhibition and ATP
step 4: decarboxylation #3 and formation of NADH
alpha-ketoglutarate + CoA-SH + NAD+ Succinyl-CoA + NADH + H+ + CO2
enzyme: alpha-ketuoglutarate dehydrogenase
last oxidative decarboxylation:
net full oxidation of all carbons of glucose
after two turns of the cycle
carbons not directly from glucose because carbons lost came from oxaloacetate
succinyl-CoA is another high-energy thioester bond
highly thermodynamically favorable/irreversible
regulated by product inhibition
Step 5: formation of GTP
succinyl-CoA + GDP + Pi ---> GTP + CoA-SH + Succinate
enzume: succinyl-CoA synthetase
synthases catalyze condensation reactions where no nucleotides are involved
synthetases: condensation reactions that use nucleotides
substrate level phosphorylation
energy of thioester allows for incorporation of inorganic phosphate
Produces GTP, which can be converted to ATP
slightly thermodynamically favorable/reversible
product concentration kept low to pull forward
Step 6: the third oxidation
succinate + FAD -----> fumarate + FADH2
enzyme: succinate dehydrogenase
bound to mitochondrial inner membrane
part of complex II in the electron-transport chain
near equilibrium/reversible

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product concentration kept low to pull forward

step 7: hydration
Fumarate + OH- ----> carbanion transition state
carbanion transition state + H+ ---> L-malate
enzyme: fumarase
stereospecific:
addition of water is always trans and forms L-malate
OH- adds to fumarate... then H+ adds to the carbanion
slightly thermodynamically favorable/reversible
product concentration kept low to pull reaction forward
last step
L-malate + NAD+ ---> NADH + H+ + Oxaloacetate
enzyme: malate dehydrogenase
final step of cycle
regenerates oxaloacetate for citrate synthase
highly thermodynamically unfavorable/reversible
oxaloacetate concentration kept VERY low by cytrase synthase
pulls the reaction forward

CAC intermediates are amphibolic (Anaplerotic reactions)

intermediates in citric acid cycle can be used in other biosynthetic pathways (removed form
cycle)
must replenish intermediates in order for the cycle and central metabolic pathway to
continue
4-carbon intermediates are formed by carboxylation of 3-carbon precursors

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Calvin's experiments
Calvin: incubated green algae with 14CO2 isotope and traced the metabolic fate of 14C
isotope
Observation 1: within less than a minute, 14C-labeled amino acids and sugars found
explanation: green algae are able to convert CO2 into small organic compounds (CO2
assimilation)
Observation 2: within 5 sec of incubation of 14CO2, labeled 3-phosphoglycerate (3PG)
was detected
explanation: 3PG is a stable intermediate and is formed by carboxylation of carbon
intermediate
Click the link for a great animation about the experiments:
http://www.snabonline.com/Content/TopicResources/Topic5/Activities/Interactives/5_6/5-6.swf
Carbon assimilation pathway: the calvin cycle (dark reaction)
Plants reduce CO2 into sugars through the calvin cycle.
Autotrophic organisms use CO2 as sole source for biosynthesis of starch, cellulose, lipids,
and proteins and other organic molecules. They use reducing equivalents of NADPH and
energy (ATP), which is generated during photosynthesis to reduce CO2 to carbon
intermediates!!!!
Calvin cycle doesn't happen in the dark because reducing equivalents and ATP are not
provided in the absence of photosynthesis
3 turns of calvin cycle consume: 3 CO2, 9 ATP, 6 NADPH and make 1 GAP
Calvin cycle step 1: CO2-fixation
3 ribulose 1,5 bisphosphate + 3 CO2 ----> 6 3-phosphoglycerate
enzyme: rubisco (ribulose 1,5B-P carboxylase) (most abundant protein in biosphere)
carboxylation of ribulose 1,5 BisP to generated 3 molecules of 3-phosphoglycerate
calvin cycle step 2: reduction
6 3-phosphoglycerate + 6 ATP + 6 NADPH + 6 H+ ----> 6 Glyceraldehyde-3-phosphate + 6
ADP + 6 NADP+ +6 Pi
mechanism: reversal of glycolysis with the exception that NADPH is used instead of NADH
Unlike GAPDH from cytoplasmic gluconeogenesis, stromal enzyme uses NADPH as
co-factor
fates of GAP:
Used to regenerate ribulose 1,5 bisphosphate (most do this)
stored as starch in chloroplast for later use
translocated to cytosol and converted to sucrose (transported to non-photosynthesizing
parts)
Calvin cycle step 3: regeneration
5 Glyceraldehyde-3-phosphate + 3 ATP ----> 3 Ribulose 1,5-bisphosphate + 3 ADP
very similar to the non-oxidative part of the pentose phosphate pathway except that it
proceeds in the opposite direction. Called reductive pentose phosphate pathway (from
hexose to pentose)
A stoichiometry problem:
3 CO2 + 9 ATP + 6 NADPH + 6 H+ ---> 1 GAP + 9 ADP + 8 Pi + 6 NADP+ (calvin cycle)
But you are short 1 Pi from balancing!
The 9th Pi is added from the cytosol

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Pi/Triose antiporter
DHAP (produced from calvin cycle) leaves stroma into cytosol through the Pi-triose
antiporter. DHAP gets dephosphroylated when it eventually turns into sucrose. The stripped
Pi then moves back into the stroma via the same transporter and this balances out the calvin
cycle.
Antiport is also used to transfer NADPH and ATP produced by photosystems into the
cytosol

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Overview
oxidative phosphorylation:
catabolism of carbohydrates, lipids, amino acids converge on cellular respiration
oxygen is reduced to H2O; electrons are donated by NADH and FADH2
takes place in mitochondria for eukaryotes
Brief review of universal electron carriers
oxidative phosphorylation is based on electron carriers
dehydrogenases collect electrons from catabolic pathways and transfer them to:
nicotamide nucleotides: NAD+ and NADP+
Flavin nucleotides: FAD and FMN
Universal electron carriers 1: Ubiquinone
Ubiquinone (coenzyme Q)
remains in lipid bilayer
very mobile
shuttles electrons between various carriers
Accepts 1 or 2 electrons

Universal electron carriers 2: Cytochromes

Electron carrier proteins
most are integral proteins of inner mitochondrial membrane
Accepts 1 electron only
complex 1- NADH:Ubiquinone Oxidoreductase
Structural features:
transfers electrons from NADH ubiquinone
Embedded in membrane
one domain extends into matrix (docking station for NADH)
Mechanistic features:
couples 2 reactions: electron transfer and proton translocation across inner mitohondrial
membrane
(1) Transfers 2 electrons from NADH to ubiquinone
(2) Transfers 4 protons through inner mitochondrial membrane per 2 electrons
Exergonic (1) drives endergonic (2)

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complex 2 succinate dehydrogenate

Transfers electrons from succinate FADH2 ubiquinone
Succinate dehydrogenase is the only membrane-bound enzyme in the Krebs Cycle
Electrons from succinate do not have enough energy to allow proton pumping cannot be
funneled through complex 1

Other bypasses of complex 1

first step of fatty acid breakdown (formation of -C=C- bond) passes electrons from acylCoA to electron transfer flavoprotein (ETF)
ETF will eventually complete electron transfer to Q:
FAD electron transfer flavoprotein ETF:ubiquinone oxidoreductase ubiquinone
(Q)
Other bypasses of complex 1
glycerol-3-phosphate from fat degradation or reduction of dihydroxyacetone phosphate
(glycolysis)
oxidized by glycerol 3-phosphate dehydrogenase (outer surface of membrane)
dehydrogenase channels electrons to ubiquinone (Q) via FAD

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complex 3 cytochrome bc1

structure:
also known as ubiquinone:cytochrome c oxidoreductase
transfers electrons from ubiquinone cytochrome c
transports 2 protons through inner membrane
mechanism:
Function: switch from 2-electron carrier (NADH, FADH2, QH2) to 1-electron carrier
(cytochromes, Cu+)
Pumps 4H+ through the membrane for every pair of electrons passed to cytochrome c (2
needed)
Cytochrome c passes electrons to complex IV
Net equation: QH2 + 2 cyt c1 (oxidized) + 2H+ (inside) ---> Q + 2 cyt c1 (reduced) + 4H
+ (outside)
2 H+ comes from the conversion of QH2 back to Q

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cytochrome IV cytochrome oxidase

structure
transfers electrons from cytochrome c O2
reduces 1 O2 to 2 H2O
mechanism
for every 4 electrons passing through complex IV:
One O2 is converted to 2 H2O using 4 H+ from matrix
involves single-electron transfers (cytochrome c)
all intermediates remain bound to complex
all intermediates are highly reactive radicals and can cause damage if released

ETC balance sheet

For each electron pair:
4 H+ are pumped out by complex I
4 H+ are pumped out by complex III
2 H+ are pumped out by complex IV
10 H+ total using NADH
pumping out H+ generates electrochemical gradient. Energy is stored as a proton-motive
force
2 components:
1) chemical potential due to [H+] gradient across membrane
2) electrical potential due to separation of charge (H+)
protons spontaneously flow down electrochemical gradient driving ATP synthesis
ATP synthesis
proton motive force provides energy to drive ATP synthesis (ADP + Pi ATP)
Requires ~50 kJ/mol under cellular conditions
ATP synthesis results from coupling proton flux to phosphorylation

84

The ATP synthase paradox

Proton motive force is required to released tightly bound ATP rather than to synthesize
it!!!!!
ATP synthase consists of two functional domains
Fo: contains a passive proton pore
F1 contains nine subunits (5 types)
'head' consists of altering alpha and beta subunits
beta subunits contain catalytic site
stator connects Fo and F1

F1 structure and dynamics

Each beta subunit adopts a different conformation
each conformation binds different ligands (none, ADP/Pi, ATP)
gamma subunit binds only 1 Beta subunit
rotation of gamma subunit (driven by proton motive force) forces beta subunits to cycle
through conformations rotational catalysis
model for ATP synthesis
movement of protons down electrochemical
gradient through c ring induces rotation of ring
and gamma stalk in plane of membrane (green
circle in middle)
rotation of gamma stalk causes beta subunits to
associate with gamma in a cyclic fashion
FOCUS ON THE PURPLE UNIT ONLY:
1) Subunit begins in the Loose
conformation. This is the conformation that
will bind the ADP and Pi. (step 1)

85

2) Gamma stalk rotates and changes the conformation of the subunit from the Loose
conformation to the Tight conformation. In the tight conformation, ADP and Pi bind to
form ATP. (step 2 and Step 3)
3) Gamma stalk rotates and changes the conformation of the subunit from the Tight
conformation to the Open conformation. This causes ATP to be released from ATP
synthase. (step 4)
Note that there are three different subunits per ATP synthase (purple subunit, blue subunit,
and yellow subunit). In one 360 degree rotation, each different color subunit goes through
all different conformations (as described above). This means that in one 360 degree rotation,
3 ATP is formed.
direction of rotation determines outcome:
direction 1: PMF-driven ATP synthesis
direction 2: ATP-driven H+ pump
ATP hydrolysis
ATP breakdown to ADP is a hydrolysis reaction!
Stoichiometry of ATP synthesis historical view
number of electrons moved and number of ATP molecules formed are whole numbers
(integers)
values of these numbers are derived from P/O ratios
Phosphates transferred (P) : oxygen oxidized (O)
Ratios were NADH = 3, succinate = 2 (Numbers you need to know for DAT)
Prokatyotes vs. eukaryotes
In eukaryotes, the total energy from glucose is about 36 ATP. However, in eukaryotes, the
total energy from glucose is about 38 ATP. Why?
Prokaryotes have no mitohcondria so they do not need to transfer pyruvate into the
mitochondrial matrix, which is done via active transport, thus costing ATP. They use cell
membrane for oxidative phosphorylation.
Note that prokaryotes do not do TCA cycle because they don't have mitochondria.

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Overview of the two stages of photosynthesis

(1) light dependent photophosphorylation (topic for this chapter)
energy from light is absorbed by chlorophyll and other pigments
absorbed energy is used: to generate ATP and to transfer electrons from water to NADP+
(oxygen is produced)
(2) carbon assimilation/carbon fixation (the calvin cyclepreviously discussed)
uses products of light reactions
NADPH and ATP reduce CO2
new organic carbon is converted into triose phosphates, sucrose, and starch
Structure of plant chloroplasts
chloroplasts are surrounded by two membranes, an outer membrane that is permeable to
small molecules and ions, and an inner membrane that encloses the internal compartment.
This compartment contains many flattened, membrane-surrounded vesicles or sacs, the
thylakoids, usually arranged in stacks called grana.
Embedded in the thylakoid membrane are the photosynthetic pigments and enzyme
complexes that carry out the light reactions and ATP synthesis.
The stroma, the aqueous phase enclosed by the inner membrane, contains most of the
enzymes for the carbon-assimilation reactions.
The calvin cycle occurs in the stroma whereas photophosphorylation occurs on the
thylakoid membranes.

Chromophores: Light-absorbing molecules

light absorption: absorbing a photon raises chromophore (electrons) to a higher energy level
Photon energy must match exactly energy gap between ground state and excited state
excited state is unstable and short-lived
Excited chromophore eventually returns to ground state
energy is released as light (emission), heat, or (biological) work
This is the idea behind photosynthesis
Primary Photosynthetic Pigments 1: chlorophylls
Green pigments in thylakoid membranes
Contain polycylic, planar rings resembling heme w/ phytol side-chain
Mg 2+ (not iron) is at center of tetrapyrrol ring
strongly absorb light due to conjugated double bonds in ring
spectra of chlorophylls a and b are not identical

87

chlorophylls are always associated with binding proteins

chlorophyll + binding protein = light harvesting complexes (LHCs)
proteins orient chlorophyll in 3D space
Energy transfer requires contact between pigments, binding proteins and membrane
components

Secondary Pigments
Accessory (secondary) pigments: carotenoids present in thylakoid membranes
secondary pigments absorb light outside the range of chlorophylls
Primary and secondary photopigments
spectra are complimentary: each 'antenna' absorbs in a specific wavelength range
pigments cover whole visible spectrum

Chlorophylls channel energy from sunlight to reaction centers

photosystems: pigments/proteins arranged into functional units
all pigments absorb light as photons
only a few chlorophylls convert light energy into chemical energy
these are part of photochemical reaction centers
rest of pigments transmits light energy to reaction centers light-harvesting (antenna)
molecules

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Energy transfer from antennas to reaction centers: exciton transfer

one pigment absorbs a photon and is excited
energy is randomly transferred to a neighboring light-harvesting molecule, exciting it
first one returns to the ground state
exciton transfer continues until it reaches a specialized pair of chlorphyll a at reaction center
energy passed to chlorophyll a in reaction center causes one electron to be promoted to next
orbital
this electron is passed to an electron acceptor molecule initiates plant electron transport
leaves an electron hole (+) in the donor chlorophyll a
Electron acceptor gains a negative charge (-)
electron is replaced through transfer from a neighboring electron donor, which becomes
positively charged

Reaction centers of higher plants

chloroplast thylakoids: two distinct reaction center types, P680 and P700
are complementary
resemble the two bacterial systems
each chloroplast has hundreds of each system in thylakoid membranes
Photosystem 2 (PSII):
contains equal amounts of chlorophylls a and b
P680 reaction center
contributes to proton gradient across thylakoid membrane
Photosystem 1 (PSI):
P700 reaciton center
high amounts of chlorophylls a and b
reaction center transfers electrons to Fd
electrons from Ferredoxin are used to reduce NADP+
Reaction centers act in tandem to move electrons from H2O to NADP+ using sunlight
Plastocyanin (Cu) moves electrons between PSII and PSI (one electron at a time)
H2O is oxidized to O2 replaces electrons transferred from PSII to PSI this is why H2O
is needed in photosynthesis
Plants: oxygenic photosynthesis

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Bacteria: anoxygenic photosynthesis

Oxygen evolving complex
Oxygen evolving complex breaks down 2 H2O molecules into 4 H+ ions and 4 e-.
The 4 e- are then used to replace the electrons that were excited by photons in P680.
Note that for this reason photosynthesis is non-cyclic electron flow!
The 4H+ are used to create the electrochemical gradient for ATP synthesis.

PSI and PSII are physically separated

PSII is located in grana stacks
PSI and ATP synthase are located in unstacked stromal thylakoids access to stroma
Cytochrome b6f distribution is more uniform
Association of PS I and PS II with LSCHII is regulated by
sunlight
protein phosphorylation
cytochrome b6f complex
function = proton pumping as electrons are transported: moves 4 H+ per pair of electrons
from stroma into thylakoid lumen. Establishes electrochemical gradient (proton motive
force)
volume of thylakoid lumen in chloroplasts is small moving a small number of protons
has large effect
result: 3 unit pH difference, i.e. 1000-fold difference in [H+]

90
Proton motive force (PMF) drives ATP synthesis

Cyclic vs. non-cyclic photophosphorylation

Non-cyclic photophosphorylation is when the electrons used in photophosphorylation are
not recycled. To re-generate electrons for photophosphorylation, oxygen is evolved as a
byproduct. The steps described above are for non-cyclic photophosphorylation.
Both photosystems (I and II) are involved
The active reaction center is P680
Electron from Photosystem I is accepted by NADP
Both ATP and NAPDH are produced
This system is predominant in green plants.
In cyclic photophosphorylation, the electrons used in the process are recycled. This sytem
is predominant in bacteria.
Only photosystem I is involved.
The active reaction center is P700
Electrons travel in a cyclic manner, traveling back to photosystem I

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Photolysis of water splitting is absentATP synthesis in photophosphorylation: overview

mechanism for ATP synthesis is analogous to that in mitochondria
ATP synthesis is catalyzed by CF1/Cfo ATPase on outer surface of thylakoid membranes
ATP is produced by rotational catalysis
Balance sheet for photophosphorylation: we have a model but all is not known
About 12 H+ move from stroma to thylakoid lumen per 4 electrons (i.e. per O2 formed)
4 H+ by oxygen-evolving complex
up to 8 H+ by cytochrome b6f complex
electrochemical potential: change in pH = 3 across thylakoid membrane
but: most of electrical potential is lost due to counterion movement unlike mitochondria
where little is lost
Energy stored in proton gradient per pole of proton: G = -17 kJ/mol
12 moles of protons translates to ~200 kJ
enough free energy to drive synthesis of several ATP
ATP yield is about 3 per mole of O2 (experimental value)
Photorespiration
Photorespiration is fixation of oxygen by rubisco instead of carbon dioxide. This is a
problem because rubsico will fix both CO2 and O2 at the same time if both are present.
This feature of rubsico probably arose because in the early earth atmosphere, there was
not much O2 so it didn't matter.
The products of photorespiration are useless and are broken down by the peroxisome.
C4 photosynthesis
Purpose is to move CO2 from the mesophyll to the bundle sheath cell to maximize
photosynthesis and minimize photorespiration and water loss from stomata.
Found in hot dry, dry climates (think of corn and sugar cane!!!!)
Requires one additional ATP, which becomes AMP This is like using up 2 ATP
Structure of a C4 leaf is called the kranz anatomy (shown below).
Mechanism is called the hatch-slack pathway (shown below).

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CAM photosynthesis
Function is to allow the calvin cycle to proceed during the day when the stomata are closed.
This in turns reduces H2O loss.
Found in hot, dry climates (think of cactus and pineapple!!!)
Special feature is that the stomata open during the night. Usually, the stomata opens during
the day!
Mechanism shown below. Note that Malic acid is created and stored in the vacuole at night.
During the day, malic acid is transported back into the vacuoule and broken down to release
CO2.

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Fatty acids can be metabolized for energy through beta oxidation

Beta-oxidation is the catabolic process by which fatty acid molecules are broken down in
the cytosol in prokaryotes and in the mitochondria in eukaryotes to generate acteyl-CoA,
which enters the citric acid cycle, and NADH and FADH2, which are co-enzymes used in
the electron transport chain.
Fatty acids are a major source of energy because beta-oxidation can create many acetyl-CoA
molecules, each of which can be used in the citric acid cycle and then eventually oxidative
phosphorylation.
Overview of beta-oxidation for saturated, even carbon fatty acids:
(1) Activation and membrane transport of free fatty acids by binding to coenzyme A.
Fatty acids cannot penetrate through the plasma membrane because of their negative
charge. Therefore, they travel through transport proteins to enter the cytosol.
Once in the cytosol, fatty acids bind to coenzyme A to form acyl-CoA, and then
moves to the mitochondria for beta-oxidation.
If the fatty acyl-CoA has a long chain, then the carnitine shuttle must be utilized
because acyl-CoA is too big to pass through the mitochondrial membrane. The acyl
group is transferred from coenzyme A to carnitine to form acyl-carnitine. Acylcarnitine then can move into the mitochondria through a special membrane protein.
Once inside the mitochondria, acyl-carnitine is converted back into acyl-CoA. The
liberated carnitine is shuttled back to the cytosol so this process can be repeated.
(2) Oxidation of the beta carbon to a carbonyl group and cleavage of two-carbon
segments resulting in acetyl-CoA
If you are interested in the exact mechanism of this pathway, go to this link
https://en.wikipedia.org/wiki/Beta_oxidation. I don't think its necessary to know for
the DAT.
(3) Oxidation of acetyl-CoA to carbon dioxide in the citric acid cycle
(4) Electron transfer from electron carriers to the electron transport chain in oxidative
phosphorylation.
Fatty acids with an odd number of carbon atoms are common in plants and marine
organisms. Therefore, humans and animals that include these things in their diets must
metabolize them in the beta oxidation pathway.
Therefore, the end product, instead of acetyl-CoA is propionyl-CoA which as 3 carbons.
This then must be chained to succinyl-CoA to enter the citric acid cycle.
Unsaturated fatty acids are catabolyzed by the beta oxidation pathway but they require two
additional enzymes to handle the double bonds.
Amino acids
Amino acids can be oxidized for energy; however, this is not the body's preferred fuel
source.
Degradation of an amino acid usually occurs in the liver and kidneys and involves
deamination, by moving its amino group to alpha-ketoglutarate (a citric acid cycle
intermediate) forming glutamate (an amino acid).
After removal of one or more amino groups, the remainder of the molecule can be used for
energy by entering glycolysis or the citric acid cycle.
Ketone bodies
Ketone bodies are one of three water-soluble molecules (acetoacetate, betahydroxybutyrate, and acetone) that are produced by the liver from fatty acids during periods
of low food intake, carbohydrate restrictive diets, starvation, or untreated type I diabetes.
They are the body's last resort fuel source.

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These ketone bodies are readily picked up by tissues and converted into acetyl-CoA
which enters the citric acid cycle and is oxidized in the mitochondria for energy.
Ketosis is a metabolic state in which most of the body's energy supply comes from ketone
bodies in the blood.
When the amount of ketone bodies rise in the blood, the pH of the blood changes,
leading to serious illness.

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4 main phases of the cell cycle

Cell cycle is the ordered sequence of events that extends from a time a cell is first formed
from a dividing parent cell until its own division into two cells.
Two main stages: (1) a growing stage called interphase and (2) the actual cell division
called the mitotic phase.
Interphase is the time when a cell's metabolic activity is very high and the cell performs its
various functions within the organism. 3 subphases:
G1 = growth and preparation of chromosomes for replication (2n). Longest phase
S = synthesis of DNA (DNA replication) a duplication of the centrosome (2 x 2n)
G2 = preparation for mitosis (2x2n)
Meitotic phase (M) is the part of the cell cycle when the cell actually divides.
2x2n 2n if mitosis.
Around 10% of cycle.
In mitosis, the nucleus and its contentsmost importantly the duplicated chromosomes
divide and are evenly distributed, forming two daughter nuclei that are identical.
During cytokinesis, which usually begins before mitosis ends, the cytoplasm is divided
into two.

G0 phase
Many times a cell will leave the cell cycle, temporarily or permanently.
It exits at the G1 and enters a stage called G0. They are busy carrying out their other
functions (secretion, attacking pathogens, etc.).
Checkpoints: quality control of the cell cycle
G1 checkpoint is the most important checkpoint. At the end of G1 phase, if the cell is not
ready to divide, the next phase will be temporarily suspended. The cell could possibly arrest
in the G0 phase and never proceed, or wait until it is ready. When the cell is ready to divide,
it will move on to the S phase.
G2 Checkpoint is at the end of G2 phase. It evaluates the accuracy of DNA replication and

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determines whether the cell is ready to begin mitosis.
M checkpoint is at the end of metaphase. It checks to see if the microtubules are properly
attached to kinetochores. If not, anaphase is suspended.

Other features of cell cycle control

Growth factors attach to plasma membrane receptors. They stimulate the cell for division.
Density-dependent inhibition: Cells stop dividing when the surrounding density becomes
too high.
Anchorage dependence: Most cells only divide when they are attached to an external
surface such as a neighboring cell.
Cyclin dependent kinases (CDKs) are enzymes that activate proteins that regulate the cell
cycle via phosphorylation. CDKs are activated by the protein cyclin.
Functional limitations of cell cycle
Surface area-to-volume ratio: volume gets much large when cells grow vs SA. When S/V
is large, exchange becomes much easier. When S/V is small, exchange is hard, leads to cell
death, or cell division to increase SA.
Genome-to-volume ratio: genome size remains constant throughout life; as cell grows,
only volume increases. G/V will be small and thus exceed the ability of its genome to
produce sufficient amounts of regulator of activities. Some large cells are multinucleated to
deal with this.

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Alternation of generations
In most plants, meiosis and fertilization divide the life of an organism into two distinct
phases or generations.
The gametophyte generation begins with a spore produced by meiosis. The spore is
haploid, and all the cells derived from it (by mitosis) are also haploid. In due course, this
multicellular structure produces gametesby mitosisand sexual reproduction then
produces the sporophyte generation.
The sporophyte generation begins with a zygote. Cells contain diploid number of
chromosomes. Cells will divide and grow. Eventually through, certain cells will undergo
mitosis, forming spores and starting a new gametophyte generation.
The gametophyte is an inconspicuous structure in angiospersm and other higher plants.

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Cancer
Cancer refers to uncontrollable cell division as a result of cell cycle regulatory mechanisms
become inactive.
A cancerous cell will exhibit defective cell differentiation.
Usually, the immune system will be able to destroy a cancerous cell. However, if the cell
evades destruction, it may proliferate to form a tumor, an abnormally growing mass of
body cells.
If the abnormal cells remain at the original site, the lump is called a benign tumor.
In contrast, a malignant tumor can spread to neighboring tissues and other parts of the
body, displacing normal tissue and interrupting organ function as it goes. The spread of
cancer cells beyond their original site is called metastasis.
A cancerous cell known as myeloma may be cultured indefinitely
a lymphocyte may be fused with myeloma cell to produce a hybridoma
sarcoma only occurs in connective tissue
carcinoma occurs in epithelial tissue
cancers of blood-forming tissues such as bone marrow, spleen, and lymph nodes, are called
leukemias and lymphomas.

Human life cycle

The development of a fertilized egg into a new adult organism is one phase aof a
multicellular organism's life cycle, the sequence of stages leading from the adults of one
generation to the adults of the next.
Having two sets of chromosomes, each inherited from one parent, is a key factor in the
life cycle of humans and all other humans that reproduce sexually.
Humans are diploid (we have 2 copies of each chromosome, 2n). Our diploid number is 46;
that is, 2n = 46.
The egg and sperm cells are collectively known as gametes.
Each gamete has a single set of chromosomes and are said to be haploid (a cell with a
single chromosome set, n = 23 for humans).
Gametes divide through the process of meiosis. In meiosis, cell division reduces the
number of chromosomes in the parent cell by half and produces four gamete cells. The
four gamete cells are not identical to one another. Meiosis occurs in 2 parts:
The first division, meiosis I, segregates the two chromosomes of the homologous
pair, packaging them in separate (haploid) daughter cells but each chromosome is
still doubled.

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Meiosis II separates the sister chromatids. Each of the four daughter cells is haploid
and contains only a single chromosome from the homologous pair.
In the human life cycle, a haploid sperm cell from the father fuses with a haploid egg cell
from the mother in the process of fertilization.
The resulting fertilized egg, called a zygote, has two sets of homologous chromosomes
and is said to be diploid (one set comes from each parent)
The life cycle is completed as a sexually mature adult develops from the zygote via
mitosis.
All sexual life cycles, including our own, involve an alternation of diploid and haploid
stages.
Producing haploid gametes prevents the chromosome number from doubling in every
generation.

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Mitosis
Why is mitosis important?
Mitosis provides for growth, cell replacement, and asexual reproduction.
Karyokinesis is nuclear division (occurs first)
Cytokinesis is cell division (occurs second)
G2 of interphase
Nuclear envelope encloses the nucleus
The nucleus contains DNA
Two centrosomes have formed by duplication of a single centrosome. Centrosomes are
regions in the animal cells that organize the microtubule of the spindle. Each centrosome
contains two centrioles.
Prophase
chromatin fibers become more tightly coiled, condensing into discrete chromosomes
Each duplicated chromosome appears as two identical sister chromatids joined at their
centromeres.
Mitotic spindle begins to form. It is composed of two centrosomes and the microtubules
that extend from them. The radial arrays of shorter microtubules that extend from the
centrosomes are called asters.
Prometaphase
Nuclear envelop fragments
Microtubules extending from each centrosome can now invade the nuclear area
Each two of the chromatids of each chromosome now has a kinetochore, a specialized
protein structure at the centromere.
Some of the microtubules attach to the kinetochores, which jerk the chromosomes back
and forth.
Nonkinetochore microtubules interact with those from the opposite pole of the spindle.
Metaphase
The centrosomes are now at opposite poles of the cell
The chromosomes have all arrived at the metaphase plate, a plane that is equidistant
between the spindle's two poles. The chromosomes' centromeres lie at the metaphase
plate.
For each chromosome, the kinetochores of the sister chromatids are attached to
kinetochore microtubules coming from opposite poles.
Anaphase
Anaphase is the shortest stage of mitosis.
Begins when the cohesin proteins are cleaved. Allows the sister chromatids of each pair
to part suddenly. Each chromatid becomes a full-fledged chromosome.
The two liberated daughter chromosomes begin moving toward opposite ends of the cell
as their kinetochore microtubules shorten.
By the end of anaphase, the two ends to he cell have equivalentand complete
collections of chromosomes.
Each chromatid in anaphase is its own chromosome, therefore the chromosome number
during anaphase is equal to 4n.
Telophase
Two daughter nuclei form in the cell. Nuclear envelops re-arise.
Chromosomes become less condensed.
Mitosis is now complete.
Cytokinesis

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Division of the cytoplasm is well under way by late telophase, so the two daughter cells
appear shortly after the end of mitosis.
In animal cells, cytokinesis involves the formation of a cleavage furrow, which pinches
the cell in two.
In plants, a cell plate forms.

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Meiosis
Chromosomes are matched in homologous pairs
In humans, a typical body cell, called a somatic cell, has 46 chromosomes.
We see that the chromosomes, each consisting of two sister chromatids, can be arranged
in matching pairs. The two chromosomes of such a matching pair are called
homologous chromosomes because they both carry genes controlling the same
inherited characteristics.
The two chromosomes of a homologous pair may have different versions of the
same gene.
Sex chromosomes the chromsomes that determine a human's sex (the 23rd pair of
chromsomes in humans. XX = female, XY = male)
Autosomes = the 22 remaining pairs of autosomes
Prophase I
Centromere movement, spindle formation, and nuclear breakdown occur as in mitosis.

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Chromosomes condense progressively throughout prophase I

Homologous pairs of chromosomes line up (synapsis), forming tetrads (4 chromatids).
Crossing over occurs between sister chromatids here. Each homologous pair has one or
more X-shaped regions called chiasmata, where crossovers have occurred.
Synaptonemal complex is a protein structure that temporarily forms between
homologous chromosomes. It gives rise to the tetrad with chiasmata and crossing over.
Later in prophase I, microtubules from one pole or the other will attach to the two
kinetochores, one at each centromere.
5 steps:
leptotene chromosomes start condensing
zygotene synapsis begins and the synaptonemal complex begins to form
pachytene synapsis is complete and crossing over occurs
diplotene synaptonemal complex disappears but the chiasmata still present
diakinesis nuclear envelope fragments, chromosomes complete condensing, and
tetrads are ready for metaphase
Metaphase I
Pairs of homologous chromosomes are now arranged at the metaphase plate, with one
chromosomes in each pair facing each pole.
Both chromatids of one homolog are attached to kintochore microtubules from one pole.
Anaphase I
Breakdown of the proteins that are responsible for sister chromatid cohesion along
chromatid arms.
Homologs move toward opposite poles, guided by the spindle apparatus.
Sister chromatid cohesion persists at the centromere, causing chromatids to move as a
unit toward the same pole.
Telphase I and cytokinesis
When telophase I begins, each half of the cell has a complete haploid set of duplicated
chromosomes. Each chromosome is composed of two sister chromatids; one or both
chromatids chormatids include regions of nonsister chromatid DNA.
Cytokinesis usually occurs simultaneously with telophase I, forming two haploid
daughter cells.
In animal cells, a cleavage furrow forms. In plants, a cell plate forms.
Prophase II
Spindle apparatus forms.
In late prophase II, chromosomes, each still composed of two chromatids, associated at
the centromere, move toward the metaphase II plate.
Metaphase II
Chromosomes are positioned at the metaphase plate as in mitosis.
Anaphase II
Breakdown of proteins holding the sister chromatids together at the centromere allows
the cromatids to separate. The chromatids move toward the opposite poles as individual
chromosomes.
Telophase II and cytokinesis
Nuclei form, the chromosomes begin decondensing and cytokinesis occurs
Meiotic division of parent cell produces 4 daughter cells, each with a haploid set of
chromosomes.

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The 4 daughter cells are genetically distinct from one another.

How crossing over works
Crossing over is an exchange of corresponding segments between nonsister chromatids of
homologous chromosomes.
The sites of crossing over appear as X-shaped regions; each is called a chiasma (plural,
chiasmata) is a place where two homologous (nonsister) chromatids are attached to each
other.
Steps of crossing over:
(1) Crossing over begins very early in prophase I of meiosis. At that time, homologous
chromosomes are paired all along their lengths, with a precise gene-by-gene alignment.
(2) The DNA molecules of two nonsister chromatidsone maternal and one paternal
break at the same place.
(3) Immediately, the two broken chromatids join together in a new way. In effect, the
homologous segments trade places, or cross over, producing hybrid chromosomes with
new combinations of maternal and paternal genes.
(4) When the homologous chromosomes separate in anaphase I, each contains a new
segment originating from its homolog.
(5) Finally, in meiosis II, the sister chromatids separate, each going to a different
gamete.
Chromosomes with a combination of genes from crossing over are called recombinant
because they result from genetic recombination, the production of gene combinations
different from those carried by the original paternal chromosomes.
In meiosis in humans, an average of one to three crossover events occur per chromosome
pair. Crossing over creates tremendous diversity in gametes.
Sources of genetic Variation FROM MEIOSIS (NO genetic variation is created from mitosis)
Crossing over during prophase I
Independent assortment of homologues during metaphase 1 (which chromosome goes to
which cell). Law of independent assortment is explained in the genetics unit.
Random joining of gametes during fertilizations

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107

We know there was life by 3.45 billion years ago

Sulfur isotopes of organic matter preserved in 3.45-billion-year-old stromatolites reveal
microbial metabolism
Stromatolite: layered calcareous structures formed by bio-films (microorganisms adhered
together) binding sedimentary gains

LUCA
Last universal common ancestor (LUCA): the population of organisms at the base of the
tree of life. All living things today are descended from this one lineage. Is there really a
LUCA?
LUCA is by far the most probable theory than the closest competing hypothesis even
when counting for exchanging material between organisms (horizontal gene transfer)
There was probably more than one self-replicating early life form. One population was
successful enough to establish itself

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What are the properties of life?

Organization: maintenance of parts (whether cells or more complex)
metabolism: control of chemical reactions to sustain life
Growth and reproduction: creation of offspring
homeostasis: the ability to regulate one's internal environment
external response: response to external environment and stimuli
What are some critical steps required for life?
Generation of simple organic molecules from inorganic molecules
origin of self replication
genotype and phenotype linkage and natural selection
moving from RNA to DNA
creation of cells (compartmentalization)
Prebiotic soup hypothesis
Prebiotic soup hypothesis: the idea that the earliest life emerged in a soup-like liquid
environment, drawing energy from the cosmic rays, volcanic eruptions, and the Earth's
internal heat
Organic from Inorganic
Many experiments have shown that life related molecules can be synthesized from simple
inorganic components
1828 urea (organic) created from inorganic salts, ammonium chloride, and cilver
cyanate
helped disprove that the chemistry of living systems were fundamentally different
from nonliving systems

Oparin and Haldane's organic soup theory

If there was oxygen, no organic molecules would have formed.
The original Earth environment was very reducing (allowing chemical parts to turn
into more complex ones)
Miller-Urey experiments
simulated ocean and atmosphere interface
methane, ammonia, and hydrogen mixed with boiling water and simulated lighning
reactions produced amino acids
these were done in reducing environments (without compounds with oxygen). This
may not be accurate.

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Reducing environments exist in hydrothermal sites.

The discovery of chemosynthesis at vents in 1977 gave some credence to deep sea
origins.

Reducing environments exist in space as well.

Amino acids were found on a 4.6 billion year old meteorite

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Could extreme pressure and heat of impact destroy amino acids?

Goldman et al. 2010 suggests glancing strikes would allow survival. Also suggested
that heat could encourage more complex amino acid complexes.
Problems with organic from inorganic
some compounds have still never been produced (nucleotides)
low quantities are produced
Origin of self replication
chicken egg problem: DNA encodes information for proteins; proteins can't replicate'
proteins are required for replication of DNA
Solution: RNA world
RNA was the information carrier and catalyst
RNA has diverse roles that include catalyst and temporary information carrier
Ribozymes = RNA enzymes
RNA world: a hypothetical early stage in the history of life in which RNA was the
fundamental unit upon which life was based, fulfilling both an information role and a
catalytic role.
DNA replaces RNA
RNA was replaced by DNA around 3.5 billion years ago as the genotype
DNA is more stable whereas RNA is more reactive
DNA have repair mechanisms (proofreading, error correction)
lower mutation rates better storage
proteins were used for catalytic functions (phenotype).
They can be more complex and diverse than RNA
Molecular bridge from RNA to DNA still unknown
Reverse transcriptase can convert from RNA to DNA today
Precursors to first organisms
Protobionts are precursors of cells. They are like cells and metabolically active but are
unable to reproduce.
Microspheres, spontaneously formed lipid or protein bilayer bubbles, are experimentally
produced protobionts that have some selective permeable qualities.
What were the first organisms like?
The first single celled life was prokaryotic (they have no nucleus or organelles)
Organisms were compartmentalized
If functions are delegated, you need to contain the parts
Also, a self replicating system, if not compartmentalized, might be coopted by other
organisms
Metabolism
Primitive heterotrophic prokaryotes: obtained materials by consuming other organic
substances (pathogenic bacteria)
Primitive autotrophic prokaryotes: mutation, heterotroph gained ability to produce its
own food cyanobacteria.
Reproduction
Reproduction may have resulted from overproduction. the cell expands so large that
splitting is more stable.
Minimal gene sets
Minimal gene set is the hypothetical minimal number of genes thought necessary to

111
allow for cellular based life. Around 206 genes (done by comparing genomes)
Early population of these organisms exchanged material most likely
Horizontal gene transfer: the transfer of genetic material from one organisms to
another that is not its offspring. This was more prevalent in the early tree of life.
Basically, early cells may have swapped DNA frequently.

Where do viruses fit in here?

Hypotheses
Escaped gene hypothesis: escaped selfish genes that have evolved protein coatings and
self replication
Reduction hypothesis: extremely reduced cellular organisms
Remnants of the RNA world
viruses may have predated or coexisted with LUCA
Oxygen and ozone layer ended abiotic chemical evolution
O2 and O3 formed by production of photosynthetic activity of autotrophs (cyanobacteria).
Ozone layer formed, which absorbs UV light, blocking energy for abiotic synthesis of
organic materials.
This terminated primitive cells.
Formation of the first eukaryotes
Endosymbiosis: a mutually beneficial relationship in which one organism lives within the
body, often within the cell, of another.
It has been shown that mitochondria and chloroplasts formed through this process
Evidence for symbiosis (commonly asked on DAT):
Membranes mitochondria have their own cell membranes, just like a prokaryotic cell
does

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DNA each mitochondrion has its own circular DNA genome, like a bacteria's genome,
but much smaller. This DNA is passed from a mitochondrion to its offspring and is
separate from the host cell's genome in the nucleus.
Reproduction Mitochondria multiply by pinching in half the same process used by
bacteria. Every new mitochondrion must be produced from a parent mitochondrion in
this way; if a cell's mitochondria are removed, it can't build new ones from scratch.

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Studying cells
Stereomicroscope: Uses visible light to view surface of sample, but only at low resolutions.
Compound microscope: Uses visible light to view a thin section of sample. May require
staining for increased viability.
Phase-contrast: Uses light phases and contrast to allow for detailed observation of living
organisms if thin.
Confocal laser scanning + fluorescence: Can look at thin slices while keeping sample
intact; can look at specific parts of cell via fluorescent tagging. Can look at living cells, but
only fluorescently tagged parts. Used to observe chromosomes during mitosis.
Scanning elctron microscope (SEM): Look at surface of (3D) objects with high resolution.
Cant use on living specimens as sample needs to be dried and coated.
CryoSEM: Like SEM but no dehydration so you can look at samples in more natural
form. Cant use on living samples.
Transmission electron microscope (TEM): look at very thin cross-sections in high detail.
Can look at internal structures, very high resolution, but cant be used on living things.
Electron tomography: 3D-Electron tomography: 3D model buildup using TEM data.
Cell fractionalization (centrifugion): cells whose membranes have been centrifuged at
various speeds for varying lengths to separate components of different sizes, densities, and
shapes. Due to differences in density.
Fastest to pellet out = nucleus
then mitochondria, chloroplats, lysosomes, peroxisomes
then ER, vesicles
then ribosomes, viruses, larger macromolecules

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Freeze fracture: split lipid bilayer of a frozen specimen. Used to study cell membranes and
organelles.
Gram straining: common technique used to distinguish gram positive from gram negative
bacteria.
Gram positive bacteria strain violet due to the presence of a thick layer of
peptidoglycan.
Gram negative bacteria strain red because of the thinner peptidoglycan wall.

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Introduction
DNA contains 4 special abilities:
Diversity of structure
Ability to replicate
Mutability
Regulated expression
Central dogma:
DNA gets transcribed into RNA which will get translated into a polypeptide

Genes and organisms

The number of genes varies greatly between organisms
Having more genes doesn't mean the organism is higher order or more complex
Organization of DNA
In viruses: DNA or RNA is surrounded by a protein coat
In prokaryotes: DNA is organized into a circular chromosome or potentially a plasmid
In eukrayotes: Most of the DNA is in the nucleus. Some of the DNA is located in the
mitochondria and the chloroplast.
The nucleus contains multiple linear chromosomes. Each chromosome contains one
double stranded DNA molecule.
Human karyotype
Diploid = 2 copies of each chromosome. Humans are diploid; we inherit one copy of
each chromosome from each of our parents. Nomenclature: 2n = _____
Haploid = 1 copy of each chromosome. Examples are sperm and egg cells.
Nomenclature: n = ______
22 pairs of autosomes (homologous chromosomes)
Just because you have the same genes doesn't mean you have the same alleles!
1 pair of sex chromosomes (XX homologous, XY not homologous)
All somatic cells in the body have the same DNA
Gene regulation
Determines when and where a given gene is expressed
non-coding DNA also encodes regulatory functions
Most human-chimp differences due to gene regulation-not genes

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Genetics and variations
Differences among individuals are called polymorphisms.
They can result from: 1) mutations 2) environment 3) mixture of both
Environmental polymorphisms are usually not heritable
Mutations vs mutants
Mutations are changes in the DNA sequence that may or may not affect phenotype.
Arise from natural processes as well as environmental factors.
Mutants are individuals that have change sin their DNA that alter the wild-type
phenotype
How can we find mutants
From natural populations:
Spontaneously find them
Survey the population for mutants
Lab populations:
mutagenesis controllable introduction of mutations
selection kill what you don't want
screen look for what you want
Forward vs reverse genetics
Forward genetics: begin with a change in phenotype and then look to see how changes
in genotype cause the observed effects.
Reverse genetics: begin with a change in genotype and then look to see how this causes
a change in phenotype.

Model organisms
Model organisms are used in genetics research frequently because they are
small,
easy to culture,
have short generation times
have small genomes,
and are easy to transport.
Nature vs. nurture
Genotype: The genetic makeup of an organism. It describes an organism's complete set

117
of genes.
Phenotype: The observable physical and/or biochemical characteristics of the
expression of a gene; the clinical presentation of an individual with a particular
genotype.

The phrase nature and nurture relates to the relative importance of an individual's
genes as compared to an individual's environment on phenotype.
Genes x Environment = Phenotype. The relative contributions of genes and the
environment on phenotype differ per phenotype.
Mendel's laws and classical genetics
Mendel's law of segregation and independent assortment
Mendel's law of segregation: During gamete formation, the alleles for the same gene
segregate from each other so that each gamete carries only one allele for each gene.

Law of independent assortment: Alleles for different traits segregate independently

during the formation of gametes.

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Mendel's law of segregation allows us to predict outcomes.
Alleles
Since human cells carry two copies of each chromosome, they have two versions of
each gene. The different versions of a gene are called alleles.
Alleles can be either dominant or recessive.
Dominant alleles show their effect even if the individual only has one copy of the
allele. A dominant allele is the stronger version of a pair of alleles. Dominant alleles
are depicted as capital letters (i.e. A).
Recessive alleles only show their effect if the individual has two copies of the allele.
Recessive alleles are depicted as lowercase letters (i.e. a).
Heterozygous refers to an individual who carries two different alleles for a particular
gene.
Homozygous refers to an individual who carries two of the same alleles for a certain
gene.
Loci
A locus in genetics is the specific location or position of a gene, DNA sequence, on a
chromosome.
Monohybrid cross
A monohybrid cross is a mating between two individuals with different alleles (two
heterozygotes) at one genetic locus of interest.
Genotypes predicted = 1 homozygous dominant, 2 heterozygous, 1 homozygous
recessive (1:2:1)

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Dihybrid cross
A dihybrid cross is a cross between two different organisms that differ in two observed
traits. They tend to result in a 9:3:3:1 ratio.

Probability stuff
Use multiplication when you see the word AND
Use addition when you see the word OR
Common crosses
True-breeding: homozygous for the trait (either dominant or recessive)
Parental cross: parental strains are crossed with one another to form the F1 generation.
P x P = F1
Parental strains are usually true-breeding
Intercross: crosses between genetically identical individuals (selfing, sibling mating)
F1 x F1 = F2
F2 x F2 = F3
etc.
Backcross: F1 progeny mated back to one of the parents
F1 x P = backcross
Testcross: Dominant phenotype x recessive phenotype. A_ x aa
A testcross allows you to determine the genotype of the organism with the dominant
phenotype (dominant homozygous or dominant heterozygous).
If all of the offspring of a testcross have dominant phenotypes, the parent organism
with the dominant phenotype has a homozygous dominant genotype (AA).
If some of the offspring of a testcross have recessive phenotypes, the parent
organism with the dominant phenotype has a heterozygous dominant genotype
(Aa).
A testcross also can be used for dihybrids (A_B_ x aabb)
Finding mutants with mutagenesis
Mutagenesis treatment with conditions that cause mutations: chemical mutagens
(carcinogens), radiation, mobile genetic elements.
Screen = look for what you want
selection = kill what you don't want
Sex-linked traits and nondisjunction
X and Y chromosome gene content

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X chromosome contains 2000-3000 genes. Nearly all genes are required in both males
and females.
Y chromosome contains ~100 genes. ~5% of gene numbers on X made up the SRY
gene. This is the master control gene for making male embryos.
X and Y genes have sequence similarity at the tip of their shorter arms. This is the
region where they pair up in meiosis.
Recombination happens only in regions that pair. Therefore, the Y chromosome has
little recombination.
X-linked inheritance
A gene located on either sex chromosome is called a sex-linked gene.
Because the human X chromosome contains many more genes tan the Y, the term has
historically referred to genes on the X chromosome.

Y-linked inheritance
Y linked traits are very rare Y-linked traits are neither dominant nor recessive because
there is only one copy.
In a pedigree, you'd expect a Y-linked trait to be transmitted from fathers to sons only,
with no affected females observed.
Three common sex-linked disorders
Hemophilia is an X-linked recessive trait that causes excessive bleeding upon injury
because the person lacks one or more of the proteins required for blood clotting.
Colorblindness is a malfunction of light-sensitive cells in the eyes. It is a disorder that
involves several X-linked genes.
Duchenne muscular dystrophy is a condition characterized by a progressive
weakening of the muscles and loss of coordination. The symptoms appear in very early
childhood and becomes progressively worse as the child ages. Most affected individuals
don't live past their early 20s.
Nondisjunction: meiosis mistakes
Nondisjunction is when homologous chromosomes do not assort correctly during
mitosis. One daughter cell would get too many chromosomes, while the other daughter
cell would be getting too few chromosomes.
Causes Aneuploidy, a genome with a wrong chromosome number (either too many
or too few).
Nondisjunction during meiosis I generates a daughter cell with n + 1 chromosomes and

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another daughter cell with n 1 chromosomes. After meiosis II, 2 daughter cells will be
n + 1 and 2 daughter cells will be n-1.
Nondisjunction during meiosis II generates 1 daughter cell with n + 1 chromosomes, 1
daughter cell with n 1 chromosomes, and 2 normal daughter cells.
Non-disjunction diseases
XYY = Jacobs syndrome
XXY = Kleinfelter syndrome
XO = Turner Syndrome
XXX = Triple X
Mosaicism in cells that undergo nondisjunction in mitosis during embryonic
development; fraction of body cells have extra or missing chromosome.
Polyploidy: all chromosomes undergo meiotic nondisjunction and produce gametes
with twice the number of chromosomes. Common in plants.
Partial monosomy is the partial chromosomal deletion of 1 homologous chromosome.

Genetic traits in humans can be tracked through family pedigrees

Mendel's laws apply to the inheritance of many human traits. We determine the
inheritance pattern of a particular human trait by assembling this information into a
family tree called a pedigree.
In genetics, the word dominant does not imply that a phenotype is either normal or
more common than a recessive phenotype. Therefore, we use the word wild-type
trait to describe traits that are prevailing in nature. Note that wild-type traits aren't
necessarily specified by dominant alleles.

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Inferring the mode of inheritance on pedigrees

Make an educated guess and see whether it is consistent with the available information.
Fill out genotypes. You can't identify all alleles for all individuals usually.
Autosomal recessive diseases tends to skip generations whereas autosomal dominant
diseases tends to be present in every generation.
Human sex-linked disorders affect mostly males. Males only have one X-chromosome,
whereas Females have two x-chromosomes. Therefore, a male only needs to inherit one
recessive allele to have a recessive phenotype, whereas a female needs to inherit two
recessive alleles to have a recessive phenotype.
Chromosomal theory of inheritance
The chromosomal theory of inheritance states that genes occupy specific loci
(positions) on chromosomes, and it is the chromosomes that undergo segregation and
independent assortment during meiosis.
Thus, it is the behavior of chromosomes during meiosis and fertilization that
accounts for inheritance patterns.
Polygenic inheritance, cytoplasmic inheritance, and maternal effects
Discrete vs continuous traits
Discrete or discontinuous phenotypes fall into distinct classes (i.e. albinism)
Continuous or quantitative traits: distribution of phenotypes varies along a continuum
(i.e. height, blood pressure)
Polygenic model for quantitative traits
The polygenic model assumes that phenotype is affected by many gene loci, each with a
similar and additive effect on the trait.
Therefore, genes controlling quantitative traits will fall in a bell-shaped distribution.
Cytoplasmic inheritance

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The egg is much larger than the sperm. The egg contains all of the cytoplasm organelles
when fertilized with a sperm. The sperm just carries over DNA.
We know that mitochondria contains its own set of DNA (mtDNA).
We only inherit our mtDNA from our mother. Therefore, any mutation seen in the
mother's mtDNA will affect the progeny.
Cytoplasmic inheritance is uniparental and the genes are NOT located in the nucleus.
Molecular basis of cytoplasmic inheritance
Mitochondria and chloroplasts have their own genomes.
Mitochondria and chloroplasts replicate themselves, and their genomes are circular, like
bacteria. Maternal effects

Maternal effects
Maternal effect is when genotype of the mother determines phenotype of the child.
Not caused by organelles.
Mediated by RNAs and proteins produced by the mother.
Typically controlled by nuclear genes.
Genetic recombination
Recombination
The formation of chiasmata (which determine the location of recombination events) are
necessary for proper chromosome segregation during meiosis.
In each cell, every chromosome is expected to have at least 1 chiasmata.
The location of the crossovers within each germ cell is random and different in each
meiosis.
The production of recombinant
phenotypes depends on:
The location of genes on the
chromosome
the location of crossing over

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Genetic distance
Genetic distance determines the proportions of recombinant gametes produced during
meiosis.
Genetic distance (cM) is proportional to physical distance (bp).
We can estimate the number of parental and recombinant gametes by looking at the
phenotypes produced by particular genetic crosses.
The maximum genetic distance that can be measured between 2 genes in one cross is 50
cM.
If over 50% of your progeny are recombinant, then the two genes are not linked.
Haplotype is a set of DNA variations, or polymorphisms that tend to be inherited
together. In other words, the two genes are linked.
Extensions to mendelism
Extensions to Mendelism: alleleism (relating genotypes to phenotypes)
Types of alleles: loss of function, gain of function, neofunctional, null allele
Dominance: complete, incomplete, codominant
Lethals: recessive, conditional (e.g. temperature sensitive)
Multiple alleles: codominance, dominance series
Genetics of sickle-cell anemia
example of pleiotropy: where one gene has effects on multiple phenotypes

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Sicke-cell anemia has pleiotropic effects:
hemoglobin protein function
cell shape
cell density
malaria resistance heterozygote (AS) confers malaria resistance because the
malaria toxin cannot effect sicke cells.
Because of the pleiotropic functions (namely malaria resistance), both the A and S
alleles of the beta-globin gene are found in human populations at high frequency.
The polymorphism is maintained by balancing selection. Heterozygote gives malaria
resistance so it gives higher fitness effects.
Different alleles are favored under different conditions:
A allele is better if no malaria-carrying mosquitoes present
S allele better if malara-carrying mosquitoes present

Multifactorial inheritance
Most traits are controlled by multiple genes. Mutations in two different genes can give
the same phenotype.
Two genes affecting the trait can show:
independence (no interaction)
redundancy
complementarity (mutual epistasis)
epistasis
suppression (another specialized case of epistasis)
Two genes: Additive effects
Additive effects are when the contribution of each gene adds up to create the
phenotype.
This is basic dihybrid cross (9:3:3:1)

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Two genes: Gene interactions
The phenotypic effect of an allelic combination at one gene is influenced by the allelic
combination at another gene.
Complementary gene interaction mutual epistasis
Mutual epistasis results when the protein each individual gene creates is not functional
alone.
When both genes creates the correct proteins, a protein complex will form and each
protein will only be functional then.
Any mutation in either gene will automatically cause a recessive phenotype.
F2 generation would see a 9:7 dominant:recessive frequency. 7 because 3 + 3 + 1.

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Redundancy
Redundancy results when two genes have the same function and only one gene is
necessary for a normal phenotype.
The only way a recessive phenotype can be seen is if the genotypes of both individual
genes are homozygous recessive.
F2 generation would produce a 15:1 dominant:recessive frequency.

Epistasis
Epistasis is when mutation at one gene masks phenotypic effects of mutation at another
gene
If the epistatic gene is recessive, then the phenotype will be the same, regardless of the
genotype of the other gene. If A is epistatic over B, then aaBB, aaBb, aabb will all
produce the same phenotype.
F2 generation would see a 9:4:3 frequency.

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Suppression
suppression results when the mutant phenotype of one gene can be suppressed (or
hidden) by another gene. The gene that does the suppression can do it through the
dominant or recessive genotype.
Produces an F2 generation ratio of 13:3 if the recessive allele was the suppressor. If the
dominant allele was the suppressor the F2 generation would produce a 15:1 ratio.

Incomplete dominance
In incomplete dominance, the heterozygous genotype would produce a phenotype that
is equivalent to mixing the other two phenotypes together. Red, white, pink
codominance
In codominance, the dominant and recessive phenotype are seen equally throughout the
heterozygous phenotype. Red, white, red + white spots

Inhertance of blood type, an example of codominance

The ABO blood group phenotype in humans involves three alleles of a single gene.
Various combinations of three alleles for the ABO blood type produce four phenotypes:
A person's blood type may be A, B, AB, or O.

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These letters refer to two agglutinogens (a type of antigen) that are attached to the
surface of red blood cells, type A and type B.
The A and B antigen molecules on the surface of red blood cells are made by two different
enzymes, each of which are encoded by different alleles of the same gene.
Matching compatible blood types is critical for safe blood transfusions.
If a donor's blood cells have an agglutinogen that is foreign to the recipient, then the
recipient's immune system produces blood proteins called antibodies that bind
specifically to the foreign agglutinogens and cause the donor blood cells to clump
together, potentially killing the recipient.
AB individuals can receive blood from anyone without fear of clumping, making them
universal recipients while donated type O blood never causes clumping, making those
with type O blood universal donors.

Another level of specificity is added to blood type by examining the presence or

absence of the Rh surface protein. Each blood type is either positive + (has the Rh
protein) or negative - (no Rh protein).
The Rh factor genetic information is inherited independently of the ABO blood type
alleles.
There are 2 different alleles for the Rh factor, known as Rh+ (produces the Rh surface
protein) and Rh- (does not produce the Rh surface protein.

Gene/enzyme hypotheses, metabolic mutants, pathways

Prototrophs vs. auxotrophs
Auxotrophs mutant that requires a specific supplement in the environment in order
for it to grow (cannot synthesize that supplement)

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Prototrophs can grow on minimal media. Wild-type. Can synthesize all nutrients
normally.
Gene, protein hypotheses
One-gene-one-enzyme hypothesis: all enzymes are composed of a single gene product
One-gene-one-polypeptide hypothesis: enzymes can be composed of more than one
gene products
This is more accurate because some enzymes require multiple subunits, which are
different polypeptides from different genes
Biochemical pathways and genes
Some genes code for enzymes which help catalyze reactions in biochemical pathways. If
one gene mutates, the enzyme that gene coded for will be synthesized incorrectly which
will prevent it from catalyzing the necessary reaction. This tends to lead to accumulation
of an intermediate.
Two types of biochemical pathways:
Convergent: two intermediates come together to create a product
Divergent: one intermediate splits into two products

Evolutionary genetics
Hardy-weinberg model
Hardy-weinberg model is a null hypothesis for population genetics
By rejecting hardy-weinberg, we can conclude that one or more of the 5 assumptions of
hardy-weinberg have been violated and are present in the population.
Assumptions of hardy-weinberg
No natural selection
No mate preference (random mating)
No mutations
No migrations
Population size is infinite
Hardy-weinberg equilibrium
If populations are in hardy-weinberg equilibrium:
the frequencies of alleles (A and B) do not change over time without an evolutionary
force
loci that are not in equilibrium will be after one generation
with allele frequencies (say A and B), we can predict genotype frequencies,
assuming no evolutionary forces.
Hardy-weinberg equations
P = dominant allele frequency, Q = recessive allele frequency
P2 + 2PQ + Q2 = 1
P2 = homozygous dominant genotype frequency

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Q2 = homozygous recessive genotype frequency

2(PQ) = heterozygous genotype frequency
Structure of DNA and RNA (also covered in cellular and molecular bio unit know all info
from both sections)
Building blocks of DNA
4 nitrogenous bases: Adenine, Guanine, Cytosine, Thymine
Purines = adenine and guanine
Pyrimidines = cytosine, thyamine, uracil

DNA backbone = alternating phosphates and deoxyriboses bonded together by

phosphodiester linkages (5' phosphate group bound to 3'-OH)
Deoxyribonucleotide (structural unit of DNA) = N base + phosphate + deoxyribose
RNA backbone = alternating phosphates and riboses
Ribonculeotide (structural unit of RNA) = N base + phosphate + ribose

Directionality of DNA = 5' to 3'

5' end is the end with the free 5' phosphate-group
3' end is the end with the free 3' OH group on the sugar

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The bases hydrogen bond with one another: one of the most important mode of
interaction between 2 complementary strands of nucleic acid
A bonds to T = 2 hydrogen bonds
C bonds to G = 3 hydrogen bonds
Hydrophilic backbones are on outside of the helix, facing the surrounding water. These
strands are antiparallel to each other one strand goes in 5' to 3' direction whereas the
other strand goes from 3' to 5'.
10.5 base pairs per helical turn when in aqueous solution
Chargaff's rules
A = T, C = G
A + T doesn't always equal C + G

Grooves on DNA
Major groove: big groove created by double helix. Many sequence specific DNA
binding proteins bind here.
Many non-specific DNA binding proteins bind to the backbone.
Minor groove: small grove created by double helix.

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Major forms of DNA

B-form DNA is the most stable structure for DNA molecule under physiological
conditions.
A-form DNA is favored in solutions devoid of water. Right-handed double helix, but the
helix is wider and its 11 base pairs per turn.
Z-form DNA has 12 bps per helical turn and is left handed. Barely a minor groove.
Been found in bacteria and eukaryotes. May play a role in regulating the expression of
genes.
Special DNA sequences
Palindromes are sequences of bases that reads the same forwards and backwards.
Occurs over BOTH strands.
Inverted repeats are sequences of bases that reads the same forwards and backwards.
Occurs over ONE strand in BOTH strands.

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RNA information
Single stranded RNA tends to create complex 3D conformations
Can base-pair with complementary DNA or RNA
Double stranded RNA usually found in the A-form
Uses ribose in the backbone, not deoxyribose
Uses uracil, not thymine
Uses ribose, not deoxyribose
Genetic technology
Southern blots
Southern blots are used to analyze the length of restriction fragments of DNA.
Steps:
1) cut DNA with restriction enzyme
2) run on gel
3) Transfer DNA to membrane
4) hybridize with radioactive probe
Northern blots
Northern blots are used to analyze length of RNA fragments.
Steps:
1) Run RNA on gel
2) transfer to membrane
3) hybridize with radioactive probe
Western blot
Western blots are used to analyze lengths of protein fragments.
Steps:
1) run protein on gel
2) transfer to membrane
3) probe blot with antibody
Approaches to introducing DNA into organisms
1) take obtained DNA
2) add additional sequences
3) transfer it into the organism
DNA cloning
DNA cloning: The process of cutting the gene out of the larger chromosome, attaching it
to a much smaller piece of carrier DNA, and allow microorganisms to make many
copies of it. The result is selective amplification of a particular gene or DNA segment.
There are five general procedures:
(1) cutting target DNA at precise locations: sequence-specific endonucleases
(restriction endonucleases) provide the necessary molecular scissors.
(2) Selecting a small carrier molecule of DNA capable of self-replication. These
DNAs are called cloning vectors (a vector is a delivery agent). They are typically
plasmids or viral DNAs.
(3) Joining two DNA fragments covalently. The enzyme DNA ligase links the
cloning vector and the DNA to be cloned. Composite DNA molecules comprising
covalently linked segments form two or more sources are called recombinant
DNAs.
(4) Moving recombinant DNA from the test tube to a host cell that will provide the

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enzymatic machinery for DNA replication.
(5) Selecting or identifying host cells that contain recombinant DNA.
Restriction endonucleases and DNA ligases yield recombinant DNA
Two classes of enzymes that cut DNA are restriction endonucleases and DNA ligases
Restriction endonucleases (also called restriction enzymes) recognize and
cleave DNA at specific sequences (restriction sequences or restriction sites) to
generate a set of smaller fragments.
They are found in a wide range of bacterial species; they are used originally to
cleave foreign DNA (self = methylated DNA)
There are 3 types of restriction endonulceases: designated I, II, and III.
Types I and III are generally large, multisubunit complexes containing both
the endonuclease and methylase activities. Both require ATP to function.
Both types can cleave DNA at 25bp-1000bp from t he recognition sequence
Type II restriction endonucleases are simpler, require no ATP, and cleaves
the DNA within the recognition sequence itself.
Restriction endonucleases make either sticky ends or blunt ends.
Sticky ends are when there are unpaired nucleotides left on one side of each
strand after cleavage. They can base-pair with each other or with
complementary sticky ends of other DNA fragments. Sticky ends are easier
than blunt ends to paste into a vector because of the overhang.
Blunt ends are when there are no unpaired bases on the ends.
Once the DNA molecule has been cleaved, a particular fragment of known size can
be partially purified by gel electrophoresis. After the target DNA fragment is
isolated, DNA ligase can be used to join it to a similarly digested cloning vector
that is, a vector digested by the same restriction endonuclease.
A polylinker is a short DNA sequence containing 2 or more different sites for
cleavage by restriction enzymes. They are introduced into vectors to make
cloning easier by providing sites that allow cloning DNA, cut with any of a
number of different restriction enzymes, into a single plasmid.
Cloning vectors allow amplification of inserted DNA sequences
Plasmids
A plasmid is a circular DNA molecule that replicates separately from the host
chromosome.
If a plasmid becomes incorporated into a chromosome, it is called an episome.
The classic E. Coli plasmid pBR322 is a good example of a plasmid with
features useful in all cloning vectors:
The plasmid pBR322 has an origin of replication, or ori, a sequence where
replication is initiated by cellular enzymes. This sequence is required to
propagate the plasmid.
The plasmid contains genes that confer resistance to the antibiotics
tetracycline and ampicillin, allowing the selection of cells that contain the
intact plasmid or a recombinant version of the plasmid.
Several unique recognition sequences in pBR322 are targets for restriction
endonulceases, providing sites where the plasmid can be cut to insert foreign
DNA.
The small size of the plasmid facilitates its entry into cells and the
biochemical manipulation of the DNA.

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In the laboratory, small plasmids can be introduced into bacterial cells by a
process called transformation and plasmid DNA are incubated together at at 0
degrees Celsius in calcium chloride solution, then subjected to heat shock by
rapidly shifting the temperature between 37-43 degrees Celsius. The calcium
ions are believed to neutralize charges on phosphates and membrane. The heat
shock causes the cells to uptake the plasmid DNA.
In an alternative method, cells incubated with the plasmid DNA are subjected
to a high voltage pulse; this approach, called electroporation, transiently
renders the bacterial membrane permeable to large molecules.
Only a few cells uptake the plasmid DNA, so a method is needed to identify
those that do.
One strategy is to utilize one of two types of genes in the plasmid, referred to
as selectable and screenable markers.
Selectable markers either permit the growth of a cell (positive selection)
or kill the cell (negative selection) under a defined set of conditions.
A screenable marker is a gene encoding a protein that causes the cell to
produce a colored or fluorescent molecule.
Bacterial artificial chromosomes
Bacterial artificial chromosomes, or BACs, are artificial vectors large enough
to be thought of as chromosomes that can hold much larger DNA segments than
plasmids.
To accommodate very long segments of cloned DNA, BAC vectors have
very stable ori sites that maintain the plasmid.
BAC also include genes that encode proteins that direct reliable distribution
of the recombinant chromosomes to ensure equal division.
The BAC vector includes both selectable and screenable markers.
Yeast Artifical Chromosomes
Yeast is very easy to maintain and grow on a large scale in the laboratory.
Plasmid vectors have been constructed for yeast.
Some of these plasmids have multiple ori sites so it can be used in more than one
speciesthese are called shuttle vectors.
Yeast artificial chromosomes (YACs) contain all the elements needed to
maintain a eukaryotic chromosome in the yeast nucleus needed for stability and
proper segregation of the chromosome ant cell division. YAC vectors can be
used to clone very long segments of DNA.
Pulsed field gel electrophoresis are used to separate the fragments of YAC
when cut up by restriction endonucleases. It is a variation of gel electrophoresis
that can separate very large DNA segments.
Cloned genes can be expressed to amplify protein production
Frequently, the product of a cloned gene, rather than the gene itself, is of interest.
Investigators can manipulate cells to express cloned genes in order to study their
protein products.
The goal is to alter the sequences around a cloned gene to trick the host organism
into producing the protein product of the gene, often at very high levels to make
purification easier.
Cloning vectors with the transcription and translation signals needed for
regulated expression of a cloned gene are called expression vectors. The rate of

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expression of the cloned gene is controlled by replacing the gene's normal

promoter and regulatory sequences with more efficient and convenient versions
supplied by the vector.
Many different systems are used to express recombinant proteins
Bacteria
Bacteria remains the most common host for protein expression because the
regulatory sequences that govern gene expression in many bacteria are well
understood and can be harnessed to express cloned proteins at high levels.
They are easy to store and grow in the laboratory, on inexpensive growth media.
Problems: many intrinsically disordered regions, proteins may not fold correctly
Yeast
Yeast is probably the best understood eukaryotic organism and one of the easiest
to grow and manipulate in the laboratory.
Yeast have tough cell walls that are difficult to breach in order to introduce DNA
vectors.
PCR
Polymerase chain reaction amplifies DNA sequences in vitro.
Requires knowledge of the DNA sequence in the region of interest (need primers)
no host cells are involved
requires very little starting material
PCR primers: you need primers (sequences of DNA that are complementary to a
sequence on a DNA strand) that flank both sides of the target region.
Number of DNA strands after n cycles of PCR = 2n * 2
Steps in one cycle (there are usually many):
1) Denaturation (95 C): Two strands of DNA are held together by hydrogen bonds.
With enough heat, the hydrogen bonds can be broken and the two strands will
separate.
2) Annealing (60 C): Once the DNA strands are separated, the solution is cooled to
allow the DNA primer to bind to the original DNA for amplification.
3) Elongation (72 C): The solution is raised in temperature again, so taq polymerase
(a heat resistant DNA polymerase) can replicate the DNA.
RT-PCR
Reverse-transcriptase PCR: amplify mRNA sequence into many DNA sequences with
the help of reverse transcriptase.
Steps:
1) reverse-transcribe the mRNA into a mRNA/cDNA hybrid
2) use RNAse to degrade the RNA. You are now left with a cDNA strand.
3) use cDNA as template in a PCR reaction.
cDNA
Complementary DNA (cDNA) is DNA that consists of only the npart of the gene that
gets translated.
Steps:
1) use intron free mRNA and then reverse transcribe it to create cDNA.
DNA microarray
DNA microarray is a method to determine which genes are expressed and which genes
are not expressed in a given sample. It can provide a snapshot of all the genes in an

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organism, informing the researcher about the genes that are expressed at a given stage in
the organisms development or under a particular set of environmental conditions.
Steps:
1) Begin with a glass slide or chip. Attach thousands of copies of DNA for the genes
you want to test for.
2) take all mRNA being transcribe and convert it to cDNA.
3) Use the cDNA as a probe and wash it over your chip. The cDNA will hybridize
(bond) to the complementary strands if they match. When they do, they will light up
with florescence. The brighter the signal, the more you know that gene is being
transcribed.
Karyotyping
Karyotyping is a method to count the number of chromosomes. Useful in diagnosing
chromsomal disorders such as down's syndrome.
Gel electrophoresis
Gel electrophoresis is a method to separate sequences of DNA, RNA, or proteins by
their size and charge.
Smaller fragments will travel further down the gel towards the positive side than the
larger fragments, which will have a tougher time to move.
The plate is positively charged, so negatively charged molecules will move faster down
the plate.
SDS Page
SDS page is a detergent used to denature proteins into their primary form and to decharge the proteins. When the proteins are ran through gel electrophoresis, then they
will only be separated by size, without having to worry about charge.
Smallest proteins travel the longest; largest proteins travel the shortest.
ELISA
ELISA is a technology to determine if a specific antigen exists. Antibodies are placed
on a microtiter plate, and if they bind to their specific antigen there will be a color
change in the microtiter plate, indicating that a specific antigen exists.
DNA replication
Replication of DNA occurs differently in prokaryotes and eukaryotes
A bacterial chromosome is a circular double stranded DNA complexes with nucleoid
proteins.
Replication begins in a specific spot called the origin of replication region (ori) and
ends at the termination region (ter).
Eukaryotic chromosomes are linear and there are more than one chromosome.
Replication begins in multiple different ori spots along the chromosome and extends
to the end of the chromosome, the telomere.
DNA replication basics
DNA replication is semiconservative, meaning that a replicated DNA molecule
contains one old and one new strand.
DNA replication occurs in a 5' to 3' direction. This is because DNA polymerase can
only add new nucleotides to the 3'-OH end.

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Eukaryotic DNA synthesis

1) DNA helicase unwinds the DNA helix. DNA gyrase relieves strain while doublestrand DNA is being unwound by helicase. DNA topoisomerase removes the supercoils;
it is ahead of the replication fork. Single-stranded DNA binding proteins (SSBs)
attach to the unwound DNA strands to prevent re-annealing of the DNA strands.
2) In leading strand synthesis, DNA polymerse III synthesizes DNA in a 5' to 3'
direction. It adds new dNTPs to the 3'-OH end. A sliding clamp tethers the DNA pol II
to the template to allow the enzyme to catalyze consecutive additions without releasing
the DNA strand it is attached to.
3) Lagging strand synthesis occurs discontinuously because the DNA is exposed in the
5' to 3' direction. DNA primase synthesizes a short RNA primer. DNA pol III extends
the RNA with DNA, forming an okazaki fragment. As the fork extends, the process
repeats, forming a continuous leading strand and multiple okazaki fragments. DNA
polymerase I removes it with RNA, replacing it with DNA. DNA ligase joins the DNA
fragments.
4) As the replicating form move son, the leading and lagging strands twist into helical
forms.
In actuality, replication does not take place in discrete steps. The replication machinery
allows all these steps to take place at the same time (concerted).
http://sites.fas.harvard.edu/~biotext/animations/replication1.swf for an excellent
animation of DNA replication!!!!!!
Replication of prokaryotic chromosomes
Replication proceeds bidirectionally from ori to ter.
Replicon is the length of DNA that is replicated following one initiation event at a
single region.
Bacteria have 3 different DNA polymerases:
DNA pol I is used for primer removal and gap filling of okazaki fragments.
DNA pol II is used for DNA repair.

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DNA pol III is used for DNA synthesis.

Completing DNA replication: Eukaryotes

The ends of the chromosomes present a special problem for the replication process.
At the tip, the lagging strand reaches a point where its system of RNA priming
cannot work, and an unpolymerized section remains and a shortened chromosome
would be the result.
To solve this problem, the tips of chromosomes, called telomeres, have adjacent repeats
of simple DNA sequences (i.e. in humans the repeat sequence is TTAGGG). These
repeats do not code for an RNA or a protein but nevertheless are important.
An enzyme called telemorase adds these simple repeat units to the chromosome ends.
The telemorase protein is a member of a class of enzymes called reverse
transcriptases (recall this from the chapter on viruses).
The telemorase carries a small RNA molecule, part of which acts as a template for
the polymerization of the telomeric repeat unit that is added to the 3' end.
This process counteracts the tendency for the teolmere to shorten at replication.

DNA Transcription
Transcription
Transcription is the creation of RNA molecules from DNA template.
Proteins are polycistronic, meaning that multiple polypeptides can be synthesized from
the same mRNA.
Eukaryotes are monocistronic, meaning that only one polypeptide can be synthesized
from the same mRNA.

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RNA synthesis occurs in the 5' to 3' direction. Transcription is occurring in the 3' to 5'
direction of the DNA-template strand.

Steps of transcription
Initiation: RNA polymerase attaches to the promoter region on DNA and unzip the
DNA into two strands. A promoter region is a sequence, usually found upstream of the
gene region, that RNA polymerase and transcription factors bind to.
In eukaryotes, RNA polymerase requires the assistance of proteins called
transcription factors, which bind to DNA control sequences called enhancers.
For prokaryotes, the pribnow box is the most common sequence of nucleotides at
the promoter. For eukaryotes and archaea, the TATA box is the most common
sequence of nucleotides a the promoter. The most common sequence of nucleotides
at the promoter region is called the consensus sequence; variations from it causes

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less tight RNA pol binding lower transcription rate.
Elongation: RNA polymerase unzips the DNA and assembles RNA nucleotides using
one strand of DNA as a template; only one strand is transcribed. The DNA strand used
for transcription is called the coding strand.
The DNA strand not used for transcription is called the anti-sense DNA strand.
Used for protection against degradation.
Termination: RNA polymerase reaches special sequences that signals for the end of
transcription. RNA polymerase will then release the DNA strand from itself.
Termination in prokaryotes:
Intrinsic (rho-independent): The mRNA contains a sequence that can base pair
with itself to form a stem-loop structure that is rich in GC content. Following the
stem-loop structure is a chain of uracils. When RNA polymerase reaches the
uracil area, it stalls and eventually detaches from the DNA template strand.

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Rho-dependent: When a certain mRNA sequence is transcribed, a rho protein
binds to the forming RNA transcript. When Rho binds, it causes RNA
polymerase to stall and detach from the DNA.

Termination in Eukaryotes:
The termination sequence is usually AAAAAAAAAAA... (poly-A) signal. When
RNA pol hits this region, it stalls and detaches from the DNA template.

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mRNA processing
In prokaryotes, the primary RNA transcript is the mature mRNA.
In eukaryotes, the primary RNA transcript undergoes modification:
5' cap: A special sequence is added to the 5' end of the mRNA, providing
stability for the mRNA and point of attachment for ribosomes.
Poly-A tail: This sequence is attached to the 3' end of the mRNA. Provides
stability and control movement of mRNA across the nuclear envelope.
RNA Splicing: Removes introns (non-coding sequences) from the RNA
transcript. Done by small nuclear ribonculeoproteins (snRNPs). Different
splicing combinations yield different polypeptides when translated. Therefore, a
combination of genes can yield many different polypeptides.
Alternative splicing allows different mRNA to be generated from same RNA
transcript by selectively removing differences of an RNA transcript into different
combinations. Each combination codes for a different protein product.

DNA Translation
Transcription and translation
Prokaryotes: transcription and translation occur simultaneously
Eukaryotes: transcription and translation are spatially and temporally separate.
Transcription occurs first in the nucleus, and translation occurs second in the cytoplasm.
Ribosomes
Ribosomes are sites of protein synthesis. It is a ribozyme: the catalytic function is
performed by rRNA.
50S + 30S = 70S (prokaryotic ribosome)
60S + 40S = 80S (eukaryotic ribosome)
Large subunit is the site of peptidyl transferase activity (tRNA binds here).
Small subunit is the initial binding of mRNA.
Exit site = E site, Peptidyl site = P site, Aminoacyl site = A site.

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tRNA
tRNA is a special RNA molecule that serves as the intermediate between RNA and
amino acids. Contains 2 sites:
One site is attached to a specific amino acid. Another site has a special 3 letter
sequence called an anticodon: this sequence binds to a complementary sequence on
the mRNA.
Aminoacyl-tRNA synthetase binds an amino acid to a specific tRNA. One enzyme for
each amino acid.

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Translation initiation
Eukaryotes:
1) Small subunit binds 5'-cap, scans mRNA for first AUG. There is only one AUG
sequence per mRNA transcript.
2) Once found, the large ribosomal subunit and the charged initiator tRNA (carrying
methionine) binds.
Prokaryotes:
1) Small subunit binds to one of the many shine-dalgarno (AUG + few other
nucleotides) sequences on the mRNA transcript. There are multiple translation
initiation sites.
2) Once found, the large ribosomal subunit and the charged initiator tRNA (carrying
n-formylmethionine) binds.
A polysome is a single mRNA molecule bound by multiple ribosomes.
Translation elongation
Prokaryotes and Eukaryotes
1) Entry of second tRNA into A site.
2) Amino acid bound to tRNA in P site bonds to amino acid bound to tRNA in A site.
A dipeptide is formed.
3) Ribosome moves down 3 more nucleotides. All tRNAs shift down one site. When
the tRNA moves from the P to the E site, the tRNA in the E site gets released. The
growing polypeptide remains in the P site.
4) Repeat steps 1-3 to grow the polypeptide chain.
Translation termination
1) Ribosome hits stop codon (UAG). Release factor binds to the A site instead of
another tRNA.
2) Polypeptide dissociates from the tRNA. tRNA and mRNA separates from the
ribosome. Ribosome dissociates into large and small subunits.

Features of the genetic code

No overlaps, no gaps between codons.
Triplet nature: three nucleotides per amino acid.

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Degenerate: more than one codon per amino acid.
The third nucleotide in the codon is the least important. Usually, this position can vary
yet still produce the same amino acid (wobble effect).
Codon bias: different species prefer different codons that code for the same amino acid.
Possible causes: mutations (some mutations are favored over others), natural selection,
accuracy of translation.

DNA error-correction and mutations

Correction mechanisms
DNA polymerase makes mistakes during DNA replication. DNA polymerase has a built
in proofreader.
Removes wrong base by 3'-5' exonuclease activity, replaces it with right one, and
resumes DNA synthesis.
Mismatch repair: enzyme repair things DNA polymerase missed.
Excision repair: enzymes remove nucleotides damaged by mutagens.
Mutagens
A mutagen is an agent/process that catalyzes mutations in the DNA sequence.
Depurination: Purine spontaneously leaves the deoxyribose sugar it was bound to.
Deamination: Amine groups on nucleotide react with water to form a ketone.
Creates wrong base.
Oxidative damage
Base analogs (structures that are similar to bases) are attached by accident.
Intercalating agents insert themselves between nitrogenous bases and causes indel
mutations.
Backbone breaks from UV ray can break DNA molecule in half.
Types of Mutations
Substitution: one nucleotide is switched with another nucleotide.
Silent mutation: A change in a single base of the DNA sequence yields the same
protein. No change in protein function. Due to wobble effect.
Missense mutation: Change in a single base of DNA sequence yields a different
amino acid. Have varying effects depends on how important the amino acid is to
the protein structure and function.
Nonsense mutation: Change in a single base of DNA sequence yields a premature
STOP codon. Have large, negative effects on protein function.
Frameshift: change in length of DNA sequence alters the reading frame of the mRNA,
causing a totally different polypeptide to be produced.

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Insertion: Insertion of one or more base pairs.
Deletion: Deletion of one or more base pairs.
Regulatory mutations: Mutations in regulatory sites affecting splicing or expression.
Chromosomal mutations:
Deletion: A segment of the chromosome is removed
Inversion: A segment of the chromosome is removed and then reinserted
backward to its original orientation
Duplication: A segment of a chromosome is copied and inserted into the
homologous chromosome.
Reciprocal Translocation: the attachment of a chromosomal fragment to a
nonhomologous chromosome and vice versa.

DNA organization
Chromatin is a complex of DNA and proteins that forms chromosomes within the nucleus
of eukaryotic cells.
Nucleosome: DNA is supercoiled around bundles of 8/9 histone proteins (beads on a
string). This exists when the cell is not dividing. One of two types:
Euchromatin: loosely bound to nucleosomes, actively being transcribed.

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Heterochromatin: areas of tightly packed nucleosomes where DNA is inactive. Contains
a lot of junk DNA.

Transposons: DNA segments that can move to a new location on the same or a different
chromosome. 2 types:
Insertion sequences that consist of only one gene that codes for enzymes that transports
it (transposase)
Insertion sequences that code for transposase and extra genes (antibiotic resistance,
replication, etc.)
Insertions of transposons into another region could cause mutation.
Two general methods of transposition (look in the picture below):
DNA transposon (cut and paste): conservative transposon is a transposable element
that excises itself and moves to a new location.
Retrotransposon (copy and paste): nonconservative transposons are transposable
elements that creates duplicate copies of themselves to be inserted elsewhere in the
genome.
Long interspaced elements (LINE) are a class of autonomous transposable
elements that code for reverse transcriptase
Short interspaced elements (SINE) are a class of nonautonomous elements that
do not code for reverse transcriptase.

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Prokaryotic transcription regulation

Structure of the Lac (lactose) operon:
-------lac I----------------------promoter --- operator - lac Z --- lac Y ---- lac A--- lac I gene: encodes for the Lac operon repressor protein.
Promoter: site where RNA polymerase binds.
Operator: site where Lac operon repressor protein binds.
Lac Z, Lac Y, Lac Z = structural genes.
How the lac operon works
The lac operon is an example of an inducible system, meaning that binding of the
effector molecule to the repressor greatly reduces the affinity of the repressor for the
operator, the repressor is released and transcription proceeds.
1) Lac I gene gets transcribed and translated to create the repressor protein.
2) When there is no lactose present in the cell, the repressor binds to the operator and
prevents RNA polymerase from transcribing the structural genes.
3) When lactose is present in the cell and there are no glucose molecules available,
lactose binds to the allosteric site of the repressor protein. This binding will cause a
conformational change in the protein, and thus a change in activity. The repressor now
cannot bind to the operator and RNA polymerase can proceed to transcribe the structural
genes. With no glucose available, there will be high cAMP levels. cAMP will bind to
the promoter and help RNA polymerase more efficiently transcribe the structural genes.
If there is glucose present in the cell, there won't be transcription of the lac operon
(even if there is lactose present as well). The activator (cAMP) will not bind to the
promoter, and transcription won't occur.
Structure of the trp (tryptophan) operon
-------P/O-------trp L--------trp E-----trpD------trpC------trpB-----trpA----------- P/O = promoter (operator sequence is found in the promoter)
L = Leader sequence (attenuator sequence is found in the leader)
trp E, D, C, B, A = structural genes
How the trp operon works
The trp operon is a repressible system, meaning that binding of the effector molecule to
the repress greatly increases the affinity of the repressor for the operator and thus the
repressor binds and stops transcription.
A key element of the trp operon is the leader sequence. This leader sequence controls the
expression of the operon through a process called attenuation. The leader sequence has
4 domains (1-4):
Domain 3 of the mRNA can base pair with either domain 2 or domain 4.
If domain 3 pairs with domain 4, a stem and loop structure form on the mRNA and
transcription stops. This structure forms when the level of tryptophan is high in the
cell.
If domain 3 pairs with domain 2, then the stem and loop structure does not form and
transcription continues through the operon normally.
If domain 4 is deleted, the stem and loop structure cannot form and transcription will
occur even in the presence of tryptophan. Domain 4 is called the attenuator because
its presence is required to reduce mRNA transcription in the presence of high levels
of tryptophan.

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Repressible enzymes
Repressible enzymes are when structural genes stop producing enzymes only in the
presence of an active repressor.
Eukaryotic transcription regulation
Regulatory proteins: repressors and activators influence RNA pol's attachment to the
promoter region.
Activators are transcription factors that help RNA polymerase binding to the correct
DNA sequence.
Silencers bind to DNA sequences and inhibit the start of translation.
Nucleosome packing: methylation of histones cause tighter packing and thus preventing
transcription. Acetylation of histones catalyzes uncoiling and promotes transcription.
Methylation of histones keeps the DNA tightly coiled and further prevents transcription.
Modifications to the histones can be inherited by offspring. Inheritance of traits
transmitted by mechanisms not directly involving the nucleotide sequence is called
epigenetic inheritance.
Short interfering RNAs block mRNA translation by altering the mRNA conformation or
configuration before it gets to the ribosome.
MicroRNAs (miRNAs): forms a complex with a protein, then the protein-miRNA
complex can bind to any complementary mRNA sequence. Binding can either degrade
the target mRNA or block its translation. The process of miRNAs blocking translation is
called RNA interference.

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Later stages of gene expression are also subject to regulation

Breakdown of mRNA
Molecules of mRNA do not remain intact forever. Enzymes in the cytoplasm break them
down, and the timing of this event is an important factor regulating the amounts of
various proteins that are produced in the cell. Long-lived mRNAs can be translated into
many more protein molecules than short-lived ones.
Prokaryotic mRNAs tend to have much shorter lifetimes than eukaryotic mRNAs.
Initiation to translation
Many proteins control the start of translation (polypeptide synthesis).
By controlling the start of protein synthesis, cells can avoid wasting energy if the needed
components are currently unavailable.
Protein activation
After translation is complete, some polypeptides require alterations before they become
functional.
Post-translational control mechanisms in eukaryotes often involve the cleavage of a
polypeptide to yield a smaller final product that is the active protein.
By controlling the timing of such protein modifications, the rate of reactions can be
further fine-tuned.
Protein breakdown
The final control mechanism operating after translation is the selective breakdown of
proteins.
This regulation allows a cell to adjust the kinds and amounts of proteins in response to
changes in its environment.
It also enables the cell to maintain its proteins in prime working order.

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Putting regulation all together (look at the picture below)

X-inactivation
During embryonic development in female mammals, one of the two X chromosomes does
not uncoil into chromatin.
It remains a dark and coiled chromosome called a Barr body. Barr bodies cannot be
expressed.
Thus, only the genes on the X chromosome will be expressed.
Either X chromosome can be inactivated, meaning genes in the female will not be expressed
similarly, so all calls in a female mammals are not necessarily functional identical.

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The genetic basis of cancer

Oncogenes and proto-oncogenes
Genes that can cause cancer when present in a single copy in the cell are called
oncogenes.
A proto-oncogene is a normal, healthy gene that, if changed, can become a cancercausing oncogene.
Many proto-oncogenes code for growth factors, proteins that stimulate cell division, or
for other proteins that somehow affect growth factor function or some other aspect of
the cell cycle. Examples of how proto-oncogenes can turn into oncogenes are shown in
the picture below:

Tumor-suppressor genes
In addition to genes whose products normally promote cell division, cells contain genes
whose normal products inhibit cell division. Such genes are called tumor-suppressor
genes because the proteins they encode prevent uncontrolled cell growth.
Any mutation that decreases the normal activity of a tumor-suppressor protein may
contribute to the onset of cancer, in effect stimulating growth through the absence of
suppression.

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Contents of Bacteria and Archaea genomes

Though archaea are more closely related to eukaryotes, they have similar genomic
architecture to bacteria
Mostly haploid
Both generally have a singular circular chromosome
Both can potentially contain plasmids: circular extrachromosomal genetic elements (often
encode for resistance to antibiotics or toxins)
Most of the genome is coding (85-95%). Very little is intergenic, non-coding regions
Have pseudogenes: nonfunctional and typically untranslated segment of DNA that arises
from a previously functional gene.
Genome size correlates highly with the total number of genes
Features of the eukaryotic genome
Contains multiple linear chromosomes that are condensed via histones
Contain at least two copies of each gene (diploid or polyploid)
Extrachromosomal plasmids are not common
97% of human DNA is non-coding.
Made up of regulatory sequences, introns, repetitive sequences, etc.
Contains trandem repeats abnormally long stretches of back to back repetitive sequences
within an effected gene.
Genome size does not correlate with the total number of genes
Features of viral genomes
Viral genomes are very small because there is high selection for smaller genomes
In many cases, genes can overlap

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Theories of evolution before Charles Darwin

Catastrophism (proposed by George Cuvier): Held that there were violent and sudden
natural catastrophes such as great floods and the rapid formation of of major mountain
chains. Plants and animals living in those parts of the world were often killed off. New life
forms move din from other areas. As a result, the fossil record for a region shows abrupt
changes in species.
Uniformitarianism (proposed by Charles Lyell): Held that natural forces now changing the
shape of the earth's surface have been operating in the past for much of the same way. In
other words, the present is the key to understanding the past.
Carolus Linnaeus developed a logical classification system for all living things (binomial
nomenclature). He described plants and animals on the basis of physical appearance and
their method of reproduction and classified them relative to each other according to the
degree of their similarities.
Jean-Baptiste Lamarck's theory of evolution:
Proposed the idea of use and disuse: body parts can develop with increased usage and
unused parts were weakened.
Believed in inheritance of acquired characteristics: body features acquired during the
lifetime can be passed down to offspring.

Darwin's theory of natural selection

3 key components that lead to an end result:
There is variation in traits.
For example, some beetles are green and some are brown.

There is differential reproduction. Since the environment can't support unlimited

population growth (there are limited resources) and individuals compete for survival, not
all individuals get to reproduce to their full potential.
Continuing on the example, green beetles tend to get eaten by birds and survive to
reproduce less often than brown beetles do.

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There is heredity.
The surviving brown beetles have brown baby beetles because this trait has a genetic
basis.

End result: The more advantageous trait, which allows the organism to have more
offspring, becomes more common in the population. If this process continues,
eventually, all individuals in the population have the advantageous trait.
The trait for brown colored exoskeleton becomes more common in the beetle
population. If this process continues, eventually, all beetles that make up the
population will be brown.

If you have variation, differential reproduction, and heredity, you will have evolution by
natural selection as an outcome.
Natural selection is responsible for producing adaptations (heritable modifications that
allow organisms to better survive in their environment) that increase an individual's fitness
(a differential effect on the reproductive success of an individual in comparison with other
individuals in the population).
Fitness is usually in reference to a particular trait or allele.
Comparative anatomy
Characteristics that results from common ancestry is known as homology.
Biologists call anatomical similarities in different organisms homologous structures
features that often have different functions but are structurally similar because of
common ancestry.
Analogy are similar traits that are due to convergent evolution, not common ancestry.
Convergent evolution is the process whereby organisms not closely related
independently evolve similar traits as a result of having to adapt to similar environments
or ecological niches.
Analogous structures are structures of different species having similar or
corresponding function but not from the same evolutionary origin (not from being
related).
Modern Evolutionary Synthesis
Do we study evolution just as first described by Darwin? No. The molecular biology

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revolution has led to the theory of modern synthesis.

Modern synthesis specifically synthesized evolution and natural selection with genetics,
systematics, paleontology, ecology, and botany.
Modern synthesis joined together micro and macroevolution.
Microevolution typically refers to short term evolution (populations and species)
Macroevolution typically refers to long term evolution (species and longer term)
Modern synthesis states that gradual evolution results from small genetic changes that
are acted upon by natural selection. The origin and diversification of species can be
explained by natural selection acting on individuals (so macroevolution can be
explained by microevolution).
Molecular biology has given us new methods, data, and theory for evolutionary biology.
Molecular biology is integral to modern evolutionary biology studies. Molecular data
(DNA sequences) is now the primary data source.
The revolution in molecular biology gave us sources of variation, mechanism of
inheritance, genotype/phenotype distinction, and data.
Sources of genetic variations in individuals
Mendelian genetics (review topics in genetics unit)
Chromosomal crossover and segregation help produce novel allele combinations in
gametes.
The random joining of gametes (fertilization in sexual reproduction) produce novel
zygote combinations.
Presence of two or more chromosomes (diploidy/polyploidy) permits the presence of a
heterozygous condition, where a recessive allele can remain in the gene pool and be
stored for later generations.
Molecular biology (review topics in genetics unit)
Differential gene expression lead to variations in phenotype.
Alternative splicing increases the variation of proteins that can be translated.
Post-translational modifications of proteins can cause variation in phenotypic traits.
Mutations influence organism evolution in multiple ways:
change the structure of the protein produced (coding region mutations), change
regulation of the gene (expression and regulatory elements), silence a gene
(mutations influencing microRNAs), change how a gene is spliced
Many mutations are lethal, deleterious, or approximately neutral. However, if a
mutation is beneficial (increases fitness), then it can be selected for through natural
selection.
Neutral variation: variation without selective value (e.g. fingerprints in
humans)
Sources of variation in populations
Unlike individuals, we don't see Mendelian ratios in populations.
For example, recessive traits and even those without selective advantage can remain in
populations.
To study variation in populations, we look at fluctuations in allele frequencies at a single
locus in a large population over time. We often ask two numerical questions:
How do allele and genotype frequencies change over time?
When is there a steady state, equilibria, or where these frequencies will not change
anymore?
The Hardy-Weinberg model (review topics in genetics unit) is used as a null hypothesis for
population genetics.
We can calculate what alleles and genotypes would be (expected) if the assumptions of

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Hardy-weinberg were met.
If the values we count in nature are different, then one of the assumptions is not met.
Relaxing assumptions of Hardy-weinberg: (1) natural selection is occurring
Directional selection: when one allele is favored over another, selection drives in one
direction. If that allele is consistently being favored over a long period of time, then the
allele will reach fixation (frequency of the allele reaches 100% for that population).
This is an example of underdominance (heterozygote disadvantage). Three scenarios:
(1) The favored allele is the dominant alleleits initial increase in frequency is the
most rapid, but its pace slows once it is common in the population.
(2) The favored allele is a codominant alleleit will reach fixation most rapidly.
(3) The favored allele is a recessive alleleit will take much longer to increase in
frequency, but once common, will go to fixation quickly.

Balancing selection is a type of selection that favors an intermediate phenotype

(heterozyote) and leads to a balanced polymorphism.
Occurs because of heterozygote advantage (overdominance): The heterozygous
allele combination confers the highest fitness increase.
Balanced polymorphism is the condition where multiple alleles are present in the
population.

Frequency independence is when there is no feedback on selection based on the

frequency of the allele in the population (what we have been looking at so far).
Frequency dependence is when the fitness of an allele is influenced by the frequency
of that allele in the population. Two types:

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Positive frequency dependence: as the allele increases in the population, the

positive influence increases (fitness of the allele increases).
Negative frequency dependence: means that as a trait increases in the population,
the negative influence increases

(fitness of the allele decreases).

Relaxing assumptions of Hardy-weinberg: (2) there are mutations and selection
Mutations are going to randomly cause the recessive allele to turn into the dominant
allele in some individuals, and vice versa.
As previously stated, some mutations are beneficial, and some are deleterious. Although
mutations will cause the number of deleterious alleles to increase in frequency, natural
selection will cause these alleles to be eliminated from the population.
Mutation-selection balance is an equilibrium in the number of deleterious alleles in a
population that occurs when the rate at which deleterious alleles are created by mutation
equals the rate at which deleterious alleles are being eliminated by selection.
The picture below depicts what the frequency of two alleles, p and q, will look like
over successive generations when the alleles are in mutation-selection balance.

Relaxing assumptions of Hardy-weinberg: (3) there is mate preference

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If inbreeding (breeding of related individuals) exists in the population, then some
offspring will be identical by descent to their ancestor, meaning they will have identical
alleles because of a shared ancestor.

Wright's F quantifies the degree of inbreeding. It is the inbreeding coefficient, the

probability that two alleles at any locus in an individual will be identical as a result of
inheritance (not mutation).
The larger F, the higher homozygosity (the higher probability of identity by descent
and inbreeding)
Inbreeding does not positively affect fitness. Inbreeding depression is the reduced
biological fitness in a given population as a result of inbreeding.
Inbreeding decreases the overall genetic variation within the gene pool, and
increases the probability of individuals for being homozygous for deleterious alleles.
With inbreeding, the allele frequencies stay the same (p and q). Inbreeding causes the
loss of heterozygotes.

Relaxing assumptions of Hardy-weinberg: (4) there is migration

Migration is simply the flow of individuals from one population to another. Migration
can introduce new alleles to the population. Over time, populations will equilibrate,
meaning that variation will eventually decrease.
Relaxing assumptions of Hardy-weinberg: (5) population size is not infinite
Wright-fisher model is essentially a small population version of the hardy-weinberg
model.
The assumptions of the wright-fisher model are the same as the hardy-weinberg

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model except the wright-fisher model assumes that the population size is not infinite.
The probability that an allele will be fixed is dependent on (1) the population size
(N) and (2) the number of allele copies in the population (k).
Genetic drift is the process of random fluctuation in allele frequencies due to sampling
effects. This is only seen in finite populations.
Because of genetic drift, allele frequencies vary over time without selection, alleles
may be fixed or lost (meaning you can lose heterozygotes), and populations may
diverge in which alleles are present without migration.
Effective population size (Ne) is the number of individuals in an ideal population
(where every individual reproduces, no migration, mutation, etc.) in which the rate
of genetic drift (measured by the decline in heterozygosity) would be the same as it
is in the actual population.
The smaller the Ne, the less variation exists in the population.

Genetic drift, mutation, and selection

Drift and selection are important in two major ways:
Beneficial mutations may not always go to fixation because initial mutations will be
so infrequent at first, selection has to be strong enough to overcome genetic drift.
Genetic drift may overpower selection in very small populations (even if they are
frequent at first.
Two important elements that determine if selection or drift will dominate are effective
population size and the strength of selection (measured by selection coefficient, s).

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Founders and bottlenecks
Two phenomena that cause short periods of small Ne are:
population bottlenecks: sharp reduction in the size of a population due to
environmental effects (i.e. earthquakes, floods, etc.) or human activities (i.e.
genocide).
founder effects: subsample of a population move to a new area
Neutral evolution
Some mutations have little to no effect: redundancy in the genetic code, synonymous
mutations, mutations in introns, pseudogenes (resemble functional genes but have lost
their function).
Neutral theory: Most molecular variation in populations is selectively neutral and most
mutations in DNA, and RNA are selectively neutral. Therefore, genetic drift is the most
important process in DNA sequence change (not selection).
Assuming the neutral theory is true, substitution rates (mutation rates) should be the
same across populations and lineages. If mutation rates are constant, then we can
estimate the timing of events by how many substitutions there are between lineages.
Molecular clock: The assumption that molecular substitutions at neutral loci occur
at a constant (clocklike rate). This allows us to apply time to phylogenies.
A complicating factor to neutral theory is saturation, a phenomenon where over time a
location in a gene region has had more than one nucleotide substitution but we only see
one, underestimating the substitution rate.

Nearly neutral theory attempts to accommodate for slightly deleterious or

advantageous substitutions that might get fixed due to drift (as a result of differences in
population size and other effects).
Moving from single genes to multiple genes
Sometimes, we need to look at multiple loci to understand evolutionary processes.
Compensatory mutations: certain advantageous mutations (i.e. resistance to a toxin)
can come at a fitness cost. This cost may be negated by additional compensatory
mutations.
Some traits are affected by many genes interacting with each other simultaneously
(review polygenic inheritance and types of gene interactions in genetics unit).
Haplotype is a set of alleles at different loci on the same chromosome.
Physical linkage: two or more loci on the same chromosome. In the absence of
recombination, loci that are physically linked segregate in the production of gametes.
Why this matters: If genes are close enough together on the same chromosome, they will
not independently segregate.

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Linkage disequilibrium: statistical association of alleles at different loci due to linkage.

For example, if A is more likely to be with B than b, then there is linkage disequilibrium.
Sources of linkage disequilibrium:
mutations
natural selection
migration
genetic drift
mating preference
How does linkage disequilibrium go away?
Recombination: the creation of new combination of alleles at a locus. Tends to
randomize genotypes at a locus, thus eliminating linkage disequilibrium from a
population.
Chromosome evolution (i.e. chromosomal mutations look this up in genetics unit)
Why does linkage disequilibrium matter?
We can look at linkage disequilibrium in populations for the signal of things like
migration and selection.
Genes closely related to other genes that confer fitness effects (positive or negative) can
change in frequency in a population over time:
Selective sweep: beneficial allele arises and goes to fixation, and because of tight
linkage, many other loci go to fixation.
Genetic hitchhiking: the process by which an allele is able to ride along with a
nearby favorable allele to which hit is physically linked and thus increase in
frequency
Background selection: The process by which an allele is lost because it is
physically linked to a nearby deleterious allele.
The hitchhiker in genetic hitchhiking, selective sweep, or background selection
can be deleterious, neutral, or beneficial.
Fitness landscapes and quantitative genetics
Fitness landscape: a heuristic representation of fitness as a function of genotype or
phenotype.

Quantitative genetics is the study of quantitative traits and the genotype-phenotype

connection. They study genotype-phenotype starting from the phenotype and go down.
A quantitative trait is a measurable phenotype that depends on the cumulative actions
of many genes and the environment (e.g. height, weight)
Tries to answer the question: how much of the phenotypic variation (in a trait) we see in
a population is due to genetic variation and not other things (like environment).

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V P =V G +V E Where VG = variation due to genes, VE = variation due to environment,
and VP = observed variation in the phenotype.
Quantitative genetics sees the evolution traits as four tasks: (1) estimate heritability, (2)
determine the response to selection, (3) examine the effect of environment, and (4)
determine the genetic location of quantitative trait loci
(1) VG is quantified as heritability. Heritability is a property of a population, not
something general about a trait. It is also a property within a population, not between
populations.

(2) One of three responses can occur to selection: directional selection (previously
explained), stabilizing selection (bell curve. Favors an intermediate (heterozygote
advantage), and disruptive selection (occurs when environment favors extreme or
unusual traits while selecting against common traits)
(3) Look for a reaction norm, the distribution of phenotypes for one genotype over
a range of environmental conditions.
(4) Quantitative trait loci (QTL): the genetic loci that contribute to a quantitative
trait. If we want to identify loci that are important for a quantitative trait we can do
QTL mapping.
Species and speciation
Why are species important?
Species are important because many species are the basic biological unit and the study
of speciation is essential for biology.
The so-called species problem is the problem of agreeing on a definition of species that is
both clear and useful.
In simple terms, species is an independently evolving lineage (or the smallest unit of
independent evolving lineage. Evolutionary species concept is a lineage that maintains
a unique identity over time.
There are problems with both definitions up above, which explains why there is a
species problem. (1) Evolutionary species concept is not helpful for identification. (2)
there are misunderstandings about identifying and defining species.
Traditionally, taxonomists identified an individual to be a species if they sufficiently looked
like a type specimen. However, variation has and continues to complicate this notion.
Cryptic species: groups of organisms that are genetically distinct and do not interbreed,
but are morphologically almost indistinguishable. Cryptic species complicate taxonomic

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sorting.
Biologists have developed four ideas of species concepts:
Evolutionary species concept
Phenetic species concept: an approach to determining species boundaries in which
species are identified as clusters of phenotypically similar individuals or populations.
Biological species concept: species are composed of actually or potentially
interbreeding individuals that are reproductively isolated. Problems:
restricted to sexual, outcrossing (not selfing) organisms
doesn't have a concept of time (i.e. can't say whether today's sunflower could
interbreed with a sunflower fossil)
there is no way to practically test reproductive isolation
hybrids
Phylogenetic species concept: species are defined as the smallest monophyletic group
What causes isolation?
Prezygotic isolating mechanisms: isolating mechanisms that prevent mating from
occurring or prevent fertilization from occurring (if mating has occurred)
Habitat isolation: species do not encounter
Behavior isolation: does not perform correct courtship rituals
temporal isolation: species mate at different seasons/time
Mechanical isolation: male/female genitalia are not compatible
Gametic isolation: male gametes do not survive in environment of female gametes
(gametes do not recognize each other)
Postzygotic isolating mechanisms: reproductive isolating mechanisms that occur after
fertilization. Hybrid inviability and sterility, and can lead to embryos that do not develop
fully.
Hybrid inviability: zygote fails to develop properly and dies before reaching
maturity
Hybrid sterility: hybrids become functional adults but cannot produce
Hybrid breakdown: hybrids produce offspring that have reduced viability/fertility
(hybrid's children cannot produce)
Modes of speciation
Divergent evolution is the accumulation of differences between groups which can lead
to the formation of new species, usually a result of diffusion of the same species to a
different and isolated environments which blocks the gene flow among the distinct
populations allowing differentiated fixation of characteristics.
Allopatric speciation: speciation between populations that are geographically
separated.
Peripatric speciation: also known as peripheral isolation is a type of allopatric
speciation where a small part of a population becomes isolated on the edges and forms a
new species.
Parapatric speciation: process of speciation that occurs when diverging populations
have distributions that abut one another.
Cline: a spatial gradient in genotypes and phenotypes that exists because of different
selective conditions
Hybrid zone: an area where diverging populations encounter, reproduce, and form
hybrid offspring. They can disappear as a result of selection against hybrids.
Sympatric speciation: process of speciation where diverging populations are not
geographically separated.

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Polyploid speciation: A polyploid is an organism with more than two copies of

chromosomes. A tetraploid would be reproductively isolated from a diploid (instant
speciation). Not uncommon in plants.
Macroevolution
Macroevolution looks at speciation and extinction to explain the evolution of individual
species and groups of species.
More specifically, they look at the rate of speciation (rate that new species form) and
rate of extinction (rate at which species go extinct).
Net diversification = speciation extinction
if speciation >> extinction = speciation explosion
if extinction > speciation = total extinction of the group
Often times, rates of speciation and extinction are pretty close
What might cause increases in speciation?
Key innovation: phenotypic or genotypic trait that is associated with an increase in
diversification.
colonization of a new area (or niche) or expansion into area (or niche)
Adaptive radiation: evolutionary lineages that have undergone rapid diversification
into a variety of lifestyles or ecological niches.
How do traits evolve and do these trends influence speciation?
Cope's rule: observation that clades tend to increase in body size over time (classic
example is the horse look at picture below for the evolution of the horse vs. body size)

In general, we can look at broader scales and ask about general trends. Three types of
trends (the picture below describes this in terms of the trait of body size, but it can apply
to any trait)

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Two general ideas about the rate of speciation

Phyletic gradualism: new species arise by a gradual transformation of an ancestral
species through slow and continual change.
Punctuated equilibrium: predicts that a lot of evolutionary change takes place in short
periods of time tied to speciation events.
Stasis: a period of little to no evolutionary change
Realistically, all the pattens are probably present in some form between the two
extremes of phyletic gradualism and punctuated equilibrium.
Extinctions
Background extinction: normal rate of extinction for a clade or taxon
Mass extinction: a statistically significant departure from background extinction that
result in a substantial loss of diversity. Five mass extinctions have been traditionally
recognized:
Ordivician-Sularian (440 mya)
Denovian (360 mya)
Permian-Triassic (250 mya)
Triassic-Jurassic (200 mya)
Cretaceous-Tertiary (65 mya)
Sexual selection
What are the costs of sex?
Twofold cost of sex: asexual lineages multiply faster than sexual lineages because all
asexual individuals can reproduce. Sexual populations are reliant on the number of
females.
Search cost: males and females must locate each other which costs time and energy and
risk of predation.
Sex (recombination) scrambles genotypes, disrupting favorable combinations; asexual
reproduction preserves advantageous genotypes.
Risk of sexually transmitted disease
Benefits of sex?
Fisher-muller hypothesis: sexual reproduction can combine beneficial mutations from

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different individuals, accelerating adaptive evolution

Generates novel phenotypes
Clearance of deleterious mutations
What causes mate choice?
Females often invest more than males. Their investment results in better outlook for
their own offspring.
Certainty of paternity: probability that a male is the genetic sire of the offspring his
mate produces.
Males are ready to mate after mating and have selection for parental care when they
are certain of paternity.
Operational sex ratio (OSR): ratio of male to female individuals who are available for
reproducing at any given time
Often the ratio of male and females in the population are close, but the number of
females ready to mate is lower.
When OSR is male biased, males compete for males and there is sexual selection.
Sexual selection: differential reproductive success resulting from competition for
fertilization can occur through competition among the same sex (intrasexual) or attraction
to the opposite sex (intersexual).
Intersexual selection:
Direct benefits: benefits that affect a particular female directly (food, nest,
protection)
Indirect benefits: benefits that affect the genetic quality of a particular female's
offspring.
Sensory bias: females choose males that have a characteristic that is similar in
nature to a preference unrelated to reproduction.
Intrasexual selection
sexual dimorphism: difference between males and females of the same species
(color, body size, structures)
sperm competition: sexual selection after mating, sperm from multiple males
compete for fertilization
Sexual conflict: evolution of phenotypic characteristics that confer a fitness benefit to
one sex but a fitness cost to the other.
Conflict and cooperation
Types of conflict
Intragenomic conflict: conflict within the genome (transposable elements, selfish
genetic elements, replication of genes to the detriment of the organism)
Intraspecific conflict: conflict within a species (can be for resources, sexual selection)
Intraspecific interactions between members of the same species are influenced by
disruptive (competition) and cohesive (reproduction and protection from predators
and weather) forces.
Interspecific conflict: conflict between species (predation, limited resources,
parasitism)
Costs and benefits of cooperation
Benefits: vigilance (increased awareness of danger), dilution effect (if a predator attacks,
less chance you will be attacked because you are with many other organisms that the
predator can attack), enhanced defense, cooperative hunting/foraging, defense of
resources
Costs: increased visibility to predators, increased competition for food, increased
competition for mates, decreased certainty of paternity, increased disease transmission

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Cooperation
Kinship cooperation: cooperation among close relatives
inclusive fitness: sum of direct and indirect fitness
direct fitness: number of viable offspring
indirect fitness: increase in reproduction of relatives due to individual's behavior
Reciprocity: exchanging actions of altruism
Altruism: behavior by an individual that increases the fitness of another individual
while decreasing the fitness of the actor.
Kin selection: natural selection that increases inclusive fitness
How does cooperation evolve? Why should natural selection favor altruism in unrelated
individuals?
Reciprocal altruism: altruistic behavior can be maintained evolutionarily if individuals
sequentially exchange acts of altruism
it may be beneficial to help an individual (even if they aren't your relative) if the
favor will be returned
Coevolution
What is the pattern of evolution of species interactions?
Coevolution: reciprocal genetic change in interacting species, owing to the natural
selection imposed by each on the other
Reciprocal selection: selection that occurs in two species due to their interactions with
one another
Pattern of coevolution doesn't have to be the same everywhere. Geographic mosaic
theory of evolution: geographic structure of populations is central to coevolution.
Antagonistic coevolution: when the effect of interaction is negative.
Specific: two species evolve in response to each other.
Guild (diffuse): several species involved and the responses are not independent
Escape and radiate: a species evolves a defense against enemies and is thereby enabled
to proliferate into a diverse clade.

Evolutionary arms race: species interact antagonistically in a way that result in each
species exerting reciprocal directional selection on the other.
Example would be in predation and herbivory interactions. The prey will evolve to
gain defense from the predator. Then the predator will evolve in response to the
prey's adaptation so they can continue eating the prey.
Cospeciation: speciation in one species leads to speciation in another.
Diversifying coevolution: an increase in genetic diversity caused by the heterogeneity
of processes across the range of ecological settings.
Life history

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Life history is the investment an organism makes in growth in reproduction.
Why do some species have many offspring and others have one?
The probability of an offspring surviving past a week affects the number of offspring
produced as shown in the picture on the next page.
trade-offs: advantage of a change in a character is correlated with a disadvantage in

other characters.
Optimallity theory: speechifying the state of a character (or reproductive strategy) that
would maximize fitness.
Lack clutch: the clutch size (number of eggs laid in a single brood by a nesting pair of
birds) that maximizes the number of surviving offspring.
Trade-off between clutch size and offspring survival.
Adaptations that have evolved as a result of coevolution:
Secondary compounds: toxic chemicals produced in plants that discourage would-be
herbivores
Camouflage (cryptic coloration): any color, pattern, shape, or behavior that enables an
animal to blend in with its surroundings. Both predator and prey can use camouflage.
Aposematic coloration: conspicuous pattern or coloration of animals that warns
predators that they sting, bite, taste bad, poisonous, or other wise to be avoided.
Mimicry occurs when two or more species resemble one another in appearance.
Mullerian mimicry occurs when several animals, all with some special defense
mechanism, share the same coloration.
Batesian mimicry occurs when an animal without any special defense mechanism
mimics the coloration of an animal that does posses a defense.
Pollination of many kinds of flowers occur as the result of coevolution of finely-turned
traits between flower and pollinators.
Biogeography
Vicariance: process by which the geographical range of a population or species is split by
the formation of a physical or biotic barrier.
Dispersal: process by which a population or species moves individuals or propagules from
one area to another.

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Biogeography: the study of the distribution of species in space and time
biomes: geographically and climatically defined regions with similar climatic conditions
ancestral range reconstruction: reconstruction of ancestral ranges based on dispersal
and vicariance analysis
disjunct distributions: non-contiguous distributions of one or more species
timing and availability of land bridges can explain disjunct distributions
Phylogeography: the study of the processes that govern the geographical distribution of
genes within species and populations.

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General ideas
Ecology is the scientific study of the interactions of organisms with the environment.
Organisms can be affected by many different variables in the environment. These variables
are grouped into two major types:
Biotic factors: all of the organisms in the area, the living component of the
environment.
Abiotic factors: The environment's nonliving components, the physical and chemical
factors (i.e. temperature).
An organism's habitat is the specific environment it lives in, includes the biotic and abiotic
factors present in its surroundings.
Ecologists study the environment on several levels.
At the organism level
Populations, a group of individuals of the same species living in a particular geographic
area.
Community, an assemblage of all the populations of organisms living close enough
together for potential interactionall the biotic factors in the environment.
Ecosystem, includes both the biotic and abiotic components of the environments.
Landscapes, arrays of ecosystems. Usually visible from the air as distinctive patches. A
landscape perspective emphasizes the absence of clearly defined ecosystem boundaries;
energy, materials, and organisms may be exchanged within a landscape.
The biosphere, which extends from the atmosphere several kilometers above the Earth
to the depths of the oceans, is all of Earth that is inhabited by life.

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Physical and chemical factors influence life in the biosphere

Energy sources
All organisms require a source of energy to live.
Solar energy from sunlight, captured during photosynthesis, powers most ecosystems.
Lack of sunlight is the most important factor limiting plant growth for terrestrial
ecosystems.
In aquatic environments, light is not uniformly available. Most photosynthesis occurs
near the surface.
In dark environments, bacteria that extract energy from inorganic chemicals power
ecosystems.
Temperature
Temperature is an important abiotic factor because of its effect on metabolism.
Few organisms can maintain a sufficiently active metabolism at temperatures close to 0
degrees Celsius, and temperatures above 45 degrees Celsius destroy the enzymes of
most organisms.
Water
Water is essential to life. Thus, for terrestrial organisms, drying out in the air is a major
danger.
Aquatic organisms are surrounded by water, their problem is maintaining adequate
internal solute concentrations.
Inorganic nutrients
The distribution and abundance of photosynthetic organisms depend on the availability
of inorganic nutrients such as nitrogen and phosphorus.
Regional climate influences the distribution of terrestrial communities
Earth's global climate patterns are largely determined by the input of radiant energy from
the sun and the planet's movement in space.
Because of earth's curvature, Earth receives an uneven distribution of solar energy. The
sun's rays strike the equatorial areas most directly (perpendicularly) whereas away from
the equator, the rays strike Earth's surface at a slant. As a result, the same amount of
solar energy is spread over a larger area. Thus any particular area of land or ocean near
the equator absorbs more heat than comparable areas in the more northern or southern
latitudes.

The seasons of the year result from the permanent tilt of the planet on its axis as it orbits the
sun.

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The globe's position relative to the sun changes through the year.
The northern hemisphere and southern hemisphere is tipped most toward the sun for a
few months and tipped furthest away from the sun for a few months. This creates
seasonal change.
The tropics, the region surrounding the equator between latitudes 23.5 degrees north
and 23.5 degrees south experience the least seasonal variation in solar radiation.

Doldrums: an area of very calm or very light winds at areas near the equator because the
high temperatures cause water to evaporate and the most air rises.
As warm equatorial air rises, it cools and releases much of its water content, creating the
abundant precipitation typical of most tropical regions.
After losing their moisture over equatorial zones, high altitude air masses spread away from
the equator until they cool and descend again at latitudes of about 30 degrees north and
south.
This descending dry air absorbs moisture from the land. As the dry air descends, some
of it spreads back to the equator. This movement creates the cooling trade winds which
dominate the tropics. As the air moves back toward the equator, it warms and picks up
moisture until it ascends again.
The latitudes between the tropics and the Arctic Circle in the north and the Antarctic circle
in the south are called temperate zones.
Generally, these regions have seasonal variations in climate and more moderate
temperatures than the tropics or the polar zones.
Notice in the picture below that some of the descending air heads into the latitudes above 30
degrees.

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At first these air masses pick up moisture, but they tend to drop it as they cool at higher
latitudes. This is why the north and south temperate zones, especially around 60 degrees,
tend to be moist.
The figure below shows the major global air movements, called the prevailing winds.

Prevailing winds (pink arrows) result from the combined effects of the rising and falling
of air masses (blue and brown arrows) and Earth's rotation (gray arrows).
Because Earth is spherical, its surface moves faster at the equator (where the diameter is
greatest) than at other latitudes.
In the tropics, Earth's rapidly moving surface deflects vertically circulating air,
making the trade winds blow from east to west.
In temperate zones, the slower-moving surface produces the westerlies, winds that
blow from west to east.
A combination of the prevailing, the planet's rotation, unequal heating of surface waters, and
the location and shapes of the continents creates ocean currents, river-like flow patterns in
the oceans.
Ocean currents have profound effects on regional climates.
Landforms can also affect local climate.
Air temperature declines about 6 degrees Celsius with every 1,000-m increase in
elevation.
Mountains affect rainfall. As moist air moves in off the Ocean and encounters the
westernmost mountains (we are assuming the air is moving west to east for this
scenario), it flows upwards, cools at higher altitudes, and drops a large amount of water.
Further inland, precipitation increases again as the air moves up and over higher
mountains. On the eastern side of the high mountain, there is little precipitation, and the
dry descending air also absorbs moisture. This effect is called a rain shadow.

Climate and other abiotic factors of the environment control the global distribution of

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organisms. The influence of these abiotic factors results in biomes, major types of
ecological associations that occupy broad geographic regions of land or water.
Terrestrial biomes are determined primarily by temperature and precipitation.
Aquatic biomes are determined primarily on salinity.
Aquatic biomes
Marine biomes
The pelagic realm of the oceans includes all open water, and the substratethe seafloor
is known as the benthic realm.
The depth of light penetration, a maximum of 200m, marks the photic zone.
In shallow areas such as the submerged parts of continents, called continental
shelves, the photic zone includes both the pelagic and benthic realms.
In these sunlit regions, photosynthesis by phytoplankton (microscopic algae and
cyanobacteria) and multicellular algae provides energy and organic carbon for a
diverse community of animals.
Zooplankton (small, drifting animals), fish, marine animals, and many other types
of animals are abundant in the pelagic photic zone.
Coral reefs are scattered around the globe in the photic zone of warm tropical waters
above continental shelves.
A reef is built up slowly by successive generations of coral animals and by
multicellular algae crusted with limestone.
Coral reefs support a huge variety of invertebrates and fishes.
Below the photic zone lies the aphotic zone. Although there is not enough light for
photosynthesis in the aphotic zone, some light does reach these depths.
This dimly lit world, sometimes called the twilight zone, is dominated by a
fascinating variety of small fishes and crustaceans.
In the intertidal zone, where the ocean meets land, the shore is pounded by waves
during the high tide and exposed to the sun and drying winds during low tide.
The rocky intertidal zone is home to many sedentary organisms which attach to
rocks and are thus prevented from being washed away when the tide comes in.

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An estuary is a biome that occurs where a freshwater stream or river merges with the
ocean.
Wetlands constitute a biome that is transitional between an aquatic ecosystemeither
marine or freshwaterand a terrestrial one.
Freshwater biomes
Freshwater biomes cover less than 1% of Earth's surface and contain a mere 0.01% of its
water but they harbor a disproportionate share of biodiversityan estimated 6% of all
described species.
Three major categories: (1) lakes and ponds, (2) rivers and streams, and (3) freshwater
wetlands.
Lakes and ponds
In lakes and large ponds, as in the oceans, the communities of organisms are
distributed according to depth of water and its distance from shore.
If the lake or pond is deep enough, there is a photic and aphotic zone.
In the benthic realm, large population of microorganisms decompose dead organisms
that sink to the bottom. Respiration by these microbes remove oxygen from water.
Temperature plays an important role in these biomes: during the summer, deep lakes
have a distinct upper layer of water that has been warmed by the sun and does not
mix with the underlying, cooler water.
The mineral nutrients nitrogen and phosphorus typically determine the amount of
phytoplankton growth in a lake or pond.
If there is an over-supply of nitrogen and phosphorus, it may produce a heavy
growth of algae, known as an algae bloom. Algae blooms reduce light
penetration and then the algae decomposes, a pond or lake can suffer severe
oxygen depletion, killing organisms that need the oxygen.

Rivers and streams

A river or stream changes greatly between its source and the point at which it
empties into the lake or ocean.
Near the source, the water is usually cold, low in nutrients, and clear. The channel is
often narrow, with a swift current that does not allow much to accumulate on the
bottom.
Downstream, a river or stream generally widens and slows. The water is usually
warmer and murkier because of sediments and phytoplankton suspended in it.
Freshwater wetlands
Range from marshes to swamps and bogs. Very rich in species diversity.

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Terrestrial biomes
Tropical forests
Tropical forests occur in equatorial areas where the temperature is warm and days are
11-12 hours long year-round.
Rainfall in these areas is quite variable, and this variability generally determines the
vegetation that grows in a particular tropical forest.
Tropical rain forests are found in very humid equatorial areas where rainfall is
abundant (200-400 cm per year). It is the most diverse of all biomes, harboring
enormous numbers of different species.
The forest contains different layers that provide many habitats: a closed upper
canopy, 1-2 layers of lower trees, a shrub understory, and a sparse ground layer of
plants.
Because of the closed canopy, little sunlight reaches the forest floor.
Epiphytes are plants that grow commensally on other plants (like vines).

Savannas
A savanna is a biome dominated by grasses and scattered trees.
The temperature is warm year around. Rainfall is low, it averages 30-50 cm per year,
with dramatic seasonal variation.
Poor soils and a lack of moisture inhibit the establishment of most trees.
Subject to frequent fires caused by lighting or human activity.
Many of the world's large herbivores and their predators inhabit savannas.

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Deserts
Deserts are the driest of all terrestrial biomes, characterized by low and unpredictable
rainfall (less than 30 cm per year).
Large tracts of desert occur in two regions of descending dry air centered around 30
degrees north and 30 degrees south latitudes.
At higher latitudes, large deserts may occur in the rain shadows of mountains.
Deserts experience large daily temperature fluctuations, with the temperature being very
hot during the day and then dropping to low temperatures at night.
The cycles of growth and reproduction of plants in the desert are keyed to rainfall.
Plants and animals adapt to conserve as much water as possible.
The process of desertification, the conversion of semi-arid regions to desert, is a
significant environmental problem.

Chaparrals
Chaparral is characterized by dense, spiny shrubs with tough, evergreen leaves.
The climate that supports chaparral vegetation results mainly from cool ocean currents
circulating offshore, which produce mild, rainy winters and hot, dry summers.
Limited to small coastal areas, including California.
Perennial shrubs and annual plants are commonly seen.
Chaparral vegetation is adapted to periodic fires, most common by lightnings.

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Temperate grasslands
Temperate grasslands have some characteristics of tropical savannas, but they are
mostly treeless, except along rivers or streams, and are found in regions of relatively
cold winter temperatures.
Precipitation, averaging between 25 and 75 cm per year, with periodic severe droughts,
is too low to support forest growth.
Fires and grazing by large animals also inhibit growth of woody plants but do not harm
the belowground grass shoots.
Large grazing animals are characteristics of grasslands.
The amount of annual precipitation influences the height of the grassland vegetation.

Temperate broadleaf forests

Temperate broadleaf forests grow throughout midlatitude regions, where there is
sufficient moisture to support the growth of large trees.
In the Northern hemisphere, deciduous trees characterize temperate broadleaf
forests.
Temperatures in temperate broadleaf forests range form very cold in the winter (-30
degrees Celsius) to very hot in the summer (30 degrees Celsius).
Annual precipitation is relatively high75 150 cm and usually evenly distributed
throughout the year as rain or snow.
These forests typically have a growing season of 5 to 6 months and a distinct annual
rhythm. Trees drop their leaves and become dormant in late autumn, preventing
water loss and then produce leaves in the spring.
The soil is rich in organic and organic nutrients due to leaf shed.
Vertical stratification: plants and animals live on ground, low branches, and treetops.
Many mammals hibernate through cold winter.

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Coniferous forests
Cone-bearing evergreen trees, such as spruce, pine, fir, and hemlock, dominate
coniferous forests. The northern coniferous forest, or taiga, is the largest terrestrial
biome on Earth.
Taiga is found across North America and Asia south of the Arctic Circle and is also
found at cool, high elevations in more temperate latitudes.
Taiga is characterized by long, cold winters and short, wet summers, which are
sometimes warm.
The soil is thin and acidic, and the slow decomposition of conifer needles make few
nutrients available for plant growth.
Most of the precipitation is in the form of snow.
The conical shape of many conifers prevents too much snow from accumulating on
their branches and breaking them.
The temperate rain forests of coastal North America (from Alaska to Oregon) are also
coniferous forests.
Warm, moist air from the Pacific Ocean supports this unique biome, which, unlike
most coniferous forests, is dominated by a few tree species.

Tundra
Tundra covers expansive areas of the Arctic between the taiga and polar ice.
The climate is often extremely cold, with little light for much of the autumn or winter.
The arctic tundra is characterized by permafrost, continuously frozen subsoilonly the
upper part of the soil thaws in the summer.
The arctic tundra may receive as little precipitation as some deserts. But poor drainage,
due to the permafrost, and slow evaporation keep the soil continually saturated.
Permafrost prevents the roots of plants from penetrating very far in the soil, which is one
factor that explains the absence of trees (extremely cold temperatures and high winds
are other factors that contribute to this)
During the brief, warm summers, when there is nearly constant daylight, plants grow
quickly and flower in a rapid burst.
High winds and colt temperatures create plant communities called alpine tundra on
very high mountaintops at all latitudes, including the tropics. There is no permafrost
beneath alpine tundra.
Animals of the tundra withstand the cold by having good insulation that retains heat.

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Polar ice
In the Northern Hemisphere, polar ice covers land north of the tundra and in the
southern hemisphere, polar ice covers the continent of Antarctica.
The temperature in these regions is extremely cold year-round, and precipitation is very
low.
Only a small portion of these landmasses is free of ice or snow, even during the
summer.
Nevertheless, small plants and invertebrates and wingless insects inhabit the frigid soil.
The terrestrial polar biome is closely interconnected with the neighboring marine biome.

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The scientific study of behavior

Behavioral ecology
Behavior is an action carried out by muscles or gland sunder the control of the nervous
system in response to an environmental cue. Collectively, behavior is the sum of an
animal's responses to internal and external environmental cues.
Behavioral ecology is the study of behavior in an evolutionary context. Tries to describe
the details of animal behavior and investigate how they develop, evolve, and contribute
to the animal's survival and reproductive success.
Questions investigated by behavioral ecologists fall into two broad categories:
Proximate questions concern the immediate reason for a behaviorhow it is
triggered by stimuli (environmental cues that cause a response), what mechanisms
play a role, and what underlying genetic factors are at work. Proximate causes are
answers to such questions about the immediate mechanism for a behavior.
Ultimate questions address why a particular behavior occurs. As a component of
the animal's phenotype, behaviors are adaptations that have been shaped by natural
selection. The answers to ultimate questions, or ultimate causes, are evolutionary
explanationsthey lie in the adaptive value of the behavior.
Simple and complex reflexes
You need to keep the conditions inside your body constant. Doing this is called
homeostasis.
Small changes inside your body can cause its cells to be damaged or destroyed. Yet,
there are big changes going on outside your body.
You need to detect a change in the environment (a stimulus) and react to the change (a
response) in a way that maintains homeostasis. When you do this without thinking, it is
called a reflex.
A reflex arc is a neural pathway that controls a reflex action. In higher animals, most
sensory neurons do not pass directly into the brain, but synapse in the spinal cord. This
allows reflex actions to occur relatively quickly.
Simple reflex: automatic 2 nerve (afferent/efferent) response to a stimulus controlled at
the spinal cord.
Complex reflex: Automatic response to a significant stimulus (controlled at brainstem
or even cerebrum). Will involve an intermediary interneuron or even the brain for
'processing' before synapsing with an efferent neuron and target tissue.
Fixed action patterns are innate behaviors
Innate behavior (instinct) is behavior that is under strong genetic control and is
performed in virtually the same way by all individuals of a species.
A fixed action pattern is an unchangeable series of actions triggered by a specific
stimulus. Once initiated, the sequence is performed in its entirety, regardless of any
changes in circumstances.
The specific stimulus is called a sign stimulus.
A graylag goose retrieving an egg (sign stimulus) is an example of a fixed action pattern.
The goose extends its neck, uses a side-to-side motion to nudge the egg back with its
back, and then sits down on the nest again.

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In its simplest form, a fixed action pattern is an innate response to a certain stimulus.
Although a fixed action pattern is a simple behavior, complex behaviors can result from
several fixed action patterns performed sequentially.
Innate behaviors are under strong genetic control, but the animal's performance of most
innate behaviors improve with experience. And despite the genetic component, input
from the environment is required to trigger the behavior.
Behavior is the result of both genetic and environmental factors
Just like phenotype, behavior is the result of the environment as well as genes.
Many environmental factors, including diet and social interactions, can modify how
genetic instructions are carried out.
Learning
Learning is a modification of behavior as a result of specific experiences. Learning enables
animals to change their behaviors in a response to changing environmental conditions. The
table below summaries the types of learning that will be discussed next.

Habituation
One of the simplest forms of learning is habituation, in which an animal learns not to
respond to a repeated stimulus that conveys little to no information.
For example, the Hydra contracts when disturbed by a slight touch; it stops
responding, however, if disturbed repeatedly by such a stimulus.
In terms of ultimate causation, habituation may increase fitness by allowing an animal's
nervous system to focus on stimuli that signal food, mates, or real danger and not waste
time or energy on a vast number of other stimuli that are irrelevant to survival and
reproduction.
Imprinting
Imprinting is learning that is limited to a specific time period in an animal's life and
that is generally irreversible.
The limited phase in an animal's development when it can learn certain behaviors is
called the sensitive period.
A classic example done by Konrad Lorenz: when the incubator-hatched graylag goslings
spent their first few hours with Lorenz, rather than their mother, they steadfastly
followed Lorenz and showed no recognition of their mother or other adults of their
species. Lorenz showed that the most important imprinting stimulus for graylag geese
was the movement of an object away from the hatchlings.

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Animal movement may be a response to stimuli or require spatial learning

Moving in a directed way enables animals to avoid predators, migrate to a more
favorable environment, obtain food, and find mates and nest sites.
The simplest movement do not involve learning.
A random movement in response to a stimulus is called a kinesis.
A kinesis may merely be starting or stopping, changing speed, or turning more or
less frequently.
In contrast to kinesis, a taxis is a response directed toward (positive taxis) or away from
(negative taxis) a stimulus.
For example, phototaxis it he movement toward or away from light and chemotaxis
is the movement toward or away from a chemical.
In spatial learning, animals establish memories of landmarks in their environment that
indicate the locations of food, nest sites, prospective mates, and potential hazards.
Movements of animals may depend on cognitive maps
An animal can move around its environment using landmarks alone. An even more
powerful mechanism is a cognitive map, an internal representation, or code, of the
spatial relationships among objects in an animal's surroundings.
Studies of cognitive maps have involved animals that exhibit migration, the regular
back-and-forth movement of animals between two geographic areas. Migration allows
many species to access food resources throughout the year and to breed or winter in
areas that favor survival.
Researchers have found that migrating animals stay on course by using a variety of
cues (i.e. gray whales use the coastline to pilot their way north and south, birds
navigate at night by the stars).
Associative learning
Associative learning, or classical conditioning, is the ability to associate one
environmental feature with another.
In one type of associative learning, an animal learns to link a particular stimulus with a
particular outcome.
For example, a dog or a cat will learn to associate a particular sound, word, or
gesture (stimulus) with a specific punishment or reward (outcome).
In another type of associative learning, called trial-and-error learning, an animal
learns to associate one of its own behaviors with a positive or negative effect. The

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animal then tends to repeat the response if it is awarded or avoid the response if it is
harmed.
For example, predators quickly learn to associate certain kinds of prey with painful
experiences.
Memory is the key to all associative learning. The brain must form a memory that
connects the environmental feature or behavior with the outcome or else associative
learning won't occur.
Social learning
Another form of learning is social learninglearning by observing the behavior of
others.
For example, many predators seem to learn some of their basic hunting tactics by
observing and imitating others.
Problem-solving behavior relies on cognition
A broad definition of cognition is the process carried out by an animal's nervous system
to perceive, store, integrate, and use information gathered by the senses.
One area of research in the study of animal cognition is how an animal's brain
represents physical objects in the environment. Some researchers have discovered
that many animals are capable of categorizing objects in their environment
according to concepts such as same and different.
Some animals have complex cognitive abilities that include problem solvingthe
process of applying past experience to overcome obstacles in novel situations.
Problem solving behavior is highly developed in some mammals, especially
dolphins and primates.
Also has been observed in some bird species.
Insight: When animal exposed to new situation without prior experience, performs a
behavior that generates a positive outcome.
Survival and Reproductive Success
Foraging
Foraging includes not only eating, but also any mechanism an animal uses to search for,
recognize, and capture food.
Because adequate nutrition is essential to survival, we should expect natural selection to
refine behaviors that enhance the efficiency of foraging.
Animals forage in a great many ways.
The mechanism that enables an animal to find particular foods efficiently is called a
search image. It is the set of key characteristics that will lead an animal to the desired
object.
A predator develops a knowledge of a prey type (i.e. looks, smell, etc.) and is
switched on for that type.
Whenever an animal has food choices, there are trade-offs involved in the selection. The
amount of energy required to capture the prey for the consumption, the danger of being
eaten by a predator, and the nutritional value of the prey varies.
Predation is one of the most significant potential costs for foraging. Studies show
that foraging in groups reduces the individual's risk of predation.
According to the optimal foraging theory, an animal's feeding behavior should provide
maximal energy gain with minimal energy expense and minimal risk of being eaten by
foraging.
Communication
Interactions between animals depend on some form of signaling between the
participating individuals.

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A signal is a stimulus transmitted by one animal to another animal.

The sending of, reception of, and response to signals constitute animal
communication, an essential element of interactions between individuals.
In general, the more complex the social organization of the species, the more
complex signaling will be required to sustain it.
Examples of communication:
Chemical chemicals used for communication are called pheromones. May be
smelled or eaten.
Chemicals that trigger reversible behavioral changes are called releaser
pheromones.
Chemicals that trigger long term physiological and behavior changes are called
primer pheromones
Visual occur during displays of aggression or during courtship
Auditory
Tactile: common in social bonding, infant care, grooming, and mating
Animals use more than one type of signal simultaneously.
Mating behaviors
Animals of many species tend to view members of their own species as competitors to
be driven away.
Careful communication is an essential prerequisite for mating.
In many species, prospective mates must perform an elaborate courtship ritual, which
confirms that individuals are of the same species, of the opposite sex, physically primed
for mating, and not threats to each other.
Movements in courtship rituals are FAPs. Thus, the entire routine is a chain of FAPs
that must be performed flawlessly if mating is to occur.
This is common among vertebrates and some groups of invertebrates.
Mating systems and parental care
The needs of the young are an important factor in the evolution of mating systems.
Animal mating systems fall into one of three categories:
Promiscuous: no strong pair-bonds or lasting relationships between males and
females
Monogamous: a bond between one male and one female, with shared parental care
Polygamous: An individual of one sex mating with several of the other
Polygamous relationships often involve a single male and many females
Parental care involves significant costs, including energy expenditure and the loss of
mating opportunities. Certainty of paternity (discussed in evolution unit) plays a big role
in the mating relationships of females and males.
Social behavior and Sociobiology
Sociobiology
Biologists define social behavior as any kind of interaction between two or more
animals, usually of the same species (i.e. aggression, cooperation)
The discipline of sociobiology applies evolutionary theory to the study and
interpretation of social behaviorthe study of how social behaviors are adaptive and
how they could have evolved by natural selection.
Territorial behavior
Many animals exhibit territorial behavior. A territory is an area, usually fixed in
location, that individuals defend and from which other members of the same species are
usually excluded.
The size of the territories varies with the species, the function of the territory, and

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the resources available.
Territories are typically used for feeding, mating, rearing young, or combinations of
these activities.
Individuals that have established a territory usually proclaim their territorial rights
continually.
Usually, intruders will avoid marked territory and a potentially confrontation with its
proprietors.
Not all species are territorial.
Agnostic behavior
In many species, conflicts that arise over limited resources such as food, mates, or
territories, are settled by agnostic behavior, including threats, rituals, and sometimes
combat that determine which competitor gains access to the resource.
Because violent combat may injure the victor as well as the vanquished in a way that
reduces reproductive fitness, we would predict that natural selection would favor
ritualized contests. And this is what usually happen sin nature.
Often the victor of an agnostic ritual gains first or exclusive access to mates, and so this
form of social behavior can directly affect an individual's evolutionary fitness.
Dominance hierarchies
Many animals live in social groups maintained by agnostic behavior.
Hens establish a clear pecking order: the alpha, or top-ranked, hen in the pecking order
is dominant; she is not pecked by any other hens and can usually drive off all the others
by threats rather than actual pecking. The alpha hen has first access to resources. The
beta, or second-ranked, hen similarly subdues all the others except the alpha, and so on
down the line to the omega, or lowest, animal.
Pecking order in chickens is an example of a dominance hierarchy, a ranking of
individuals based on social interactions.
Once a hierarchy is established, each animal's status in the group is fixed, often for
several months or even years.

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What is population ecology?

Ecologists usually define a population as a group of individuals of a single species that
occupy the same general area.
These individuals rely on the same resources, are influenced by the same environmental
factors, and are likely to interact and breed with one another.
Population ecology is concerned with changes in population size and factors that regulate
populations over time.
Use statistics to describe a population.
Examine population dynamics, the interactions between biotic and abiotic factors that
cause variation in population sizes.
Density and dispersion patterns are important population variables
Population density is the number of individuals of a species per unit area or volume.
Because it is impractical or impossible to count all individuals in a population in most
cases, ecologists use a variety of sampling techniques to estimate population densities.
Within a population's geographic range, local densities may vary greatly. The dispersion
pattern of a population refers the way individuals are spaced within their area. Three types:
A clumped dispersion pattern is one in which individuals are grouped in patches (most
common in nature). Clumping often results from an unequal distribution of resources in
the environment. Clumping may reduce the risk of predation or be associated with social
behavior.
A uniform dispersion pattern (an even one) often results from interactions between the
individuals of a population. Animals may exhibit uniform dispersion as a result of
territorial behavior.
In a random dispersion pattern, individuals are placed in an unpredictable way,
without a pattern. However, varying habitat conditions and social interactions make
random dispersion rare.
Estimates of population density and dispersion patterns enable researchers to monitor
changes in a population and to compare and contrast the growth and stability of populations
in different areas.

Life tables track survivorship in populations

Life tables track survivorship, the chance of an individual in a population surviving to
various ages.

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Life tables can be used to construct survivorship curves, which plot survivorship as the
proportion of individuals from an initial population that are alive at each age.
By using a percentage scale instead of actual ages on the x-axis, we can compare species
with widely varying life spans on the same graph.
Three types of survivorship curves:
Type I curve (e.g., humans and mammals) usually produce very few offspring, but give
them good care, increasing the likelihood that they will survive to maturity. Most
individuals survive to the older age intervals.
Type II curve (e.g., invertebrates, lizards, and rodents) is intermediate, with
survivorship constant over the lifespan. That is, individuals are no more vulnerable at
one stage of the life cycle than at another.
Type III curve indicates low survivorship for the very young, followed by a period
when survivorship is high for those few individuals who live to a certain age. Species
with this type of survivorship typically produce very large numbers of offspring but
provide little or no care for them.

Idealized models predict patterns of population growth

Population size fluctuates as new individuals are born or immigrate into an area and others
die or emigrate. Other populations change rapidly, even explosively.
Using idealized models, population ecologists can predict how the size of a particular
population will change over time under different conditions.
The exponential growth model
The rate of population increase under ideal conditions, called exponential growth, can
be calculated using the simple equation G = rN where G stands for the growth rate of the
population (number of new individuals added per time interval), N is the population size
(the number of individuals in the population at a particular time), and r stands for the
per capita rate of increase (the average contribution of each individual to population
growth).
number of births
Per capita rate of increase =
total number of people
In a population growing in an ideal environment with unlimited space and resources, r is
the maximum capacity of members of that population to reproduce. Thus, the value of r
depends on the kind of organism.
When a population is expanding without limits, r remains constant and the rate of
population growth depends on the number of individuals already in the population (N).
Biotic potential: Maximum growth rate under ideal conditions (unlimited resources and
no restrictions).

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intrinsic rate of growth is when reproductive rate (r) is maximum (biotic potential)
The exponential growth model is unrealistic because any population will eventually be
limited by the resources available.

Limiting factors and the Logistic Growth Model

Environmental factors that restrict population growth are called limiting factors.
The logistic growth model is a description of an idealized population growth that is
slowed by limiting factors as the population size increases. The formula for logistic
( K N)
growth is G=rN
K
The only new symbol in this equation is K, which stands for carrying capacity (the
maximum population size that a particular environment can sustain). Changes in
abiotic or biotic factors might increase or decrease carrying capacity.
With the logistic growth model, the rate increases until around N = 1/2K. Beyond 1/2K,
population growth rate decreases until N = K. At N = K, the growth rate is equal to zero.
The model predicts that a populations growth will be small when the population is
either small or large, and highest when the population is at an intermediate level relative
to carrying capacity.
When population is small, growth rate is small because N is small.
When population is high, limiting factors cause the growth rate to be small.

Multiple factors may limit population growth

Density-dependent factorslimiting factors whose intensity is related to population
densityappear to limit growth in natural populations.
The most obvious is intraspecific competition.
Density-dependent factors often depress a population's growth by increasing death rate.
A population-limiting factor whose intensity is unrelated to population density is called a
density independent factor.

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Over the long term, most populations are probably regulated by a mixture of factors.
Population cycles
Population cycle: predictable fluctuations in population over a period of time.
When population grows over carrying capacity, it may be limited (lower) than the initial
K due to the damage caused to the habitat lower new carrying capacity K or it may
crash to extinction.
boom-and-bust cycle: characterized by rapid exponential growth (boom) followed by
time which population falls back to a minimal level (bust).
May be caused by winter food shortages.
May be due to predator-prey interactions.
Could be affected by a combination of limited food resources and excessive predation.

R-selection vs. K-selection

K-selected population members have low reproductive rates and are roughly constant in
size (at K). Have a carrying capacity that the population levels out at. Carrying capacity is a
density dependent factor. (like humans)
R-selected population Rapid exponential population growth, numerous offspring, fast
maturation, little postnatal care. Generally found in rapid changing environments affected
by density independent factors. Characterized by opportunistic species. (i.e. bacteria)

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The human population

The human population continues to increase, but the growth rate is slowing.
The world population is undergoing a change known as a demographic transition, a shift
from zero population growth in which birth rates and death rates are high but roughly equal,
to zero population growth characterized by low but roughly equal birth and death rates.
Demographic transition comes with economic development.
Reduced family size is the key to demographic transition.
A demographic tool called an age-structure diagram is helpful for predicting a population's
future growth. The age structure of a population is the number of individuals in different
age-groups.
Population momentum refers to population growth that would occur even if levels of
childbearing immediately declined to replacement level (number of births = number of
deaths).
For countries with above-replacement fertility, population momentum represents natural
increase to the population.
For below-replacement countries, momentum corresponds to continued population
decline.
Ecological footprint: estimate of the amount of land required to provide the raw materials
an individual or nation consumes, including food, fuel, water, housing, and waste disposal.

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Community Structure and Dynamics

What is a community?
A biological community is an assemblage of all the populations of organisms living
close enough together for potential interaction.
Ecosystems define the boundaries of the community according to the research questions
they want to investigate.
A community can be described by its species competition. Community ecologists seek
to understand how abiotic factors and interactions between populations affect the
composition and distribution of communities.
Interspecific interactions are fundamental to community structure
Organisms engage in interspecific interactionsrelationships with individuals of other
species in the communitythat greatly affect population structure and dynamics.
Interspecific interactions are classified according to the effect on the populations
concerned, which may be helpful (+) or harmful (-) or neutral (o).
Types:
Interspecific competition occurs when populations of two different species
compete for the same limited resource.
In general, the effect of interspecific competition is negative for both populations
(-/-).
However, it may be far more harmful for one population than the other.
Commensalism: one species benefits while the other one is unaffected (+/o).
In mutualism, both populations benefit (+/+).
Plants and mycorrhizae, herbivores and the cellulose-digesting microbes that
inhabit their digestive tracts, lichens, nitrogen fixing bacteria and legumes, and
reef-building corals and photosynthetic dinoflagellates are important examples of
mutualism.
obligate mutualism: each partner can only survive and reproduce successfully
in the presence of the other
facultative mutualism: mutualism is beneficial but not essential for the survival
of each
symbiosis is a long term interaction between two or more species.
In parasitism, a parasite lives in a host with minimum expenditure of energy and
benefit at the expense of the host (+/-).
Parasites can be ectoparasites (cling to the exterior of the host) or
endoparasites (live within the host).
Examples of ectoparasites are ticks, lice, mites and mosquitoes, which attach
temporarily to feed on blood or other body fluids.
Bacteria and viruses are examples of endoparasites.
All viruses are parasites.
In predation, one species (the predator) kills and eats another species (the prey)
(+/-).
Herbivory is the consumption of plant parts or algae by an animal (+/-).
Types of predation and herbivory
A true predator kills and eats other animals.
Parasites spend most of their life cycles living on or in the host. The host doesn't
usually die (if at all) until the parasite completes one life cycle.

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A parasitoid is an inset that lays eggs on its host. After the eggs hatch, the larvae obtain
nourishment by consuming host tissues. The host eventually dies, but not until the larvae
complete development and have begun pupation.
Carnivores are animals that eat animals.
Omnivores are animals that eat plants and animals.
A herbivore is an animal that eats plant.
Granivores are seed eaters
Grazers are animals that eat grasses
Browsers eat leaves
Saprophytism: protists and fungi that decompose dead matter externally and absorb the
decomposed nutrients.
Competition may occur when a shared resource is limited
Each species in a community has an ecological niche, defined as the sum of its use of
the biotic and abiotic resources in its environment.
Reminder about competition:
Interspecific competition is competition among members of different species.
Intraspecific competition is competition among members of the same species.
Release from competitive exclusion two species compete for the exactly the same
resource (or occupy the same niche). One is likely to be more successful (no two species
can sustain coexistence if they occupy the same niche). No two species can occupy the
same niche.
Interspecific competition occurs when the niches of two populations overlap and both
populations need a resource that is in short supply.
In general, competition lowers the carrying capacity for the competing populations
because the resources used by one population are not available to the other
population.
What else can happen if the niches of two populations overlap?
Resource partitioning two species occupy the same niche but pursue slightly
different resources or securing their resources in different ways, individuals
minimize competition to maximize success (SLIGHTLY DIFFERENT niches
Character displacement (niche shift) As a result of resource partitioning, certain
traits allow for more success in obtaining resources in their partitions. This reduces
competition and causes a divergence of features between the two species.
Fundamental niche: The potential area and resources an organism is capable of using.
The presence of limiting factors prevent species from occupying the fundamental niche.
Realized niche: niche that an organism occupies in absence of competing species in its
fundamental niche.
Even in the presence of a competing species, both species may be able to occupy
their respective realized niches if there is no overlap between both species' realized
niches.
Trophic structure is a key factor in community dynamics
Every community has a trophic structure, a pattern of feeding relationships consisting
of several different levels.
The sequence of food transfer up the trophic levels is known as a food chain.
The transfer of food moves chemical nutrients and energy from organism to
organism up through the trophic levels in a community.
Starting at the bottom, the trophic level that supports all others consists of autotrophs

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(self-feeders), which ecologists call producers.

Photosynthetic producers use light energy to power the synthesis of organic
compounds.
Plants are the main producers on land whereas in water, the producers are mainly
photosynthetic unicellular protists and cyanobacteria (collectively called
phytoplankton).
All organisms in the trophic levels above the producers are heterotrophs (otherfeeders), or consumers, and all consumers are directly or indirectly dependent on the
output of producers.
Herbivores, which eat plant, algae, or phytoplankton, are primary consumers.
Herbivores have a long digestive tract with greater surface area and time for more
digestion.
Have symbiotic bacteria in digestive tract to help break down cellulose which the
herbivore itself cannot.
Above primary consumers, the trophic levels are made up of carnivores and
insectivores, which eat the consumers form the level below.
Secondary consumers prey on primary consumers.
On land, they include many small mammals such as a mouse eating a herbivorous
insect.
In aquatic environment, secondary consumers are mainly small fishes that eat
zooplankton.
Higher trophic levels include tertiary (third-level) consumers, such as snakes that eat
mice and other secondary consumers.
Most ecosystems have secondary and tertiary consumers.
Some ecosystems have a higher level, quaternary (fourth-level) consumers.
These include hawks in terrestrial ecosystems and killer whales in the marine
environment.
In another trophic level, consumers that derive their energy from detritus, the dead
material produced at all the trophic levels. By breaking down detritus, decomposers link
all trophic levels. Different organisms consume detritus in different stages of decay.
Scavengers, which are large animals, such as crows and vultures, feast on dead
carcasses.

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The diet of detritivores is made up primarily of decaying organic material.

Decomposers, mainly prokaryotes and fungi, secrete enzymes that digest molecules
in organic material and convert them to inorganic form. The breakdown of organic
materials into inorganic ones is called decomposition.
Food chains interconnect, forming food webs
A more realistic view of the trophic structure of a community is a food web, a network
of interconnecting food chains.
Greater number of pathways in a community food web, the more stable the
community is.
Notice that a consumer may eat more than one type of producer, and several species of
primary consumers may feed on the same species of producer.
Food webs, like food chains, do not typically show detritivores and decomposers, which
obtain energy from dead organic material from all trophic levels.
Species diversity includes relative abundance and species richness
A community's species diversity is defined by two components: species richness, or the
number of different species in a community, and relative abundance, the proportional
representation of a species in a community.

In the pictures above, the species diversity in woodlot B is greater than in A. Although
there are four species in each lot, woodlot A mostly has the first species whereas each
species is relatively equal in abundance in woodlot B.
Plant species diversity in a community often has consequences for the species diversity
of animals in the community.
Certain herbivores eat certain plants. Therefore, if there are a wider variety of plants,
there will be a wider variety of herbivores (primary producers), and so on.
Species diversity also has consequences for pathogens.
When many potential hosts are living close together, it is easy for a pathogen to
spread from one to another. In woodlot A, a pathogen that infects the most abundant
tree would be rapidly transmitted across the entire forest.
Keystone species have a disproportionate impact on diversity
Less abundant species may exert control over community composition. A keystone
species is a species whose impact on its community is much larger than its biomass or
abundance would indicate.
A keystone species occupies a niche that holds the rest of its community in place.

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Example:
Experimenter removed a predator, a sea star (a keystone species), from experimental
areas within the intertidal zone along the Washington coast.
The result was that the sea star's main prey, the mussel, outcompeted many of the
other shoreline organisms for the important resource of space on the rocks.
The number of different organisms present in experimental areas dropped from more
than 15 species to fewer than 5 species.
Disturbance is a prominent feature of most communities
Disturbances (blowouts) are events such as storms, fires, floods, droughts, or human
activities that damage biological communities and alter the availability of resources.
The type of disturbances and their frequency and severity vary from community to
community.
Communities change drastically following a severe disturbance that strips away
vegetation and even soil. The disturbed area may be colonized by a variety of species,
which are gradually replaced by a succession of other species, in a process called
ecological succession. As it progresses, diversity and total biomass increase. A final
successional stage of constant species composition is called a climax community (this
usually never occurs). Succession has a factor of randomness that makes it hard to
predict.
When ecological succession begins in a virtually lifeless area with no soil, it is
called primary succession. Pioneer species are plants and animals that are the first
to colonize a newly exposed habitat (usually opportunistic, r-selected species); can
tolerate harsh conditions (lichens and mosses).
As environment changes, r-selected will be replaced by stable k-selected species
(live longer, slow succession) and reach climax where it remains for hundreds of
years.

Secondary succession occurs where a disturbance has cleared away an existing

community but left the soil in tact.

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Invasive species can devastate communities

For long as people have traveled from one region to another, they have carried
organisms along, sometimes intentionally and sometimes by accident.
Many of these non-native species have established themselves firmly in their new
locations.
Furthermore, many have become invasive species, spreading far beyond the original
point of introduction and causing environmental or economic damage by colonizing and
dominating wherever they find a suitable habitat.
Not every organism introduced to a new habitat is successful, and not every species
that is able to survive in its new habitat becomes invasive. There is no single
explanation for why any non-native species turns into a destructive pest.
Humans fight invasive species with biological control, the intentional release of a
natural enemy to attack and decrease the invasive species population.
Subject to a coveolutionary arms race by the prey (invasive species) and the
predator.
Ecosystem structure and dynamics
Ecosystem ecology emphasizes energy flow and chemical cycling
An ecosystem consists of all the organisms in a community as well as the abiotic
environment with which the organisms interact.
Ecosystem ecologists are especially interested in energy flow, the passage of energy
through the components of the ecosystem, and chemical cycling, the transfer of
materials within the ecosystem.
General energy flow in an ecosystem:
Energy typically enters the ecosystem in the form of sunlight.
Plants (producers) convert the light energy into chemical energy through the process
of photosynthesis.
Animals (consumers) take in some of this chemical energy in the form of organic
compounds when they eat the
plants.
Decomposers obtain chemical
energy when they decompose the
dead remains of plants and animals.
Every use of chemical energy by
organisms involves a loss of some
energy to the surroundings in the
form of heat.
General chemical cycling in an
ecosystem:
In ecosystems the supply of
chemical elements used to construct
molecules is limited.
Chemical elements such as carbon
and nitrogen are cycled between the abiotic and biotic components of the ecosystem.
Plants acquire the chemical elements and use them to build organic molecules.
Animals consume the organic molecules.
When the plants and animals become detritus, decomposers return most of the
elements to the soil and air in inorganic form.

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Primary production sets the energy budget for ecosystems
Each day, Earth receives 1019 kcal of solar energy. Only about 1% of this is converted to
chemical energy by photosynthesis.
Ecologists call the amount, or mass, of living organic material in the ecosystem the
biomass.
The amount of solar energy converted to chemical energy (in organic compounds) by an
ecosystem's producers for a given area and for a given time period is called primary
production.
Different ecosystems vary considerably in their primary production as well as in their
contribution to the total production of the biosphere.
Net primary production refers to the amount of biomass produced minus the amount
used by producers as fuel for their own cellular respiration.
Energy supply limits the length of food chains
When energy flows as organic matter through the trophic levels of an ecosystem, much
of it is lost at each link in a food chain.
A pyramid of production illustrates the cumulative loss of energy with each transfer in
a good chain.
Each tier of the pyramid represents the chemical energy present in all of the
organisms at one trophic level of a food chain.
The width of each tier indicates how much of the chemical energy of the tier below
is actually incorporated into the organic matter of that trophic level.
Producers convert only 1% of the energy in the sunlight available to them to primary
production.
Ideally, 10% of the energy available at each trophic level becomes incorporated into
the next higher level (usually ranges from 5% to 20%).

An important implication of this stepwise decline of

energy in a trophic structure is that the amount of
energy available to top-level consumers is small
compared with that available to lower-level
consumers.
This explains why top-level consumers such as
lions and hawks require so much geographic
territory; it takes a lot of vegetation to support
trophic levels so many steps removed from
photosynthetic production.
This also explains why the population of toplevel consumers is most sensitive to population
fluctuations of lower levels.

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Chemicals are cycled between organic matter and abiotic reservoirs
Because chemical cycles in an ecosystem include both biotic and abiotic (geologic and
atmospheric) components, they are called biogeochemical cycles.
The figure to the right is a general scheme for the cycling of a nutrient within an
ecosystem.
Note that the cycle has abiotic reservoirs, where chemicals accumulate or stockpiled
outside of living organisms.
Steps of a general biogeochemical cycle:
(1) Producers incorporate chemicals from the abiotic reservoirs into organic
compounds
(2) Consumers feed on the producers, incorporating some of the chemicals into their
own bodies.
(3) Both producers and consumers release some chemicals back into the
environment in waste products.
(4) Decomposers break down the complex organic molecules in detritus. The
products of decomposition are inorganic compounds, which replenish the abiotic
reservoirs.
Biogeochemical cycles can be local or global.
Soil is the main reservoir for nutrients in a local cycle (i.e. phosphorus)
Chemicals that exist primarily in gaseous form (i.e. carbon and nitrogen), the cycling
is essentially global.
The water cycle
All parts of the biomes are linked by the global water cycle. Organisms on earth need
water for almost all metabolic processes.
Abiotic reservoir: surface and atmospheric water.
Enter food chain: plants absorb water from soil; animals drink and eat other organisms
Recycling: transpiration
Return to abiotic: evaporation and runoff

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The carbon cycle
Carbon, the major ingredient of all organic molecules, has an atmospheric reservoir and
cycles globally.
Abiotic reservoir: CO2 in atmosphere, fossil fuels, peat, sedimentary rocks, and as
dissolved carbon compounds in the oceans.
Enter food chain: Photosynthesis (carbon fixation in Calvin cycle) by primary
producers, which will then get eaten up by consumers.
Return to abiotic: cellular respiration, combustion of wood and fossil fuels,
decomposition of detritus

The phosphorus cycle

Organisms require phosphorus as an ingredient of nucleic acids, phospholipids, ATP, and
as a mineral component of bones and teeth.
Unlike the carbon cycle and other major biogeochemical cycles, the phosphorus cycle
does not have an atmospheric component (only rocks).
Abiotic reservoir: rocks, minerals soil
Enter food chain: weathering (break down) of rock release soluble phosphate to the soil.
Plants then uptake the soluble phosphate
through the soil and build them into
organic compounds. Consumers obtain
phosphorus in organic form by eating
plants.
Return to abiotic: decomposers release
phosphate to the soil by decomposing
animal waste and the remains of dead
plants and animals. Some phosphate drains
from terrestrial ecosystems into the sea,
where it may settle and eventually become
part of new rocks. This phosphorus will
not cycle back into living organisms until
geologic processes uplift and expose them

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to weathering, a process that takes millions of years.
Because phosphates are transferred from terrestrial to aquatic ecosystems much more
rapidly than they are replaced, the amount in terrestrial ecosystems gradually diminishes
over time. As a result, the phosphate availability is often quite low and commonly a
limiting factor for population growth.
The nitrogen cycle
As an ingredient of proteins and nucleic acids, nitrogen is essential to the structure and
functioning of all organisms. In particular, it is a crucial and often limiting plant
nutrient.
Abiotic reservoir: Atmospheric N2 (makes up 80% of the atmosphere) and nitrogen in
the soil
Atmospheric N2 cannot be absorbed by plants. The process of nitrogen fixation
converts N2 to compounds of nitrogen that can be used by plants.
Fixation occurs in lightning strikes and is done by free-living bacteria in the soil or
bacteria living symbiotically in the roots of certain species of plants (most
commonly legumes)
N2 is converted into ammonia (NH3), which then picks up another H+ to become
ammonium (NH4+).
NH4+ is then converted into NO2- (nitrite)and NO3- (nitrate) by nitrifying bacteria.
Nitrates and nitrites are more readily absorbed by plants.
Enter food chain: Plants uptake nitrites, nitrates, and/or ammonium and then synthesize
organic molecules. Higher order consumers gain nitrogen from their prey.
Return to abiotic: Consumers excrete waste nitrogen, decomposition of detritus releases
ammonium from organic compounds back into the soil (nitrifying bacteria can convert
this ammonium back into nitrites or nitrates), denitrifying bacteria strips oxygens from
nitrites and nitrates, releasing N2 back into the atmosphere (this occurs in low-oxygen
conditions), aerobic denitrification produces N2O.
Although not shown in the figure, some NH4+ and NO3- are made in the atmosphere by
chemical reactions involving N2 and ammonia gas. The ions produced by these chemical
reactions reach the soil in precipitation and dust, which can be then used as nitrogen
sources for organisms.

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The loss of biodiversity

The loss of biodiversity includes the loss of ecosystems, species and genes
Biodiversity encompasses more than in individual speciesit includes ecosystem
diversity, species diversity, and genetic diversity.
Ecosystem diversity
The world's natural ecosystems are rapidly disappearing. As natural ecosystems are
lost, so are essential services (e.g., water purification)
Species diversity
When ecosystems are lost, populations of the species that make up their biological
communities are also lost.
Ecologists refer to the loss of a single population of a species as extirpation.
Although extirpation and declining population size are strong signals that a species
is in trouble, it is still possible to save it.
Extinction means that all populations of a species have disappeared, an irreversible
situation.
Genetic diversity
The genetic diversity within and between populations is the raw material that makes
microevolution and adaptation to the environment possiblea hedge against future
environmental changes.
If local populations are lost and the total number of individuals of a species declines,
so, too, do the genetic resources for that species.
Severe reduction in genetic variation threatens the survival of a species.
Major causes of threats to biodiversity loss
Habitat loss: Human alteration of habitats poses the single greatest threat to biodiversity.
Agriculture, urban development, forestry, mining, and environmental pollution have
brought about massive destruction and fragmentation of habitats.
Deforestation: clear-cutting of forests. Causes erosion, flooding, and changes in
water patterns.
Desertification: overgrazing of grasslands that border deserts transform the
grasslands into deserts.
Invasive species: Ranking section behind major habitat loss is invasive species, which
disrupt communities by competing with, preying on, or parasitizing native species.
Overharvesting: The third major threat to biodiversity is over-exploitation of wildlife of
harvesting at rates that exceed the ability of populations to rebound.
Pollution: Pollutants released by human activities can have local, regional, and global
effects.
Small pollutants, such as oil spills, contaminate local areas.
Ozone depletion in the upper atmosphere is another example of global impact of
pollution. The ozone layer protects Earth from the harmful UV rays in sunlight.
In addition to being transported to areas far away from where they originate, many
toxins produced by industrial waste or applied as pesticides become concentrated as
they pas through the food chain. This concentration, or biological magnification,
occurs because the biomass at any given trophic level is produced from a larger
toxin-containing biomass ingested from the level below.
Eutrophication is the process of nutrient enhancement in lakes and subsequent
increase in biomass. Lakes polluted with nutrients (i.e. from fertilizer runoff)
stimulate algal blooms (massive algae/phytoplankton growth) which respire and
deplete oxygen. Breakdown of the dead algae and phytoplankton by decomposers
deplete even more oxygen. Many animals die of oxygen starvation.

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Acid rain: Burning of fossil fuels release SO2 and NO2 in the air. When they react
with water vapor, they turn into sulfuric acid and nitric acid. Both acids kill plants
and animals when they rain to earth.
Global climate change: burning of fossil fuels and forests increase CO2 in atmosphere.
CO2 is part of a class of molecules called greenhouse gases, gases that can absorb heat,
allowing less heat to escape back into space. The increase of greenhouse gases in the
atmosphere leads to the greenhouse effect, an increase in global temperatures. The
increase in global temperature leads to a rise in sea level by melting ice (affecting
weather patterns).
Climate change is an agent of natural selection
Why do some species appear to be adapting to global climate change while others are
endangered by them?
Most of the adaptations can be attributed to phenotypic plasticity, the ability to change
phenotype in response to local environmental conditions.
Phenotypic plasticity allows organisms to cope with short-term environmental
changes.
Phenotypic plasticity is itself a trait that has a genetic basis and can evolve.
Conservation biology and restoration ecology
Protecting endangered populations is one goal of conservation biology
Conservation biology is a goal-oriented science that seeks to understand and counter
the loss of biodiversity.
Sustaining ecosystems and landscapes is a conservation priority
One of the most harmful effects of habitat loss is population fragmentation, the
splitting and consequent isolation of portions of populations.
To counteract the effects of fragmentation, conservation biology often aims to sustain
the biodiversity of entire ecosystems and landscapes.
Ecologically, a landscape is a regional assemblage of interacting ecosystems.
Landscape ecology is the application of ecological principles to the study of the
structure and dynamics of a collection of ecosystems.
Where habitats have been severely fragmented, a movement corridor, a narrow strip or
series of small clumps of high-quality habitat connecting otherwise isolated patches, can
be a deciding factor in conserving biodiversity.
Establishing protected areas slows the loss of biodiversity
Conservation biologists tend to protect certain areas to maintain biodiversity. Choosing
locations for protection often focuses on biodiversity hot spots.
These relatively small areas have a large number of endangered and threatened
species and an exceptional concentration of endemic species, those that are found
nowhere else.
Because endemic species are limited to specific areas, they are highly sensitive to
habitat degradation. Thus, biodiversity hots spots can also be hot spots of extinction.
Zoned reserves are an attempt to reverse ecosystem disruption
One type of protection is called a zoned reserve, an extensive region of land that
includes one or more areas undisturbed by humans.
The lands surrounding these areas continue to be used to support the human population,
but they are protected from extensive alteration.
As a result, they serve as a buffer zone, or shield, against further intrusion into the
undistributed areas.
Restoration ecology is a developing science
The expanding field of restoration ecology uses ecological principles of returning

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degraded areas to their natural state.
One of the major strategies in restoration ecology is bioremediation, the use of living
organisms to detoxify polluted ecosystems.

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Systematics connects classification with evolutionary history

Systematics is a discipline of biology that focuses on classifying organisms and determining
their evolutionary relationships.
The evolutionary history of a species or group of species is called phylogeny.
In the 18th century, Carolus Linnaeus introduced a system of naming and classifying species,
a discipline called taxonomy.
Biologists assign each species a two-part scientific name, or binomial.
The first par is the genus to which ha species belongs.
The second part of the binomial is unique for each species within the genus.
In addition to naming species, Linnaeus also grouped them into a hierarchy of categories.
It places similar genera in the same family, puts families into orders, orders into
classes, classes into phyla, phyla into kingdoms, and kingdoms into domains.
Biologists typically use phylogenetic trees to depict hypotheses about the evolutionary
history of a species.
Prokaryotes
Prokaryotes are diverse and widespread
Despite their small size, prokaryotes have an immense impact on our world. They are
found wherever there is life, including in and on the bodies of multicellular organisms.
When we discuss prokaryotes, we tend to focus on bacterial pathogens, disease-causing
agents. But benign or beneficial prokaryotes are far more common than harmful
prokaryotes.
Prokaryotes are essential to the health of the environment. They function as
decomposers, making them indispensable components of the chemical cycle.
There are two major domains of prokaryotes, Archarea and Bacteria.
Prokaryotes have unparalleled nutritional diversity
Two sources of energy are used by prokaryotes:
Like plants, prokaryotic phototrophs capture energy from sunlight. Prokaryotic
cells do not have chloroplasts, but some have thylakoid membranes where
photosynthesis takes place.
Prokaryotes called chemotrophs harness the energy stored in chemicals, either
organic molecules or inorganic molecules.
Sources of carbon:
Autotrophs, including plants and some prokaryotes and protists, obtain their carbon
atoms from carbon dioxide (CO2).
Most prokaryotes, as well as animals, fungi, and some protists, are heterotrophs,
meaning they obtain their carbon atoms from the organic compounds of other
organisms.
The terms used to describe how an organism obtains energy and carbon are combined to
describe its modes of nutrition:
Photoautotrophs harness sunlight for energy and use CO2 for carbon.
Photoheterotrophs obtain energy from sunlight but get their carbon atoms from
organic sources.
Chemoautotrophs harvest energy from inorganic chemicals and use carbon and
CO2 to make organic molecules. Because they don't depend on sunlight,
chemoautotrophs can thrive in conditions that seem totally inhospitable to life.
Chemoheterotrophs acquire both energy and carbon from organic molecules, and
are by far the largest and most diverse group of prokaryotes.

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Biofilms are complex associations of microbes

In many natural environments, prokaryotes attach to surfaces in highly organized
colonies called biofilms.
Biofilms form on almost any support, including rocks, soil, organic material, metal,
plastic, and TEETH.
You have biofilm on your teethdental plaque is a biofilm that can cause tooth
decay.
Biofilms are common among bacteria that cause disease in humans.
Bacteria and archaea are the two main branches of prokaryotic evolutionarily
Archaea:
Archaea are prokaryotes but differ from bacteria.
Archael cell walls (different from bacteria) contain various polysaccharides and
proteins, but not peptidoglycan.
Phospholipid components (different from eukaryotes and bacteria): glycerol is
different and the hydrocarbon chains are branched with ether-linkages instead of
ester-linkages.
Similarity with eukaryotes (Archaea is more similar to eukaryotes than bacteria):
DNA of both archaea and eukaryotes are associated with histones, but bacterial
DNA is not.
Ribosome activity is not inhibited by certain antibiotics such as streptomycin and
chloramphenicol unlike bacteria.
Bacteria:
Distinct from archaea and eukaryotes by these features:
cell wall made up peptidoglycan
bacterial DNA not associated with histones
ribosome activity is inhibited by streptomycin and chloramphenicol
How bacteria are classified
Mode of nutrition/how they metabolize resources

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Ability to produce endospores (resistant bodies that contain DNA and a small
amount of cytoplasm surrounded by a durable wall)
Means of motility: flagella, corckscrew motion, or gliding through slime material
Shapes: cocci (spherical), bacilli (rod-shaped), spirilla/spirochetes (spiral)
Thick peptidoglycan cell wall (gram-positive), thin peptidoglcyan cell wall
covered with lipopolysaccharides (gram-negative).
Archaea thrive in extreme environmentsand in other habitats
A group of archaea called the extreme halophiles (salt lovers) thrive in very salty
places.
Most are aerobic and heterotrophic whereas others are anaerobic and photosynthetic
with the pigment bacteriorhodopsin.
Extremely salty environments may turn various colors as a result of the dense
growth and colorful pigments of halophilic bacteria.
Another group of archaea, the extreme thermophiles (heat lovers), thrive in very hot
temperatures. Typically sulfur-based.
Acidophile is an organism with an optimal growth at pH levels 3 or below. Aklaliphile
is an organism with optimal growth at pH levels 9 or above.
A third group of archaea, the metahnogens, live in anaerobic (oxygen-lacking)
environments and give off methane as a waste product. They are obligate anaerobes.
Bacteria include a diverse assemblage of prokaryotes
Domain bacteria is currently divided into multiple groups based on comparisons of
genetic sequences:
Proteobacteria are all gram-negative and share a particular rRNA sequence. With
regard to other characteristics, however, this large group encompasses enormous
diversity.
Include species that live symbiotically with other species. Symbiosis is a close
association of two or more species.
A second major group of bacteria, gram-positive bacteria, have gram-positive cell
walls (review prokaryote structure chapter).
Cyanobacteria are the only groups of prokaryotes with plantlike, oxygen-generating
photosynthesis. Provide an enormous amount of food for freshwater and marine
ecosystems. Include species that live symbiotically with other species.
Contain accessory pigment phycobillins
Some are specialized cells called heterocysts that produce nitrogen-fixing
enzymes
Known as blue-green algae.
The chlamydias, which live in eukaryotic host cells, live inside eukaryotic host cells
(the sexually transmitted disease Chlamydia is part of this group).
Spirochetes, the fifth group, are helical bacteria that spiral through their
environment by means of rotating, internal filaments. Some are notorious pathogens.
Chemosynthetic: autotrophs; some are nitrifying bacteria
Nitrogen-fixing: heterotrophs that fix nitrogen, lives in nodules of plants
(mutualism)
Some bacteria cause disease
All organisms are almost constantly exposed to pathogenic bacteria. Most often, our
body's defenses prevent pathogens from affecting us. Occasionally, however, a pathogen
establishes itself in the body and causes illness.

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Most bacteria that cause illness do so by producing a poisoneither an exotoxin or an

endotoxin.
Exotoxins are proteins that bacteria cells secrete into their environment.
Endotoxins are lipid components of the outer membrane of gram-negative bacteria
that are released when the cell dies or is digested by a defensive cell.
Koch's postulates are used to prove that a bacterium causes a disease. For a human
disease, the researcher must be able to:
(1) find the candidate bacterium in every case of the disease
(2) isolate the bacterium from a person who has the disease and grow it in pure
culture
(3) show that the cultured bacterium causes the disease when transferred to a healthy
subject
(4) isolate the bacterium from the experimentally infected subject.
Protists
Protists are an extremely diverse assortment of eukaryotes.
Protists are a diverse collection of mostly unicellular eukaryotes. They are difficult to
characterize because of this. Most are unicellular.
Protists obtain their nutrition in a variety of ways:
Some protists are autotrophs, producing their food by photosynthesis; these are
called algae (another useful term that is not taxonomically meaningful).
Other protists, informally called protozoans, are heterotrophs, eating bacteria and
other protists. Some are fungus-like and some are parasitic.
Parasites derive their nutrition from a living host, which is harmed by the
interaction.
Still other protists are mixotrophs, capable of both photosynthesis and heterotrophy,
depending on the availability of light and nutrients.
Most protists are aquatic but others inhabit the bodies of various host organisms.
Protists are more complicated than any prokaryotes because their cells have a
membrane-enclosed nucleus (containing multiple chromosomes), have organelles, and
their flagella and cilia have 9+2 pattern of microtubules. However, they are considered
the simplest eukaryotes.
Secondary endosymbiosis is the key to much of protist diversity
Why are protists so diverse?
Scientists think that heterotrophic eukaryotes evolved first; these had mitochondria but
not chloroplasts.
As shown in the figure below, autotrophic eukaryotes are though to have arisen later
from a lineage of heterotrophic eukaryotes descended from an individual that engulfed
an autotrophic cyanobacterium through primary endosymbiosis.
If the cyanobacterium continued to function within its host cell, its photosynthesis
would have provided a steady source of food for the heterotrophic host and thus
given it a significant selective advantage.
And because the cyanobacterium had its own DNA, it could reproduce to make
multiple copies of itself within the host cell.
Over time, the descendants of the original cyanobacterium evolved into chloroplasts.
The chloroplast-bearing lineage of eukaryotes later diversified into the autotrophs green
algae and red algae.
Over subsequent occasions during eukaryotic evolution, green algae and red algae

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themselves became endosymbionts following ingestion by heterotrophic eukaryotes.
Heterotrophic host cells enclosed the algal cells in food vacuoles but the algaeor parts
of themsurvived and became cellular organelles.
This process, in which an autotrophic eukaryotic protist became endosymbiotic in a
heterotrophic eukaryotic protist, is called secondary endosymbiosis. This is a major
key in protist diversity.

Chromoalveolates represent the range of protist diversity

Chromalveolata is a large, extremely diverse group that includes
autotrophic, heterotrophic, and mixotrophic species and multicellular as
well as unicellular species.
Autotrophic chromalveolates include diatoms, unicellular algae that have a
unique glassy cell wall called a test which is made up of silicon dioxide.
The cell wall of a diatom consists of
two halves that fit together like the
bottom and the lid of a shoe box.
Are an important food source in all
aquatic environments.
Dinoflagellates are a group that includes unicellular
autotrophs, heterotrophs, and mixotrophs, and are
also very common components of marine and
freshwater plankton (communities of
microorganisms that live near the water's surface).
Bloomspopulation explosionsof autotrophic
dinoflagellates sometimes warm coastal waters
to turn pinkish orange, a phenomenon known as
red tide. Toxins produced by red-tide
dinoflagellates have killed large numbers of fish.
Have two flagella: one is posterior, while the
second is transverse (across the body) and rests in an encircling mid groove
perpendicular to the first flagellum.
Some produce nerve toxins that concentrate in filter-feeding shellfish, which can
cause illness in humans

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Brown algae are large, complex, autotrophic chromalveolates. They owe their brownish
color to some of the pigments in their chloroplasts.
All are multicellular, and most are marines.
Seaweed and kelp are brown algae. Kelp are anchored to
the seafloor by their root-like structures, which allow
them to grow very tall. Form kelp forests which many
marine animals use as their feeding grounds.
Have flagellated sperm cells.
Water molds are heterotrophic, unicellular chromalveolates
that typically decompose dead plants and animals in
freshwater habitats.
Because many species resemble fungi, water molds were
classified as fungi until molecular comparisons revealed
they were protists.
Parasitic water molds sometimes grow on the skin or gills
of fish.

Ciliates are a group of unicellular protists that includes heterotrophs and mixotrophs.
Named for their use of cilia to move and to sweep food into their mouth.
Have specialized features such as mouths, anal pores, contractile vacuoules, two
kinds of nuclei (one large and one small), and other features.
Perhaps the most complex of all cell.
Paramecium is the prime example of ciliates.
Rhizarians include a variety of amoebas
The clade Rhizaria was recently proposed based on similarities in
DNA, although some believe that the rhizarians should be placed in
Chromalveolata. The largest two groups are the foraminiferans and
the radiolarians.
Amoebas move and feed by means of pseudopodia, which are
temporary extensions of the cell.
Pseudopodia encircle food and absorb it by phagocytosis.
Most amoebas in Rhizaria are distinguished from other amoebas
by their threadlike (rather than lobe-shaped pseudopodia).
Foraminiferans are found both in the ocean and cell water.
They have porous shells, called tests, composed of organic material hardened by
calcium carbonate.

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The pseudopodia, which function in feeding and locomotion, extend through small
pores in the test.
90% of forams that have
been identified are fossils.
The fossilized tests, which
are a component of
sedimentary rock, are
excellent markers for
correlating the ages of rocks
in different parts of the
world.
Like forams, radiolarians
produce a mineralized support
structure, in this case an
internal skeleton made up of
silica dioxide.
The cell is also surrounded by a test composed of organic materials.
Most species of radiolarians are marine.
When they die, their hard parts settle to the bottom of the ocean and become part of
the sediments. In some areas, radiolarians are so abundant that sediments, known as
radiolarian ooze, are hundreds of meters thick.

Some excavates have modified mitochondria

Excavata (the excavates) have recently been proposed as a clade on the basis of their
molecular and morphological characteristics.
The name revers to an 'excavated feeding groove possessed by some members of
the groups.
Many excavates have modified mitochondria that lack functional electron transport
chains and use anaerobic pathways to extract energy.
Some excavates are parasites.

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Other Protozoans
Protozoa are animal-like protists. They are heterotrophs that consume either living cells
or dead organic matter.
Apicomplexans
Parasites of animals
Characterized by apical complex, a complex of organelles located at each end
(apex) of the cell.
No physical means of motility
Form spores that are dispersed by one or more hosts.
Unikonts include protists that are closely related to fungi and animals
Unikonta is a controversial grouping that joins two well established clades:
amoeboazoans, which are protists, and a second clade that includes animals and fungi.
Amoebozoans, including many species of free-living amoebas, some parasitic amoebas,
and the slime molds, have lobe-shaped pseudopodia.
Its pseudopodia arch around the prey and will inclose in a food vacuoule.
The yellow, branching growth on a dead log is an amoebozoan called a plasmodial
slime mold.
Grow as a plasmodium feeding on decaying vegetation. Plasmodium is a single,
multinucleate mass of cytoplasm undivided by plasma membranes. Despite growing
as a plasmodium, plasmodial slime molds are unicellular organisms.
The plasmodium extends pseudopodia through soil and rotting logs, engulfing food
by phagocytosis as it grows. Within the fine channels of the plasmodium, cytoplasm
streams first one way and then the other in pulsing flows that probably help with
nutrient distribution.
When food becomes unavailable or when the environment desiccates (dries up),
stalks bearing more capsules form.
Haploid spores released from the capsule germinate into haploid amoeboid or
flagellated cells, which fuse to form a diploid cell.
The diploid cell grows into the spreading
plasmodium.
Cellular slime molds are also common on
rotting logs and decaying organic matter.
Exhibit both funguslike and protozoalike
characteristics during their life cycle.
Spores germinate into amoebas which feed
on bacteria
When food sources are depleted, the
amoebas aggregate into a single unit,
which migrates as a slug. The individual
cells of the slug mobilize to form a stalk with a capsule at the top similar to the
spore-bearing bodies of many fungi. Spores are then released, which repeat the
cycle.
The stimulus for aggression is cyclic AMP, which is secreted by the amoebas that
experience food deprivation first.
Other fungi-like protists

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Oomycota are either parasites or saprobes.
Saprobes are organisms that gets nutrition from nonliving/decaying organic matter.
They form filaments (hyphae) which secret enzymes that digest the surrounding
substances. The breakdown products are then absorbed.
The filaments of Oomycota lack septa, or cross walls, which in many of the true
fungi have.
Because they lack septa, they are coenocytic, containing many nuclei within a single
cell.
Cell walls made up of cellulose, not chitin like fungi
Archaeplastids include red algae, green algae, and land plants
Almost all of the members of the supergroup Archaeplastida are
autotrophic.
The warm costal waters of the tropics are home to the majority of species
of red algae.
Contain red accessory pigments called phycobilins that masks the
green of chlorophyll.
Most are multicellular, while some are unicellular.
Multicellular red-algae are typically soft-bodied, but some have cell
walls encrusted with hard, chalky deposits.
Gametes do not have flagella.
Green algae, which are named for their grass-green chloroplasts, include
unicellular and colonial species as well as multicellular seaweeds.
Have chlorophyll a and b.
Have cellulose cell walls
Store carbohydrates as starch
Some species have isogamous gametes, where both sperm and egg are motile and
equal in size
Some species have ansiogamous, where the sperm and egg differ in size
Some species are oogamous, where a
large egg cell remains with the parent
and is fertilized by a small, motile
sperm.
A lineage of Chlorophytes, the
charophytes, are believed to be the
ancestors of plants.
Multicellularity evolved several times in
eukaryotes
Multicellular organisms have evolved from
three different ancestral lineages:
chromalveolates (brown algae), unikonts
(fungi and animals), and archaeplastids
(red algae and green algae).
According to one hypothesis, two separate unikont lineages led to fungi and animals. It
is estimated that the ancestors of animals and fungi diverged more than 1 billion years
ago.
Evidence suggests that a group of unikonts called choanoflagellates are the closest

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living protist relatives of animals.
A different group of unikont protists is thought to have given rise to fungi.
Evidence suggests that a group of single-celled protists called nucleariids, amoebas
that feed on algae and bacteria, are the closest living relatives of fungi.
A group of green algae called charophytes are the closest living relatives of of land
pants.

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Plant Evolution and Diversity

Plants have adaptations for life on land
Except for primitive bryophytes, the dominant generation of all plants is the diploid
sporophyte generation. A diploid structure is more apt to survive genetic damage
because two copies of each chromosome allow recessive mutations to be masked.
All plants are covered a waxy cuticle, a waxy covering on aerial parts that reduces
desiccation (prevents water loss). Gas exchange cannot occur directly through the
cuticle, but through tiny pores called stomata that are regulated.
Plants must obtain nutrients from both soil and air, two very different media. Roots,
stems, and leaves help meet this resource challenge. Leaves developed as centers for
photosynthesis. Stems developed to provide a framework to support leaves. The
elongation and branching of plant's stems and roots maximize exposure to the resources
in the soil and the air. Roots developed to obtain water and minerals from the soil and to
anchor the plant.
A plant must be able to connect its subterranean and aerial parts, conducting water and
minerals upward from its roots to its leaves and distributing sugars produced in the
leaves throughout its body. Development of a vascular system allows the plant to
distribute water and nutrients throughout all parts.
Because air provides much less support than water, plants must be able to hold
themselves up against the pull of gravity. The cell walls of some plant cells, including
xylem, are thickened and reinforced by a chemical called lignin.
In the more primitive plant divisions, flagellated sperm require water to swim to eggs. In
the more advanced divisions (Coniferophyta and Anthophyta), the sperm, packaged as
pollen, are adapted for delivery by wind or animals. In all plants, the fertilized egg
(zygote) develops into an embryo while attached to and nourished by the parent plant.
This multicellular, dependent embryo is the basis for designating plants as
embryophytes, distinguishing them from algae.
In the most advanced divisions, the Anthophyta, the gametophytes are enclosed (and
thus protected) inside an ovary.
Plants of the Coniferophyta and Anthophyta have developed adaptations to seasonal
variations in the availability of water and light.
For example, some trees are deciduous; that is, they shed their leaves to minimize
water loss during slow-growing seasons.

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Plant diversity reflects the evolutionary history of the plant kingdom

1) After plants originated from an algal ancestor approximately 475 million years ago,
early diversification gave rise to bryophytes: seedless, nonvascular plants, including
mosses, liverworts, and hornworts.
They resemble other plants in having apical meristems and embryos that are retained
on the parent plant, but they lack true roots and leaves.
Cell walls are not made up of lignin, meaning that bryophytes with an upright
growth habit lack support.
Must remain small and water must be readily available for absorption through
surface tissues and as a transport medium for sperm. Bryophytes have flagellated
sperm.
2) The origin of vascular plants (tracheophytes) occurred about 425 million years ago.
Their lignin-hardened vascular tissues provide strong support, enabling stems to stand
upright and grow tall on land. Two clades of vascular plants are informally called
seedless vascular plants: the lycophytes and the pterophytes.
Both lycophytes and pterophytes require moist conditions for fertilization, and they
disperse their offspring as spores that are carried by air currents.
Lycophytes (e.g., club mosses, spike mosses, quillworts) produce clusters of sporebearing sporangia in conelike structures called strobili.
Three important pterophytes are ferns, horsetails, and whisk ferns.
Ferns produce clusters of sporangia called sori that develop on the under-surface
of fern fronds (leaves).
Horsetails have hollow, ribbed stems that are joined at nodes. Nodes occur at
intervals along the stem, produce small leaves and, in some species, branches.
Stems, branches, and leaves are green and photosynthetic and have a rough
texture to the presence of silicon dioxide. Sporangia are called strobili.
Whisk ferns have branching stems without roots. Leaves are very small or
absent. The absence of roots and leaves is considered a secondary lossthat is,
these structures were lost as whisk ferns diverged from their ancestors.
3) The first vascular plants with seeds evolved about 360 million years ago. Seeds and

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pollen are key adaptations that improved the ability of plants to diversify in terrestrial
habitats.
A seed consists of an embryo packaged with a food supply within a protective outer
covering. This survival packet facilitates wide dispersal of plant embryos.
Two major clades: Gymnosperms and Angiosperms.
Gymnosperms were among the earliest seed plants. Coniferophyta (conifers) +
other minor divisions make up the gymnosperms. They have seeds produced in
unprotected megaspores (naked seeds) near the surface of the reproductive
structure. A vast majority do not have flagellated sperm. Fertilization and seed
development are lengthy: 1-3 years.
Coniferophyta are the cone bearing plants. Male and female reproductive
structures are borne in pollen-bearing male cones and ovule-bearing female
cones.
Angiosperms, or Anthophyta, are the flowering plants. No flagellated sperm. More
specialized vascular tissues. Numerous variations in habitat in growth. Can survive
in a variety of environmental conditions.
Alternation of Generations and Plant Life Cycles
Review alternation of generations in life cycles and cancer chapter in cell/molec bio unit
The life cycle of a moss is dominated by the gametophyte (Bryophyte life cycle)

(1) Haploid gametes are produced in protective structures called gametangia. The male
gametangium, or antheridium (plural, antheridia), produces flagellated sperm that
swim through water to fertilize eggs produced by the female gametangium, or
archegonium (plural, argegonia).
(2) After fertilization, the zygote remains in the gametangium. Zygote is diploid.
(3) There it divides by mitosis, developing into a sporophyte embryo and then a mature
sporophyte, which remains attached to the gametophyte.
(4) Meiosis occurs in the sporangia at the tips of the sporophyte stalks. After meiosis,
haploid spores are released from the sporangium.
(5) The spores undergo mitosis and develop into the gametophyte plants.
Note: The haploid gametophyte stage is the dominant stage of the life cycle of
bryophytes

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Ferns, like most plants, have a life cycle dominated by the sporophyte (Tracheophyte life
cycle)

(1) Fern gametophytes often have a distinctive heart-like shape, but they are quite small
and inconspicuous. Like Bryophytes, Tracheophyte gametophytes produce antheridium
and archegonium.
(2) Like Bryophytes, Tracheophytes have flagellated sperm that require moisture to
reach an egg. Although eggs and sperm are usually produced in separate locations on the
same gametophyte a variety of mechanisms promote cross-fertilization between
gametophytes.
(3) The zygote remains on the gametophyte as it develops into a new sporophyte.
(4) Unlike Bryophytes, the gametophyte dies and the sporophyte becomes an
independent plant.
(5) The black dots in the photograph are clusters of sporangia, in which cells undergo
meiosis, producing haploid spores. The spores are released and develop into
gametophytes by mitosis.
Note: Tracheophytes (and all other vascular plants) have a dominant sporophyte
generation in their life cycle, unlike Bryophytes (gametophyte dominated).
A pine tree is a sporophyte with gametophytes in its cones (Gymnosperm life cycle)
In seed plants, a specialized structure within the sporophyte houses all reproductive
stages, including spores, eggs, sperm, zygotes, and embryos. In gymnosperms, such as
pines and other conifers, this structure is called a cone.
Each leaf, or scale, of the cone contains sporangia that produce spores by meiosis.
Unlike seedless plants, however, the spores are not released. Rather, spores give rise to
gametophytes within the shelter of the cone. The gametophytes later produce gametes,
which unite to form a new sporophyte.
A Gymnosperm bears two types of cones, which produces spores that develop into the

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male and female gametophytes.

The smaller ones, called pollen cones (1 in the figure below), produce the male
gametophytes). Pollen cones contain many sporangia, each of which makes numerous
haploid spores by meiosis.
Male gametophytes, or pollen grains, develop from the spores. Pollen grains are
released by the cones and are carried by the wind to another cone that contains a
female gametophyte
(2) An ovulate cone, which produces the female gametophyte, is larger than a pollen
cone. Each of its stiff scales bears a pair of ovules.
(3) Pollination occurs when a pollen grain lands on an ovulate scale and enters the
ovule. After pollination, the scales of the cone grow together, sealing it until the seeds
are mature. Meiosis then occurs in a spore mother cell within the ovule.
(4) Over the course of many months, one surviving haploid spore cell develops into the
female gametophyte, which make eggs.
(5) Meanwhile, a tiny tube grows out of each pollen grain, digests its way through the
ovule, and eventually releases sperm, which are simply nuclei rather than independent
cells, near an egg. Fertilization typically occurs more than a year after pollination. (More
on how fertilization works in seed, vascular plants in the chapters on plant structure and
function)
(6) Usually, all eggs in an ovule are fertilized, but ordinarily only one zygote develops
fully into a sporophyte embryo.
(7) The ovule matures into a seed, which contains the embryo's food supply and has a
tough seed coat. In a typical Gymnosperm, seeds are shed about two years after
pollination.
(8) The seed is dispersed by the wind, and when conditions are favorable, it germinates,
and its embryo grows into a pine seedling.

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The flower is the centerpiece of angiosperm reproduction
Like pine cones, flowers are the sites of pollination and fertilization. Flowers house
separate male and female sporangia and gametophytes, and the mechanisms of sexual
reproduction, including pollination and fertilization, are similar to Gymnosperms. And
like cones, flowers are also short stems bearing modified leaves.
Parts of a flower:

The structures of the flower are attached in a circle to a receptacle at the base of the
flower.
The outer layer of the circle consists of the sepals, which are usually green. They
enclose the flower before it opens.
When the sepals are peeled away, the next layer is the petals, which are conspicuous
and attract animal pollinators.
Plucking off a flower's petals reveals the filaments of the stamens (male
reproductive structure). The anther, a sac at the top of each filament, contains male
sporangia and will eventually release pollen. The filament holds the anther.
At the center of the flower is the carpel (pistil), the female reproductive structure. It
holds the ovary, a unique angiosperm adaptation that encloses the ovules. The ovary
matures into a fruit, which aids seed dispersal. The style is a tube on top of the ovary
that connects it to the stigma, a structure that receives pollen during fertilization.
Complete flowers contain all four floral organs. Incomplete flowers lack one or more
floral organs, for example stamens or carpels. Clusters of flowers are called
inflorescences.
The angiosperm plant is a sporophyte with gametophytes in its flowers (Angiosperm life
cycle)
(1) Meiosis in the anthers of the flower produces haploid spores that undergo mitosis
and form the male gametophytes, or pollen grains.
(2) Meiosis in the ovule produces a haploid spores that undergoes mitosis and forms the
few cells of the female gametophyte, one of which becomes an egg.
(3) Pollination occurs when a pollen grain, carried by the wind or an animal, lands on
the stigma.
(4) As in gymnosperms, a tube grows from the pollen grain to the ovule, and a sperm
fertilizes the egg, forming a zygote. (More on how fertilization works in seed, vascular
plants in the chapters on plant structure and function)

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(5) A seed develops from each ovule. Each seed consists of an embryo (a new
sporophyte) surrounded by a food supply and a seed coat. (seed formation is discussed
more in depth in the chapters on plant structure and function)
(6) While the seeds develop, the ovarys wall thickens, forming the fruit that encloses
the seeds. (fruit formation is discussed in more detail in the chapters on plant structure
and function)
(7) When conditions are favorable, a seed germinates. As the embryo begins to grow, it
uses the food supply from the seed until it can begin to photosynthesize. Eventually, it
develops into a mature sporophyte plant, completing the life cycle.

The structure of a fruit reflect its function in seed dispersal

A fruit, the ripened ovary of a flower, is an adaptation that helps disperse seeds.
Many angiosperms produce fleshy, edible fruits that are attractive to animals as food.
While the seeds are developing, these fruits are green and effectively camouflaged
against green foliage. When ripe, the fruit turns a bright color, advertising its
presence to animals.
When an animal digests a fruit, most of the tough seeds pass unharmed through its
digestive tract. The animal may deposit the seeds some distance away from where it ate
the fruit.

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Diversity of Fungi
Fungi absorb food after digesting it outside their bodies
All fungi are heterotrophs that acquire their nutrients
by absorption. They secrete powerful enzymes that
digest macromolecules into monomers and then
absorb the small nutrient molecules into their cells.
Fungi are more similar to human cells than bacterial
cells.
Fungi are essential decomposers in most ecosystems.
The feeding structures of a fungus are a network of
threadlike filaments called hyphae. Hyphae branch
repeatedly as they grow, forming a mass called a
mycelium
The umbrellas that many recognize as fungi are
reproductive structures. The reproductive structures
are made up of hyphae.
Fungal hyphae are surrounded by a cell wall. Most
fungi, unlike plants, have cell walls made up of
chitin, a strong, flexible nitrogen-containing
polysaccharide, identical to the chitin found on the
exoskeletons of many arthropods.
In most fungi, the hyphae consist of chains of cells
separated by cross-walls (septum) that have pores large enough to allow ribosomes,
mitochondria, and even nuclei to flow from cell to cell.
Some fungi lack cross-walls entirely (coencytic) and have many nuclei within a single
mass of cytoplasm.
Fungi cannot run or fly in search of food, but their mycelium makes up for the lack of
mobility by being able to grow at a phenomenal rate, branching throughout a food
source and extending its hyphae into new territory.
Because a fungus's hyphae grow longer without getting thicker, the fungus develops a
huge surface area from which it can secrete digestive enzymes and through which it can
absorb food.
Some fungi are parasites, obtaining nutrients at the expense of living plants or animals.
Many parasitic fungi have hyphae called haustoria that penetrate their host.
Plants are more susceptible to fungal infections than animals.
The general term for a fungal infection is called mycosis.
A popular human fungal infection is athlete's foot.
Some fungi live symbiotically with other organisms.
Of special significance is the symbiosis between fungi and plant roots called a
mycorrhiza. Mycorrhizae absorb phosphorus and other essential minerals from the
soil and make them available to the plant. Sugars produced by the plant through
photosynthesis nourish the fungus, making the relationship mutually beneficial.
Lichens is a mutualistic association between fungi and algae. the algae, which is
usually a chlorophyta or cyanobacteria, provides sugar from photosynthesis. If the
algae is nitrogen-fixing, then nitrogen is also provided. The fungus, which is most
often an ascomycete, provides water and protection from the environment. Some
fungi produce pigments that shield algae from UV radiation or excess light.

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Fungi produce spores in both asexual and sexual life cycles
Fungal reproduction typically involves the release of vast numbers of haploid spores,
which are transported over great distances by wind or water. A spores that lands in a
most place where food is available germinates and produces a new haploid fungus.
Spores can be produced sexually or asexually.

Sexual reproduction:
In many fungi, sexual reproduction involves mycelia of different mating types.
Hyphae from each mycelium release signaling molecules that grow toward
eachother.
(1) When the hyphae meet, their cytoplasms fuse. This stage is called plasmogamy.
But this fusion of cytoplasm is often not followed immediately by the fusion of
parental nuclei. Thus, many fungi have what is called a heterokaryotic stage, in
which cells contain two genetically distinct haploid nuclei. A pair of haploid nuclei
one from each strain, is called a dikaryon.
(2) Hours, days, or even centuries may pass before the parental nuclei fuse, forming
the usually short-lived diploid phase. This stage is called karyogamy.
(3) Zygotes undergo meiosis, producing haploid spores.
Asexual reproduction:
(4) In asexual reproduction, spore-producing structures arise from haploid mycelia
that have undergone neither a heterokaryotic stage nor meiosis. There are two types
of asexual spores:
Sporangiospores are produced in sack-like capsules called sporangia that are
born on a stalk called a sporangiophore.
Conidia are formed at the tips of specialized hyphae, not enclosed inside sacks.
Hyphae bearing conidia are called conidiophores.
Two general types of asexual reproduction:
fragmentation of the hyphae and regeneration
budding the pinching off a small hyphal outgrowth
Many fungi that reproduce sexually can also produce asexually.
Asexual reproduction is the only known means of spore production in some fungi,
informally known as imperfect fungi, formally known as Duteromycota. No sexual
reproduction takes place.
The term mold refers to any rapidly growing fungus that reproduces asexually by
producing spores, often at the tips of specialized hyphae.
The term yeast refers to any single-celled fungus. Yeast typically reproduces
asexually by budding.

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Fungi are classified into five groups

The chytrids, the only fungi with flagellated spores, are thought to represent the earliest
lineage of fungi.
Common in lakes, ponds, and soil.
The zygomycetes, or zygote fungi, are characterized by their protective
zygosporangium, where zygotes produce haploid spores by meiosis.
Example: bread mold
Lack septa, except when filaments border reproductive filaments.
The glomeromycetes form a distinct type of mycorrhiza in which hyphae invade plant
roots branch into tiny treelike structures known as arbuscules.
Lack septa, but do not produce zygospores.
Occur only in mutualistic associations with roots of plants
About 90% of all plants have symbiotic partnerships with glomeromycetes as
mycorrhizae.
The ascomycetes, or sac fungi, are named for sack-like structures called asci (plural:
ascus) that produce spores in sexual reproduction.
Example: yeast
Have septa and reproduce sexually by producing haploid ascospores.
After plasmogamy of hyphae from unlike strains, a dikaryotic hypha produces more
filaments by mitosis.
Karyogamy and meiosis subsequently occur in terminal hyphal cells producing 4
haploid cells.
These 4 cells divide by mitosis to produce 8 haploid ascospores in a sac called an
ascus. 8 ascospores grouped together into fruiting bodies called ascocarps.
Basidiomycetes, or club fungi are named after their club-shaped, spore-producing
structure called a basidium.
Example: mushrooms
Many species excel at breaking down the lignin found in wood and thus play key
roles as decomposers.
Plasmogamy between two unlike hyphae is followed by mitosis and the growth of
dikaryotic hyphae to form a fruiting body is called a basidiocarp.

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Fungal groups differ in their life cycles and reproductive stages
Life cycle of Zygomycetes
As hyphae grow with food, the fungus produces asexually, forming spores in
sporangia at the tips of upright hyphae. When the food is depleted, the fungus
reproduces asexually
(1) Hyphae from mycelia of different mating types fuse
(2) Produce a cell containing multiple nuclei from two parents
(3) This young zygosporangium develops into a thick-walled structure that can
tolerate dry or harsh environments
(4) When conditions are favorable, the parental nuclei fuse to form diploid zygotes,
which undergo meiosis, producing haploid spores called zygospores.

Life cycle of Basidiocarps

(1) The heterokaryotic stage begins when hyphae of two different mating types fuse
(2) The fusion creates a heterokaryotic mycelium, which grows and produces the
mushroom.
(3) In the club shaped cells called basidia, which line the gills of a mushroom, the
haploid nuclei fuse, forming diploid nuclei. Each diploid then undergoes meiosis,
forming haploid spores called basidiospores.
(4) A mushroom can release as many as a billion spores.
(5) If spores land on moist matter that can serve as food, they germinate and grow
into haploid mycelia.

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Animal evolution and diversity

What is an animal?
Animals are multicellular, heterotrophic eukaryotes that (with a few exceptions) obtain
nutrients by ingestion. Animals' dominant generation in the life cycle is the diploid
generation. Most are motile during at least some point in the life cycle. Lastly, all
animals undergo a period of embryonic development during which 2-3 layers of tissue
form.
Ingestion means eating food. This mode of nutrition contrasts animals with fungi.
Animals digest food within their body after ingesting other organisms.
Animal cells lack cell walls that provide strong support in the bodies of plants and
fungi. They are held together by extracellular structural proteins, the most abundant
of which is collagen, and by unique types of intercellular junctions.
All but the simplest animals have muscle cells for movement and nerve cells for
conducting impulses.
Other unique features are seen in animal reproduction and development. Most
animals are diploid and reproduce sexually; eggs and sperms are the only haploid
cells.
General life cycle of an animal:
(1) male and female adults make haploid gametes by meiosis
(2) an egg and sperm fuse, producing a zygote
(3) the zygote divides by mitosis
(4) division of the zygote forms an early embryonic stage called a blastula
(5) in the sea star and most other animals, one side of the blastula folds inward,
forming a gastrula
(6) Gastrulation causes the endoderm, ectoderm, and mesoderm to form.
(7) After the gastrula stage, many animals develop directly into adults. Others (such
as the sea star shown in the picture) develop into one or more larval stages at first.
A larva is an immature individual that looks different from the adult animal.
(8) The larva undergoes a major change of body form, called metamorphosis, in
becoming and adult capable of reproducing sexually.

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Animal diversification began more than half a billion years ago
The lineage that gave rise to animals is thought to have diverged from a flagellated
unikont ancestor more than 1 billion years ago.
Animal diversification appears to have accelerated rapidly from 535-525 million years
ago, during the Cambrian period. Because many animal body plans and new phyla
appear in the fossils from such an evolutionarily short time span, biologists call this
episode the Cambrian explosion.
Scientists are not sure what caused the Cambrian explosion.
Of the 35 or so animal phyla, all of the animals in all but one phylum are invertebrates.
Invertebrates lack a vertebral column (backbone).
Animals can be characterized by basic features of their body plan
Symmetry: Animals can have radial symmetry, the type of symmetry found in a
flowerpot. There is a top and bottom side, but not front, back, left, or right sides. Other
animals have bilateral symmetry, the type of
symmetry found in a shovel. Have 2 axes of
orientation: front to back and top to bottom. Have
a dorsal (top) side and a ventral (bottom) side, a
left and a right side, an anterior (front) end and a
posterior (back) end.
The symmetry of an animal reflects its
lifestyle. A radial animal is typically sedentary
or passively drifting, meeting its environment
equally on all sides. In bilaterally symmetric animals, the brain, sense organs, and
mouth are usually located in the head. This arrangement facilitates mobility.
The animal phyla that have bilateral symmetry belong to the clade called
bilaterians.
Body plans also vary in the organization of tissues. Most animals, collectively called the
eumetazoa, have closely functioning cells organized into tissues. They have two
(diplopblastic) or three (triploblastic) layers of tissue called germ layers. In another
group of animals, the parazoa, cells are not
organized into true tissues, and organs do not
develop.
Animals arising from embryos may be
characterized by the presence or absence of a
body cavity. A body cavity is a fluid-filled space
between the digestive tract and outer body wall
cushions the internal organs and enables them to
grow and move independently of the body wall.
In soft-bodied animals, a noncompressible fluid
in the body forms a hydrostatic skeleton that
provides a rigid structure against which muscles
contract, moving the animal.
During embryonic development in more
advanced animals, a body cavity called a coelom
develops from tissue derived from the
mesoderm. The fluid-filled coelom cushions the
internal organs and allows for their expansion
and contraction. Acoelomate animals lack a
coelom, while pseudocoelomate animals have a

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cavity that is not completely lined by mesodermderived tissue.
Two markedly different cleavage patterns occur to
produce two groups of animals, the protostomes and
duterostomes.
Protostomes have spiral, determinate cleavages.
Solid masses of the mesoderm split and form the
coelom. The blastopore turns into the mouth.
Duterostomes have radial and indeterminate
cleavages. Folds of the archentron form the
coelom. The anus develops from the blastopore.
Cephalization is a trend whereby nervous tissue,
over many generations, becomes concentrated toward
one end of an organism. This process eventually
produces a head with sensory organs. In animals with
bilateral symmetry, there is a progressively greater
increase in nerve tissue concentration at the anterior
end as organism increase in complexity.
The digestive systems of animals vary. Simpler clades have a gastrovascular cavity: a
central body cavity in the sacklike body of certain animals that functions in both the
digestion and distribution of nutrients. An
alimentary canal, which is found in more
developed clades, is a digestive tract consisting
of a tube running between a mouth and an anus
(food goes in the mouth and out of the anus).
Alimentary canals are also organized into
specialized compartments that carry out digestion
and nutrient absorption stepwise.
Many animals have segmented body parts. A segmented boy allows for greater
flexibility and mobility, and it
probably evolved as an
adaptation facilitating
movement. In some cases, the
body parts are the same and
repeat, while in other cases the
body parts are modified and
adopt specialized functions.
The body plans of animals can be
used to build phylogenetic trees
Because animals diversified so
rapidly on the scale of geologic
time, it is difficult to sort out the
evolutionary relationships
among the various phyla using
only the fossil record. The
picture to the right represents a
morphology-based phylogenetic
tree of the major phyla of the
animal kingdom.

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Invertebrate Diversity
Sponges have a relatively simple, porous body
Sponges (phylum Porifera) are the simplest of all animals. They have no nerves or
muscles, though their individual cells can sense and react to changes in the environment.
Most sponges lack body symmetry, although some are radially symmetric.
Sponges have no respiratory system, circulatory system, excretory system.
Reproduce asexually (budding) or sexually (sponges are hermaphrodites).
Does not have coelom.
A simple sponge resembles a thick-walled sac perforated with holes. Water enters
through the pores into a central cavity, then flows out through a larger opening called the
osculum.
The body of a sponge consists of two layers of cells separated by a gelatinous region.
Since the cell layers of sponges are loose associations of cells, they are not considered
true tissues and are classified with parazoa.
The inner cell layer consists of flagellated collar cells called choanocytes, which
help to sweep water through the sponge's body.
Amoebocytes, which wander through the middle body region, produce supportive
skeletal fibers composed of a flexible protein called spongin and mineralized
particles called spicules made up of CaCO3 or SiO2.
Sponges are examples of suspension feeders, animals that collect food particles from
water passed through some type of food-trapping equipment.
Choanocytes trap food particles in mucus on the membranous collars that surround
the base of their flagella and then engulf the food by phagocytosis. Amoebocytes
pick up food packaged in food vacuoules from choanocytes, digest it, and carry the
nutrients to other cells.
Adult sponges are sessile, meaning they are anchored in placethey cannot escape from
predators.
Sponges produce defensive compounds such as toxins and antibiotics to deter
pathogens, parasites, and predators.

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Cnidarians are radial animals with tentacles and stinging cells
Cnidarians (e.g., hydras, sea anemones, corals, and jellies) are characterized by radial
symmetry and bodies arising from two tissue layers (diploblastic).
The simple body of most cnidarians has an outer epidermis and an inner cell layer that
lines the digestive cavity. A jelly-filled middle region may contained scattered amoeboid
cells.
Have no respiratory system, excretory system, or circulatory system. Does not have
coelom.
Contractile tissues and a nerve net occur in their simplest forms in cnidarians.
Undergoes asexual or sexual reproduction.
Cnidarians exhibit two kinds of radially symmetric body forms.
A polyp (found in Hydras) is a sessile, cylinder-shaped body with rising tentacles.
A medusa (found in jellyfish) is a floating, umbrella-shaped body with dangling
tentacles.
Cnidarians are carnivores that use their tentacles to capture small animals and protists
and to push the prey into their mouths.
Cnidarians have a gastrovascular cavity for digestion and absorption of nutrients.
The fluid of the gastrovascular cavity also acts as a hydrostatic skeleton, supporting the
body and helping to give cnidarians its typical shape.
Phylum Cnidaria is named for its unique stinging cells, called cnidocytes, that function
in defense and capturing prey.
Each cnidocyte contains a fine thread coiled within a capsule. The stinging organelle
is called a nematocyst. When it is discharged, the thread can sting or entangle prey.

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Flatworms are the simplest bilateral animals
Flatworms, phylum Platyhelminthes, are the simplest of the bilaterians with
cephalization.
Most Flatworms have a gastrovascular cavity with only one opening. Fine branches
of the gastrovascular cavity distribute food throughout the animal.
Triploblastic, acoelomates, eumetazoa
Nervous system: two nerve cords, anterior centralized ganglia (brain)
No circulatory system and no respiratory system
Excretory system consists of protonephridia and flame cells.
Reproduction: asexual (fragmentation and regeneration) or sexual (hemaphroditism)
Three major groups of flatworms:
Free-living flatworms (planatians) has a head with a pair of light-sensitive eyecups
and a flap at each side that detects chemicals. Dense clusters of nerve cells form a
simple brain, and a pair of nerve cords connect with small nerves that branch
throughout the body. When a planarian feeds, it sucks food through the mouth at the
tip of a muscular tube that projects from the mid-ventral surface of the body. Crawl
using cilia.
Flukes live as parasites in other animals. Many flukes have suckers that attach to
their host and a tough protective opening. Many flukes have complex life cycles that
facilitate dispersal of offspring to new hosts. Larvae develop in an intermediate host.
The larvae then infect the final host in which they live as adults.
Tapeworms are another parasitic group of flatworms. They inhabit the digestive
tract of vertebrates. They absorb nutrients across their body surface and have no
digestive tract. Because of this adaptation to their parasitic lifestyle, tapeworms are
an exception to the original definitions of animal; other animals ingest nutrients.
Have segments called proglottids but are not considered true segments because
they only develop secondarily for reproduction. Like flukes, tapeworms have a
complex life cycle, usually involving one or more hosts. They take advantage of
predator-prey relationships of their hosts.
The term worm is commonly applied to any slender, elongated invertebrate.

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Nematodes have a pseudocoelom and a complete digestive tract
Nematodes, also called roundworms, make up the phylum Nematoda.
Free-living or parasitic.
Free living soil dwellers help decompose and recycle nutrients
Nematodes are responsible for trichinosis in humans, when ingested via
incompletely cooked meat.
Nervous system: nerve chord and ring
No respiratory and excretory systems
Not segmented
As bilaterians, these animals have bilateral symmetry and as an embryo with three
layers (triploblastic, eumetazoa).
Roundworms have a fluid-filled body cavity (a pseudocoelom, not completely lined
with mesoderm) and a digestive tract with two openings (alimentary canal). The
fluid in the pseudocoelom helps distribute nutrients absorbed by the digestive system
throughout the body. It also functions as a hydrostatic skeleton.
Nematodes are cylindrical with a blunt head and a tapered tail. Several layers of tough,
nonliving material called a cuticle cover the body and prevent the nematode from drying
out. In parasitic species, the cuticle protects the nematode from the host's digestive
system.
When the worm grows, it periodically sheds it cuticle (molts) and secretes a new, larger
one.

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Phylum Rotifera
Rotifers are aquatic organisms. Some are benthic (living at the bottom) but most are
free-living in fresh water.
Bilateral, triploblasts, eumetazoa
No circulatory and respiratory systems
Digestive system: alimentary canal with mouth and anus
Nervous system: cerebral ganglia (brain) with some nerves extending through the body
Their body is spherical or cylindrical, ending in a bifurcate foot.
The anterior part is modified to a ciliary organ, the corona or wheel organ.
Body cavity is a pseudocoelom.
The pharynx is armed with jaws (the mastax); complete digestive system. Rotifers are
filter-feeders.
Excretory system consists of protonephridia and flame cells.
Sexes are dioecious, meaning there are distinct male and female individual organisms.
The male is generally smaller than the female.
Parthenogenesis is common.

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Diverse molluscs are variations on a common body plan
Slugs, snails, oysters, clams, octopuses, and squids are just a few of the great variety of
animals known as molluscs.
Molluscs are soft-bodied animals, but most are protected by a hard shell.
Basic body plan of a mollusc:
A muscular foot which functions
in locomotion.
A visceral mass containing most
of the internal organs.
The main body cavity is a
hemocoel, through which blood
circulates.
A mantle, a fold of tissue that
drapes over the visceral mass and
secretes a shell in molluscs such
as clams and snail. Made up of
CaCO3.
In many molluscs, the mantle
extends beyond the visceral
mass, producing a water-filled
chamber called the mantle
cavity, which houses the gills.
A radula is a unique rasping organ that is used to scrape up food.
Most molluscs have separate sexes, with reproductive organs located in the visceral
mass.
The life cycle of many marine molluscs includes a ciliated larva called a
trochophore.
Molluscs have a true coelom and a mainly open circulatory system.
Nervous system: ventral nerve chords and brain
Respiratory system: gills
Digestive system: alimentary canal with mouth, anus, and radula
Excretory system: Nephridia
Embryonic development: Protostome
Three diverse groups of molluscs:
The largest group of molluscs is called the gastropods, found in fresh
water, salt water, and terrestrial environments. Most gastropods are protected by a
single, spiraled shell into which the animal can retreat when threatened. Many
gastropods have a distinct head with eyes at the tips of tentacles.
The bivalves include numerous species of clams, oysters, mussels, and scallops.
They have shells divided into two halves that are hinged together. Most bivalves are
suspension feeders. The mantle cavity contains gills that are used for feeding as well
as gas exchange. Most bivalves are sedentary, living in sand or mud.
The cephalopods differ from gastropods and bivalves in being adapted to the
lifestyle of fast, agile predators. Cephalopods use break-like jaws and a radula to
crush or rip prey apart. The mouth is at the base of the foot, which his drawn out into
several long tentacles for catching and holding prey. All cephalopods have large
brains and sophisticated sense organs that contribute to their success as mobile
predators.

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Annelids are segmented worms
A segmented body resembling a series of fused rings is the hallmark of phylum
Annelida. An earthworm, a typical annelid, uses its flexible, segmented body to crawl
and burrow rapidly into the soil.
They are found in damp soil, in the sea, and in most freshwater habitats. Most are
bottom-dwelling scavengers that burrow in the sand and mud.
Triploblasts, eumetazoa, protostome, no respiratory system
Three main groups of annelids:
Earthworms and their relatives. The picture below shows the segmented anatomy
of an earthworm.
Internally, the coelom is partitioned by membrane walls.
Many of the internal body structures are retreated within each segment.
The nervous system includes a simple brain and a ventral nerve cord with a
cluster of nerve cells in each segment.
Have metanephridia as excretory organs.
The digestive tract (alimentary canal) is not segmented; it passes through the
segment walls from the mouth to anus.
Have a closed circulatory system. The main vessels of the earthworm circulatory
systema dorsal blood vessel and a ventral blood vesselare connected by
segmental vessels. The heart is simply an enlarged region of the dorsal blood
vessel plus five pairs of segmental vessels on the anterior end.
Earthworms move by coordinating the contraction of longitudinal and circular
muscles. These muscles work against the coelomic fluid in each segment, which
acts as a hydrostatic skeleton.
Are hermaphrodites but they don't fertilize their own eggs.

Polychaetes
The polychaetes, which are mostly marine, form the
largest group of annelids.
They live in tubes and extend feathery appendages coated
with mucus that trap suspended food particles. Freeswimming polychaetes travel in the open ocean by
moving their paddle-like appendages on each segment.

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In polychaetes, stiff bristles on the appendages help the worm wriggle about in
the search of small invertebrates to eat. In many polychaetes, the appendages are
richly supplied with blood vessels and are either associated with the gills or
function as gills themselves.
The third main group of annelids is the leeches, which hare notorious for their
bloodsucking habits. Most species are free-living carnivores that eat small
invertebrates such as snails and insets.

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Arthropods are segmented animals with joined appendages and an exoskeleton
Over a million species of arthropods have been identified. The diversity and success of
arthropods are largely related to their segmentation, their hard exoskeleton, and their
jointed appendages.
The appendages are variously adapted for sensory reception, defense, feeding,
walking, and swimming.
The arthropod body, including the appendages, is covered by an exoskeleton, an
external skeleton that protects the animals and provides points of attachment for the
muscles that move appendages. The exoskeletons
in arthropods is a cuticle, a nonliving covering in
arthropods that is hardened by layers of protein
and chitin, a polysaccharide.
As it grows, an arthropod must periodically
shed its old exoskeleton and secrete a larger
one, a complex process called molting.
The body of most arthropods arises from several
distinct groups of segments that fuse during
develop: the head, the thorax, and the abdomen.
In some arthropods (i.e. the lobster), the
exoskeleton of the head and the thorax is partly
fused, forming a body region called the
cephalothorax. Each segment group is
specialized for a different function.
Arthropods have an open circulatory system.
Nervous system: fused ganglia, ventral nerve cord
Bilateral, triploblastic, eumetazoa, protostome, coelomate
Excretory system: malphagian tubules
Respiratory system: varies between spiracles and tracheal tubes, book lungs, and gills
Four major groups of arthropods:
Chelicerates are marine organisms that were abundant in the sea some 300 million
years ago. Living chelicerates include the scorpions, spiders, ticks, and mites,
collectively called arachnids. Most arachnids live on land. Use trachea or book
lungs for respiration.

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Millipedes are wormlike terrestrial creatures that eat decaying plant matter. They
have two pairs of short legs per body segment. Centipedes are terrestrial carnivores
with a pair of poison claws used in defense and to paralyze prey. Each of their body
segment bears a single pair of long legs.
Crustaceans are nearly all aquatic. Lobsters, crayfish, barnacles, crabs, and shrimps
are part of this group. Use gills to breathe.

Insects are the most diverse group of animals on the planet, comprising over 70% of
all animal species. They are distributed worldwide and have a remarkable ability to
survive challenging environments.
Use spiracles and tracheal tubes to breathe.
What characteristics account for the success of insects? They have shared
features with other arthropods (segmented body, exoskeleton, joined
appendages), flight, a waterproof coating on the cuticle, a complex life cycle,
short generation times, and large numbers of offspring.
Life cycles: More than 80% of insect species undergo complete
metamorphosis. The larval stage is specialized for eating and growing. A larva
typically molts several times as it grows, then exists as an encased, nonfeeding
pupa while its body grows. The inset emerges as an adult that is specialized for
reproduction and dispersal. Other inspect species undergo incomplete
metamorphosis, in which the transition from larva to adult is achieved through
multiple molts, but without forming a pupa.

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Modular body plan: like other arthropods, insects have specialized body regions
a head, thorax, and an abdomen. These regions arise from the fusion of
embryonic segments during development. The insect body plan is essentially
modular: each embryonic segment is a separate building block that develops
independently of other segments. As a result, a mutation that changes homeotic
gene expression can change the structure of one segment or its appendages
without affecting any of the others. This explains much of the extraordinary
diversification that is observed in insects. Head typically bears a pair of sensory
antennae, a pair of eyes, and several pairs of mouthparts. The mouthparts are
adapted for particular kinds of eating. As a result of the variety in mouthparts,
insects have adaptations that exploit almost any conceivable food source. Most
adult insects have three pairs of legs, which may be adapted for any type of
locomotion basically. Insects learned to fly without sacrificing any legs because
wings are extensions of the cuticle.
Protective color patterns: In many groups of insects, adaptations of body
structures have been coupled with protective coloration (camouflage, mimicry,
aposematic coloring).

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Echinoderms have spiny skin, an endoskeleton, and a water vascular system for movement
Echinoderms, such as sea stars, sand dollars, and sea urchins, are slow-moving or
sessile marine animals.
Exhibit bilateral symmetry as larvae but then radial symmetry as an adult.
Triploblast, eumetazoa, coelomate
open circulatory system with no heart
nervous system: nerve ring and radial nerves
no respiratory system and no excretory system
digestive: alimentary canal with mouth and anus
Have prickly bumps or spines. They are extensions of the hard calcium-containing
plates that form the endoskeleton, or internal skeleton, under the thin skin of the animal.
Unique to echinoderms is the water vascular system, a network of water-filled canals
that branch into extensions called tube feet, which function in locomotion, feeding, and
gas exchange.
A sea star pulls itself slowly over the seafloor using its suction-cup-like tube feet.
When it encounters prey, it grips the prey with its tube feet.
Some echinoderms such as sea stars are capable of regeneration.
Though echinoderms have many unique features, we see evidence of their relation to
other animals in their embryonic developments. They are duterostomes, meaning that
they are more closely related to humans than any other protostome phylum.

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Our own phylum, Chordata, is distinguished by four features
4 unique features of chordates:
(1) a dorsal, hollow nerve cord
(2) a notochord, a flexible, supportive, longitudinal rod located between the
digestive tract and the nerve cord
(3) pharyngeal slits located in the pharynx, the region just behind the mouth
(4) a muscular post-anal tail (a tail posterior to the anus)
Body segmentation is also a chordate characteristic.
Two main groups of invertebrate chordates (have been extensively studied to examine
the origin of vertebrates):
Adult tunicates are stationary and look more like small sacs. They often adhere to
rocks and boats, and are common on coral reefs. Has no trace of a notochord, nerve
cord, or tail, but it does have prominent pharyngeal slits that function in feeding. The
tunicate larva, however, is a swimming, tadpole-like organism that exhibits all four
distinctive chordate features. They are suspension feeders. Tunicates likely represent
the earliest branch of the chordate lineage.
Lancelets, another group of marine invertebrate chordates, also feed on suspended
particles. They are small, blakelike chordates that live in marine sands. They clearly
illustrate all four chordate features throughout their lives, unlike tunicates.
Vertebrate chordates will be discussed in the next chapter.

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Derived characters define the major clades of chordates

Here is the proposed phylogeny for phylum Chordata:

The tunicates are thought to be the first group to branch from the chordate lineage.
Unlike tunicates, all other chordates have a brain, albeit a small one in the lancelets (only a
swollen tip of the nerve cord).
The next transition was the development of a head that consists of a brain at the anterior end
of the dorsal nerve cord, eyes and other sensory organs, and a skull. These innovations
opened up completely new way of feeding for chordates: active predation. All chordates
with a head are called craniates.
The origin of a backbone came next. The vertebrates are distinguished by a more extensive
skull and a backbone, or vertebral column, composed of a series of bones called
vertebrae. The vertebrae encloses the nerve cord.
The next major transition was the origin of jaws, which opened up new feeding
opportunities.
The evolution of lungs or lung derivatives, followed by muscular lobed fins with skeletal
support, opened the possibility of life on land.
Tetrapods, jawed vertebrates with two pairs of limbs, were the first vertebrates on land.
The evolution of amniotes, tetrapods with a terrestrially adapted egg, completed the
transition to land.
Hagfishes and lampreys lack hinged jaws
The two most primitive surviving craniates are hagfishes and lampreys. They have bilateral
symmetry, triploblasts, eumetazoa, coelomate, two chambered heart circulatory system,
complete brain, gills for breathing, and alimentary canal.
In hagfishes, the notochord is the body's main support in the adult. The notochord also
persists in the adult lamprey, but rudimentary vertebral structures are also present.

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Consequently, lampreys are considered vertebrates, but hagfishes are not.
Hagfishes scavenge dead or dying vertebrates on the cold, dark seafloor. Although nearly
blind, they have excellent senses of smell and touch. They feed by entering the animal
through an existing opening or by creating a hole using sharp, tooth-like structures on the
tongue that grasp and tear flesh.

Lamprey larvae resemble lancelets. They are suspension feeders that live in freshwater
streams, where they are buried in sediment. Most lampreys migrate to the sea or lakes as
they mature into adults. Most species of lamprey are parasites.

Jawed vertebrates with gills and paired fins include sharks, ray-finned fishes, and
lobe-finned fishes
Jawed vertebrates' success probably relates to their paired fins and tail, which
allowed them to swim after prey, as well as to their jaws, which enabled them
to catch and eat a wide variety of prey.
Hinged jaws are thought to have evolved by modification of skeletal supports
of the anterior pharyngeal (gill) slits.
Three lineages of jawed vertebrates with gills and paired fins are commonly
called fishes.

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All are triploblasts, eumetazoa, coelomates, have two chambered hearts, complete
brains, gills, and alimentary canals.
Class Chondrichthyes (sharks and rays)
Have a flexible skeleton made of cartilage.
Some sharks are suspension feeders while others are adept predators. Sharks and most
other aquatic vertebrates have a lateral line system, a row of sensory organs running
along each side that are sensitive to changes in water pressure and can detect minor
vibrations caused by animals swimming nearby. Bodies of sharks are streamlined for
swimming in the open ocean.
Rays are adapted for life on the bottom of the ocean. Their bodies are dorsoventrally
flattened, with eyes on the top of the head. The tails of stingrays bear sharp spines with
venom and glands at the base.

Class Actinopterygii (ray-finned fish)

In ray-finned fishes, which include tuna, trout, and
goldfish, the skeleton is made of bonecartilage
reinforced with a hard matrix of calcium phosphate.
Their fins are supported by thin, flexible skeletal
rays.
Most have flattened scales covering their skin that
secrete a coating of mucus that reduces drag during
swimming.
On each side of the head, a protective flap called an
operculum covers a chamber housing the gills.
Movement of the operculum allows the fish to
breathe without swimming.
Ray-finned fishes also have a lung derivative that
helps keep them buoyantthe swim bladder.
Class Sarcopterygii (lobe-finned fish)
The key derived character of the lobe-fins is a series of rod-shaped bones in their
muscular pectoral and pelvic fins.
A lineage of the lobed-finned fish, the tetrapods, were the first to adapt to life on land.

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Amphibians are tetrapodsvertebrates with two pairs of limbs

Amphibians include salamanders, frogs, and caecilians. They are bilateral, triploblasts,
eumetazoa, coelomates, have three chambered hearts, complete brains, gills, and alimentary
canals.
Most amphibians are found in damp habitats, where their most skin supplements their lungs
for gas exchange.
Amphibian skin usually has poison glands that may play a role in defense.
Many amphibians live a double life. For example, frogs spend much of its time on land,
but lay their eggs in water. Eggs are encapsulated in a jellylike material so they must be
surrounded by moisture to prevent them from drying out.
The larval stage, called a tadpole, is a legless, aquatic algae-eater with gills, a lateral line
system, and a long, finned tail. In changing into a frog, the tadpole undergoes a radical
metamorphosis.
Not all amphibians live such a double life; some are strictly terrestrial and some are strictly
aquatic.
The term toad is a term generally used to refer to frogs that have rough skin and live
entirely in terrestrial habitats.
Amphibians were the first vertebrates to colonize the land. However, the distribution of
amphibians was limited by their vulnerability
to dehydration.

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Reptiles are amniotestetrapods with a terrestrially adapted egg

Reptiles, birds, and mammals are amniotes. The major derived character of this clade is the
amniotic egg. The amniotic egg contains specialized extraembryonic membranes, so called
because they are not part of the embryo's body. The amnion is a fluid-filled sac surrounding
the embryo.
The clade of amniotes called reptiles includes lizards, snakes, turtles, crocodilians, birds,
and dinosaurs. They are bilateral, triploblasts, coelomates, have three chambered hearts,
complete brains, lungs, and alimentary canals.
Lizards are the most numerous and diverse reptiles other than birds.
Reptiles have several other adaptations other than the amniotic egg for terrestrial living not
found in amphibians.
Reptilian skin, covered with scales waterproofed with the tough protein keratin, keeps
the body from drying out.
Reptiles cannot breathe through their dry skin and obtain most of their oxygen with their
lungs, using their rib cage to help ventilate lungs.
Many reptiles are cold-blooded because they do not use their metabolism to produce
body heat. They regulate temperature through their behavior. A better term than coldblooded is ectothermic, meaning they absorb external heat rather than generating
much of their own.

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Birds are feathered reptiles with adaptations for flight

Almost all birds can fly, and nearly every part of a bird's body reflects adaptations that
enhance flight. The forelimbs have been remodeled as feather-covered wings that act as
airfoils, providing lift and maneuverability in the air. Large flight muscles anchored to a
central ridge along the breastbone provide power. Few birds are flightless (i.e. ostrich).
They are bilateral, triploblasts, eumetazoa, coelomates, have four chambered hearts,
complete brains, lungs, and alimentary canals.
Many features help reduce weight for flight:
birds lack teeth
their tail is supported by only a few small vertebrae
their feathers have hollow shafts
their bones have a honeycombed structure
Flying requires a great amount of energy and birds have a high rate of metabolism. Highly
efficient circulatory systems help support the high metabolic rate. They are endothermic,
using heat generated by metabolism to maintain a warm, steady body temperature.
Insulating feathers help to maintain their warm body temperature.
Birds have excellent eyesight to aid flight.
Birds typically display very complex behaviors, particularly during breeding seasons.
Courtship often involves elaborate rituals.
Strong evidence indicates that birds evolved from a lineage of small, two-legged dinosaurs
called theropods.

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Mammals are amniotes that have hair and produce milk

Two featureshair and mammary glands that produce milkare the distinguishing traits of
mammals. They are bilateral, triploblasts, eumetazoa, coelomates, have four chambered
hearts, complete brains, lungs, and alimentary canals.
Like birds, mammals are endothermic. Hair provides insulation that helps maintain a warm
body temperature.
Efficient respiratory and circulatory systems (including a four-chambered heart) support the
high rate of metabolism characteristic of endotherms.
Differentiation of teeth adapted for eating many kinds of foods is also characteristic of
mammals.
Other than the platypus, all mammals are born rather than hatched. During development, the
embryos remain inside the mother and receive their nourishment directly from her blood.
Mammalian embryos produce extraembryonic membranes that are homologous to those
found in the amniotic egg. Membranes from the embryo join with the lining of the uterus to
form a placenta, a structure in which nutrients from the mother's blood diffuse into the
embryo's blood.
Three major lineages of mammals: monotremes, marsupials, and eutheriansdiffer in
reproductive patterns.
The only existing egg-laying mammals, known as monotremes, are echidnas (spiny
anteaters) and the duck-billed platypus.
Marsupials have a brief gestation and give birth to tiny, embryonic offspring that
complete development while attached to the mother's nipples. The nursing young are
usually housed in an external pouch.
Eutherians are mammals that bear fully developed live young. They are commonly
called placental mammals because their placentas are more complex than those of
marsupials, and the young complete their embryonic development in the mother's uterus
attached to the placenta.

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Plant structure and function

The two major groups of angiosperms are the monocots and eudicots
Plant biologists have traditionally placed most angiosperms into two groups, called
monocots and eudicots. The names monocot and eudicot refer to the first leaves on the
plant embryo. These embryonic leaves are called seed leaves, or cotyledons. Cotyledons
provide nutrition
A monocot embryo has one seed leaf (one cotyledon); a dicot embryo has two seed
leaves (two cotyledons).
The great majority of dicots, called the eudicots (true dicots), are evolutionarily
related, having diverged from a common ancestor about 125 million years ago; a few
smaller groups of dicots have evolved independently. In this unit, we will focus on
monocots and eudicots.
Monocots and eudicots vary over four other characteristics:
Leaf venation the pattern of veins in leaves. Eudicots have a netted, branching,
venation pattern whereas monocots have a parallel venation pattern.
Flower parts numbers of petals, sepals, stamens, and other flower parts. Eudicots
are in 4s, 5s, or multiples thereof whereas monocots are in 3s or multiples thereof.
Vascular bundles arrangement of bundles of vascular tissue (xylem and phloem)
in stems. Eudicots are organized in a circle whereas monocots are scattered.
Root form of root. Eudicots have taproots (a large, single root), whereas monocots
have a fibrous system (A cluster of many fine roots)

A typical plant body contains three basic organs: roots, stems, and leaves
Plants, like most animals have organs comprised of different tissues, which in turn are
composed of one or more cell types. An organ consists of several types of tissues that
together carry out a particular function.
A plant's root system anchors it in the soil, absorbs and transports minerals and water,
and stores food.
Near the root tips, a vast number of tiny tubular projections called root hairs
enormously increase the root surface area for absorption of water and minerals.
Each root hair is an extension of an epidermal cell (a cell in the outer layer of the

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root). As the plant gets older, root hairs die. New epidermal cells form, which will
form new root hairs. Therefore, roots must constantly grow to provide new root hairs
for the absorption of water. The older epidermal cells protect the root.
The shoot system of a plant is made up of stems, leaves, and adaptations for
reproduction, which in angiosperms are the flowers.
The stems are the parts of the plant that are generally above ground and support and
separate the leaves (thereby promoting photosynthesis) and flowers. A stem has
nodes, the points at which leaves are attached, and internodes, the portions of the
stem between nodes.
The leaves are the main photosynthetic organs in most plants, although green stems
also perform photosynthesis. Most leaves consist of a flattened blade and a stalk, or
petiole, which joins the leaf to a node of the stem.
The two types of buds are undeveloped shoots.
When a plant stem is growing in length, the terminal bud (also called the apical
bud), at the apex (tip) of the stem has developing leaves and a compact series of
nodes and internodes.
The axillary buds, one in each of the angles formed by a leaf and the stem, are
usually dormant.
In many plants, the terminal bud produces hormones that inhibit the growth of
axillary buds, a phenomenon called apical dominance (more on this later).
By concentrating resources on growing taller, apical dominance is an evolutionary
adaptation that increases the plant's exposure to light. However, branching is also
important for increasing the exposure of the shoot system to the environment, and
under certain conditions, the axillary buds begin growing.

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Many plants have modified roots, stems, and leaves
The plant's three basic organsroots, stems, and leaveshave become
adapted for a variety of functions.
Certain plants (monocots) have unusually large taproots that store food in
the form of carbohydrates such as starch. The plants consume the stored
sugars during flowering and fruit production.
Examples of modified stems:
The strawberry plant has a horizontal stem called a stolon that grows
along the ground. Stolons enable a plant to reproduce asexually, as
plantlets form at nodes along their length.
Rhizomes are horizontal stems that grow near the soil surface. They store
food and, having buds, can also form new plants.
A potato plant has rhizomes that end in enlarged structures specialized for storage
called tubers.
Cacti have modified leaves that protect the plant from being eaten by animals. The
main part of the cactus is the stem, which is adapted for photosynthesis and water

Examples of modified leaves:

Grasses and many other monocots have long leaves without petioles.
Some eudicots, such as celery, have enormous petioles.
Some plants have a modified leaf called a tendril, with its tips coiled around a
support structure. Tendrils help plants climb.

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Three tissue systems make up the plant body
Organs of plants contain tissues; a tissue is a group of cells that perform a specialized
function.
The dermal tissue system is the plant's outer protective covering. It forms the first line
of defense against physical damage and infectious organisms like our skin.
In many plants, the dermal tissue system consists of a single layer of tightly packed
cells called the epidermis. The epidermis of leaves and most stems has a waxy
coating called the cuticle, which helps prevent water loss. The cuticle is made up of
a waxy material called cutin.
Roots do not have a cuticle because having a cuticle would prevent them from
absorbing water.
The second tissue system is the vascular tissue system. Made up of of the xylem and
phloem.
Xylem tissue contains water-conducting cells that convey water and dissolved
minerals upward from roots.
Phloem tissue contains cells that transport sugars and other organic nutrients from
leaves or storage tissues to other parts of the plant.
Tissues that are neither dermal nor vascular make up the ground tissue system. It
accounts for most of the bulk of a young plant, filling the spaces between the epidermis
and vascular tissue system.
Ground tissue internal to vascular tissue is called pith, and ground tissue external to
the vascular tissue is called cortex.
Ground tissue has diverse functions, including photosynthesis, storage, and support.
The picture on the next page shows how the three tissue systems are organized in typical
plant roots, stems, and leaves.
The views at the bottom left shows in cross section the three tissue systems in a young
eudicot root.
Water and minerals that are absorbed from the soil must enter through the epidermis.
In the center of the root, the vascular tissue system forms a vascular cylinder, with
the cross sections of xylem cells radiating from the center like the spokes of a wheel
and phloem cells filling in the wedges between the spokes. The outer part of the
vascular cylinder consists of one to several layers of cells called the pericycle, from
which lateral roots arise.
The ground tissue system of the root, the region between the vascular cylinder and
the epidermis, consists entirely of cortex. The cortex cells store food as starch and
take up minerals that have entered the root through the epidermis. The innermost
layer of the cortex is the endodermis, a cylinder one cell thick. It is a selective
barrier, determining which substances pass between the rest of the cortex and the
vascular tissue.
The bottom right of the picture shows a cross section of a young monocot root.
Like eudicots, the monocot root has an outer layer of epidermis (dermal tissue),
surrounding a large cortex (ground tissue), with a vascular cylinder (vascular tissue)
at the center surrounded by the pericycle.
But in a monocot root, the vascular tissue consists of a central core of cells (pith)
surrounded by a ring of xylem and a ring of phloem.
As the center of the picture indicates, the young stem of a eudicot looks quite different
from a young stem of a monocot.
Primary tissue in the stem contain many of the same characteristics as that in the

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root. However, the endodermis and the casparian strips are lacking.
Both stems have their vascular tissue system arranged in numerous vascular bundles.
However, in monocots stems the bundles are scattered, whereas in eudicots they are
arranged in a ring.
This ring separates the ground tissue into cortex and pith regions. The pith fills the
center of the stem and is often important in food storage. In a monocot stem, the
ground tissue is not separated into these regions because the vascular bundles do not
form a ring.

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The picture below illustrates the arrangement of a typical plant leaf.
The epidermis is the protective covering of one or more layers of cells. The
epidermis is covered by the cuticle, a protective layer of the waxy material cutin.
The cuticle reduces transpiration, or the loss of water through evaporation.
The palisade mesophyll consists of parenchyma cells equipped with numerous
chloroplasts and large surface areas, specializations for photosynthesis.
Photosynthesis in leaves occurs primarily in this tissue.
The spongy mesophyll consists of parenchyma loosely arranged below the palisade
mesophyll. The numerous intercellular spaces provide air chambers that provide
carbon dioxide to photosynthesizing cells and oxygen to respiring cells.
Guard cells are specialized epidermal cells that control the opening and closing of
stomata. Stomata are openings in the epidermis that allow gas exchange between
the inside of the leaf and the external environment.
The leaf's vascular tissue system is made up of a network of veins. A vein is a
vascular bundle composed of xylem and phloem tissues surrounded by a protective
sheath of cells called bundle sheath cells. The vein also functions as a skeleton that
reinforces the shape of the leaf.
Bundle sheath cells surround the veins in such a way that no vascular tissue is
exposed to inter-cellular space. In this way, air bubbles cannot enter vessels
where they could impede the movement of water.

Plant cells are diverse in structure and function

Plant cells have three unique features: chloroplasts (the sites of photosynthesis), a
central vacuoule (contains fluid that helps the cell maintain turgor) and a protective cell
wall made up of cellulose surrounding the plasma membrane.
The picture on the next page highlights the adjoining cell walls of two cells. Many plant
cells, especially that provide structural support, have a two-part cell wall:
A primary cell wall is laid down first, and then a more rigid secondary cell wall
forms between the plasma membrane and the primary wall.
The primary cell walls in adjacent cells in plant tissues are held together by a sticky
layer called the middle lamella.
Pits, where the cell wall is relatively thin, allow migration of water between plant
cells.
Plasmodesmata are open channels in adjacent cell walls through which cytoplasm
and various molecules can flow from cell to cell.

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5 types of cells in plants:

Parenchyma cells are the most abundant type of cell in most plants. They usually
only have primary cell walls, which are thin and flexible. They perform most of the
metabolic functions of a plant and food storage. Most parenchyma cells can divide
and differentiate into other types of plant cells under certain conditions, such as
during the repair of an injury.
Collenchyma cells also lack secondary walls, but they have unevenly thickened
primary walls. They provide flexible support in actively growing parts of the plants;
young stems and petioles often have collenchyma cells just below their surface
Scherenchyma cells have thick secondary cell walls usually strengthened with
lignin, the main chemical component of wood. They cannot elongate and are thus
found only in regions of the plant that have stopped actively growing in length.
When mature, most scherenchyma cells are dead. Their cell walls form a rigid
skeleton that supports the plant. Two types of scherenchyma cells:
One, called a fiber, is long and slender and is usually arrange din bundles.
Sclereids, which are shorter than fiber cells, have thick, irregular, and very hard
secondary walls.

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Xylem tissue includes two types of water-conducting cells: tracheids and vessel
elements. Both have rigid, lignin-containing secondary cell walls. Most xylem cells are
dead at maturity; that is, they are essentially cell wall, completely lacking cellular
components, and contain only the material being transported.
Tracheids are long, thin cells with tapered ends.
Vessel elements are wider, shorter, and less tapered. A column of vessel members is
called a vessel. Water passes from one vessel member to another through areas
devoid of both primary and secondary cell walls. These areas are called
perforations and are literally holes between cells.
Vessel elements are more efficient at moving water than tracheids; therefore, vessel
elements are considered a more evolutionarily advanced feature. They are found
most predominantly among the flowering plants.

Phloem tissue is made up of cells called sieve-tube elements arranged end to end to
form fluid-conducting columns called sieve tubes.
Sieve-tube elements remain alive at maturity, although they lose most organelles,
including the nucleus and ribosomes. This reduction in cell contents enables
nutrients to pass more easily through the cell.
The end walls between sieve-tube members, called sieve plates, have pores that
allow fluid to flow from cell to cell along the sieve tube.
Alongside each sieve-tube element is at least one companion cell, which is
connected to the sieve-tube element by numerous plasmodesmata. One companion
cell may serve multiple sieve-tube elements by producing and transporting proteins
to all of them.

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Plant growth
Primary growth lengthens roots and shoots
The growth of a plant differs from that of an animal in a fundamental way. Most animals
are characterized by determinate growth; that is, they cease growing after reaching a
certain size. Most species of plants, however, continue to grow as long as they live, a
condition called indeterminate growth. Indeterminate growth allows a plant to
continuously increase its exposure to sunlight, air, and soil.
Flowering plants are characterized as annuals, biennials, or perennials, based on the
length of their life cycle, the time of germination through flowering and seed production
to death.
Annuals complete their life cycle in a single year or less (i.e. grains, legumes).
Biennials complete their life cycle in two years, with flowering and seed production
usually occurring during the second year (i.e. beets, parsley, turnips)
Perennials are plants that live and reproduce for many years (i.e. trees, shrubs)
Growth in all plants is made possible by tissues called meristems. A meristem consists
of undifferentiated cells that divide when conditions permit, generating additional cells.
Some products of this division remain in the meristem and produce still more cells,
while others differentiate and are incorporated into tissues and organs of the growing
plant.
Meristems at the tips of roots and in the buds of shoots are called apical meristems.
Cell division in the apical meristem produces the new cells that enable a plant to
grow in length, a process called primary growth. Tissues produced by primary
growth are called primary tissues. Primary growth enables roots to push through
the soil and allows shoots to grow upward.
Mechanisms of primary growth:
The picture to the right illustrates primary growth in a root. The root tip is covered
by a thimble-like root cap that protects the delicate,
actively dividing cells of the apical meristems.
Growth in length occurs just behind the root tip,
where the three zones of cells at successive stages of
primary growth are located (each zone overlaps).
The zone of cell division includes the root apical
meristem and the cells that derive from it. New root
cells are produced in this region, including cells of
the root cap. In the zone of elongation, root cells
elongate. It is cell elongation that pushes the root tip
farther in into the soil. The cells lengthen, rather
than expand equally in all directions, because of the
circular arrangement of cellulose fibers in parallel
bands in their cell walls. The cells elongate by
taking up water and as they do, the cellulose fibers
separate, somewhat like an expanding accordion.
The three tissue systems of a mature plant complete
their development in the zone of differentiation.
Cells of the vascular system differentiate into
primary xylem and primary phloem.
Differentiation of cells results from differential gene
expression.

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The micrograph to the right shows a section

through the end of a growing shoot that was cut
lengthwise from its tip to just below its
uppermost pair of axillary buds. You can see the
apical meristem, which is a dome-shaped mass
of dividing cells at the tip of the terminal bud.
Elongation occurs just below this meristem, and
the elongating cells push the apical meristem
upward. As the apical meristem advances
upward, some of its cells remain behind, and
these become new axillary bud meristems at the
base of the leaves. Two stages in the growth of a
shoot: Stage (1) is like the micrograph and in
stage (2), the apical meristem has been pushed
upward by elongating cells underneath.
Secondary growth increases the diameter of woody
plants
Woody plants (such as trees) grow in diameter in
addition to length, thickening older regions where
primary growth has ceased. This increase in
thickness of stems and roots, called secondary
growth, is caused by the activity of dividing cells
that are called lateral meristems. These diving cells
are arranged into two cylinders, known as the
vascular cambium and the cork cambium, that
extend along the length of roots and stems. Tissues produced by secondary growth are
called secondary tissues.
The vascular cambrium is a cylinder of meristem cells one cell thick between the
primary xylem and primary phloem. Secondary growth adds layers of vascular tissue on
either side of the vascular cambium, which increases root and stem thickness. Gives rise
two two new tissues: secondary xylem to its interior and secondary phloem to its
exterior.
Secondary xylem makes up the wood of a plant. Over the years, a woody stem gets
thicker and thicker, as its vascular cambrium produces layer upon layer of secondary
xylem. The cells of the secondary xylem have thick walls rich of lignin, giving wood
its characteristic hardness and strength.

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Annual growth rings result from the layering of secondary xylem. In many
environments, conditions vary during the year, creating seasons during which plants
alternate growth with dormancy. During periods of growth, the vascular cambrium is
actively dividing, and when the season draws to an end, divisions and growth
gradually come to a halt. When the next season begins, the vascular cambrium
begins dividing again The layers are visible as rings because of uneven activity of
the vascular cambrium during the year as previously explained.
The epidermis and the cortex, both the result of primary growth, make up the young
stem's external covering. When secondary growth begins, the epidermis is sloughed off
and replaced with a new outer layer called cork. Mature cork cells are dead and have
thick, waxy walls that protect the underlying tissues of the stem from water loss,
physical damage, and pathogens.
Cork is produced by meristem tissue called the cork cambium, which first forms
from parenchyma cells in the cortex. The cork cambrium produces new cells on the
outside and sometimes on the inside. On the inside, the phelloderm may be
produced. Together, the cork cambrium and the phelloderm is called the periderm.
As the stem thickens and the secondary xylem expands, the original cork and cork
cambium are pushed outward and fall off. A new cork cambium forms to the inside.
When no cortex is left, it forms from parenchyma cells in the phloem.
Everything external to the vascular cambrium is called bark. The main components
of bark are the secondary phloem, the cork cambium, and cork. The youngest
secondary phloem (next to the vascular cambium) functions in sugar transport. The
older secondary phloem dies, as does the cork cambium you see here. Pushed
outward, these tissues and cork produced by the cork cambium help protect the stem
until they, too, are sloughed off as part of the bark. Keeping pace with secondary
growth, cork cambium keeps regenerating from the younger secondary phloem and
keeps producing a steady supply of cork.
The bulk of a tree trunk log is dead tissue. The living tissue sin it are the vascular
cambium, the youngest secondary phloem, the cork cambium, and cells in the wood
rays.
The wood rays consist of parenchyma cells that transport water and nutrients, store
organic nutrients, and aid in wound repair.
The heartwood, in the center of the trunk, consists of the older layers of secondary
xylem. These cells no longer transport water; they are clogged with resins and other
compounds that make heartwood resistant to rotting.
The lighter-colored sapwood is a younger secondary xylem that does conduct xylem
fluid (sap).

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Reproduction of flowering plants

The development and pollen and ovules culminates in fertilization
Microsporangia produce the microspores (male spores), and the macrosporangia
produce the macrospores (female spores). Summary of reproduction in seed plants:
Microsporangium produces numerous microspore mother cells, which divide by
meiosis to produce 4 haploid cells, the microspores.
Microspores mature into pollen grains. A pollen grain represents the male
gametophyte generation.
The pollen grain further divides into three cells (in flowering plants) or four cells (in
conifers). One of these cells is a vegetative, or tube, cell that controls the growth of
the pollen tube. Other cells become the sperm cells.
The megasporangium, called the nucellus, produces a macrospore mother cell, which
divides by meiosis to produce 4 haploid cells. One of these cells survives to become the
megaspore and represents the female gametophyte generation.
Megaspore divides by mitosis to produce one egg (in flowering plants) or two eggs
(n conifers).
Other accessory cells, in addition to the egg may be produced: one of two tissue
layers called integuments surround the megasporangium.
The integuments, nucellus, and megaspore daughter cells are collectively called the
ovule.
An opening through the integuments for pollen access to the egg is called the
micropyle.
When a pollen grain lands on the sticky sigma (pollination), a pollen tube, an
elongating cell that contains the vegetative nucleus, grows down the style toward an
ovule. There are two sperm cells inside the pollen tube.
Ovules within the ovary consist of a megaspore mother cell surrounded by the
nucellus and integuments. The megaspore mother cell divides by meiosis to form 4

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haploid cells, the megaspores. One surviving megaspore divides 3 times by mitosis
to produce 8 nuclei. 6 of the nuclei undergo cytokinesis and form plasma
membranes. The result is an embryo sac. At the micropyle end of the embryo sac
are the three cells, an egg cell and two synergids. At the opposite end of the
micropyle are the three antipodal cells (play a part in embryo nutrition). In the
middle are the two haploid nuclei, the polar nuclei.
When the pollen tube enters the embryo sac through the micropyle, one sperm
fertilizes the egg, forming a diploid zygote. The nucleus of the second sperm fuses
with both polar nuclei, forming a triploid nucleus. The triploid nucleus divides by
mitosis to produce the endosperm, which provides the nourishment for subsequent
development of the embryo and seedling. The
fertilization of the egg and the polar nuclei each by
a separate sperm nucleus is called double
fertilization.
The ovule develops into a seed
After fertilization, the ovule, containing the triploid
central cell and the diploid zygote, begins developing
the seed.
Endosperm development usually precedes embryo
development.
Embryonic development begins when the zygote
divides by mitosis into two cells (basal and terminal
cells).
Repeated division of one of the cells then
produces a ball of cells that becomes the embryo.
The other cell divides to form a thread of cells that
pushes the embryo into the endosperm. The bulges
seen on the embryo are the developing cotyledons.
The dormant embryo contains a miniature root and
shoot, each equipped with an apical meristem. After
the seed germinates, the apical meristem will sustain
primary growth as long as the plant lives.
The result of embryonic development is a mature
seed. The embryo, surrounded by its endosperm food
supply, becomes dormant; it will not develop further until the seed germinates.
Dormancy is a key adaptation because it allows time for a plant to disperse its seeds and
increases the chance that a new generation of plants will begin growing only when
environmental conditions favor survival.
The seed consists of an embryo, a hard, resistant seed coat (formed from the
integuments), and some kind of storage material.
The major storage material is the endosperm (a nutritious package of food for the
embryo).
Monocots have only one seed leaf inside the seed coat. It is often only a thin leaf,
because the endosperm to feed the new plant is not inside the seed leaf. Dicots have
two seed leaves inside the seed coat. They are usually rounded and fat, because they
contain the endosperm to feed the embryo plant.
The embryo consists of the following parts:
The top portion of the embryo (above the cotyledons), the epicotyl, becomes the
shoot tip.

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Often attached to the epicotyl are young

leaves usually called the plumule.
(sometimes the plumule refers to the epicotyl
and the leaves)
Below the epicotyl and attached to the
cotyledons is the hypocotyl. It becomes the
young shoot.
In some embryos, a radicle develops below
the hypocotyl. The radicle develops into the
root.
In many monocots, a sheath called the
coleopitle surrounds and protects the
epicotyl. In a developing young plant, the
coleopitle emerges first, appearing as a leaf.
The first true leaves, however, emerge from
the plumule within the coleopitle.
Grasses, such as maize and wheat, have a special cotyledon called a
scutellum. Two sheathes enclose the embryo of a grass seed: a coleopitle
and a coleorhiza (covers the young root).
The ovary develops into a fruit
A fruit is a specialized vessel that houses and protects seeds and helps
disperse them from the parent plant.
Fruits are classified by their development:
simple: a single or several fused carpels
aggregate: a single flower with multiple separate carpels
multiple: a group of flowers called an inflorescence
Steps of fruit formation: (1) soon after pollination, (2) the flower drops its
petals, and the ovary starts to grow. The ovary expands tremendously, and its
wall thickens, (3) forming the fruit.
An accessory fruit contains other floral parts in addition to ovaries.
Seed germination continues the life cycle
At germination, the plant does not begin life but rather resumes the growth
and development that were temporarily suspended during seed dormancy.
Germination depends on imbibition, the uptake of water due to low water
potential of the dry seed. The hydrated seed expands, rupturing its coat. The
inflow of water triggers metabolic changes in the embryo that makes it start
growing again.
Enzymes begin digesting stored nutrients in the endosperm or cotyledons, and these
nutrients are transported to the growing regions of the embryo.
The radicle (embryonic root) emerges first.
Next, the shoot tip breaks through the soil surface.
In many eudicots (garden bean), a hook forms the hypocotyl, and growth pushes the
hook above ground. The hook straightens and pulls the cotyledons up.
In many monocots (maize), the coleopitle pushes up through the soil.

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Asexual reproduction produces plant clones

Many angiosperm species reproduce both asexually and sexually.
Sexual reproduction results in offspring that are genetically different from their
parents.
Asexual reproduction results in a clone of genetically identical organisms.
Mechanisms of Asexual Reproduction
Fragmentation, separation of a parent plant into parts that develop into whole
plants, is a very common type of asexual reproduction.
In some species, a parent plant's root system gives rise to adventitious shoots that
become separate root systems.
Apomixis is the asexual production of seeds from a diploid cell.
Advantages and disadvantages of asexual vs. sexual reproduction
Asexual reproduction is also called vegetative reproduction. It can be beneficial to
a successful plant in a stable environment. However, a clone of plants is vulnerable
to local extinction if there is an environmental change.
Sexual reproduction generates genetic variation that makes evolutionary adaptation
possible. However, only a fraction of seedlings survive
Mechanisms that prevent self-fertilization
Many angiosperms have mechanisms that make it difficult for a flower to selffertilize.
Dioecious species have staminate and carpellate flowers on separate plants.
Others have stamens and carpels that mature at different times or are arranged to
prevent selfing.
The most common is self-incompatibility, a plant's ability to reject its own pollen.
Recognition of a self pollen triggers a signal transduction pathway leading to a block
in growth of a pollen tube.
The uptake and transport of plant nutrients
Plants acquire nutrients from air, water, and soil
The success of plants depend son their ability to gather and conserve resources from
their environment (air, water, and soil).
The transport of materials is central to the integrated functioning of the whole plant.
Adaptations for acquiring resources were key steps in the evolution of vascular plants
Adaptations in each species represent compromises between enhancing photosynthesis
and minimizing water loss.
Stems serve as conduits for water and nutrients and as supporting structures for leaves.
There is a generally a positive correlation between water availability and leaf size.
Phyllotaxy, the arrangement of leaves on a stem, is specific to each species. Most
angiosperms have alternate phyllotaxy with leaves arranged in a spiral. The angle
between leaves is 137.5o and likely minimizes shading of lower leaves.

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Light absorption is affected by the leaf area index, the
ratio of total upper leaf surface of a plant divided by the
surface area of land on which it grows.
Self-pruning is the shedding of lower shaded leaves
when they respire more than they photosynthesize.
Leaf orientation affects light absorption. In low-light
conditions, horizontal leaves capture more sunlight. In
sunny conditions, vertical leaves are less damaged by sun and allow light to reach lower
leaves.
Shoot height and branching pattern also affect light capture. There is a trade-off between
growing tall and branching.
The root system mines soil. Taproot systems anchor plants and are characteristic of
gymnosperms and eudicots. Root growth can adjust to local conditions (i.e. roots branch
more in a pocket of high nitrate than low nitrate). Roots are less competitive with other
roots from the same plant than with roots from different plants.
Different mechanisms transport substances over long or short distances
There are two major pathways through plants: apoplast and symplast.
The apoplast consists of everything external to the plasma membrane. It includes
cell walls, extracellular spaces, and the interior of vessel elements and tracheids.
The symplast consists of the cytosol of the living cells in a plant, as well as the
plasmodesmata.
Three transport routes for water and solutes are:
The apoplastic route, through cell walls and extracellular spaces.
The symplastic route, through the cytosol.
The transmembrane route, across cell walls.

Review diffusion and osmosis chapter in cellular and molecular bio unit.
Aquaporins are transport proteins in the cell membrane that allow the passage of water.
These affect the rate of water movement across the membrane.

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Efficient long distance transport of fluid requires bulk flow, the movement of fluid
driven by pressure. Efficient movement is also achieved in the fact that tracheids and
vessel elements have no cytoplasm, and sieve-tube elements have few organelles in their
cytoplasm.
Transpiration drives the transport of water and minerals from roots to shoots via xylem
Plants can move a large volume of water from their roots to shoots.
Moving water and minerals into the roots
Most water and mineral absorption occurs near root tips, where root hairs are located
and the epidermis is permeable to water. After soil solution enters the roots, the
extensive surface area of cortical cell membranes enhances the uptake of water and
selected minerals.
The concentration of essential minerals is greater in the roots than in the soil because
of active transport.
Transport of water and minerals into the xylem
The endodermis is the innermost layer of cells in the root cortex. It surrounds the
vascular cylinder and is the last checkpoint of selective passage of minerals from the
cortex into the vascular tissue. Water can cross the cortex via the symplast or
apoplast.
The waxy casparian strip of the endodermal wall blocks the apoplastic transfer
of minerals from the cortex to the vascular cylinder. Water and minerals in the
apoplast must cross the plasma membrane of an endodermal cell to enter the
vascular cylinder.
The endodermis regulates and transports needed minerals from the soil into the
xylem. Water and minerals move from the protoplasts of endodermal cells into their
cell walls. Diffusion and active transport are involved in this movement from
symplast to apoplast.
Water and minerals now enter the tracheids and vessel elements.

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Bulk flow transport via the xylem
Xylem sap, water and dissolved minerals, is transported from roots
to leaves by bulk flow.
The transport of xylem sap involves transpiration, the evaporation
of water from a plant's surface. Transpired water is replaced as water
travels up from the roots.
At night, root cells continue pumping mineral ions into the xylem of the vascular
cylinder, lowering the water potential. Water flows in from the root cortex,
generating root pressure. Root pressure sometimes results in guttation, the
exudation of water droplets on the tips or edges of leaves. Positive root pressure
is relatively week and is a minor mechanism of xylem flow.
According to the cohesion-tension hypothesis, transpiration and water cohesion
pull water from shoots to roots. Xylem sap is normally under negative pressure, or
tension.
Water vapor in airspaces of a leaf diffuses down its water potential gradient and
exits the leaf via stomata. As water evaporates, the air-water interface retreats
further into the mesophyll cell walls. The surface tension of water creates a
negative pressure potential. This negative pressure pulls water in the xylem into
the leaf. The transpirational pull on xylem sap is transmitted from leaves to
roots.
Water molecules are attracted to cellulose in xylem cell walls through adhesion.
Adhesion of water molecules to xylem cell walls helps offset the force of gravity.
Water molecules are attracted to each other through cohesion. Cohesion make sit
possible to pull a column of xylem sap.
Thick secondary cell walls prevent vessel elements and tracheids from
collapsing under negative pressure.

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Bulk flow differs from diffusion. It is driven by differences in pressure potential, not
solute potential. It occurs in hollow dead cells, not across the membranes of living cells.
It moves the entire solution, not just water or solutes. It is much faster than diffusion.
The rate of transpiration is regulated by stomata
Leaves generally have broad surface areas and high surface-to-volume ratios. These
characteristics help increase photosynthesis and increase water loss through stomata
(this is a trade-off).
Guard cells help balance water conservation with gas exchange for photosynthesis.
About 95% of the water a plant loses escapes through stomata. Each stoma is flanked by
a pair of guard cells, which control the diameter of the stoma by changing shape.
Stomatal density is under genetic and environmental control.
Mechanisms of stomatal opening and closing:
Changes in turgor pressure open and close stomata. When turgid, guard cells bow
outward and the pore between them opens. When flaccid, guard cells become less
bowed and the pore closes.
This results primarily from the reversible uptake and loss of potassium ions by guard
cells. When potassium ions enter the guard cell, the osmolarity of the internal
surroundings of the guard cell is increased compared to the extracellular space. As a
result, water moves into the guard cells. When water flows into the guard cells, the
stomata opens.
Because ions are flowing into the cell, a charge gradient is created. To relieve this
gradient, chloride ions are pumped into the cell along with potassium ions in some
plants. In other plants, hydronium ions are pumped out.

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Stimuli for stomatal opening and closing:
Stomata close when temperatures are high. This reduces loss of water but shuts
down photosynthesis.
Stomata opens when carbon dioxide concentrations are low inside the leaf. Allows
photosynthesis but risks water loss.
Stomata close during the night and opens during the day. May be due to carbon
dioxide levels: CO2 levels are low during the day because the plant is actively doing
photosynthesis but at night, CO2 levels are high because the plant is only respiring.
The hormone abscisic acid is produced in response to water deficiency and causes
the closure of stomata.
Effects of transpiration on wilting and leaf temperature
Plants lose a large amount of water by transpiration. If the lost water is not replaced by
sufficient transport of water, the plant will lose water and wilt.
Transpiration also results in evaporative cooling, which can lower the temperature of a
leaf and prevent denaturation of various enzymes involved in photosynthesis and other
metabolic processes.
Xerophytes are plants adapted to arid climates.
Some desert plants complete their life cycle during the rainy season.
Others have leaf modifications that reduce the rate of transpiration.
Some plants use a specialized form of photosynthesis called crassulacean acid
metabolism (CAM).
Sugars are transported from sources to sinks via the phloem
The products of photosynthesis are transported to the phloem by a process of
translocation. In angiosperms, sieve-tube elements are the conduits for translocation.
Phloem sap is an aqueous solution that is high in sucrose. It travels from sugar source to
sink.
A sugar source is an organ that is a net producer of sugar, such as mature leaves.
A sugar sink is an organ that is a net consumer or storer of sugar, such as a tuber or
bulb.
Starch is an important player, since it is essentially insoluble in water. Any cell that
converts extracellular soluble sugars into starch acts as a sink. Oppositely, any cell
can act as a source if it breaks down starch into soluble sugars.
A storage organ can be both a sugar sink in summer and sugar source in winter.
Sugar must be loaded into sieve-tube elements before being exposed to sinks.
Depending on the species, sugars may move by symplastic or both symplastic and
apoplastic pathways.
Companion cells enhance solute movement between the apoplast and symplast.
In many plants, phloem loading requires active transport. Proton pumping and
cotransport of sucrose and H+ enable the cell to accumulate sucrose. At the sink, sugar
molecules diffuse from the phloem to sink tissues and are followed by water.

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Phloem sap moves through a sieve tube by

bulk flow driven by positive pressure called
the pressure flow mechanism. Steps:
(1) sugar is loaded from a photosynthetic
cell into a phloem tube by active
transport. Sugar loading at the source end
raises the solute (sugar) concentration
inside the phloem tube.
(2) The high solute concentration draws
water into the tube by osmosis, usually
from the xylem. The inward flow of water
raises the water pressure at the source end
of the phloem tube.
(3) At the sugar sink, both sugar and
water leave the phloem tube. As the sugar
departs the phloem, lowering the solute
concentration at the sink end, (4) water
flows by osmosis back into the xylem.
The exit of water lowers the water
pressure in the tube.
The building of water pressure at the
source end of the phloem tube and the
reduction of that pressure at the sink cause phloem sap to flow from source to sink
down a gradient of water pressure. Sieve plates allow free movement of solutes as
well as water. Thus, sugar is carried
along from the source to sink a the same
rate as the water.
Plant nutrients and the soil
Soil contains a living, complex ecosystem
Plants obtain most of their water and
minerals from the upper layers of soil.
Living organisms play an important role in
these soil layers. This complex ecosystem is
fragile.
The basic properties of soil are texture and
composition.
Soil texture: soil particles are classified
by size; from smallest to larges they are
called sand, silt, and clay. Soil is
stratified into layers called soil horizons.
Topsoil consists of mineral particles,
living organisms, and humus, the
decaying organic material. Soil solution
consists of water and dissolved minerals
in the pores between soil particles.
Loams are the most fertile topsoils and
contain equal amounts of sand, silt, and
clay.
Soil composition: A soil's composition

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refers to its inorganic and organic chemical components. Cations adhere to
negatively charged soil particles; this prevents them from leaching out of the soil
through percolating groundwater. Topsoil contains organic components such as
bacteria, fungi, algae, other protists, insects, earthworms, nematodes, and plant roots.
These organisms help to decompose organic material and mix the soil
Cation exchange is a mechanisms by which the root hairs take up certain positively
charged ions (cations).
Inorganic cations such as calcium, magnesium, and potassium adhere by chemical
attraction to the negatively charged surfaces of clay particles. This adhesion helps
prevent these positively charged nutrients from draining away during heavy rain or
irrigation.
In cation exchange, root hairs release hydrogen ions into the soil solution. The
hydrogen ions help displace cations on the clay particle surfaces, and root hairs can
then absorb them.

In contrast to cations, anions are not usually bound tightly to soil particles. Unbound
ions are readily available to plants, but they tend to drain out of the soil quickly due to
irrigation or rainfall.
Plants require essential elements to complete their life cycle
More than 50 chemical elements have been identified among the inorganic substances in
plants, but not all of these are essential to plants. There are 17 essential elements,
chemical elements required for a plant to complete its life cycle.
Nine of the essential elements are called macronutrients because plants require them in
large amounts. The remaining eight are called micronutrients because plants need
them in very small amounts.
Plant nutrition often involves relationships with other organisms
Plants and soil microbes have a mutualistic relationships. Dead plants provide energy
needed by soil-dwelling microorganisms. Secretions from living roots support a wide

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variety of microbes in the near-root environment.

The layer of soil bound to the plant's roots is the rhizosphere. The rhizosphere contains
bacteria that act as decomposers and nitrogen-fixers.
Free-living rhizobacteria thrive in the rhizosphere, and some can enter roots.
They can play several roles: produce hormones that influence plant growth, produce
antibiotics that protect roots from disease, and absorb toxic materials or make
nutrients more available to roots.
Mycorrhizae are mutualistic associations of fungi and roots (previously discussed in
other chapters).
Some plants have nutritional adaptations that use other organisms in nonmutualistic
ways. Three unusual adaptations are:
Epiphytes: grows on another plant and obtains water and minerals from rain
Parasitic plants: absorb sugars and minerals from their living host plant
Carnivorous plants
Plant responses to internal and external signals
Signal transduction pathways link signal reception to response
Review cell signaling chapter in cellular and molecular bio unit.
Morphological adaptions for growing in darkness is called
etiolation. After being exposed to light, a plant undergoes
changes called de-etiolation, in which shoots and roots grow
normally.
A plant's response to a stimuli is an example of cell-signal processing. Therefore, it
will follow a signaltransduction pathway.
De-etiolation activates enzymes
that function in photosynthesis
directly, supply the chemical
precursors for chlorophyll
production, and affect the levels of
plant hormones that regulate
growth.
Plant hormones help coordinate
growth, development, and responses to
stimuli
Plant hormones are chemical
signals that modify or control one
or more specific physiological
processes within a plant.
Plant hormones are produced in very low concentration, but a minute amount can
greatly affect growth and development of a plant organ. In general, they control plant
growth and development by affecting the division, elongation, and differentiation of
cells.
Auxin
The term auxin refers to any chemical that promotes elongation of coleoptiles.
Indoleacetic acid (IAA) is a common auxin in plants; in this chapter the term auxin
refers specifically to IAA. Auxin is a modified tryptophan amino acid.
Auxin is produced in shoot tips and is transported down the stem. Auxin transporter
proteins move the hormone from the basal end of one cell to the apical end of a
neighboring cell. Auxin is actively transported (using ATP) from cell to cell in a specific

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direction (polar transport).
Auxin plays a major role in cell elongation. According to the acid growth hypothesis,
auxin stimulates proton pumps in the plasma membrane.
(1) The proton pumps lower the pH in the cell wall, (2) activating expansins,
enzymes that loosen the cell wall. (3) The cross-linking molecules are now more
exposed to enzymes that loosen the cell wall. (4) The cell then swells with water and
elongates because its weakened wall no longer resists the cell's tendency to take up
water via osmosis.

Auxin promotes cell elongation only within a certain concentration range. Above a
certain level, it usually inhibits cell elongation in stems, probably by inducing the
production of ethylene; a hormone that generally counters the effects of auxin.
Auxin influences plant responses to light (phototropism) and gravity (geotropism).
Auxin's role in plant development:
Polar transport of auxin plays a role in pattern formation of the developing plant
Reduced auxin flow from the shoot of a branch stimulates growth in lower branches
Auxin transport plays a role in phyllotaxy, the arrangement of leaves on the stem
Polar transport of auxin from leaf margins directs leaf venation pattern
The activity of the vascular cambium is under control of auxin transport
Cytokinins
Cytokinins are so named because they stimulate cytokinesis (cell division). Structurally,
they are variations of the nitrogen base adenine. Two types: naturally occurring zeatin
and artificially produced kinetin.
Cytokinins are produced in actively growing tissues such as roots, embryos, and fruits.
Cytokinins work together with auxin to control cell
division and differentiation.
Cytokinins, auxin, and strigolactone interact in the
control of apical dominance, a terminal bud's
ability to suppress development of axillary buds. If
the terminal bud is removed, plants become bushier.
Cytokinins slow aging of some plant organs by
inhibiting protein breakdown, stimulating RNA and
protein synthesis, and mobilizing nutrients from

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surrounding tissues.
Cytokinins influence the direction of organ development (organogensis).
Gibberellins
Gibberellins have a variety of effects, such as
stem elongation, fruit growth, and seed
germination.
Gibberellins are produced in young roots and
leaves.
They stimulate growth of leaves in stems. In
stems, gibberellins stimulate cell elongation
and cell division. High concentrations of
gibberellins cause the rapid elongation of
stems called bolting.
In many plants, both auxin and gibberellins
must be present for fruit development.
After water is imbibed, release of gibberellins
from the embryo signals seeds to germinate.
Brassinosteroids
Brassinosteroids are chemically similar to the sex hormones of animals.
They induce cell elongation and division in stem segments.
They slow leaf abscission and promote xylem differentiation.
Abscisic acid
Abscisic acid (ABA) slows growth.
In buds, it delays growth and causes the formation of scales in preparation for
overwintering.
Two of the many effects of ABA: seed dormancy and drought tolerance.
Seed dormancy ensures that the seed will germinate only in optimal conditions. In
some seeds, dormancy is broken when ABA is removed by heavy rain, light, or
prolonged cold. Precocious (early) germination can be caused by inactive or low
levels of ABA.
ABA is the primary internal signal that enables plants to withstand drought. ABA
accumulation causes stomata to close rapidly.
Strigolactones
Hormones called strigolactones stimulate seed germination, help establish mycorrhizal
associations, and help control apical dominance.
Ethylene
Plants produce ethylene in response to stresses such as drought, flooding,
mechanical pressure, injury, and infection.
Ethylene induces the triple response to mechanical stress, which allows
a growing shoot to avoid obstacles. It consists of a slowing of stem
elongation, thickening of stem, and horizontal growth.
Senescence is the programmed death of cells or organs. A burst of
ethylene is associated with apoptosis.
A change in the balance of auxin and ethylene controls leaf abscission, the process that
occurs in auto when a leaf falls off the plant.
The base of the leaf stalk separates from the stem. The separation region is called the
abscission layer. The abscission layer consists of a narrow band of cells with thin
walls that are further weakens when enzymes digest the cell walls. The leaf drops off
when its weight splits the abscission layer apart.

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A burst of ethylene production in a fruit triggers the ripening process. Ethylene triggers
ripening, and ripening triggers release of more ethylene. Ethylene gas fills the
intercellular spaces within the fruit and stimulates its ripening by enzymatic breakdown
of cell walls.
Also involved in stimulating the production of flowers.
Plant responses to stimuli
Tropisms and phototropism
Any growth response that results in plant organs curving toward or away from stimuli s
called a tropism.
The growth of a shoot in response to light is called phototropism. It is achieved by the
action of the hormone auxin.
Mechanism of action:
Auxin is produced in the apical meristem, moves downward by active transport into
the zone of elongation, and generates growth by stimulating elongation.
When all sides of the apical meristem are equally illuminated, growth of the stem is
uniform and the stem grows strength.
When the stem is unequally illuminated, auxin moves downward into the zone of
elongation but concentrates on the shady side of the stem.
The higher concentration of auxin in the shady side of the stem causes
differential growth; that is, the shady side grows more than the sunny side.
When this happens, the stem bends toward the light

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Action spectrums
Light cues many key events in plant growth and
development. Effects on light on plant morphology are
called photomorphogenesis.
Plants detect not only the present of light but also its
direction, intensity, and wavelength (color)
A graph called an action spectrum depicts relative
response of a process to different wavelengths.
Action spectra are useful in studying any process that
depends on light.
Plants have internal clocks
An innate biological cycle of about 24 hours is called a
circadian rhythm. It persists even when an organism is
sheltered from environmental cues. Thus, circadian
rhythms occur with or without external stimuli.
Circadian rhythms are controlled by internal timekeepers
known as biological clocks.
Although a biological clock continues to mark time in the absence of environmental
cues, it requires daily signals from the environment to remain tuned to a period of
exactly 24 hours.
Circadian rhythms can be entrained to exactly 24 hours by the day-night cycle.
Plants mark the seasons by measuring photoperiod
A biological clock does not only time a plant's everyday activities, but may also
influence seasonal events that are important in a plant's life cycle.
The environmental stimulus plants most often use to detect the time of year is called
photoperiod, the relative lengths of day and night. Photoperiodism is a physiological
response to photoperiod.
Plants whose flowering is triggered by photoperiod fall into one of two groups:
One group, the short-day plants, generally flower in late summer, fall, or winter,
when light periods shorten.
In contrast, long-day plants usually flower in late spring or early summer, when
light periods lengthen.
Day-neutral plants do not flower in
response to daylight changes.
Flowering and other responses to photoperiod
are actually controlled by the length of
continuous darkness, not the length of
continuous daylight.
Short-day plants will only flower if it stays
dark long enough and long-day plants will
flower if the dark period is short enough.
A short day-plant will not flower (1) until it is
exposed to a continuous dark period (2)
exceeding a critical length. The short-day plant
will not blossom if the nighttime part of the
photoperiod is interrupted (3) even by a brief
flash of light. There is no effect if the daytime
portion of the photoperiod is broken by a brief
exposure to darkness.

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In long-day plants, flowering occurs when the night length is shorter (4) than the critical
length. A dark interval that is too long will prevent flowering. Additionally, flowering
can be induced in a long-day plant by a flash of light (6) during the night.
Photoreceptors include light detectors that may help set the biological clock
Different plant responses can be mediated by the same or different photoreceptors.
There are two major classes of light receptors: blue-light photoreceptors and
phytochromes.
Various blue-light photoreceptors control hypocotyl elongation, stomatal opening, and
phototropism.
Phytochromes are pigments that regulate many of a plant's responses throughout its life
(e.g., seed germination, shade avoidance).
Phytochromes change back and forth between two forms that differ slightly in
structure: Pr (absorbs red light), and Pfr (absorbs far-red light). When the Pr form
absorbs red light (660 nm), it is quickly converted to Pfr, and when Pfr absorbs far-red
light (730 nm), it is slowly converted back to Pr.

Each night, new phytochrome molecules are synthesized only in the Pr form. Thus,
molecules of Pr slowly accumulate in the continuous darkness that follows sunset.
After sunrise, the red wavelengths of sunlight cause much of the phytochrome to be
rapidly converted from the Pr form to Pfr. Sunlight contains both red light and far-red
light, but the conversion to Pfr is faster than the conversion to Pr.
It is the sudden increase in Pfr each day at dawn that resets a plant's biological clock.
Interactions between phytochrome and the biological clock enable plants to measure the
passage of night and day. In doing so, the clock monitors photoperiod and, when
detecting seasonal changes in day and night length, cues responses such as seed
germination, flowering, and the beginning and end of bud dormancy.
The consequences of the phytochrome switch are shown in the picture below.
Bar (1) shows the results we saw for both short-day and long-day plants that receive
a flash of light during their critical dark period. R stands for red light, FR stands for
far-red light.
Bar (2) reveals that the effect of a flash of red light that interrupts a period of
darkness can be reversed by a subsequent flash of far-red light. Both types of plants
behave as though there is no interruption in the night length.
Bars (3) and (4) indicate that now matter how many flashes of red or far-red light a
plant receives, only the wavelength of the last flash of light affects the plant's
measurement of night length.

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Phytochromes control more than just the biological clock

Phytochrome can detect if enough light has been exposed to a seed before it germinates.
When the critical exposure is exceeded, production of gibberellins or destruction of
ABA occurs and germination follows.
The phytochrome system also provides the plant with information about the quality of
light. It can determine shade from the sun. Shaded plants receive more far-red than red
light. In the shade avoidance response, the phytochrome ratio shifts in favor of Pr when a
tree is shaded.
A flowering hormone?
Photoperiod is detected by leaves, which cue buds to develop as flowers. The flowering
hormone is called florigen. It is produced in leaves and travels to shoot tips.
Other tropisms
Gravity
Response to gravity is known as gravitropism.
Both auxins and gibberellins are involved but their action depends on their relative
concentrations and the target organ. Mechanism of action for auxin:
If a stem is horizontal, auxin produced at the apical meristem moves down the
stem and concentrates on its lower side. Since auxin stimulates cell elongation,
growth of the lower side is greater than that of the upper side, and the stem bends
upward as it grows.
If a root is horizontal, auxin is produced at the apical meristem (root tip), and, as
in stems, concentrates on the lower side of the root. However, in roots, auxin
inhibits growth.
Roots show positive gravitropism whereas shoots show negative gravitropism.
Plants may detect gravity by the settling of statoliths, dense cytoplasmic
components.
Touch
Thigmotropism is a response to touch.
When vines and other climbing plants contact some object, they respond by
wrapping around it.
Mechanism is not well understood.
Drought
During drought, plants reduce transpiration by closing stomata, slowing leaf growth,

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and reducing exposed surface area.
Growth of shallow roots is inhibited, while deeper roots continue to grow.
Flooding
Enzymatic destruction of root cortex cells creates air tubes that help plants survive
oxygen deprivation during flooding.
Salt stress
Plants respond to salt stress by producing solutes tolerated at high concentrations.
This process keeps the water potential of cells more negative than that of the soil
solution.
Heat stress and cold stress
Heat-shock proteins help protect other proteins from heat stress.
Many plants, as well as other organisms, have antifreeze proteins that prevent ice
crystals from growing and damaging cells.

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Types of reproduction
Asexual and sexual reproduction
In sexual reproduction, the fusion of haploid gametes form a diploid cell, the zygote.
Eventually, the animal that develops from a zygote can give rise to gametes by meiosis.
In humans:
The female gamete, the egg, is large and non-motile
The male gamete, the sperm, is much smaller and motile
In asexual reproduction, new individuals are generated without the fusion of egg and
sperm.
Reproduction relies entirely on mitotic cell division

Mechanisms of asexual reproduction

Budding is when new individuals arise from outgrowths of existing ones (reef building
coral)
Common among invertebrates is fission, the separation of a parent organism into two
individuals of approximately equal size (similar to mitosis).
Parthenogenesis is when an egg develops without being fertilized (bees, wasps, ants, etc.)
Progeny can be haploid or diploid
Asexual reproduction can be a two-step process:
fragmentation: breaking of the body into several pieces
regeneration: regrowth of lost body parts
If more than one piece grows and develops into a complete animal, the effect is
reproduction
Reproductive cycles
Most animals exhibit cycles in reproductive activity, often related to changing seasons.
Found in asexully and sexually reproducing animals
Cycles controlled by hormones. Secretion of hormones is regulated by environmental
cues.
Because reproductive cycles are regulated by environmental cues, global climate change
can affect reproduction.
Ovulation, the release of mature eggs, occurs at the midpoint of a cycle.
Variation in patterns of sexual reproduction
Hemaphroditisim is when an individual has both male and female reproductive systems.

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Types of fertilization
Introduction
the union of sperm and egg, fertilization, can be either internal or external.
In external fertilization, t he female releases eggs into the environment where the male
fertilizes them.
Moist habitat is almost always required for external fertilization, to prevent gametes
from dying out and allow the sperm to swim to the eggs
Other species have internal fertilization, where sperm is deposited in or near the female
reproductive tract, and fertilization occurs within that tract.
It is an adaptation that enables sperm to reach en egg even when the environment is dry
Usually requires copulation (sexual intercourse) and complex reproductive systems
Non-placental internal development: certain animals (e.g. marsupials, tropical fish)
have no placenta. There is limited exchange of food and oxygen between mother and
young.
Placental internal development: lots of exchange of food and oxygen between mother
and young.
monotremes are egg laying mammals (platypus)
marsupials are mammals where the young is carried in a pouch
a viviparous mammal is one in which the offspring develop within the uterus
an oviparous mammal is one in which the parent lays eggs (birds, some amphibians, most
repitles)
oviviparous animal is a combination. The young are hatched from eggs, but the eggs are
kept in the mother's body until they are ready to hatch.
Ensuring the survival of offspring
Internal fertilization is typically associated with the production of fewer gametes than
external fertilization but results in the survival of a higher fraction of zygotes.
This is because the environment of internal fertilization is shielded from predators and
also contains mechanisms that provide greater protection and care of the embryos.
Gamete production and delivery
Sexual reproduction in animals relies on sets of cells that are precursors for eggs and sperm.
These precursor cells are created very early in life and remain inactive until later in life,
where they are amplified to increase production of gametes.
Animals also employ a variety of reproductive systems
Gonads are organs that produce gametes.
More elaborate reproductive systems include sets of structures that carry, nourish, and
protect the gametes.
In many insect species, the female reproductive system contains one or more
spermathecae, sacs in which sperm may be stored for extended periods.
Vertebrate reproductive systems display limited but significant variations.
Some vertebrates have a 2 chamber uterus, others only have a 1 chamber uterus.
In many nonmammalian vertebrates, the digestive, excretory, and reproductive systems
have a common opening to the outside, the cloaca.
Animals often mate with more than one member of the other sex.
Male and female reproductive anatomy

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Male reproductive anatomy

Testes
The male gonads, or testes produce sperm in highly coiled tubes called seminiferous
tubules.
Sertoli cells are the nurse cells of the testes that helps in the process of
spermatogenesis. Activated by follicle-stimulating hormone (FSH).
Intersticial cells (leydig cells) produce male sex hormones (testosterone) in the
presence of luteinizing hormone (LH).
The scrotum is the small muscular sac that contains and protects the testicles. Keeps the
testes cooler than the rest of the body for proper production of sperm.
Ducts (path of sperm is SEVEnUP)
From the seminiferous tubules of a testis, the sperm pass into the coiled duct of an
epidiymis. Takes 3 weeks for sperm to pass through this (enough time for it to grow and
mature).
During ejaculation, the sperm are propelled from each epidiymis through a muscular
duct, the vas deferens.
Each vas deferens, one from each epididymis (one for each testes), extends around
and behind the urinary bladder, where it joins a duct from the seminal vesicle,
forming a short ejaculatory duct.
The ejaculatory duct opens to the urethra, the outlet tube for both the excretory
system and the reproductive system.
Penis
The human penis contains the urethra as well as three cylinders of spongy erectile
tissue.
During sexual arousal, the erectile tissue fills with blood from the arteries and the
increased pressure blocks of the veins. This causes an erection.
The main shaft of the penis is covered by relatively thick skin.
The head, or glans, of the penis has a much thinner outer layer and is more sensitive to
stimulation
the human glans is surrounded by a fold of skin called the prepuce, which is removed
during circumcision.
Accessory glands
three sets of accessory glandsthe seminal vesciles, the prostate glands, and the
bulbourethral glandsproduce secretions that combine with sperm to form semen, the
fluid that is ejaculated.
Two seminal vesicles contribute about 60% of the volume of the semen. Provides
mucus (liquid for sperm), fructose as ATP, and prostaglandins
The prostate gland secretes its products directly into the urethra through the small
ducts. Neutralizes acidity of urine that may still be in urethra, vagina acidity, and
seminal fluid.
Bulbourethral glands secrete small amount of fluid of unknown function into the
urethra.

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Human Female reproductive anatomy

Ovaries
The female gonads are a pair of ovaries that flank the uterus and are held in place by
ligaments.
Outer layer is packed with follicles, each consisting of an oocyte, a partially developed
egg, surrounded by support cells.
Support cells nourish and protect oocyte during development.
Oviduct and uterus
Oviduct, or fallopian tube, extends from the uterus to each ovary.
The cilia that lines the oviduct helps facilitate movement of the egg.
The uterus is a thick, muscular organ that can expand during pregnancy to
accommodate a fetus.
The inner lining of the uterus is the endometrum (richly supplied with blood vessels).

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The neck of the uterus, the cervix opens up to the vagina.
Vagina
Vagina is a muscular but elastic chamber that is the site of insertion of the penis. Also
serves as the birth canal where a baby is born.
The clitoris consists of erectile tissue supporting a rounded glans.

Mammary glands
Mammary glands (only in mammals) are present in both sexes, but they normally produce
milk only in females.
Spermatogenesis
Begins at puberty within the seminiferous tubules of testes

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The father cell of sperm is clalled the spermatogonia cells primary spermatocytes
(mitosis) (meiosis I) 2 secondary spermatocytes (meiosis II) 4 spermatids
Sertoli cells nourish the newly formed sperm cells and help make them motile.
Sperm
Sperm are compact packages of DNA specialized for effective male genome delivery
Sperm head: contains chromosomes and the acrosome.
Acrosome is at the tip of the sperm head and contains enzymes which are used to
penetrate the egg
Midpiece: flagellum (9+2 microtubule array) and lots of mitochondria for ATP generation
Tail: remainder of flagellum; sperm is propelled by whiplike motion of tail and midpiece

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Oogenesis
Oogonia (fetal cells) (mitosis) primary oocytes (meisosis) and remain at prophase I
until puberty menstural cycle releases 1 egg per month released egg continues
development through remainder of meiosis I in a follicle (protects and nourishes oocyte)
(completion of meiosis I) secondary oocyte and polar body (meiosis) and remains at
metaphase II until sperm enters the egg completion of meiosis II at fertilization

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Hormonal control of reproductive cycles
Hormones from multiple glands govern reproduction in males and females.
The hypothalamus secretes gonadotropin-releasing hormone (GnRH), which then directs the
anterior pituitary to secrete the gnoadotropins, follicle stimulating hormone (FSH) and
lutenizing hormones (LH).
Are called gonadotropins because they act on male and female gonads, and they support
gametogenesis by stimulating sex hormone production, among with other mechanisms.
Sex hormones:
androgens = testosterone
estrogens = estradiol and progesterone
gonads are major source of sex hormones
Sex hormones regulate gametogenesis both directly and indirectly, but they also have other
actions.
Hormonal control of the male reproductive system
FSH and LH, released by the anterior pituitary in response to GnRH from the hypothalamus,
direct spermatogenesis by acting on different types of cells in the testis.
Hormonal upregulation:
FSH stimulates sertoli cells, located within the seminiferous tubules, to nourish
developing sperm.
LH causes leydig cells, to produce testosterone and other androgens, which promote
spermatogenesis.
Negative feedback routes:
Testosterone regulates blood levels of GnRH, FSH, and LH.
Inhibin, a hormone that in males is produced by sertoli cells, acts on the anterior
pituitary gland to reduce FSH secretion.
Hormonal control of female reproductive cycles
The cyclic shredding of the blood-rich endometrium from the uterus, a process that occurs
in a flow through the cervix and vagina, is called menstruation.
Menstrual cycle refers to the changes that occur about once a month in the uterus
The cyclic changes in the uterus is called the ovarian cycle.
Menstrual cycle
menarche is a girl's first menstrual period
Hypothalamus and anterior pituitary initiate the reproductive cycle. Low levels of estrogen
and progesterone lead to the secretion of GnRH, which in turn, stimulates production of
FSH and LH.
FSH stimulates the development of the follicle and the oocyte.
FSH also stimulates the secretion of estrogen from the follicle.
The rising levels of estrogen stimulate the anterior pituitary to create lots of LH. The surge
of LH triggers ovulation.
After ovulation, the follicle, now called the corpus luteum, continues to develop under the
influence of LH and secretes both estrogen and progesterone.
Estrogen and progesterone stimulate the development of the endometrium. Estrogen
thickens the endometrium whereas progesterone develops and maintains the endometrial
wall.
If no implantation occurs, negative feedback from the high levels of estrogen and
progesterone cause the anterior pituitary to crease production of FSH and LH through the

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hypothalamus. In absence of FSH and LH, the corpus luteum deteriorates. The deterioration
stops production of estrogen and progesterone. When estrogen and progesterone stop getting
produced, the growth of the endometrium cannot be supported. As a result, the endometrium
disintegrates; sloughing off during menstruation.
If implantation of the embryo occurs, the implanted embryo will secrete human chorionic
gonadotropin (HCG) to sustain the corpus luteum. As a result, the corpus luteum will
produce estrogen and
progesterone to maintain the
endometrium. Estrogen and
progesterone production will
then be maintained by the
placenta later on.
Ovarian cycle
follicular phase:
development of the egg and
secretion of the estrogen from
the follicle.
Ovulation: the midcycle
release of the egg
Luteal phase: the secretion
of estrogen and progesterone
from the corpus luteum after
ovulation.
the menstrual cycle consists of
the menstrual flow phase,
proliferative phase, and secretory
phase
menstrual phase is when the
endometrium is shed
proliferative phase is when
estrogens allow the
endometrium to thicken as
allow glands and arteries to
grow during the secretory
phase
secretory phase is when the
corpus luteum produces
progestrone which allows the
endometrium to be receptive
to implantation of the
blastocyst. Progesterone
levels are at the highest
during this phase.
Birth control pills contain
synthetic estrogen and progestin.
Estrogen and progestin stops
pituitary gland from releasing
FSH and LH.

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Four stages of growth and development in an animal:

(1) Gametogenesis spermatogenesis and oogenesis
(2) Embryonic development fertilization of egg until birth
(3) Reproductive maturity puberty
(4) Aging until death
Stages 2 and 3 can collectively be called ontogeny: the origination and development of
an organism, from the time of fertilization of the egg to the organism's mature form.
Fertilization
1a) Capacitation: Secretions from the uterus wall and uterine tube destabilize the plasma
membrane surrounding the head of the sperm, making the head more fluid which helps it
prepare for fertilization, and makes the sperm hyperactive (Faster and wiggle more)
1b) Contact: The sperm contacts the egg's jelly coat, triggering exocytosis of the sperm's
acrosome. The sperm then moves through the corona radiata (dense layer of granulosa
cells surrounding the oocyte) and eventually reaches the zona pellucida.
2) Acrosomal reaction: the hydrolytic enzymes make a hole in the jelly coat. Actin
filaments extend from the sperm onto sperm-binding receptors (ZP3) on the plasma
membrane (zona pellucida) of the egg. The binding to the ZP3 receptors triggers the
acrosome reaction during which the enzymatic contents of the acrosome are released. Helps
the sperm create a hole through the zona pellucida.
In non-mammals, the zona pellucida plays an important role in preventing crossbreading of different species (especially in species that fertilize outside the body).
Zona pellucida is commonly used to control wildlife populations by
immunocontraception. When the zona pellucida of one animal species is injected into
the blood stream of another, it results in sterility of the second species due to immune
responsefertilization cannot occur because antibodies have already bound the zona
pellucida, preventing sperm from binding.
3) contact and fusion of sperm and egg membranes: fusion triggers depolarization of the
membrane, which acts as a fast block to polyspermy (prevents other sperm from fusing)
4) cortical reaction: cortical granules in the egg fuse with the plasma membrane. The
secreted contents clip off the sperm-binding receptors and cause the fertilization envelope to
form. This acts as a slow block to polyspermy.
5) Entry of sperm nucleus. This triggers meiosis II
6) fusion of nuclei and replication of DNA: sperm and ovum nuclei fuse to create the
zygote

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Cleavage
The zygote undergoes a succession of rapid cell divisions that characterize the cleavage
stage of early development.
during cell cleavage the nuclear to cytoplasmic ratio increases
G1 and G2 phase of cell cycle basically skipped, cells are in S and M phase.
No increase in mass
Cleavage partitions of the cytoplasm of the larged fertilized egg into many smaller cells
called blastomeres.
Pattern of cleavage divisions differs among species.

Common characteristics of early cleavage:

Embryo polarity (asymmetric cleavage): Egg has an upper, animal pole, and a lower,
vegetal pole. The yolk (stored nutrients) will be distributed unequally, pooling at the
vegetal pole.
Polar and equatorial cleavages: The yolk begins to affec the relative size of cells
produced in the two hemispheres. This division is equatorial if the line is perpentiduclar
to the line connecting the poles. The division can also be polar if the line is the same line
connecting the poles.
Holoblastic vs meroblastic: Holoblastic is when the cleavage furrow passes entirely
through the egg whereas meroblastic means when the cleavage furrow does not pass
entirely through the egg.
Radial and spiral cleavages: In duterostomes, early cleavages are radial, forming cells
at the animal and vegetal poles that are aligned together, the top cells directly above the
bottom cells. In protosomtes, cleavages are spiral, forming cells that are shifted with
respect to those below them.
Indeterminate and determinate cleaves: A cleavage is said to be indeterminate if it
produces blastomeres that, if separated, can individually complete normal development.
Blastomeres produced by a determinate cleavage cannot develop into a complete
embryo if separated from other blastomeres.
Radial cleavages in duterostomes are usually indeterminate, whereas spiral
cleavages in protostomes are usually determinate.
Successive cleavage divisions result in a solid ball of cells called a morula (8 cell stage, the
cells are totipotent).
As cell divisions continue, liquid fills the morula and pushes cells out to form a circular
cavity surrounded by a single layer of cells. The hollow sphere of cells is called the blastula

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(128 cell stage) and the cavity is called the blastocel.
Formation of the gastrula occurs when a group of cells invaginate (move inward) into the
blastula, forming a two layered embryo with an opening from the outside into a center
cavity. Special features:
Archentron: The center cavity formed by gastrulation. Completely surrounded by
endoderm cells. Develops into the digestive tract of an animal.
Blastopore: opening into the archentron. Becomes the mouth (in protostomes) or the
anus (in duterostomes).
Three germ layers: A third cell layer forms in between the outer and inner layers of the
invaginated embryo. These three cell layers, the ectoderm, mesoderm, and endoderm
(outside, middle, and inside layer, respectively) are the three primary germ layers from
which all subsequent tissues develop.
Ecotderm: forms epidermis skin, nervous and sensory systems, pituitary gland, jaws
and teeth, germ cells
Mesoderm: muscle, bone, kidneys, blood, gonads, and connective tissues
Endoderm: epithelial lining of most organs, thymus, thyroid, and parathryoid glands,
liver, and the lungs

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Embryonic membrane development

In birds, reptiles, and humans, called the amniotes, extraembryonic (outside the embryo)
membranes develop, as follows:
Chorion: The chorion is the outer membrane that surrounds the embryo. In birds and
reptiles, it acts as a membrane for gas exchange. In mammals, the chorion implants into
the endometrium. Later, the chorion forms the placentaa blaned of maternal and
embryonic tissues across which gases, nutrients, and wastes are exchanged.
Amnion: The amnion is a membrane encloses the amniotic cavity, a fluid-filled cavity
that cushions the developing embryo.
Allantois: A sac that buds off from the archentron. Eventually, it encircles the embryo,
forming a layer below the chorion. In birds and reptiles, it initially stores waste
products. Later in development, it fuses with the chorion, and together they act as one
membrane for gas exchange. In mammals, the allantois transports waste product to the
placenta. Eventually forms the umbilical cord.
In birds and reptiles, a yolk sack membrane digests enclosed yolk. Yolk is a part of an
egg that feeds the developing embryo. Blood vessels transfer nutrients to the embryo. In
placental mammals, the yolk sack is empty as the umbilical cord/placenta delivers
nutrients.
Organogenesis
The development of organs is called organogenesis. Features characteristic of chordates:
Notochord: cells along the dorsal surface of the mesoderm germ layer form the
notochord, a stiff rod that provides support in lower order chordates. In most vertebrates,
a more complex, joined skeleton develops around the ancestral notochord, and the adult
retains only remnants of the embryonic notochord.
Neutral tube: In the ecotderm layer directly above the notochord, a layer of cells form
the neural plate. The plate indents, forming the neural groove, and then rolls up into a
cylinder, the neural tube. The neural tube develops into the nervous system. Additional
cells roll off the top of the developing neural tube and form the neural crest. These cells
form various tissues: including teeth, bone, and muscles of the skull, etc.

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Important variations in other animals in development

Frog (an amphibian)
When the sperm penetrates a frog egg, a reorganization of the cytoplasm results in the
appearance of a gray, crescent-shaped region, called the gray crescent.
The dorsal lip, which forms at the site of the grey crescent, is the site of initiation of
gastrulation in the amphibian embryo. The bottom and sides of the blastopore edge are
called the ventral and lateral lips.
Cells from the vegetal pole rich in yolk material form a yolk plug near the dorsal lip.

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Bird
Most of the yolk in the bird is not involved in cleavages. Instead, the cleavages occur in
a blastula that consists of a flattened, disk-shaped region that sits on top of the yolk. This
is called a blastodisc. When gastrulation occurs, invagination occurs along a line called
the primitive streak. As cells migrate into the primitive streak, the crevice formed
becomes an elongated blastopore.

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Humans
At the end of cleavage, the embryo is a blastocyst, the mammalian version of a blastula.
Clustered at one end of the blastocyst cavity is a group of cells called the inner cell
mass (embryonic disk) and at the other end is another ring of cells called the
trophoblast.
5 days after fertilization, the blastocyst performs zone hatching: the zona pellucida
degenerates and is replaced by an underlying layer of trophoblastic cells so it can
implant in the uterus.
The trophoblast have several functions. First, it accomplishes implantation by
embedding into the endometrium of the uterus. It produces human chorionic
gonadotropin, which maintains progesterone production of the corpus luteum (which,
in turn, will maintain the endometrium). Later, the trophoblast forms the chorion, the
extraembryonic membrane that will eventually turn into the placenta.

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Within the trophoblast, a bundle of cells called the inner cell mass (embryonic disk)
clusters at one end and flattens into the embryonic disk. This is analogous to the
blastodisk of birds and reptiles. A primitve streak develops, gastrulation follows, and
development of the embryo and the extraembryonic membranes ensues.
Fertilization (syngamy) takes place in the fallopian tubes (oviduct). Cleavage occurs
while the fertilized egg is still moving through the oviduct. The embryo is at the blastula
stage by the time it reaches the uterus for implantation.

Factors that influence development and differentiationInfluence of the egg cytoplasm.

Cytoplasmic material is distributed unequally in the egg and subsequent daughter cells
during cleavage (i.e. yolk and gray crescent). Nonuniform distribution of the cytoplasm
results in embryonic axes. When cleavages divide the egg, the quality of cytoplamic
substances will vary among daughter cells. Substances unique to certain daughter cells may
influence their subsequent development.
Embyronic induction is the influence of one cell group or group of cells over neighboring
cells. Cells that exert this influence are called organizers; they do this by secreting
chemicals that diffuse to neighboring cells, influencing their development.
The dorsal lip functions as an organizer for the notochord.
Homeotic genes contribute to the control of development by turning on and off other genes
that code for substances that directly affect development. A homeobox is an 180 nucleotide
sequence that is highly conserved between many species that are homeotic genes.
Apoptosis, programmed cell death, is a normal part of development. Damaged cells
undergo apoptosis; if not, cancer may develop.
During embyronic development, the individual digits separate after being fused. This
best illustrates apoptosis.
The fate of a cell is said to be determined if its final form cannot be changed. Cells are
more likely to be determined later in the developmental sequence than earlier.
By tracing the fates of cells during development, a lineage map can be built (tells you
which cells arose from which cells).
Stem cells
Many early animal embryos contain stem cells capable of giving rise to differentiated cells
of any type (embryonic stem cells).
Stem cells can be isolated from early embryos at the blastula stage, or the blastocyst stage in

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humans. These cells can differentiate into many different types of cells.
Adult body has stem cells (adult stem cells), but they can only generate a few different
types of cells.
Totipotent stem cells are the most versatile of stem cell types. Can give rise to ANY and
ALL human cells. Can give rise to an entire organism. First few divisions in embryonic
development produce totipotent cells.
Pluripotent stem cells can give rise to all tissue types, but CANNOT give rise to an entire
organism.
Multipotent stem cells give rise to a limited range of cells within a tissue type.
Fertilization, Pregnancy and Labor
Human oocytes can be fertilized most successfully by the use of micro-injection
Fraternal twins result from more than one egg being fertilized; identical twins result from
indeterminate cleavage
Ectopic pregnancy results when the zygote makes contact and starts to grow in improper
places.
Tubal pregnancies are when the zygote implants itself into the fallopian tube
Erythroblastosis fetalis = A fatal disease in pregnant women that is caused by
incompatibility between a mother's blood and her unborn baby's blood. Because of the
incompatibility, the mother's immune system may launch an immune system against the
baby's red blood cells. As a result, the baby may die. Two types:
Rh incompatibility disease: Rh+ fetus; Rh- mother
ABO incompatibility disease
first trimester of pregnancy is where organs are formed
at approximately 8 weeks, the embryo is called a fetus
at 5 weeks, eyes, heart, liver, pancreas, and limb buds have begun development
Labor (three stages) a series of strong uterine contractions
1. Cervix thins out and dilates, amniotic sac ruptures and releases fluids
2. Rapid contractions followed by birth
3. Uterus contracts and expels umbilical cord and placenta
Evolution and development (evo-devo)
Evolution and development is the combination of developmental biology and evolutionary
biology.
Studies the evolution of the timing and rate of development, the evolution of function,
and the evolution of the regulation and expression of genetic networks.
Ontogeny recapitulates phylogeny is an idea that suggests embryonic stages of
development of an organism repeat the evolutionary history of the species. This idea is
not true, but is rather seen as an historical-side note.
How do proteins take new functions?
Subfunctionalization: gene duplication produces gene copies that diverge and divide
the work initially undertaken by the gene before duplication.
Neofunctionalization: duplicated genes diverge and one copy takes on a new function.
Promiscuous proteins: proteins capable of carrying out more than one function (usually
sone strongly and one weakly)
Gene recruitment: the co-option of a particular gene or network for a totally different
function as a result of mutation.
Gene duplication: any duplication of DNA that contains one or many genes

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How do genes duplicate?
Slippage during replication
Ectopic recombination: error in recombination where unequal parts of the homologous
chromosomes recombine
Retrotransposition
Whole genome duplication (e.g., polyploidy)
Gene duplication
homologs: genes that share common ancestry.
paralogs: homologous genes within a genome separated by a gene duplication event.
orthologs: homologous genes separated by a speciation event.
Complex adaptations: suites of coexpressed traits that together experience selection for a
function
What guides the development of organisms?
Homeotic genes: genes associated with mapping body shape during development
In insects, molting and metamorphosis are regulated by the hormone ecdysone

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Body organization and types of tissues
Hierarchical organization of body plans
Cells are organized into tissues, groups of cells with a similar appearance and a common
function.
Different types of tissues are further organized into functional units called organs.
Organs are generally made up of 4 types of tissue:
Nervous tissue
Epithelial tissue
Muscle
Connective tissue
Groups of organs that work together, providing an additional level of organization and
coordination, make up an organ system.
Types of animal tissues
Epithelial cells or epithelia cover the outside of the body and line organs and cavities
within the body.
Epithelial cells are closely packed, often with tight junctions.
They function as a barrier against mechanical injury, pathogens, and fluid loss.
Also form active interfaces with the environment.
Different cell shape and arrangements correlate to distinct functions.
They are polarized, meaning that they have two different sides.
The apical surface faces the lumen (cavity) or outside of the organ and is therefore
exposed to fluid or air. Specialized projections often cover this surface.
The opposite side of each epithelium is the basal surface.
Connective tissue consists of a sparse population of cells scattered through an extracellular
matrix. It holds many tissues and organs together and in place.
Three different types of connective tissue fibers:
Collagenous fibers provide strength and flexibility
Reticular fibers join connective tissue to form adjacent tissues
Elastic fibers make tissues elastic
Loose connective tissue is the most common tissue: binds epithelia to underlying
tissues and holds organs in place.
Fibrous connective tissues is dense with collagenous fibers.
Bone generates the skeleton of animals.
Adipose tissue stores fat in adipose cells.
Blood carry nutrients from one place to another.
Cartilage contains collagenous fibers embedded in chondroitin sulfate. Very strong.
cartilage tissue is surrounded by a dense fibrous connective tissue called
Perichondrium
Muscle tissue is the tissue responsible for nearly all types of body movement.
Skeletal muscle is responsible for voluntary movements.
Smooth muscle, which lacks striations, is responsible for involuntary body movements.
Cardiac muscle forms the contractile wall of the heart and is involuntary.
Nervous tissue functions in the receipt, processing, and transmission of information.
Contains neurons, which transmits nerve impulses, and support cells called glial cells.
Peritoneum is the tissue that covers all the digestive organs and lines in the body cavity.
Homeostasis
Regulating and conforming

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An animal is a regulator for an environmental variable if it uses internal mechanisms to

control internal change in the face of external fluctuation.
An animal is a conformer for a particular variable if it allows its internal conditions to
change in accordance with external changes in the variable.
An animal may regulate some processes and conform to other processes.
Homeostasis
Homeostasis means steady state, referring to the maintenance of internal balance.
In achieving homeostasis, animals maintain a relatively constant internal environment even
when the external environment changes significantly.
Mechanisms of homeostasis
An animal achieves homeostasis by maintaining a variable at a particular value, or set
point.
A fluctuation in the variable above or below the set point serves as the stimulus detected by
a sensor.
Upon receiving a signal from the sensor, a control center generates an output that triggers a
response, a physiological activity that helps return the variable to the set point.
Feedback control in homeostasis
Negative feedback is a control mechanism that reduces the stimulus.
For example, you sweat to decrease the effects of heat (increase body temperature).
Positive feedback (e.g. orgasm) is a control mechanism that amplifies, rather than reduces,
the stimulus.
Does not play a major role in homeostasis, but helps drive processes to completion.
Alterations in homeostasis
A circadian rhythm is a set of physiological changes that occur roughly every 24 hours.
One way in which homeostasis may be altered is through acclimatization, the gradual
process by which an animal adjusts to changes in its external environment.
Acclimatization is a temporary change during an animal's lifetime and does not bring
about any changes within the genetic code.

Thermoregulation
Endothermy and Ectothermy
Endothermic means that the organism is warmed by internal mechanisms.
Can maintain a stable body temperature in the face of large fluctuations in the
environmental temperature.
Ectothermic means that the organism gains heat from external sources.
Mainly adjust their body temperature by behavioral means.
Ectotherms generally need to consume much less food than endotherms of equivalent
size.
Organisms may be both ectothermic and endothermic in some way.
Variation in body temperature
A poikilotherm is an animal whose body temperature varies with its environment.
A homeotherm has a relatively constant body temperature.
There is no fixed relationship between endothermy, homeothermy, poikilothermy, and
ectothermy.
Balancing heat loss and gain
The essence of thermoregulation is maintaining a rate of heat gain that equals the rate of

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heat loss.
Many of these mechanisms involve the integumentary system, the outer covering of
the body, consisting of the skin, hair, and nails.
Radiation is the emission of electromagnetic waves by all objects warmer than absolute
zero.
Evaporation is the removal of heat from the surface of a liquid that is losing some of its
molecules as gas.
Convection is the transfer of heat by the movement of air or liquid past a surface.
Conduction is the direct transfer of thermal motion (heat) between two molecules of
objects in contact with each other.
Insulation
A major thermoregulatory adaptation is insulation, which reduces the flow of heat between
an animal's body and its environment.
Insulation may include hair or feathers, as well as layers of fat formed by adipose tissue.
Circulatory adaptations
Nerve signals that relax the muscles of vessel walls result in vasodilation, a widening of
superficial blood vessels. As a result, blood flow of the skin increases. Done in hot
temperatures.
Vasodilation warms the skin and increases the transfer of body heat to the environment.
Vasoconstriction reduces blood flow and heat transfer by decreasing the diameter of
superficial vessels. Done in cold temperatures.
In many birds and mammals, reducing heat loss from the body comes from countercurrent
heat exchange, the transfer of heat between fluids that are flowing in opposite directions.
Arteries and veins are located adjacent to each other. As warm blood moves from the
body to the core in the arteries, it transfers heat to the colder blood returning from the
extremities in the veins.

Cooling by evaporative heat loss

Many terrestrial animals lose water by evaporation from their skin and respiratory surfaces.
Water absorbs considerable heat when it evaporates (high specific heat); this heat is carried

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away from the body surface with water vapor. This is evaporative heat loss.
Behavioral responses
Many ectotherms maintain a nearly constant body temperature by engaging in relatively
simple behaviors.
When cold, they seek warm places, orienting themselves toward heat sources and
expanding their portion of body surface exposed to the heat source.
When hot, they bate, moving to cool areas, or turn in another direction, minimizing their
absorption of heat form the sun.
Adjusting metabolic heat production
Endotherms can vary heat production, thermogenesis, to match changing rates of heat loss.
It is increased by such muscle activity as moving or shivering.
Nonshivering thermogenesis occurs in brown adipose tissues. The breakdown of the
adipose tissues eventually generates a proton gradient. Instead of using the gradient to
synthesize ATP, the gradient is used to generate heat.
Physiological Thermostats
The sensors for thermoregulation are concentrated in the hypothalamus
within the hypothalamus, a group of nerve cells functions as a thermostat, responding to
body temperatures outside the normal range by activating mechanisms that promote heat
loss or gain.

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Respiratory system
Partial pressure gradients in gas exchange
Partial pressure is the pressure exerted by a particular gas in a mixture of gasses. A gas
always undergoes net diffusion from a region of higher partial pressure to a region of lower
partial pressure.
Respiratory media
The conditions for gas exchange vary considerably, depending on whether the respiratory
mediumthe source of oxygenis air or water.
Gas exchange with air is much easier than gas exchange with water due to differing
diffusional coefficients. Do2 in air is higher than DO2 in water.
Aquatic animals that need to extract oxygen out of water have developed special adaptations
to do this.
Respiratory surfaces
The respiratory surface is the part of an animal's body where gas exchange occurs.
The cells that carry out gas exchange have a plasma membrane that must be in contact with
an aqueous solution. Respiratory surfaces are always moist.
The movement of oxygen and carbon dioxide across respiratory surfaces takes place by
diffusion.
Respiratory surfaces tend to be large and thin to maximize surface area to maximize the
flux of these gases.
In sponges, cnidarians, and flatworms, every cell in the body is close enough to the external
environment so that gases can diffuse quickly between any cell and the environment. The
skin serves as the respiratory organ.
In other animals, the bulk of the body's cells lack immediate access to the environment.
External vs internal respiration
External respiration refers to the entrance of air into the lungs and the gas exchange
between the alveoli and the blood
Internal respiration includes the exchange of gas between blood and the cells and the
intracellular processes of respiration.
Gills in aquatic animals
Gills are outfoldings of the body surface that are suspended in the water. They often have a
total surface area much greater than that of the rest of the body's exterior.
Movement of the respiratory medium over the respiratory, a process called ventillation,
maintains the partial pressure gradients of oxygen and carbon dioxide across the gill that are
necessary for gas exchange.
In fishes, the efficiency of gas exchange is maximized by countercurrent exchange, the
exchange of a substance or heat between two fluids moving in opposite directions.
In a fish gill, the two fluids are blood and water.
As blood enters a gill capillary, it encounters water that is completing its passage
through the gill (almost depleted of oxygen). The partial pressure of oxygen in the water
is greater than that of the blood in the capillaries, and oxygen transfer takes place.
Because blood flows in the direction opposite to that of water passing over the gills,
at each point in its travel blood is less saturated with oxygen than the water it meets.
Even as the blood continues its passage, its partial pressure of oxygen steadily
increases, but so does that of the water it encounters, since each successive position
in the blood's travel corresponds to an earlier position in the water's passage over the
gills.

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Tracheal systems in insects

The tracheal system is a network of airtubes that branch throughout the body.
The largest tubes, called tracheae, open tot he outside.
The finest branches, tracheoles, extend close to the surface of nearly every cell, where

gas is exchanged by diffusion across the moist epithelium that lines the tips of tracheal
branches.
Lungs
Lungs are localized respiratory organs. They are an infold of the body surface that are
typically subdivided into numerous pockets. It is the largest internal organ.
In humans, the right lung is larger than the left lung. The right lung has 3 lobes whereas the
left lung has 2 lobes.

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Pleurae is the thin, smooth membranous outer covering of the lungs.

Because the respiratory surface of a lung is not in direct contact with all other parts of the
body, the gap must be bridged by the circulatory system.
Book lungs are stacks of flattened membranes enclosed in an internal chamber.
Mammalian respiratory systems

Air enters through the nostrils. The air is then filtered by hairs, warmed, humidified, and
sampled for odors through the nasal cavity.
Mucus secreted by goblet cells traps large dust particles, pollen, and other particulate
contaminants.
The nasal cavity leads to the pharynx, an intersection where the paths for air and food
cross.
All the contaminants and mucus are swept back here by cilia for disposal via spitting or
swallowing. Called the mucus escalator.
smoking can damage the cilia of the respiratory cells and allow toxins to remain in
lungs
The larynx is the upper part of the respiratory pathway. It is the voice-box; if non-gas
enters, cough reflex activates.
Also controls action of the epiglottis. If food is moving down the pharynx, the larynx
will tip the epiglottis over the glottis, which is the opening of the trachea so food can
move down through the esophagus. If air is moving through, the epiglottis is covering
the esophagus, so air can travel down through the glottis.

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The trachea is the windpipe.
The walls of the trachea is reinforced by ringed cartilage that is C-shaped (for strength
and to keep the airway open).
Covered by ciliated mucus cells.
The trachea branches into two bronchi, one leading to each lung. Within each lung, the
bronchi branch repeatedly into finer and finer tubes called bronchioles.
Gas exchange in mammals occur in alveoli, air sacs clustered at the tips of the thinnest
bronchioles.
emphysema is a pathology marked by destruction of alveoli
Oxygen diffuses through the alveolar wall through the pulmonary capillary wall, into
blood, and into red blood cells. Carbon dioxide moves in the opposite direction starting
at the red blood cells and moving into the alveoli.
Alveoli lack cilia or significant air currents to remove particles from the surface so they
are highly susceptible to contamination.
White blood cells patrol the alveoli, engulfing foreign particles.
Alveoli produces a mixture of phospholipids and proteins called surfactant, which coats
the alveoli and reduces surface tension which prevents collapse.
Breathing
How an amphibian breathes
An amphibian such as a frog ventilates its lungs by positive pressure breathing, inflating
the lungs with forced airflow.
Muscles lower the floor of an amphibian's oral cavity, drawing in air through its nostrils.
With the nostrils and the mouth closed, the floor of the oral cavity rises, forcing air
down the trachea and into the lungs.
During exhalation, air is forced back out by the elastic recoil of the lungs and by
compression of the muscular body wall.
How a bird breathes
To bring fresh air into their lungs, birds use eight or nine air sacs situated on either side of
the lungs.
The air sacs do not function directly in gas exchange but acts as bellow that keep air
flowing through the lungs.
Instead of having alveoli, sites of gas exchange in bird lungs are tiny channels called
parabronchi.
Two cycles of inhalation and exhalation are required to pass one breath through the system:
First inhalation: air fills the posterior air sacs
First exhalation: posterior air sacs contract, pushing air into the lungs
Second inhalation: air passes through the lungs and fills the anterior air sacs
Second exhalation: as anterior air sacs contract, air that entered the body at first
inhalation is pushed out of the body.

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How a mammal breathes

Tidal breathing is breathing in and out through the same tubing, inhibiting gas exchange
during exhalation.
Deoxygenated air is mixed with some fresh air during inhalation, some of it is rebreathed
Much less efficient than birds as a result
Mammals employ negative pressure breathingpulling, rather than pushing, air into their
lungs.
Using muscle contraction to expand their thoracic cavity, mammals use lower air
pressure in their lungs below the air outside the body. The pressure gradient causes air to
flow into the lungs.
During exhalation, the muscles controlling the thoracic cavity relax, and the volume of the
cavity is reduced. The increased air pressure in the alveoli forces air up into the breathing
tubes and out of the body.
Expanding the thoracic cavity during inhalation involves the animal's rib muscles and the

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diaphragm, a sheet of skeletal muscle that forms the bottom wall of the cavity.
The diaphragm is a skeletal muscle and is controlled by the phrenic nerve It is also the
only organ which only and all mammals have, and without which no mammal can live.
Inhalation is an active process diaphragm and the intercostal muscles (between ribs)
contract and flattens. This causes an increase in volume and a decrease in pressure in the
lungs. The pressure gradient is created and there is a bulk flow of air into lungs.
Exhalation is a passive process decrease in lung volume causes an increase in air
pressure. Air then rushes out and the diaphragm relaxes and expands.

The volume of air inhaled and exhaled with each breath is called tidal volume.
The tidal volume during maximal inhalation and exhalation is called vital capacity.
The air that remains after a forced exhalation is called the residual volume.
As you get older, residual volume increases while vital capacity decreases.
Control of breathing in humans
Most of the time your breathing is regulated by involuntary mechanisms.
The neurons mainly responsible for regulating breathing are in the medulla oblongata, near
the base of the brain. Neural circuits in the medulla form a pair of breathing control
centers that establish the breathing rhythm.
chemoreceptors located on the aorta and carotid arteries are involved in blood gas content
monitoring.
When you breathe deeply, a negative-feedback mechanism prevents the lungs from over
expanding: during inhalation, sensors that detect stretching of the tissue send nerve impulses
to control circuits in the medulla, inhibiting further inhalation.
In regulating breathing, the medulla uses the pH of the surrounding tissue fluid as in
indicator as blood carbon dioxide concentration.
Blood carbon dioxide is the main determinant of the pH of cerebrospinal fluid, the fluid
surrounding the brain and the spinal cord.
Carbon dioxide diffuses from the blood and into the cerebrospinal fluid, where it reacts
with water to form carbonic acid. Carbonic acid then dissociates into bicarbonate
anion and hydrogen ion.
In response to decreasing pH, the medulla will increase the depth and rate of breathing

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until the pH returns to a normal value.
Respiratory pigments
coordination and circulation of gas exchange
During inhalation, fresh air mixes with air remaining in the lungs.
The resulting mixture formed in the alveoli has a higher Po2 and a lower PCO2 than the blood
through the alveolar capillaries.
As a result, there is a net diffusion of oxygen out of the alveoli and there is a net
diffusion of carbon dioxide into the alveoli.
By the time leaves the lungs in the pulmonary veins, its Po2 and Pco2 match the values for
those gases in the alveoli (because they are in equilibrium).
In the systemic capillaries, the partial pressure gradients favor oxygen to diffuse out of the
blood and carbon dioxide to diffuse into the blood.
After the blood unloads oxygen and loads carbon dioxide, it is return to the heart and
pumped to the lungs again. And the cycle re-begins.
Respiratory pigments
Animals transport most of their oxygen bound to proteins called respiratory pigments.
Respiratory pigments greatly increase the amount of oxygen that can be carried within
the circulatory fluid.
The main respiratory pigment of all most all vertebrates and many invertebrates is
hemoglobin.
In vertebrates, it is contained in erythrocytes (RBCs) and has 4 subunits, each with a
cofactor called a heme group with an iron atom at its center.
Each heme binds one molecule of oxygen, so 1 hemoglobin molecule can carry 4
molecules of oxygen.
Hemolgobin binding to oxygen is reversible, allowing it to load O2 in one area and
unload it elsewhere.
Binding for O2 is cooperative, meaning that when one oxygen molecule binds, the other
subunits conformations change, increasing their affinities for oxygen.
As we have seen, high amounts of carbon dioxide lowers the pH of its surroundings by
reacting with water to form carbonic acid. Low pH decreases the affinity of hemoglobin
for oxygen, an affect called the Bohr shift. This is to facilitate hemoglobin to release
oxygen to offset the increased carbon dioxide concentrations.
2,3-diphosphoglycerate (2,3-DPG) is produced from an intermediate compound in
glycolysis and decreases the affinity of hemoglobin for oxygen.
Produced when there are low oxygen levels so that hemoglobin can be stimulated to
release its bound oxygen molecules.
During high levels of oxygen, oxyhemoglobin inhibits the enzyme that synthesizes
2,3-DPG.
Chloride shift: carbonic anhydrase is in red blood cells so charge must be maintained
when bicarbonate ions (negative charge) leaves the cell. When bicarbonate diffuses out
into the plasma, chloride anions enter.
Haldane effect: Deoxygenation of the blood increases hemoglobin's ability to carry carbon
dioxide whereas oxygenated blood decreases hemoglobin's ability to carry carbon dioxide.
CO2 does not dissolve in blood well, so we need to convert it into H2CO3 to increase the
dissolving ability.
At tissues we have high concentrations of carbon dioxide (from respiration). It will

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diffuse into the blood cell, where carbonic anhdyrase will turn it into H2CO3, which
then becomes bicarbonate and H+. This explains why high [CO2] lead sot low pH.
At the lungs, CO2 wants to leave the blood and into the alveoli while oxygen wants to
leave the alveoli and into the blood cells. However, the CO2 is in the bicarbonate form,
so it will have to re-enter the RBC where the carbonic anhydrase will reverse the
reaction and turn it back into CO2. It will then diffuse out of the lungs.
Consider hemoglobin: hemoglobin is going to interact with H+ (Bohr shift) to form an
alternative version of hemoglobin that doesn't bind to oxygen as well and therefore will
end up binding to CO2 instead. So in the presence of high [CO2] and [H+], the
hemoglobin structure is altered to the alternative form that will release oxygen and will
bind to CO2.
Bigger picture: tissues are high [CO2] and [H+] and they are not getting a lot of oxygen
so we want to oxygenate them. When hemoglobin arrives at these tissues, the low pH
causes Bohr shift which stimulates the hemoglobin to release its oxygen molecules to
the tissues and will stimulate the hemoglobin to attach to CO2 molecules. When
Hemoglobin binds to CO2, it prevents the CO2 from forming carbonic acid. In this sense,
hemoglobin is acting as a buffer by binding to CO2 molecules to prevent more CO2
molecules from turning into carbonic acid and decreasing the pH. At the lungs, carbonic
acid will be re-converted back into CO2. This will raise the pH and cause the
hemoglobin molecule to return back to its normal form with higher affinities for oxygen.
CO2 leaves to the alveoli while oxygen diffuses in and becomes bound to the
hemoglobin.

Factors that affect dissociation curve of hemoglobin:

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the dissociation curve of hemoglobin is sigmodial.
Curve is shift right (oxygen is released easier, lower oxygen affinity) increase of CO2
pressure, H+ concentrations, temperature, and exercise. CADET face right!
Myoglobin is the oxygen binding pigment in muscles.
It has a hyperbolic dissociation curve.
No cooperative binding
single subunit
Saturates very quickly and releases in very low oxygen emergency muscle situations
Fetal hemoglobin has a dissociation curve shifted to the left compared to an adult.
By shifting the curve to the left, the fetal hemoglobin has a higher binding affinity to
grab oxygen from maternal blood.

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Circulatory systems in other animals
Protozoans and other unicellular animals
Movement of gas through simple diffusion within the cell
Gastrovascular cavities
Gastrovascular cavity is a digestion and circulatory system with only one opening
usually seen in Cnidarians.
Fluid bathes both the inner and outer tissue layers, facilitating exchange of gases and
cellular waste. Only the cells lining the cavity have direct access to nutrients released by
digestion. However, the body wall is 2 cells thick so the diffusion distance is really
small.
In a hydra, thin branches of the gastrovascular cavity extend into the animal's tentacles.
In jellies and other cnidarians, the gastrovascular cavity has a much more elaborate
branching pattern.
Flatworms and planarians survive without a circulatory system due to the combination of a
gastrovascular cavity and a flat body.
Flat body optimizes exchange with environment by increasing surface area and
minimizing diffusion distances.
Open and closed circulatory systems
A circulatory system has 3 basic components:
circulatory fluid
set of interconnecting vessels
a muscular pump, the heart
In an open circulatory system, the circulatory fluid, called hemolymph is also the
interstitial fluid that bathes body cells.
Arthropods have open circulatory systems.
Heart contraction pumps hemolymph through the circulatory vessels into
interconnected sinuses, spaces surrounding the organs.
Within the sinuses, chemical exchange occurs between the hemolymph and body cells.

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In a closed circulatory system, a circulatory fluid called blood is confined to vessels and is
distinct from the interstitial fluid.
One or more hearts pump blood into large vessels that branch off into smaller ones that
infiltrate the organs.
Chemical exchange occurs between the blood and the interstitial fluid, as well as
between the interstitial fluid and the body cells.
Annelids, cephalopods, and all vertebrates have closed circulatory systems.

Open circulatory systems require less energy input than closed circulatory systems.
Closed circulatory systems allows animals to be larger.
Organization of vertebrate circulatory systems
The closed circulatory system of humans and other vertebrates is called the cardiovascular
system.
Blood flow through blood vessels is unidirectional
Blood vessels are only distinguished by the direction in which they carry blood
Arteries carry blood from the heart to organs throughout the body.
Within organs, arteries branch into arterioles.
Arterioles convey blood to capillaries, microscopic vessels with very thin, porous walls.
Networks of capillaries, called capillary beds, infiltrate tissues, passing within a few
cell diameters of every cell in the body. Exchange of gases and nutrients occur between
the interstitial fluid and capillary beds.
At their downstream end, capillaries converge into venules, and venules converge into
veins, the vessels that carry blood back to the heart.
Portal veins (exception to the general rule) carry blood between pairs of capillary beds
in the digestive system to capillary beds in the liver.
The hearts of all vertebrates contain two or more muscular chambers.
The chambers that receive blood entering to the heart are called atria (singular, atrium)
and the chambers responsible for pumping blood out of the heart are called ventricles.

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Single circulation
In bony fishes, rays, and sharks, the heart consists of two chambers: an atrium and a
ventricle.
The blood passes through the heart once in each complete circuit through the body, an
arrangement called single circulation.
Blood pumped out from the ventricles go to the capillary bed in the gills, where oxygen
diffuses into the blood and carbon dioxide diffuses out of the blood.
As blood leaves the gills, the capillaries converge into a vessel that carries oxygen-rich
blood to capillary beds throughout the body.
Deoxygenated blood then travels back to the heart (atria).
Double circulation
The circulatory systems of amphibians, reptiles, and mammals have two circuits, an
arrangement called double circulation.
The pumps for the two circuits are combined into a single organ, the heart (allows for
coordination of both circuits).
One pump, the right side of the heart, delivers oxygen-poor blood to the capillary beds of
the gas exchange tissues where oxygen/carbon dioxide exchange occurs. This is called the
pulmonary circuit if the capillary beds are all in the lungs. It is called a pulmocutaneous
circuit if it includes capillaries in both the lungs and the skin, as in many amphibians.
After oxygen-enriched blood leaves the gas exchange tissues, it enters the other pump, the
left side of the heart. The heart will propel the blood to capillary beds in organs and tissues
throughout the body, where appropriate exchanges will occur between capillaries and the
interstitial fluids. Deoxygenated blood then travels back to the heart, completing the
systemic circuit.

Mammals and birds have 4 chambered hearts

Repitles and amphibians have 3 chambered hearts
Fish have 2 chambered hearts

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Crocodiles and alligators have 4 chambered hearts
The heart
Mammalian circulation

Contraction of the right ventricle pumps blood to the lungs via pulmonary arteries.
As blood flows through capillary beds in the left and right lungs, it loads oxygen and
unloads carbon dioxide.
Oxygen-rich blood returns to the lungs via the pulmonary veins to the left atrium of the
heart.
Oxygen-rich blood flows into the left ventricle.
Blood leaves the left ventricle via the aorta, which conveys blood to arteries leading
throughout the body.
The first branches leading from the aorta are the coronary arteries, which supply blood to
the heart muscle itself.
Then branches lead to capillary beds in the head and arms, where the appropriate exchanges
occur.
The aorta descends into the abdomen, supplying oxygen-rich blood leading to capillary beds
in the abdominal organs and legs, where the appropriate exchanges occur.
Deoxygenated blood in the upper half of the body is channeled into a large vein, the
superior vena cava. The inferior vena cava drains blood form the bottom half of the body.
The two venae empty their blood into the right atrium, for which oxygen-poor blood flows
into the right ventricle and restarts the cycle.
Mammalian heart structure

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The two atria have relatively thin walls and serve as collection chambers for blood
returning to the heart from the lungs or other body tissues.
The two ventricles have thicker walls and contract much more forcefully. The left ventricle
contracts with more force than the right ventricle since it needs to pump blood to the entire
body.
The heart contracts and a rhythmic cycle called the cardiac cycle.
When the heart contracts, it pumps blood; when it relaxes, its chambers fill with blood.
The contraction phase is called systole, and the relaxation phase is called diastole.
The volume of the blood each ventricle pumps per minute is called the cardiac output
(heart reat * stroke volume = cardiac output). Two factors:
Rate of contraction, or heart rate (beats per minute)
stroke volume, the amount of blood pumped by a ventricle in a single contraction.
Stroke volume = end diastole volume end systolic volume
Four valves prevent backflow and keep blood moving in the right direction. Made up of
connective tissue, valves open when pushed from one side and close when pushed from the
other.
Atrioventricular (AV) valves lie between each atrium and ventricle.
Pressure generated by contraction of the ventricles closes the AV valves, preventing
blood from flowing back into the atria.
Papillary muscles are located in the ventricles and bind to the AV valve to prevent
inversion of these valves during systole.
Valve on the right side of the heart has 3 cusps and is called the tricuspid valve
The valve on the left side has 2 cusps and is called the mitral valve.
Semilunar valves are located at the two exits of the heart: where the aorta leaves the left
ventricle and where the pulmonary artery leaves the right ventricle.
Pushed open by pressure generated from contraction of ventricles.
Relaxation of ventricles closes the semilunar valves and prevents backflow.
If blood squirts backward through a defective valve, it may produce an abnormal sound
called a heart murmur.
Maintaining the heart's rhytmic beat
Some cardiac muscle cells are autorhythmic, meaning they can contract and relax
repeatedly without any signal from the nervous system.
The sinoatrial (SA) node sets the rate and timing at which all cardiac muscle cells contract.
It is autorhythmic and is located in the wall of the right atrium, near where the superior
vena cava enters the heart.
Some arthropods have SA nodes located in the nervous system, outside the heart.
Produces electrical impulses. Since cardiac muscle cells are electrically coupled through
gap junctions, impulses from the SA node spread rapidly throughout heart tissue.
Impulses from the SA node spread rapidly through the walls of the atria, causing both atria
to contract in unison.
When the atria contracts, the impulses originating at the SA node reach other autorhythmic
cells located in the wall between the left and right atria. The cells form a relay point called
the atrioventricular (AV) node.
The impulses at the AV node are delayed by about 0.1 seconds before spreading to the
heart so that the atria can completely empty.
The signals from the AV node are sent through the bundle of His, nodal tissue that passes

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down between both ventricles and then branches into the ventricles through the Purkinjie
fibers. This impulse results in the contraction of the ventricles.
Physiological cues can later heart tempo by regulating the SA node.
The parasympathetic and sympathetic nervous systems are largely responsible for this.
Sympathetic nervous system speeds up SA node and heartbeat, and the
parasympathetic nervous system slows down SA node and heartbeat.
Body temperature affects SA node.
An increase in 1 degree Celsius increases heart rate by 10 beats per minute.
Blood Vessels
Blood vessel structure
Blood vessels contain a central lumen (cavity) lined with an endothelium, a single layer of
flattened epithelial cells.
The smooth surface of the endothelium minimizes resistance to the flow of blood
Capillaries are the smallest blood vessels and have very thin walls, which consist of an
endothelium and a surrounding extracellular layer called the basal lamina.
Exchange of substances between blood and the interstitial fluid only occurs in capillaries
because the walls are thin enough to permit this exchange.
The walls of arteries and veins have more complex organization than those of capillaries.
The outer layer is connective tissue that contains elastic fibers, that provides strength.
The layer next to the endothelium contains smooth muscle.
The walls of arteries are thick and strong, accommodating blood pumped at high
pressure by the heart and are elastic.
Veins have a thinner wall than arteries. Also contain valves which maintains a
unidirectional flow of blood.
Blood flow velocity
The velocity of blood slows as it moves from arteries to arterioles to the much narrower
capillaries.
TOTAL cross sectional area is inversely proportional to velocity.
As capillaries have the highest total cross sectional area, velocity is lowest.
The larger the blood vessel, the lower the total cross sectional area, and the higher the
velocity (arteries > arterioles and veins > venules)
Note: the greatest resistance to blood flow is located in the arterioles.
Blood pressure
Contraction of a heart ventricle generates blood pressure, which exerts a force in all
directions.
Arterial blood pressure is highest when the heart contracts during ventricular systole. The
pressure at this time is called systolic pressure.
The rhythmic bulging of the artery is the pulse.
During diastole, the elastic walls of the artery snap back. As a consequence, there is a lower
but still substantial blood pressure when the ventricles are relaxed. This is the diastolic
pressure.
Regulation of blood pressure
As the smooth muscles in the arteriole walls contract, the arterioles narrow, a process called
vasoconstriction. This increases the artery blood pressure.
When the smooth muscles in the arteriole relax, the arterioles undergo vasodilation, an

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increase in diameter that causes blood pressure in the arteries to fall.

Nitric oxide is the major inducer of vasodilation and endothelin, a peptide, is the major
potent inducer of vasoconstriction.
Capillary function
Given that capillaries lack smooth muscle, how is blood flow in the capillary beds altered?
One mechanism is constriction or dilation of the arterioles that supply capillary beds.
A second mechanism involves precapillary sphincters, rings of smooth muscle located
at the entrance to each capillary bed.
These sphincters regulate and redirect the passage of blood into particular sets of
capillaries.
Two opposing forces control the movement between the capillaries and the surrounding
tissues:
Blood pressure tends to drive fluid out of the capillaries
the presence of blood proteins tend to pull fluid back. The dissolved proteins in the
blood generates osmotic pressure
Blood pressure > osmotic pressure, so this leads to a let loss of fluid from the capillaries.
The net loss is generally greatest at the arterial end of these vessels, where the blood
pressure is highest.

Double capillary beds occur in the glomerulus, around the loop of henle, small intestine,
liver, hypothalamus, and anterior pituitary gland. The capillary bed pools into another
capillary bed without first going to the heart (transports products in high concentration
without spreading to the rest of the body)
Capillary bed 1 drains into the portal vein and capillary bed 2 drains into vein that
returns to the heart
Fluid return by the lymphatic system
The lost fluid and proteins return to the blood via the lymphatic system, which includes a
tiny network of vessels intermingled among capillaries of the cardiovascular system, as well
as larger vessels into which small vessels empty.
After entering the lymphatic system by diffusion, the fluid lost by capillaries is called

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lymph; its composition is about the same as that of the interstitial fluid.
The lymphatic system drains into large veins of the cardiovascular system at the base of
the neck.
Lymph vessels have valves to prevent backflow
Along a lymph vessel are small, lymph-filtering organs called lymph nodes, which play an
important role in the body's defense.
Contains phagocytic cells (leukocytes) that filter the lymph and serve as immune
response centers.
The spleen is an organ that makes lymphocytes, filters the blood, stores blood cells, and
destroys old blood cells.
Blood components
Blood composition and function
Blood is 55% plasma and 45% other cellular components.
Vertebrate blood is a connective tissue of consisting of cells suspended in a liquid matrix
called plasma.
Many of the dissolved solutes are inorganic ions sometimes referred to as electrolytes.
Some ions buffer the blood
Some ions maintain the osmotic balance of blood
Affects the composition of the intersitial fluid
Plasma proteins acts as buffers against pH and helps maintain the osmotic balance
Contains nutrients, metabolic wastes, respiratory gases, and hormones.
Has a much higher protein concentration than interstitial fluid, although the two fluids
are otherwise similar.
Cellular elements
Red blood cells, or erythrocytes, are by far the most numerous blood cells. The main
function is oxygen transport.
Contains hemoglobin, an iron-containing protein that transports oxygen (up to 4
molecules per molecule).
Lacks organelles and a nucleus to maximize hemoglobin content.
NOTE that erythrocytes derive their energy from glycolysis and not from the TCA
cycle and oxidative phosphorylation!
erythropoietin is a hormone released from the kidneys and will stimulate red blood
cell formation in the bone marrow
White blood cells are leukocytes. Their function is to fight infections.
Diapedesis is the process
by which white blood cells
become part of the
interstitial fluid (slip
through endothelial lining)
Platelets are pinched-off
cytoplasmic fragments of
specialized bone marrow cells.
Functions in blood clotting.
Do not contain a nucleus.
Derived from
megakaryocytes.
Maintenance of body pH

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body fluid is relatively constant at 7.4 this consistency is attained by the removal of CO2
by the lungs and hydrogen ions by the kidneys and buffer systems (look in general
chemistry notes for an explanation for buffers).
Phosphate buffer system is the predominant buffer system that operates in the internal
fluid of all cells.
Carbonic-acid-bicarbonate buffer system is by far, the most important buffer for
maintaining acid-base balance in the blood.

Disorders:
Respiratory: affects the blood acidity by causing changes in PCO2 (high CO2 = acidic)
Metabolic: affects the blood acidity by causing changes in HCO3- (High HCO3- = basic)
Blood clotting
Platelets adhere to exposed collagen of damaged vessel and cause neighboring platelets to
form the platelet plug (temporary sealing the break in the vessel wall).
Both the platelets and damaged tissue release clotting factor called thromboplastin.
Thromboplastin converts inactive plasma protein prothombrin to thrombin
Thrombin converts fribrinogen into fibrin
Fibrin threads coat damaged area and trap blood cells to form a clot. Serum is the fluid left
after blood clotting.
A thrombus is a blood clot that forms in a vessel abnormally.

Fetal circulation important for the DAT

oxygenated, nutrient-rich blood from placenta is carried to fetus via umbilical vein
Blood bypasses the liver through the ductus venosus. The ductus venosus provides a direct
communication between the umbilical vein and the inferior vena cava. Oxygenated blood
from the ductus venosus combines with the deoxygenated blood in the inferior vena cava
and continues to the heart.
Blood travels to the fetus heart through the inferior vena cava and mixes with deoxygenated
blood returning from the superior vena cava. Blood then enters the right atrium of the
heart.
Because fetal lungs are not functional, most blood will bypass the right ventricle and be
shunted to the left atrium via the foramen ovale. Blood will then travel into the left
ventricle and be distributed throughout the fetal body via the aorta.
Some blood will enter the right ventricle from the right atrium and proceed to the
pulmonary trunk. However, most of this blood will be shunted away from the
pulmonary arteries and into the aorta via the ductus arteriosus.
Blood circulates through the fetal body and returns to the placenta via the umbilical
arteries. These arteries are also carrying deoxygenated blood back to the placenta.
The placenta re-oxygenates blood returning from the umbilical arteries and repeats the

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fetal cardiovascular cycle by recycling the newly oxygenated blood to the fetus through the
umbilical vein.
Click the link below, and select fetal system for an excellent animation to understand this!
http://www.indiana.edu/~anat550/cvanim/fetcirc/fetcirc.html

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Features of diet
Chemcial energy and food
The energy content of food is measured in kilocalories (1 kcal = 1,000 calories)
The rate of energy consumption by an animal is called its metabolic rate. It is the sum of
all the energy used by biochemical reactions over a given time interval.
The number of kilocalories a resting animal requires to fuel essential biochemical processes
for a given time is called the basal metabolic rate (BMR).
Any activity will consume kilocalories in addition tot he BMR.
Essential Nutrients
Some cellular processes require materials that an animal cannot assemble from simpler
organic precursors.
These materialspre-assembled organic molecules and mineralsare called essential
nutrients.
Essential nutrients include essential amino acids and fatty acids, vitamins and minerals.
Essential nutrients serve key functions in cells such as serving as substrates of enzymes
(as coenzymes), and as cofactors in biosynthetic pathways.
Essential amino acids are the 8 amino acids that cannot be synthesized within the body.
Essential fatty acids are fatty acids that contain double bonds that cannot be normally
synthesized within the body.
Vitamins are organic molecules that are required in the diet in very small amounts.
Are either fat-soluble or water-soluble.
Minerals are inorganic nutrients that are usually required in small amounts.
Dietary deficiencies
A diet that lacks one or more essential nutrients or consistently supplied less chemical
energy than the body requires results in malnutrition, failure to obtain adequate nutrition.
A diet that fails to provide adequate sources of energy results in undernutrition.
Digestion in other animals
Main stages of food processing
The first stage, ingestion, is the act of eating or feeding.
During digestion, the second stage of food processing, food is broken down into molecules
small enough for the body to absorb.
Mechanical digestion breaks food into smaller pieces, increasing the surface area
available for chemical processes.
Chemical digestion is necessary because animals cannot directly use the proteins,
carbohydrates, nucleic acids, fats, and phospholipids in foods.
Enzymatic hydrolysis breaking macromolecules into smaller components through
breaking bonds by adding water.
In the third stage, absorption, the animal's cell take up (absorb) small molecules.
Elimination completes the process as undigested material passes out of the digestive
system.
4 main feeding mechanisms of animals
Many aquatic animals are filter feeders (whale), which strain small organisms or food
particles from the surrounding medium.
Substrate feeders (caterpillar) are animals that live in or on their food source.
Most animals, including humans, are bulk feeders (humans), which eat relatively large
pieces of food.
Fluid feeders (mosquito) suck nutrient rich fluid from a living host.

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Intracellular digestion
Food vacuoules, cellular organelles in which hydrolytic enzymes break down food, are the
simplest digestive compartments. The hydrolysis of food inside vacuoules is called
intracellular digestion.
This usually occurs after phagocytosis or pintocytosis.
Amoeba captures food via phagocytosis. The engulfed food becomes a food vacuoule. A
lysosome fuses with the food vacuoule, and its enzymes breakdown the food.
The cilia of paramecium sweeps food into its cytopharynx. The food vacuoule forms and
moves toward the anterior of the cell, where it will fuse with a lysosome and become
degraded.
Extracellular digestion
In most animal species, hydrolysis occurs largely by extracellular digestion, the f body.
Many animals with relatively simple body plans have a digestive compartment with a single
opening called a gastrovascular cavity. It functions in digestion as well as in the
distribution of nutrients throughout the body.
A hydra uses its tentacles to stuff captured prey through its mouth into its
gastrovascular cavity. Specialized gland cells of the hydra's gastrodermis, the tissue
layer that lines the cavity, then secretes digestive enzymes that break the soft tissues of
the prey into tiny pieces. Other cells of the gastrodermis engulf these food particles, and
most of the hydrolysis of macromolecules occur intracellularly.

Most animals have a digestive tube extending between two openings, a mouth and an anus.
This is a complete digestive tract, or more commonly, an alimentary canal.

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The alimentary canal of an earthworm includes a muscular pharynx that sucks food
through the mouth. Food passes through the esophagus and is stored and moistened in
the crop. Mechanical digestion occurs in the muscular gizzard, which pulverizes food

with the aids of small bits of sand and gravel. Further digestion and absorption occurs in
the intestine. The intestine contains typholosole which helps increase surface area for
absorption.
A grasshopper has several digestive chambers grouped into three main regions: a
foregut, with an esophagus and a crop; a midgut; and a hindgut. Food is stored and
moistened in the crop, but most digestion occurs in the midgut. Pouches called gastric
cecae extend from the beginning of the midgut and function in digestion and absorption.

Many birds have a crop for strong food and a stomach and gizzard for mechanically
digesting it. Chemical digestion and absorption of nutrients occurs in the intestine.

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Digestion in plants and fungi

Plants do not have a digestive system. Most of digestion occurs intracellularly. The
processes are similar to animals.
Plants store starch primarily in seeds, stems, and roots
When nutrients are required, polymers are broken down into the appropriate monomers
by enzymatic hydrolysis.
Some plants use extracellular digestion
Venus flytrap enzymes diggest trapped flies (serves as nitrate source). However, it is
still autotrophic.
Fungi rhizoids of bread mold secrete enzymes into bread, producing simple digestive
products which are then absorbed by diffusion into rhizoid.

Human Digestive System

Introduction
In mammals, the digestive system consists of the alimentary canal and various accessory
glands that secrete digestive juices through the ducts into the canal.
Accessory glands are salivary galnds, pancreas, liver, and the gallbladder.

Food is pushed along the alimentary canal by peristalsis, alternating waves of contraction
and relaxation in the smooth muscles lining the canal.
At some junctions between specialized compartments, the muscular layer forms ringlike
valves called sphincters. They regulate passage of material between compartments.
The oral cavity, pharnyx, and esophagus
Ingestion and the initial steps of digestion occur in the mouth, or oral cavity.
Mechanical digestion occurs through chewing of food.
The salivary glands deliver saliva through ducts to the oral cavity. Saliva initiates
chemical digestion while also protecting the oral cavity.
The enzyme amylase hydrolyzes starch into smaller polysaccharides and maltose.
The protective effect of saliva is provided by mucus, which protects the lining of the
mouth from abrasion and lubricates food for easier swallowing.
The tongue aids digestive processes by evaluating ingested material to determine if

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it should be ingested and then enabling its further passage if it is deemed okay. It
also helps manipulate the mixture of saliva and food into a ball shape called a bolus.
papillae are projections on the tongue surface and are involved in the sensation
of taste.
The pharynx, or throat region, opens to two passageways: the trachea (windpipe) and
the esophagus.
The esophagus connects to the stomach. When a food bolus arrives at the pharynx,
the larynx tips a flap of tissue called the epiglottis down, preventing food from
entering the trachea. The upper esophageal sphincter (blocks esophagus) relaxes,
allowing the bolus to pass through. Once food enters here, peristaltic contractions of
smooth muscle move each bolus to the stomach.
Digestion in the stomach
The stomach, which is located just below the diaphragm, stores foods and begins digestion
of proteins.
Secretes a digestive fluid called gastric juice and mixes with the food. This mixture of
ingested food and gastric juice is called chyme.
Components of gastric juice:
Hydrochloric acid which disrupts the ECM that binds cells together. Also creates a low
pH environment in the stomach (pH = 2), which kills most bacteria, and denatures
proteins in food.
Pepsin, a protease, cleaves peptide bonds to turn proteins into smaller polypeptides.
Works best in a very acidic environment.
The interior surface of the stomach wall is highly folded and dotted with pits leading into
tubular gastric glands. The gastric glands have all three types of cells that secrete the
different components of the gastric juice.
Parietal cells use an ATP-driven pump to expel hydrogen ions into the lumen. Also
pumps out chloride ions. Only in the lumen the H+ and the Cl- ions combine to form
HCl.
G cells secrete gastrin, a large polypeptide hormone which is absorbed into the
blood. It stimulates parietal cells to secrete HCl.
Gastrin also stimulates ECL cells, neuroendocrine cells in the digestive tract.
They release histamine which in turn stimulates parietal cells to produce
hydrochloric acid.
Chief cells release pepsin into the lumen in an inactive form called pepsinogen. HCl
converts pepsinogen into active pepsin. Then pepsin itself activates the remaining
pepsinogens. Example of positive feedback.
Mucous cells secrete mucus, which lubricates and protects the cells lining the stomach.

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Peptic ulcers are caused by failure of mucosal lining to protect stomach. Can also
be caused by excess stomach acid or H. pylori as well.

Chemical digestion by gastric juice is facilitated by the churning action of the stomach.
Churning is the coordinated series of muscle contractions and relaxations that mixes the
stomach contents about every 20 seconds.
The lower esophageal sphincter, or cardiac sphincter, is the sphincter between the
esophagus and the stomach that normally opens only when bolus arrives.
Occasionally, a person experiences acid reflux, a backflow of chyme from the stomach
into the lower end of the esophagus.
The controlled release of chyme into the small intestine is controlled by the pyloric
sphincter.

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Digestion in the small intestine

The small intestine is the alimentary canal's longest compartment and most of the
enzymatic hydrolysis of macromolecules from food occurs here.
The first section of the small intestine forms the duodenum. Most of the digestion is
completed in this section. It is here that chyme from the stomach mixes with the digestive
juices from the pancreas, liver, and gallbladder, as well as gland cells of the intestinal wall
itself.
The pancreas aids chemical digestion by producing an alkaline solution rich in
bicarbonate as well as several enzymes.
The bicarbonate neutralizes the acidity of the chyme and acts as a buffer.
Pancreatic enzymes secreted are trypsin and chemotrypsin, proteases secreted into
the duodenum in inactive forms. Trypsin gets activated first by enteropeptidase
(enzyme secreted from intestinal glands when food passes through duodenum), and
then it activates the other enzymes.
Pancreas also secretes lipases (digestion of fats) and pancreatic amylase (digestion
of starch).
Liver produces bile, a substance that helps digest fats and other lipids. Bile contains
salts, which acts as emulsifiers. Bile is stored and concentrated in the gallbaldder.
The epithelial lining of the duodenum is a source of several digestive enzymes. Some
are secreted into the lumen of the duodenum, whereas others are bound to the surface of
epithelial cells.
Peristalisis moves the mixture of chyme and digestive juices along the small intestine.
The remaining regions of the small intestine, the jejunum and the ilenum, are the major
sites for absorption of nutrients.
Absorption in the small intestine
Most of the absorption occurs at highly folded surface of the small intestine.
Large folds in the lining encircle the intestine and are studded with finger-like
projections called villi. In turn, each epithelial cell of a villus has on its apical surface
many microscopic projections called microvilli.
This confers extremely high surface area, which greatly increases the rate of
absorption.
Depending on the nutrient, transport across epithelial cells can be passive or active.
Goblet cells secrete mucus to lubricate and protect epithelial cells from
mechanical/chemical damage.
The capillaries and veins that carry nutrient-rich blood away from the villi converge into
the hepatic portal vein, a blood vessel that leads directly to the liver.
By channeling all nutrients through the liver, it allows it to regulate the distribution
of nutrients to the rest of the body.
Also allows liver to remove toxic substances.

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Some products of fat digestion take a different path.
Hydrolysis of fats by lipase in the small intestine generates fatty acids and
monoglycerides.
They are absorbed by epithelial cells and then recombined into triglycerides.
They are then coated with phospholipids, cholesterol, and proteins, forming globules
called chylomicrons.
Chylomicrons are first transported from an epithelial cell in the intestine to a lacteal, a
lymph filled vessel at the core of each villus. The lacteal passes the chylomicrons to the
heart.
Small intestine also absorbs water and ions.

Functions of the liver

Blood storage
Blood filtration kupfer cells (macrophages) phagocytize bacteria picked up in intestines
Carbohydrate metabolism liver maintains normal blood glucose levels via
gluconeogenesis (generation of glucose) and glycogenesis (generation of glycogen)
All carbohydrates absorbed into the blood are carried by the hepatic portal vein into the
liver.
Protein metabolism liver deaminates amino acids, forms urea from ammonia in blood,
synthesizes plasma proteins, synthesizes nonessential amino acids.

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Detoxification detoxidifes chemicals, secreted by liver as part of bile

Erythrocyte destruction kupfer cells destroy irregular erythrocytes (most are done by
spleen)
Vitamin storage and iron storage
if blood glucose levels are high glycogenesis
if blood glucose levels are low
glycogenolysis
Produces bile
Jaundice is yellowing of the skin due to excess bilirubin (typically liver failure).
Processing in the large intestine
The alimentary canal ends with the large intestine, which includes the colon, cecum, and
rectum. The small intestine connects to the large intestine at a T-shaped junction.
One long arm is the colon, which leads to the rectum and anus.
The other arm is a pouch called the cecum, which is important for fermenting ingested
material.
The appendix, a finger-like extension of the human cecum, has a minor and dispensable
role in immunity.
The colon completes reabsorption of water that began in the small intestine. What remain
are the feces, the wastes of the digestive system, which becomes increasingly solid by the
end.
If less water than normal is reabsorbed by the colon, the result is diarrhea
If too much water is reabsorbed by the colon, the result is constipation.
A rich community of mostly harmless bacteria lives on the unabsorbed organic material in
the colon. The main source of vitamin K and vitamin B come from these symbiotic
bacteria.
The terminal portion of the large intestine is the rectum, where the feces are stored until
they can be eliminated.
Between the rectum and anus are two sphincters, the inner one being involuntary
and the outer one being voluntary.

Regulation of digestion
Hormonal control of digestion
A branch of the nervous system called the enteric division is dedicated to regulating
digestive events and peristalisis in the small and large intestines.
Gastrin is produced by the stomach lining, and the effects have been discussed above.
Secretin is produced by cells lining duodenum when food enters; this stimulates pancreas
to produce bicarbonate (neutralizes the chyme).
Enteropeptidase is produced by cells lining the duodenum when food enters; this
stimulates the pancreas to deposit its mass of digestive enzymes into the duodenum.
Somatostatin is produced by delta cells of the pancreas. It will suppress the release of
gastrointestinal hormones such as gastrin, secretin, and cholecystokinin. This suppression
will decrease the rate of gastric emptying along with reducing blood flow within the
intestines.
Cholecystrokinin is produced by small intestine in response to fats; stimulates gallbladder
to release bile and pancreas to release its enzymes.
If the chyme is rich in fats, high levels of secretin and cholecystrokinin released act on
the stomach to inhibit peristalsis and secretion of gastric juices, thereby slowing down
digestion.
Gastric inhibitory peptide is produced in response to fat/protein digestates in the

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duodenum; mild decrease of stomach motor activity.

Glucose homeostasis
When the blood glucose level rises above the normal range, the secretion of insulin triggers
the uptake of glucose from the blood into body cells, thereby decreasing the blood glucose
concentration.
Insulin does not act on the brain.
When the blood glucose level drops below the normal range, the secretion of glucagon
promotes the release of glucose into the blood by breaking down storage carbohydrates
(glycogen).
Both hormones are produced in the pancreas.
Alpha cells within the pancreatic islets create glucagon and beta cells create insulin.
Diabetes Mellitus
Diabetes mellitus is caused by a deficiency of insulin or a decreased response to insulin in
target tissues.
Cells do not take in glucose to break down for energy; instead the cells mainly use fat.
Type 1 diabetes is when the immune system destroys the beta cells within the pancreas and
thus destroys the person's ability to synthesize insulin.
Type 2 diabetes is characterized by a failure of target cells to respond normally to insulin.
Insulin is produced, but target cells fail to take up glucose from the blood, and blood
glucose levels remain elevated.
Regulation of appetite and consumption
Secreted by the stomach wall, ghrelin is one of the signals that triggers feelings of hunger
as mealtimes approach.
A rise in blood sugar level after a meal stimulates the pancreas to secrete insulin. Among
other functions, insulin suppresses appetite by acting on the brain.
Produced by adipose tissue, leptin suppresses appetite. When the amount of body fat
decreases, leptin levels fall, and appetite increases.
The hormone PYY, secreted by the small intestine after meals, acts as an appetite
suppressant that counters the appetite stimulant ghrelin.

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Osmoconformers vs. osmoregulators
Osmoregulatory challenges and mechanisms
An osmoconformer has its internal osmolarity isoosmotic with its surroundings.
Marine animals are all osmoconformers.
An osmoregulator has its internal osmolarity independent compared to its surroundings.
Enables animals to live in environments that are inhabitable for osmoconformers, such
as freshwater and terrestrial habitats, or to move between marine and freshwater
environments.
Many marine vertebrates and some marine invertebrates are osmoregulators. Their body is
hypotonic to the environment and water will naturally flow out. Mechanisms:
Gain of water and salt ions from eating food and drinking seawater.
Osmotic water loss through gills and other pats of the body surface.
Excretion of salt ions from gills.
Excretion of salt ions and small amounts of water in scanty urine from kidneys.
Freshwater fish are osmoregulators. Their body is hypertonic to the environment, meaning
water will naturally flow in.
Gain of water and some ions in food. NO DRINKING.
Uptake of salt ions by gills.
Osmotic water gain through gills and other parts of body surface.
Excretion of salt ions and large amounts of water in dilute urine form kidneys.

Transport epithelia in osmoregulation

In most animals, osmoregulation and metabolic waste disposal rely on transport epithelia
one or more layers of epithelial cells specialized for moving particular solutes in
controlled amounts in specific directions.
Typically arranged into complex tubular networks with extensive surface areas.
In birds, the transport epithelium are the pair of nasal salt glands.
Salt glands use active transport to secrete excess salts. They maintain salt balance and
allow for saltwater to be drank.

Nitrogen waste
Forms of Nitrogenous Waste
Animals that secrete nitrogenous wastes as ammonia need access to lots of water because
ammonia can be tolerated at very low concentrations. Most common in aquatic species.
Most terrestrial animals and many marine species secrete urea. The advantage is that urea
has very low toxicity. The disadvantage is that it requires tremendous amounts of energy.
Insects, land snails, and many reptiles, including birds, create uric acid as their primary

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nitrogenous waste. The advantage is that uric acid is not toxic and it can be disposed with
minimal water loss. Disadvantage is that it requires lots of energy.
Structure of excretory systems
Excretory processes
Hydrostatic pressure drives a process of filtration, where a tubule collects a filtrate from
the blood. Proteins and other large molecules can't be filtered out of the blood while small
solutes can.
The transport epithelium then reclaims valuable substances from the filtrate and returns
them to body fluids. This is reabsorption.
Other substances, such as toxins and excess ions, are extracted from body fluids and added
to the contents of the excretory tubule. This is called secretion
The altered filtrate (urine) leaves the system and the body. This is called excretion.
Excretory systems in simple organisms
All of the cells in protozoans and cnidarians are in contact with the external, aqueous
environment. Water soluble wastes (i.e. ammonia, carbon dioxide) exit by simple diffusion.
Protists such as paramecium and amoebas possess contractile vacuoules which pump water
out of the cell by active transport.
Excess carbon dioxide, waste oxygen, and water leave plants by diffusion through stomata
and lenticels in a process called transpiration.
Protonephridia
Platyhelminthes and Rotifera have units called protonephridia, which form a network of
dead-end tubules.
The tubules, which are connected to external openings, branch throughout the flatworm
body.
Cellular units called flame bulbs cap the branches at each protonephridium.
During filtration, the beating of the cilia draws water and solutes from the interstitial
fluid through the flame bulb, releasing filtrate into the tubule network.
The filtrate then moves outward through the tubules and empties as urine into the
environment.

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Metanephridia
Annelids have metanephridia, excretory organs that collect fluid directly from the coelom.
Each segment of an annelid has a pair of metanephridia, which are immersed in
coleomic fluid and enveloped by a capillary network.
A ciliated funnel surrounds the internal opening of each metanephridium.
As the cilia beat, fluid is drawn into a collecting tubule, which includes a storage
bladder that opens to the outside.

Malphagian tubules
Arthropods have organs called malphagian tubules that remove nitrogenous wastes and
also function in osmoregualtion.
They extend from dead-end tips immersed in the hemolymph to openings in the
digestive tract.
There is NO filtration step.
The transport epithelium that lines the tubules secretes certain solutes from the
hemolymph into the lumen of the tubule.
Water follows the solutes into the tubule by osmosis, and the fluid then passes into the
rectum.
There, most solutes are pumped back into the hemolymph, and water reabsorption by
osmosis follows.
Wastes are eliminated as dry matter along with feces.

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Mammalian Excretory system

Excretory organs
In the lungs, CO2 and water vapor diffuse from the blood and are continually exhaled.
The liver produces nitrogenous wastes, blood pigment wastes, and other chemical
wastes.
excess bilirubin causes jaundice (usually a liver issue)
The skin sweat glands excrete water and dissolved salts to regulate body temperature.
The excretory system consists of kidneys, a pair of organs for transporting and storing
urine.
Urine produced by each kidney exits through a duct called the ureter; the two ureters
drain into a common sac called the urinary bladder.
During urination, urine is expelled from the bladder through a tube called the urethra
Sphincter muscles near the junction of the urethra and bladder regulate urination.
Kidney structure
Each kidney has an outer renal cortex and an inner renal medulla. Both regions are
supplied with blood by a renal artery and drained by a renal vein.
Within the cortex and the medulla lie tightly packed excretory tubules and associated
blood vessels.
The fluid that will be excreted as urine is collected in the inner renal pelvis, and exits
the kidney via the ureter.
Nephron Types

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Weaving back and forth across the renal cortex and medulla are the nephrons, the
functional units of the vertebrate kidney.
85% of the nephrons are cortical nephrons, which reach only a short distance into the
medulla.
The remainder, the juxtamedullary nephrons, extend deep into the medulla.
They are essential for production of urine that is hyperosmotic to body fluids, a key
adaptation for water conservation in mammals.

Nephron organization
Each nephron consists of a single long tubule as well as a ball of capillaries called the
glomerulus. The blind end of the tubule forms a cup-shaped swelling, called Bowman's
capsule, which surrounds the glomerulus.
Filtrate is formed when blood pressure forces fluid from the blood in the glomerulus
into the lumen of Bowman's capsule.
Processing occurs as the filtrate passes through three major regions of the nephron: the
proximal tubule the loop of Henle, and the distal tubule.
A collecting duct receives processed filtrate from many nephrons and transports it to the
renal pelvis.
Each nephron is supplied with blood by an afferent arteriole an offshoot of the renal
artery that branches and forms the capillaries of the glomerulus. The capillaries
converge as they leave the glomerulus, forming an efferent arteriole.
Branches of this vessel form the peritubular capillaries, which surround the proximal
and distal tubules. Other branches extend downward and form the vasa recta, hairpinshaped capillaries that serve the renal medulla, including the long loop of Henle of
juxtamedullary nephrons.
How the whole excretory process occurs
From blood filtrate to urine
The porous capillaries and specialized cells of Bowman's capsule are permeable to water
and small solutes, but not blood cells or large molecules.
The filtrate produced in the capsule contains salts, glucose, amino acids, vitamins,
nitrogenous wastes, and other small molecules.
Concentration of these substances in the initial filtrate are the same as those in blood
plasma.

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Reabsorption in the proximal tubule is critical for the recapture of ions, water, and valuable
nutrients from the huge volume of the initial filtrate.
NaCl gets reabsorbed. Epithelial cells pump Na+ into interstitial fluid, and this transfer
of positive charge out of the tubule drives the passive transport of Cl-.
Glucose, amino acids, and K+ ions are reabsorbed through active or passive
transportation from the filtrate interstitial fluid peritubular capillaries.
Water gets reabsorbed through passive transport.
Processing of filtrate in proximal tubule help remains constant pH in body fluids:
Cells in transport epithelium secrete H+ and NH3 into the tubule, which then
combines to form NH4+ in the tubule. The more acidic the filtrate is, the more
ammonia the cells secrete into the tubule.
Proximal tubules also reabsorb the buffer HCO3- (bicarbonate) from the filtrate,
contributing further to balance pH.
Reabsorption of water continues as the filtrate moves into the descending loop of hemle.
Numerous water channels formed by aquaporins make the transport epithelium freely
permeable to water.
The osmolarity of the interstitial fluid of the kidney increases progressively from the
outer cortex to the inner medulla. As a result, the kidney osmolarity makes it favorable
to water to be reabsorbed.
The filtrate reaches the tip of the loop and then returns to the cortex in the ascending loop
of Henle.
Two specialized regions: a thin segment near the loop tip and a thick segment adjacent
to the distal tubule.

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As filtrate ascends in the thin segment, NaCl diffuses out passively into the
interstitial fluid. This helps maintains the osmolarity of the interstitial fluid of the
medulla.
In the thick segment of the ascending limb, NaCl must be pumped out actively into
the epithelium.
The distal tubule plays a key role in regulating K+ and NaCl concentration of body fluids
and pH regulation.
K+ is actively secreted from the epithelium and into the distal tubule. The amount
secreted will regulate the K+ concentration in body fluids.
Water is passively reabsorbed.
NaCl is actively reabsorbed from the filtrate. The amount reabsorbed will regulate NaCl
concentration in body fluids.
Contributes to pH regulation by actively secreting H+ into the tuubule and actively
reabsorbing HCO3-.
The collecting duct carries the filtrate through the medulla to the renal pelvis. Final
processing of the filtrate by the transport epithelium of the collecting duct forms the urine.
Hormonal control determines the extent to which the urine becomes concentrated.
When kidneys are conserving water, aquaporin channels in the collecting duct allow
H2O molecules to be reabsorbed passively. At the same time, the epithelium remains
impermeable to salt and urea. This creates a hyperosomotic urine. In the inner
medulla, the duct becomes permeable to urea. Since the urine is hyperosmotic, urea
passively gets reabsorbed.
When kidneys are producing dilute urine, the kidney actively reabsorbs NaCl
without allowing water to follow by osmosis.
Solute gradients and water conservation
The primary solutes affecting osmolarity are NaCl and urea.
The nephron uses countercurrent system to maximize the activities it wants to do.
The nephron uses a countercurrent multiplier system in which it expends energy to
create concentration gradients.
The countercurrent multiplier system makes the medulla very salty which facilitates
water reabsorption.
Types of urine produced in other animals
Mammals can produce hyperosmotic urine.
Birds can produce hyperosmotic urine, but their main water conservation adaptation is uric
acid. birds have a long loop of henle, thus concentrated urine
Reptiles can only produce isoosmotic or hypoosmotic urine.
Freshwater fishes cannot produce hyperosmotic urine.
Amphibians cannot produce hyperosmotic urine.
Homeostatic regulation of the kidney
Hormonal control
The hypothalamus in the brain controls hormones that regulate osmolarity.
Antidiuretic hormone (ADH) or vasopressin helps increase the reabsorption of water in
the collecting duct.
ADH is produced in the posterior
pituitary
hypothalamus
and gland.
stored in the posterior pituitary gland.
When blood osmolarity rises, the hypothalamus trigger release of ADH from the
posterior pituitary.

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ADH brings about changes that make the epithelium more permeable to water (recruits
more aquaporins to the epthelium) and thus able to reabsorb more water.
The increase in water reabsorption concentrates urine, reduces urine volume, and lowers
blood osmolarity back toward the set point.
As the osmolarity of the blood falls, a negative-feedback mechanism reduces the activity
of osmoreceptor cells in the hypothalamus, and ADH secretion is reduced.
The second regulatory mechanism that helps maintain homeostasis by acting upon the
kidney is the renin-angiotensisn-aldosterone system (RAAS).
The RAAS system involves the juxtaglomerular apparatus (JGA), a specialized tissue
consisting of cells of and around the afferent arteriole, which supplies blood to the
glomerulus.
When blood pressure or volume drops in the afferent arteriole (for instance, as a result
of dehydration), the JGA releases the enzyme renin.
Renin initiates a sequence of steps that cleave a plasma protein secreted from the liver
called angiotensinogen ultimately yielding a peptide called angiotensin II.
Angiotension II stimulates the adrenal glands to release a hormone called aldosterone.
Aldosterone causes the nephrons' distal tubules and collecting duct to excrete K+ and
reabsorb more Na+ and water, increasing blood volume and pressure.
Atrial natriuretic peptide (ANP) opposes the RAS.
The walls of the atria of the heart release ANP in response to an increase in blood
volume and blood pressure.
ANP inhibits the release of renin from the JGA.

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Neuron structure and organization
Neuron structure and function
Neurons are cells that transformation within the body.
Most of a neuron's organelles, including its nucleus, are located in the cell body.
A typical neuron has numerous highly branched extensions called dendrites.
The dendrites receive signals from other neurons.
A neuron as a single axon, an extension that transmits signals to other cells.
Axons are much longer than dendrites.
The axon divides into many branches at its end.
The greater the diameter of the axon, the faster impulses will propagate. This is because
larger diameter axons have less resistance to flow of ions.
Each branched end of an axon transmits information to another cell at a junction called a
synapse.
The part of each axon branch that forms this specialized junction is a synaptic terminal.
At most synapses, chemical messengers called neurotransmitters pass information
from the transmitting neuron to the receiving cell.
In describing a synapse, we refer to the transmitting neuron as the presynaptic cell and
the neuron, muscle, or gland cell that receives the signal as the postsynatpic cell.
The connection shaped base of an axon connected to the cell body is called the axon
hillock. This is typically where signals that travel down the axon are generated.
Mylein sheath is an electrically insulating material (made of lipid) that forms around the
axon of a neuron. This increases the speed at which an action potential moves down the
axon.
Mylein sheath is created by glial cells:
Central nervous system neuronal mylein sheath is created by glial cells called
oligodendrocytes.
Peripheral nervous system neuronal mylein sheath is created by glial cells called
Schwann cells.
In myleinated axons, voltage-gated sodium channels are restricted to gaps in the mylein
sheath called nodes of Ranvier.
The extracellular fluid is only in contact with the axon membranes at the nodes.
Depolarization occurs at the nodes of Ranvier.
The mechanism for propagating action potentials along an axon is called saltatory
conduction, because the action potential appears to jump along the axon from
node to node.

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The neurons of vertebrates and most invertebrates require supporting cells called glial cells,
or glia.
They nourish neurons, insulate the axons of neurons, and regulate the extracellular fluid
surrounding neurons.
Nissl bodies are areas of the rough ER that are involved in neuron protein synthesis.
Microglia are the phagocytic cells of the CNS.
Glia sometimes function in replenishing certain groups of neurons and in transmitting
information.
Glial cells vastly outnumber neurons.
Special cells in the CNS:
Astrocytes maintain the integrity of the blood-brain barrier, regulate nutrient and
dissolved gas concentrations, and absorb and recycle neurotransmitters.
Ependymal cells line the brain ventricles and aid in the production circulation, and
monitoring of cerebrospinal fluid.

Introduction to information processing

Introduction
Information processing by a nervous system occurs in three stages:
sensory input: the conduction of signals from sensory receptors to the central nervous
system
integration: analysis and interpretation of the sensory signals and the formulation of the
appropriate responses
motor output: the conduction of signals from the integration centers to effector cells,
which perform the body's responses.
In all but the simplest animals, specialized populations of neurons handle each stage of
information processing.
Sensory (afferent) neurons transmit information about external stimuli or internal

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conditions
Neurons in the brain or ganglia integrate (analyze and interpret) the sensory input. The
vast majority of the neurons in the brain are interneurons (association neurons), which
form the local circuits connecting neurons in the brain.
A vast majority of nerves (~99%) are interneurons
Neurons that extend out of the processing centers trigger output in the form of muscle or
gland activity. These are called motor (efferent) neurons.
In many animals, the neurons that carry out integration are organized in a central nervous
system (CNS).
These constitute all nerves DIRECTLY inside the brain and spinal cord.
The neurons that carry information into and out of the CNS constitute the peripheral
nervous system (PNS).
These constitute all nerves that ARE NOT DIRECTLY inside the brain and spinal cord.
Satellite cells surround the neuron cell bodies in the ganglia. Ganglia are clusters of
neuron cell bodies.

When bundled together, the axons of neurons form nerves, a communication line consisting
of a bundle of neurons tightly rapped in connective tissue.
A plexus is a network of nerve fibers.
The vagus nerve is one very important parasympahetic nerve that innverates many of
the thoracic and abdominal viscera.
Depending on its role in information processing, a neuron can vary from simple to quite
complex.
Ion pumps and channels establish resting potential
Formation of resting potential
There is a charge gradient between the interior of a neuron and the extracellular space. This
charge difference is called a membrane potential.
For a resting neuron, one that is not sending a signal, the membrane potential is called the
resting potential and is typically between -60 and -80 mV.
The sodium-potassium pump plays a key role in establishing the resting potential.
This pump uses the energy of ATP hydrolysis to actively transport out 3 Na+ and actively
pump in 2 K+ into the cell.
The concentration gradients of ions across the plasma membrane represent a form of
potential energy that can be harnessed for cellular processes.
Some ion channels along the membrane of the neuron are always open. These ion channels
are called leak channels and only allow the passive movement of potassium ions.

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Since the internal [K+] is greater than the external [K+], there will be a net movement of
potassium ions out of the cell. This helps generate the internal negative charge of the
neuron.
As there are no leak channels for Na+, sodium cannot move in or out of the neuron
freely.

Action potentials basics

Hyperpolarization and depolarization
Changes in membrane potential occur because neurons contain gated ion channels, ion
channels that open or close in response to stimuli.
When the gate opens, ions flow the channel, changing the membrane potential.
Hyperpolarization is an increase in the absolute value of Vm. The membrane potential
moves farther from 0.
Depolarization is a decrease in the absolute value of Vm. The membrane potential moves
closer to 0.
Graded potentials and action potentials
Threshold is the membrane potential to which an action potential will occur if reached.
In many mammalian neurons, the threshold is -55 mV.
Graded potentials are shifts in the membrane potential that do not reach the threshold
needed for an action potential.
Can be a hyperpolarization or a depolarization.
An action potential occurs when a depolarization causes the membrane potential to reach
the threshold.
Action potentials are all-or-nothing, meaning that if the membrane potential hits the
threshold, an action potential will occur.
Action potentials arise because some of the ion channels in neurons are voltage-gated ion
channels, opening or closing when the membrane potential passes a particular level.
Once a certain membrane potential is experienced, the voltage-gated ion channels will

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open, causing further depolarization.

This positive-feedback mechanism explains the all-or-nothing phenomenon of action
potentials.
Sub-maximal vs. maximal stimulus
A sub-maximal stimulus is the amount of voltage necessary to elicit a response between
the threshold and the maximum response.
Maximal stimulus is the amount of voltage necessary to elicit a maximal response.

Mechanism of action potential

Mechanism
When the membrane of the axon is at the resting potential, most voltage-gated sodium and
voltage-gated potassium channels are closed.
A stimulus (any factor that causes a nerve signal to be generated) opens up some sodium
channels. Na+ inflow through those channels depolarizes the membrane. If the
depolarization reaches the threshold, it triggers an action potential.
Once threshold is crossed, the positive-feedback cycle of the voltage-gated ion channels
rapidly brings the membrane potential close to ENa. This is called the rising phase
ENa is the equilibrium value of sodium. The sodium-potassium pump generates an
electrochemical gradient between inside the neuron and the extracellular space via
active transport. Higher concentration of Na+ outside than inside.
When the voltage-gated ion channels open, Na+ are allowed to passively diffuse to either
side. Since an electrochemical gradient is generated at the resting potential, there is a net
movement of Na+ ions into the neuron. This causes the neuron to become positively
charged.
Two events prevent the membrane potential from actually reaching ENa: (1) Voltage-gated
Na+ channels inactivate soon after opening, halting Na+ inflow and (2) Most voltage-gated
potassium channels open, causing a rapid outflow of K+. Both events quickly bring the
membrane potential back toward EK. This stage is called the falling phase.
EK is the equilibrium value for potassium. The sodium-potassium pump generates an
electrochemical gradient between the inside of the neuron and the extracellular space via
active transport. Higher concentration of K+ inside than outside.
When the voltage-gated ion channels open, K+ can passively diffuse to either side. K+
will spontaneously move out into the extracellular space. This brings the internal
membrane potential down toward EK.
In the final phase of an action potential, called the undershoot, the membrane's
permeability to K+ is higher than at rest, so the membrane potential is closer to EK than it is
to the resting potential. The gated potassium channels eventually close and the membrane
potential returns to resting potential.
This is also called the refractory period, where a second action potential cannot be
initiated. This limits the maximum frequency at which an action potential can be
generated. It is due to inactivation of sodium channels.
Conduction of action potential across axon
Action potential that starts at the axon hillock moves along the axon only toward the
synaptic terminals.
At the site where the action potential is imitated, usually the axon hillock, Na+ inflow
during the rising phase creates an electrical current that depolarizes the neighboring
region of the axon membrane (zone of depolarization). The depolarization is large
enough to reach threshold, causing an action potential in the neighboring region. This

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process is repeated across the axon.
Behind the zone of depolarization is the zone of repolarization caused by K+ outflow.
In this zone, sodium channels remain activated. Therefore, an action potential cannot be
generated here.
Greater diameter and more heavily myelinated axons will propagate faster impulses.
The larger the diameter, the less resistance to flow of ions
A more heavily myelinated axon will have more saltatory conduction
The rate at which action potentials are produced conveys information about the strength of
the input signal.

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Synaptic communication
Introduction
Information is transmitted at the synaptic terminals. Basic steps:
At the terminal of the presynaptic neuron, the neuron synthesizes the neurotransmitter
and packages it in multiple membrane-enclosed compartments called synaptic vesicles.
The arrival of an action potential at the presynaptic terminal depolarizes the plasma
membrane, opening voltage-gated channels that allow Ca2+ ions to diffuse into the
terminal.
The resulting rise in Ca2+ concentration in the terminal causes the neurotransmitter to be
released.
Once released, the neurotransmitter diffuses across the synaptic cleft, the gap that
separates the presynaptic and the postsynaptic neurons.
Upon reaching the postsynaptic membrane, the neurotransmitter binds binds to an
activates a specific response in the membrane.
The leftover neurotransmitter in the synaptic cleft may be taken back into the nerve
terminal (active transport), be degraded by enzymes, or diffuse out of the synapse.

Generation of postsynatpic potentials

The receptor protein that binds and responds to neurotransmitters is a ligand-gated ion
channel, often called an ionotropic receptor.
Binding of the neurotransmitter to a particular part of the receptor opens the channel and
allows specific ions to diffuse across the postsynaptic membrane.
The result is a postsynaptic potential, a graded potential in the postsynaptic cell.
At some synapses, the ionotropic receptor is permeable to Na+ and K+. When this receptor
opens, the membrane potential depolarizes to a value midway between EK and ENa.
This depolarization brings the postsynaptic neuron above the threshold. This is called a

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excitatory postysynaptic potential (EPSP).

At other synapses, the ionotropic receptor is selectively permeable for only K+ and Cl-.
When this receptor opens, the postsynaptic membrane hyperpolarizes.
The hyperpolarization produce din this manner is called an inhibitory postsynaptic
potential (IPSP) because it moves the membrane potential further from threshold.
Neurotransmitters can also bind to metabotropic receptors, a receptor that activates a
signal transduction pathway in a postsynaptic neuron that creates a second messenger.
The second messenger can alter the postsynaptic neuron in diverse ways, such as
altering the number of open potassium channels.
Metabotropic receptors have a slower onset than ionotropic receptors but last longer.
Metabotropic receptors do not directly pump ions like ionotropic receptors!
Summation of postsynaptic potentials
One postsynaptic potential usually isn't strong enough to produce an effect.
One neuron is linked up to many other neurons, so it can receive multiple postsynaptic
potentials in rapid succession from different presynaptic neurons. When this happens, the 2+
postsynaptic potentials add up in effect to produce one main effect.
EPSPs produced nearly simultaneously by DIFFERENT synapses on the same
postsynaptic neuron can add together, an effect called spatial summation.
In addition, two EPSPs can occur at a single synapse in such a rapid succession that the
postsynaptic neuron's membrane potential hasn't returned to resting potential before the
arrival of the second EPSP.
When this happens, the EPSPs add together, an effect called temporal summation.

Neurotransmitters
Types
Acetylcholine is vital for nervous system function that includes muscle stimulation,
memory formation, and learning. Two main acetylcholine receptors:
One is a ligand-gated ion channel, which functions at the vertebrate neuromuscular
junction, the site where a motor neuron forms a synapse with a skeletal muscle cell.
When acetylcholine is released by a motor neuron binds to this receptor, the ion channel
opens forming an EPSP. This is excitatory.
The second is a metabotropic receptor found in locations that include the vertebrate
CNS and heart. Acetylcholine released by neurons activate a G protein signal
transudction pathway that leads to open potassium channels. This is an IPSP, or an
inhibitory effect.
Gamma-aminobutyric acid (GABA) is the neurotransmitter at most inhibitory synapses in
the brain.
Binding of GABA to receptors in postsynatpic cells increases membrane permeability to
Cl-, resulting in an IPSP.
Norepinephrine is an excitatory neurtornasmiter in the autonomic nervous system, a branch
of the PNS.
Dopamine and seratonin are released at many sites in the brain and affect sleep, mood,
attention, and learning.
Nervous systems
Vertebrate central nervous system
During embryonic development, the central nervous system develops from the notochord
a hallmark of chordates.

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Meninges cover around the brain and spinal cord.
The brain is made up of outer gray matter and inner white matter. Surrounded by
cerebrospinal fluid.
There are 12 pairs of cranial nerves that are sensory, motor, and mixed. Most cranial
nerves are mixed.
The forebrain has activities that include the processing of olfactory input (smells),
regulation of sleep, learning, and any complex processing.
The cerebrum is the largest part of the brain.
Divided into the left and right cerebral hemispheres. Left hemisphere controls
right side of body and vice versa. In a phenomenon known as lateralization,
areas in the two hemispheres become specialized for different functions during
brain development in humans and children. In most people, the left hemisphere
becomes adept at language, logic, and mathematical operations, as well as
detailed skeletal motor control and the processing of fine visual and auditory
details. The right cerebral hemisphere is stronger at spatial relations, pattern, and
face recognition, and nonverbal thinking.
A thick band of axons called the corpus calossum enables the right and left
hemmispheres to communicate.
Under the corpus callosum, groups of neurons called the basal nuclei are
important in motor coordination.
Divided into 4 lobes:
Frontal lobe concerned with reasoning, planning, parts of speech,
movement, emotions and problem solving.
Parietal lobe concerned with perception of stimuli such as touch, pressure,
temperature and pain.
Temporal lobe concerned with perception and recognition of auditory
stimuli (hearing) and memory.
Occipital lobe concerned with many aspects of vision.
The outer layer of the cerebrum is called the cerebral cortex and is vital for
perception, voluntary movement, and learning. The cerebral cortex is mostly
made up of association areassites of higher mental activities (thinking). The
inner portion is called the medulla.
Olfactory bulb controls smell.
The thalamus is the main input center for sensory information going to the
cerebrum. Takes in sensory information and relays it to the correct areas.
The hypothalamus constitutes the control center that includes the body's thermostat
as well as the central biological clock.
telencephalon = cerebral cortex + olfactory bulb
diencephalon = thalamus + hypothalamus
The midbrain, located centrally in the brain, coordinates routing of sensory input.
The hindbrain controls involuntary activities, such as blood circulation.
The pons is a relay center to allow communication between the cortex and the
cerebllum.
Medulla oblongata controls breathing, heart rate ,and gastrointesitnal activity.
The cerebellum coordinates movement and balance and helps in learning and
remembering motor skills. Controls muscular coordination.
The midbrain and portions of the hindbrain give rise to the brainstem, the part of the
brain that is connected to the spinal cord.

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It controls the flow of messages between the brain and the rest of the body, and
controls basic body functions such as breathing, swallowing, heart rate, blood
pressure, consciousness, and whether one is awake or sleepy.
Consists of the midbrain, pons, and the medulla oblongata.

The spinal cord runs lengthwise inside the vertebral column, known as the spine. It
conveys information to and from the brain and generates basic patterns of locomotion.
The central canal is the space that runs longitudinally through the length of the entire
spinal cord. It is filled with cerebrospinal fluid, which supplies the CNS with nutrients
and hormones and carrying away wastes.
Made up of gray and white matter:
Gray matter is primarily made up of neuron cell bodies.
White matter consists mainly of bundled axons.
Makes up the outer layer of the spinal cord.
Acts independently of the brain as part of simple nerve circuits that produce reflexes,
the body's automatic responses to certain stimuli. Does NOT travel through brain!
Sensory information enters through the dorsal horn and motor information exits
through the ventral horn.
Peripheral nervous system
Sensory information reaches CNS along PNS neurons designated as afferent neurons.
Following processing within the CNS, instructions travel to muscles glands, and endocrine
cells along PNS neurons called efferent neurons.
PNS has two different components:
The motor system consists of neurons that carry signals to skeletal muscles. Can be
voluntary or involuntary.
The autonomic nervous system consists of neurons that carry signals to smooth and
cardiac muscles. It is generally involuntary. 3 subdivisions:
The enteric division of the autonomic nervous system are active in controlling the
digestive tract, pancreas, and gallbladder.
The sympathetic division corresponds to the fight-or-flight response. Major
neurotransmitter is norepinephrine.
The paraympathetic division causes the opposite response of the sympathetic
division and promotes calming and a return to self-maintenance functions. Major
neurotransmitter is acetylcholine.

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Innate immunity
Innate immunity of invertebrates
Innate immunity provides an immediate defense against infection. Cells of innate system
recognize and responds to pathogens in a generic way, but, unlike the adaptive immune
system, does not confer long-lasting or protective immunity to the host. Nonspecific
immune system.
Binding of an innate immune receptor to a foreign molecule activates internal defenses,
enabling responses to a very broad range of pathogens.
Found in all animals
Innate immunity in invertebrates
Insects rely on their exoskeleton as a first line of defense against infection.
Composed largely of the polysaccharide chitin, the exoskeleton provides an effective
barrier defense against most pathogens.
Chitin also lines insect's intestine, where it blocks infection by many pathogens ingested
with food.
Lysozyme, an enzyme that breaks down bacterial cell walls, further protects the insect's
digestive system.
Any pathogen that breaches the barrier defenses encounters a number of internal immune
defenses.
Hemocytes travel throughout the body in the hemolymph, the circulatory fluid.
They ingest and break down bacteria and other foreign substances through
phagocytosis.
Also release chemicals that kill pathogens and entrap large parasites.
Encounters with pathogens in the hymolymph can cause hemocytes and other cells to
secrete antimicrobial peptides, which are short chains of amino acids that circulate
throughout the body of the insect and inactivate or kill fungi and bacteria by disrupting
their plasma membranes.
Immune cells of insects bind to molecules found only on the outer layers of fungi or
bacteria.
Innate immune responses are distinct for different classes of pathogens.
Innate immunity in vertebrates
Barrier defenses block the entry of pathogens.
They include the skin and the mucous membranes lining the digestive, respiratory,
urinary, and reproductive tracts. The mucous membranes produce mucus, a viscous
fluid that traps pathogens and other particles.
The skin functions as not only a physical barrier but also a hostile barrier. It is
covered with oily and acidic (pH 3-5) secretions from sweat glands, making it hard
for life to grow on it.
Lysozymes in tears, saliva, and mucous secretions destroys the cell walls of susceptible
bacteria as they enter the openings around the eyes or the upper respiratory tract.
Microbes that go through the digestive tract must contend with the acidic environment
of the stomach, which kills most pathogens.
Symbiotic bacteria in the digestive tract and vagina out-competes many other
organisms.
Many pathogens that get through barrier defenses are engulfed by phagocytic cells that use
several types of receptors to detect pathogens.
Toll-like receptors can detect a broad range of human pathogens, as well as a variety of
other molecules that activate tissue damage, by a process called pattern recognition.

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These receptors initiate the innate and the adaptive immune response.
Types of phagocytic cells:
Neutrophils, which circulate in the blood, are attracted by chemicals from infected
tissues in a process called chemotaxis and then engulf and destroy the infecting
pathogens.
Are the most common WBC.
Move into tissues via diapedesis.
Monocytes move into tissues (diapedesis) where they develop into macrophages,
which phagocytize cell debris and pathogens.
Are also antigen-presenting cells.
Dendritic cells mainly populate tissues, such as skin, that contact the environment.
They stimulate adaptive immunity against pathogens as they encounter and engulf.
Antigen-presenting cells.
Eosinofils, often found beneath mucosal surfaces, are important in defending against
multicellular invaders.
Basophils store histamine and work in inflammatory response. Are the least common
WBC.
Mast cells secrete histamine and work in the allergic and inflammatory response.
Natural killer cells circulate through the body and detect the abnormal array of surface
proteins characteristic of some virus-infected and cancerous cells.
They do not engulf cells; instead, they secrete chemicals that lead to cell death.
Many cellular innate defenses in vertebrates involve the lymphatic system. The lymphatic
system consists of a branching network of vessels, numerous lymph nodeslittle round
organs packed with macrophages and white blood cells called lymphocytesthe bone
marrow, and several organs.
The lymphatic vessels carry a fluid called lymph, which is similar to the interstitial fluid
that surrounds body cells but contains less oxygen and fewer nutrients.
Two main functions: to return tissue fluid back to the circulatory system and to fight
infection.
Some of the fluid that enters tissue spaces from the blood in a capillary bed does not
reenter the blood capillaries but instead is returned to the blood via lymphatic vessels.
Fluid enters the lymphatic system by diffusing into tiny, dead-end lymphatic capillaries
that are intermingled among the blood capillaries. Lymph drains from the lymphatic
capillaries into larger lymphatic vessels. Eventually fluid reenters the circulatory system
via two large lymphatic vessels that fuse with the vein in the chest.
When your body fights infection, lymph that circulates around carries microbes, parts of
microbes, and their toxins picked up from infections. Once inside lymphatic organs,
macrophages that reside there engulf the invaders as part of the innate immune response.
Lymph nodes fill with huge numbers of defensive cells, causing the tender swollen
glands in your neck and armpits that your doctor looks for as a sign of infection.
Some macrophages reside in lymph nodes.
Dendritic cells can migrate to the lymph nodes after interacting with pathogens. Also
stimulates adaptive immunity within the lymph nodes.

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In mammals, pathogen recognition triggers the production and release of a variety of

peptides and proteins that attack pathogens or impede their production.
Interferons are proteins that provide innate defense by interfering with viral infections.
They limit the cell-to-cell spread of viruses in the body.
The complement system consists of roughly 30 proteins in blood plasma.
These proteins circulate around the blood in an inactive form and are activated by
substances on the surfaces of pathogens.
Activation leads to lysis of the cells. Activation also can help attract phagocytes to
these foreign cells.
Functions in the inflammatory response as well as the adaptive defenses.
The inflammatory response is the changes brought about by signaling molecules released
upon injury or infection.
One important inflammatory molecule is histamine, which is stored in densely packed
vesicles of mast cells, found in connective tissue.
Histamine released at sites of damage triggers nearby blood vessels to dilate and become
more permeable. The dilation causes capillaries to leak fluid into the neighboring
tissues, causing localized swelling.
Complement system helps phagocytes engulf foreign cells and help lyse foreign cells.
Phagocytes are attracted to injury by chemical gradients of complement, engulf
pathogens and damaged cells.
When macrophages and neutrophils are activated, the cells discharge cytokines,
signaling molecules that modulate immune responses.
Cytokines promote blood flow to the injury site or infection.
The result in the of the increased blood flow is the accumulation of pus, a fluid rich in
white blood cells, dead pathogens, and cell debris from damaged tissue.
Fever is a systemic inflammatory response.

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In response to certain pathogens, substances released by activated macrophages cause
the body's thermostat to reset to a higher temperature.
Higher temperature is beneficial to help fighting off infections.

Adaptive immunity players

Introduction
In adaptive immunity, molecular recognition relies on a vast arsenal of receptors, each of
which recognizes a feature typically found on only a particular part of a particular molecule
in a particular pathogen.
Recognition and response occurs with tremendous specificity.
Is activated after the innate immune response and develops more slowly.
Receptors provide pathogen-specific recognition
The adaptive response relies on T and B cells, which are types of white blood cells called
lymphocytes.
Lymphocytes originate from stem cells in the bone marrow.
Lymphocytes that go to the thymus (an organ above the heart) mature into T cells.
Lymphocytes that remain and mature in the bone marrow develop as B cells.
Lymphocytes of a third type remain in the blood and become natural killer cells
active in innate immunity.
Any substance that elicits a B or T cell response is called an antigen. They are typically
foreign and are large molecules, either proteins or polysaccharides that protrude from the
surface of foreign cells or viruses.
In adaptive immunity, recognition occurs when a B or T cell binds to an antigen via a
protein called an antigen receptor.
All of the antigen receptors made by a single B or T cell are identical.
Each antigen receptor binds to just one part of one molecule from a particular pathogen.
The small, accessible portion of an antigen that binds to an antigen receptor is called an
epitope.
A single antigen usually has several epitopes, each binding to a receptor with
different specificity.
Each B or T cell displays specificity for a particular epitope, enabling it to respond
to any pathogen that produces molecules containing that epitope.
The antigen receptors of the B cells can bind to epitopes of intact antigens on pathogens
or circulating free in body fluids.

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Antigen recognition by B cells and Antibodies

Each B cell antigen receptor is a Y-shaped molecule consisting of 4 polypeptide chains:
two identical heavy chains and two identical light chains, with disulfide bridges linking the
chains together. A transmembrane region anchors the receptor. A short tail region at the end
of the transmembrane region extends into the cytoplasm.
The light and heavy chains each have a constant region, where amino acid sequences
vary very little among the receptors.
Within the two tips of the Y shape, each chain has a variable region, so named because
its amino acid sequence varies extensively from one B cell to another. The combination
of the V region makes up the antigen binding site. Note that the antigen-binding site is
at the N-terminus!

Binding of a B cell antigen receptor to an antigen is an early step in B cell activation,

leading to the formation of cells that secrete a soluble form of the receptor. The secreted
protein is called an antibody.
Antibodies have the same Y-shaped structure as B cell antigen receptors but are secreted
rather than membrane bound.
Antibodies bind to intact antigens in the blood and the lymph.
in a typical antibody, heavy and light chains are linked by hydrogen bonds
Antigen recognition by T cells
The T cell antigen receptor consists of two different polypeptide chains, an alpha and beta
chain, linked by a disulfide bridge. At the base of the T cell antigen receptor is a
transmembrane region that anchors the receptor. At the outer tip of the molecule, the
variable regions o the alpha and beta chains together form a single-antigen binding site.
The remainder of the molecule is made up of the constant regions.
T cells can bind only to fragments of antigens that are displayed, or presented, on the
surface of host cells, unlike B cells.

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The host protein that displays the antigen fragment on the cell surface is called the major
histocompatibility complex (MHC) molecule. Most body cells only have MHC II but
antigen presenting cells have MHC II and I.
Recognition of a protein antigens by T cells begin when a pathogen or part of a
pathogen either infects or is taken by a host cell.
Inside the host cell, enzymes cleave the antigen into smaller peptides and then the
antigen fragments bind to the MHC molecules inside the cell.
Movement of the MHC molecule and the bound antigen fragment up to the cell surface
results in antigen presentation, display of the antigen fragment in an exposed groove of
the MHC protein.
The appropriate T cell can then bind to the antigen fragment and the MHC molecule.
B and T cell development
4 major characteristics of adaptive immunity:
immense diversity of lymphocytes and receptors, enabling immune system to detect
pathogens never encountered
adaptive immunity normally has self-tolerance, the lack of reactivity against an animal's
own molecules and cells
cell proliferation triggered by activation greatly increases number of B and T cells
specific for the antigen
there is a stronger and more rapid response to an antigen encountered previously
The capacity to generate diversity in B and T cells is built into the structure of Ig genes.
A receptor light chain is encoded by three gene segments: a variable (V) segment, a
joining (J) segment, and a constant (C) segment.
The V and J segments together encode the variable region of the receptor chain while
the C segment encodes for the constant region.
Assembling a functional Ig gene requires rearranging the DNA. Early in B cell
development, an enzyme complex called recombinase links one light-chain V segment
to one J segment. This leads to the creation of many different types of short and long
chains, and thus many different types of antigen-binding sites. This is called VJ
recombination.
Mutations in VJ recombination can add additional variation.

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Origin of self-tolerance
As lymphocytes mature in the bone marrow or thymus, their antigen receptors are tested for
self-reactivity. If this fails the test, they are destroyed by apoptosis.
Proliferating of B and T cells
An antigen is presented to a steady stream of lymphocytes in the lymph nodes until a match
is made.
Once the match is made, the B or T cell undergoes multiple cell divisions. The daughter
cells are clones of the original cell.
Some of the clones become effector cells, short-lived cells that take effect immediately
against the antigen and any pathogens producing that antigens.
The effector forms of B cells are plasma cells, which secretes antibodies.
The effector forms of T cells are helper T cells and cytotoxic T cells.
The remaining cells in the clone become memory cells, long-lived cells that can give
rise to effector cells if the same antigen is encountered later in the animal's life.
This whole process is called clonal selection because an encounter with an antigen selects
which lymphocyte will divide to produce a clonal population for a particular epitope.
Primary vs. secondary immune response
Immunological memory is responsible for the long-term protection that a prior infection
provides against many diseases.
The production of effector cells from a clone of lymphocytes during the first exposure to an
antigen is the basis for the primary immune response
If an individual is exposed again to the same antigen, the response is faster, of greater

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magnitude, and more prolonged. This is called the secondary immune response.
Adaptive immunity mechanism
Humoral vs. cell-mediated response
The humoral immune response occurs in the blood and lymph. In the humoral response,
antibodies help neutralize or eliminate toxins in the blood and lymph.
In the cell-mediated immune response, specialized T cells destroy infected host cells.
Helper T cells: A response to nearly all antigens
A type of T cell called a helper T cell triggers the humoral and cell-mediated immune
responses. They secrete signals which help initiate productions of antibodies that neutralize
pathogens and activate T cells that will kill the infected cells. Two requirements for helper T
cells to activate:
A foreign molecule must be present that can bind specifically to the antigen receptor of
the T cell
The antigen must be displayed on the surface of an antigen-presenting cell.
Can be a dendritic cell, macrophage, or B cell.
Most body cells have class I MHC molecules, but antigen-presenting cells have
class I and class II molecules.
An accessory protein called CD4 helps the helper T cell bind to the class II MHC
molecule. When the helper T cell binds to the antigen-presenting cell cytokines are
exchanged.
Once the helper T cell has been activated, they produce interleukins to stimulate
proliferation of T cells, B cells and macrophages.
Cytotoxic T cells
Cytotoxic T cells use toxic proteins to kill cells infected by viruses or other intracellular
pathogens before fully mature.
To become active, cytotoxic T cells require signals from helper T cells and interaction
with an antigen-presenting cell.
The accessory protein CD8 binds to the class I MHC molecule to keep the 2 cells in
contact.
The cytotoxic T protein kills the host cell by secreting proteins that disrupt membrane
integrity and trigger cell death.
T suppressor cells
T suppressor cells serve to town down the T cell response to self cells or following an
infection.
Activation and function of B cells
Activation of B cells involve both helper T cells and proteins on the surface of pathogens.
When an antigen first binds to receptors on the surface of a B cell, the cell takes in a few
foreign molecules by receptor-mediated endocytosis.
The class II MHC protein of the B cell presents an antigen fragment to a helper T cell. The
T cell attaches to that antigen. The direct cell-to-cell contact is usually critical to B cell
activation.
A single activated B cell gives rise to thousands of clones. These clones begin producing
and secreting antibodies.
Antibody function
Antibodies do not actually kill pathogens, but by binding to pathogens, they interfere with
pathogen activity or mark pathogens in various ways for inactivation or destruction.
Types of antibodies:

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IgG is most abundant antibody
IgM is the first antibody to appear in response to an antigen
IgA is present in mucosal secretions
IgE is present in the allergic response
IgD crosses the placenta and activates T-cells
Neutralization is a process in which antibodies bind to proteins on the surface of a virus
and makes it impossible for the virus to infect the cell.
In opsonization, antibodies bound to antigens on bacteria do not block infection, but instead
present a readily recognized structure for macrophages or neutrophils.
Antibodies can also work with proteins of the complement system.
Binding of complement protein to an antigen-antibody complex on a foreign cell
triggers the generation of a membrane attack complex that forms a pore in the
membrane of the cell and causes lysis.

Active vs. passive immunity

Active immunity are the defenses that arise when a pathogen infects the body and prompts
a primary or secondary immune response.
Passive immunity is when the antibodies in the blood of a pregnant female cross the
placenta to her fetus.
Newborn infants are protected by passive immunity also by drinking breast milk. Breast
milk contains antibodies.
Antibiotics are chemicals derived from bacteria or fungi that are harmful to other
microorganisms.
Vaccines are substances that stimulate the production of memory cells. Inactivated viruses
or fragments of viruses, bacteria, or other microorganisms are used as vaccines. Once
memory cells have formed, the introduction of a live microorganism will stimulate a swift
response by the immune system before any disease can become established.
vaccine = active immunity that is artificially acquired
Transplant rejection (immune system)
Transplanted tissues or organs are detected as nonself by the recipients immune system
because the antigens on the donated organ are those of the donor, not the recipient.

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As a result, the recipient's immune system will attack the transplanted organ.
Take immunosuppressing drugs to help prevent transplant rejection. They work by lowering
the body's immune response to antigens.
The recipient who is taking these drugs are immunocompromised because the immune
system is not functioning at full capacity.
Disorders of the immune system
Malfunction or failure of the immune system causes disease
When the immune system fails to function properly, serious disease can result.
Autoimmune diseases result when the immune system goes awry and turns against
some of the body's own molecules.
Immunodeficiency diseases are when an immune response is defective or absent. These
people are susceptible to frequent and recurrent infections (i.e. AIDS).
Allergies
Allergies are hypersensitive (exaggerated) responses to otherwise harmless antigens in
our surroundings.
Antigens that cause allergies are called allergens (i.e. protein molecules on pollen
grains)
Two stages of an allergy attack:
(1) sensitization: Occurs when a person is first exposed to an allergen. After an
allergen enters the bloodstream, it binds to effector B cells (plasma cells) with
complementary receptors. The B cells then proliferate through clonal selection and
secrete large amount of antibodies to this allergen. Some of these antibodies attach
by their base to the surface of mast cells, body cells that produce histamine and other
chemicals that trigger the inflammatory response.
(2) when the person is exposed to the same allergen later: the allergen enters the
body, binds to antibodies attached to mast cells, causing the mast cells to release
histamine which triggers the allergic symptoms. Like in inflammation, histamine
causes blood vessels to dilate and leak fluid so it causes nasal irritation, itchy skin,
and tears.

Antihistamines are drugs that interfere with histamine's action and give temporary relief
from an allergy.

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Vertebrate skeletal muscle structure and function
The skeleton and muscles interact in movement
Muscles are connected to bones by tendons.
A muscle pulls the bone to which it is attachedit can only move the bone in one
direction. A different muscle is needed to reverse the action. Thus, back-and-forth
movement of body parts involves antagonists, a pair of muscles (or muscle groups) that
can pull the same bone in opposite directions.
An example of antagonists are the biceps and triceps.

Structure of skeletal muscle

Vertebrate skeletal muscle, which moves bones and body, has a hierarchy of smaller and
smaller units.
fascia is loose connective tissue that covers the surface of muscle
Within a typical skeletal muscle is a bundle of muscle fibers that run parallel to the length
of the muscle.
Each fiber is a single cell with multiple nuclei.
Each nucleus is derived from one of the embryonic cells that fused to form the muscle
cell.
Sarcoplasm is the cytoplasm of a fiber cell.
Sarcolemma is the plasma membrane of muscle cells.
It can propagate an action potential
It is invaginated by transverse tubules, channels for ion flow.
It wraps several myofibrils together to form a muscle cell/muscle fiber
Mitochondria is present in large amounts for ATP synthesis
Inside a muscle cell lies a longitudinal bundle of myofibrils, which contain the thick and
thin filaments.
Thin filaments is comprised of two strands of actin that are coiled around each
other.
Thick filaments, which are staggered arrays of myosin molecules.
The interaction between thick and thin filaments produces muscle cell contraction.
the alternating between the thin actin filaments and the thick myosin filaments is
responsible for striations in the skeletal muscle.
The myofibrils in muscle fibers are made up of repeating sections called sarcomeres, which
are the basic contractile units of skeletal muscle.
Thin filaments attach at Z lines which are located at the boundary of a single sarcomere,
while thick filaments are anchored at M lines centered in the sarcomere.

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The I band is the region containing thin filaments.
The H zone is the region containing thick filaments.
The A band is the region of actin and myosin overlapping.
The H zone and I band reduce during contraction, but the A band does NOT.

The sliding-filament model

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According to the well-accepted sliding-filament model, the thin and thick filaments ratchet
past each other, powered by myosin muscles.
1) The myosin head is bound to ATP and it is in its low-energy configuration.
2) The myosin head hydrolyzes ATP to ADP and phosphate and is now in its high-energy
conformation.
3) The myosin head binds to actin on its myosin-binding site, forming a cross-bridge.
4) Releasing ADP and Pi, myosin returns to its low-energy configuration, sliding the thin
filament toward the center of the sarcomere.
5) Binding of a new molecule of ATP releases the myosin head from actin, and a new cycle
begins.
Without new ATP, the cross bridges remain attached to the myosin head. This is why dead
corpses are stiff.
At rest, most muscle fibers contain only enough ATP for a few contractions. Powering
repetitive contractions requires two other storage compounds:
Creatine phosphate, which will transfer a group from phosphocreatine to ADP in an
enzyme-catalyzed transphosphorylation reaction.
Glycogen can be broken down into glucose, which can be metabolized quickly to create
ATP.
During intense muscle activity, oxygen becomes a limiting reagent and ATP is instead
generated by lactic acid fermentation.
This generates much less ATP per glucose molecule and creates the burning sensation in
the muscles.

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The role of calcium and regulatory proteins

Tropomyosin, a regulatory protein, and the troponin complex, a set of additional
regulatory proteins, are bound to the actin strands of thin filaments.
In a muscle fiber at rest, tropomyosin covers the myosin-binding sites on the actin (thin)
filaments, preventing actin from interacting.
When Ca2+ ions accumulates in the cytosol, it binds to the troponin complex, causing
tropomyosin bound along the actin strands to shift position and expose the myosinbinding sites. When the Ca2+ concentration falls, the binding sites are covered, and
contraction stops.
Whereas contraction of a single skeletal muscle fiber is a brief all-or-none twitch,
contraction of a whole muscle is graded; you can voluntarily alter the extend and strength
of its contraction.
The nervous system produces graded contractions of whole muscles by varying (1) the
number of muscle fibers that contract and (2) the rate at which muscle fibers are
stimulated.
The strength of a contraction of a single muscle fiber cannot increase but the strength of
overall contraction can be increased by recruiting more muscle fibers.
A motor unit consists of a single motor neuron and all the muscle fibers it controls.
Usually small motor units are activated first, then larger ones are activated as needed.
This creates a smooth increase in force.
Fine movement uses small motor units only.
1) Acetylcholine (Ach) is released at the synaptic terminal of a motor neuron. It diffuses
across the synaptic cleft and binds to the receptor proteins on the muscle fiber's plasma
membrane, triggering an action potential in the muscle fiber.
2) The action potential is propagated along the plasma membrane and down transverse
tubules.
3) The action potential propogating down the T tubules make close contact with the
sarcoplasmic reticulum (SR), a specialized endoplasmic reticulum. Close contact of the
AP with the SR triggers the release of Ca2+ ions from the SR.
4) Ca2+ ions bind to the troponin complex in the thin filament, exposing the myosin binding
sites.
5) Cycles of myosin cross-bridge formation and the breakdown, coupled with ATP
hydrolysis, slide thin filament toward center of sacromere. The muscle contracts.
6) Cytosolic Ca2+ is removed by active transport into the SR after the action potential ends.
7) Tropomyosin blockage of myosin-binding sites is restored; contraction ends, and the
muscle fiber relaxes.

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Types of muscles
Types of muscle responses
Simple twitch is the response of a single muscle fiber to a brief stimulus. Three phases:
Latent period is the time between stimulation and onset of contraction. During this
time, the action potential propagates along the sacrolemma and Ca2+ ions are released
to open up the myosin-binding sites.
Contraction
Relaxation is the absolute refractory period. The muscle is now unresponsive to a
stimulus during this time.
Summation occurs when two contractions combine additively and become stronger. They
are more prolonged than a simple twitch.
This occurs when a second action potential arrives before the muscle fiber has
completely relaxed.
Tetanus is the continuous sustained contraction because the rate of muscle stimulation is so
fast that the twitches blur into one smooth constant.
Tonus is the unconscious low level contraction of your muscles while they are rest. It is a
state of partial contraction.

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Your muscles are never completely relaxed.

This is what makes your muscles feel somewhat firm while you are resting and not
intentionally tensing them.
5 types of muscle contractions
Isotonic contraction is when a muscle shortens against a fixed load while the tension on the
muscle remains constant
A concentric contraction is a type of dynamic contraction where the muscle fibers shorten
and the tension on the muscle fiber increases.
An eccentric contraction is a type of dynamic contraction where the muscle fiber lengthens
and the tension on the muscle increases.
Dynamic contraction involves both concentric and eccentric type of contractions.
An isometric contraction occur when both ends of the muscle are fixed and no change in
length occurs during the contraction, but the tension increases.
Types of muscle fibers
Skeletal muscle is voluntary, striated, and moves bone. It is multi-nucleated. They generally
don't undergo mitosis to create new cells (hyperplasia), but will increase in size
(hypertrophy). There are multiple types:
Fibers that rely mostly on aerobic respiration are called oxidated fibers.
They have many mitochondria for ATP synthesis.
They have a rich blood supply for easy access to nutrients.
Have a large amount of the oxygen-storing protein myoglobin.
Slow oxidative muscle fibers have a low rate of myosin ATPase activity. They have
the smallest diameter and are the most highly resistant to fatigue. Red color. Are
slow-twitch fibers, meaning that they contract slowly but they contract for a much
longer period of time than fast-twitch fibers. Muscles that need to be active
continuously have many of these fibers.
Fast oxidative muscle fibers have a high rate of myosin ATPase activity. They have
an intermediate diameter and are intermediate in resistance to fatigue. Red to pink
color. They are fast-twitch fibers, meaning that they contract very fast. Fast-twitch
fibers enable brief, rapid, powerful contractions.
In contrast, glycolytic fibers rely on glycolysis as their major source of ATP production.
They have the largest diameter and the low concentrations of myoglobin.
They have high myosin ATPase activity.
Fast-twitch fiber
Typically white color.
Usually used for power.
Cardiac muscle is only found in the heart. It is striated and involuntary. They are mononucleated or bi-nucleated.
High amounts of mitochondria
NO summation or tetanus due to long refractory period
Ion channels in the plasma membrane of cardiac muscle cells cause rhythmic
depolarizations that trigger action potentials WITHOUT nervous system input
(myogenic). Action potentials last much longer than skeletal muscles.
Adjacent cardiac muscle cells are electrically coupled by specialized regions called
intercalated disks. This enables the action potential generated by specialized cells in
one part of the heart to spread, causing the whole heart to contract.
Smooth muscle is found mainly in hollow organs such as the digestive tract and blood

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vessels. They lack striations, are mono-nucleated, and are involuntary.
Thick filaments are scattered throughout the cytoplasm and thin filaments are attached
to structures called dense bodies, some of which are tethered to the plasma membrane.
There is less myosin than in skeletal muscle and the myosin is not associated with
specific actin strands.
The contraction of the thin and thick filaments causes the dense bodies to move closer,
which causes the shortening of the intermediate filaments found throughout the cell.
This causes the cell to get smaller and contract as a whole.
These muscles are stimulated by the autonomic nervous system.
Smooth muscle can respond to hormones, change in pH, oxygen and carbon dioxide
levels, temperatures on top of neuronal responses.
Two main types:
Single unit (visceral) smooth muscle is connected by gap junctions and contract as
a single unit (stomach uterus, urinary bladder).
In multiunit smooth muscle, each fiber is directly attached to neurons and can
contract independently (iris, bronchioles).
Movement in lower forms
Unicellular locomotion
Protozoans and primitive algae use flagella by means of power stroke or recovery stroke.
Amoeba extend pseudopodia; advancing the cell membrane as it extends forward.
Invertebrate locomotion
A hydrostatic skeleton consists of fluid held under pressure in a closed body
compartments. Invertebrates with these skeletons control their form and movement by using
muscles to change the shape of the fluid filled compartments.
Flatworms uses bi-layered longitudinal and circular muscles to contract against the
hydrostatic skeleton. Contraction causes hydrostatic skeleton to flow longitudinally,
lengthening the animal
Segmented worms (annelids) advance by action of muscles on hydrostatic skeleton.
Bristles in the lower part of each segment setae, anchor the worm in the earth while
muscles push ahead.

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Sensory receptors
Types
Mechanoreceptors sense physical deformation caused by forms of mechanical energy such
as pressure, touch, stretch, motion and sound.
Chemoreceptors include both general receptors, those that transmit information about total
solute concentration and specific receptors, those that respond to individual kinds of
molecules (Taste and smell).
Electromagnetic receptors detect forms of electromagnetic energy such as light, electricity,
and magnetism.
Thermoreceptors detect heat and cold.
Nociceptors detect pain.
Important information
Sensory receptors respond strongly to own stimuli and weakly to others.
The neural pathways separate for each type of receptor and all terminate somewhere in the
CNS.
The Eye
Pathway of light stimuli
Cornea (focuses light) pupil (controls amount of light that enters the eye; diameter
controlled by iris) lens (focuses image; controlled by cilliary muscles) Retina
(location of rods and cones).
Cones detect high-intensity illumination and are sensitive to color.
Rods detect low intensity illumination, are important in night vision, and do not detect
color.
Rod pigment rhodopsin is struck by photons from light, causing hyperpolarization
transduction into neural action potential sent to brain.
Photoreceptor cells synapse to bipolar cells ganglion cells axons of ganglion
cells bundle to optic nerve.
Point at which optic nerve exits is called the blind spot (no photoreceptors here)
Eye has virtrous and aqueous humor:
Virtrous humor is the clear gel that fills the space between the lens and retina of the
eyeball. It is jelly like, maintains eye shape and optical properties.
Aqueous humor is the thin, watery fluid that fills the space between the cornea and the
iris. This fluid nourishes the cornea and the lens and give the eye its shape. \

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Eye disorders
Myopia nearsightedness
Hyperopia farsightedness
Astigmatism irregularly shaped cones. Causes blurred vision at any distance.
Cataracts lens becomes opaque and light cannot enter
Glaucoma increase in pressure of eye due to blocking of outflow of aqueous humor.
Causes blurred vision, distorted vision, or vision loss.

The ear
Structure
The Ear transduces sound energy into impulses.
Outer ear auricle/pinna (what we think of as the ear) and the auditory canal; direct
sound into external auditory canal
Middle ear amplifies sound; tympanic membrane (eardrum) begins the middle ear and
vibrates at the same frequency as incoming sound ossicles: malleus, incus, and stapes
(transmit sounds from the air to the cochlea)
Inner eat wave moves through the cochlea as the vibration of ossicles exert pressure on
fluid. As waves move through the ear the pressure alternates, moving the vestibular
membrane in and out; this movement is detected by hair cells (sensory receptors of the
ear) that are located in the organ of Corti transduced neural signal action potential
The inner ear also has semicircular canals that are responsible for balance (fluid + hair
cells sense orientation + motion)

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Invertebrate sekeletons
Arthropods have an exoskeleton composed of hart chitin. Chitin helps necessitate molting
for growth.
Vertebrate skeleton organization
Axial skeleton is the part of the skeleton that consists of the bones of the heat and the trunk
of a vertebrate.
The appendular skeleton supports the attachment and functions of the upper and lower
limbs of the human body. Consist of pectoral girdle, pelvic girdle, upper limbs (arms) and
lower limbs (legs).
Joints are areas where different bones meet:
Stutures are immovable joints that holds together the bones of the skull.
Moveable joints are bones that move relative to each-other.
Ligaments are bone-to-bone connectors that strengthen joints.
ACL ligament limits rotational knee movement and connects femur and tibia.
Tendons are muscle-to-bone connectors that bend skeleton at moveable joints.
Origin is the point of attachment of muscle to stationary bone.
Insertion is the point of attachment of muscle to bone that moves.
Extension is the straightening of a joint.
Flexion is the bending of a joint.
A fibrous joint connect bones without allowing any movement.
Cartilaginous joints are bones that are attached by cartilage that allow for little
movement.
Synovial joints allow for much more movement. They are most common.
They are filled with synovial fluid which acts as a lubricant.
Ball-and socket joints (I.e where the humerus joins the pectoral girdle), enable us to
rotate our arms and legs and move them in several places.
Hinge joints permit movement in a single plane (i.e. elbows and knees)
A pivot joint enables us to rotate the forearm at the elbow and move the head from side
to side.

Vertebrate sekeleton parts

vertical column: cervical, thoracic, lumbar, sacrum, coccyx
upper limbs: humerous, radius, ulna, carpal, metacarpal
lower limbs: femur, tibia, fibula patella, tarsal, metatarsal
Cartillage avascular connective tissue (supplied with nutrients via diffusion) and it is
softer and more flexible.
Made up of specialized cells called chondrocytes that produce a ground substance
(supports the cells and fibers and helps determine the consistency of the ECM).
Made up of mostly collagen

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Found on the ear, nose, larynx, trachea, and joints
In fetal development, the greater part of the skeleton is cartilaginous. The cartilage is
replaced by bone, a process that ends at puberty.
3 types (differ in the amount of cartillage):
hyaline is most common reduced friction/absorbs shock in joints
fibrocartilage
elastic
How cartilage is made (chondrogenesis):
1) Condensed mesenchyme tissue differentiates into chondroblasts
2) Chondroblasts secrete collagen, hydroxylysine, ground substance, and elastin
fiber. Chondroblasts that get trapped in the ECM are called chondrocytes.
Bone is connective tissue that is hard and strong, while elastic and lightweight.
Functions: supports soft tissue, protects internal organs, assists in body movement,
stores minerals (mainly calcium), produces blood cells, and stores energy in the form of
adipose cells in bone marrow.
Contains blood and nerves.
4 different types of cells:
Osteoprogenitor/Ostreogenic cells differentiate into osteoblasts
Osteoblasts (Bone Building) secrete collagen and organic compounds upon which
bone is formed.
Incapable of mitosis
As matrix is released around them, they are enveloped by the matrix and
differentiate into osteocytes.
Osteocytes are incapable of mitosis and exchange nutrients and waste material with
the blood.
Osteoclasts reabsorb (destroy) bone matrix, releasing minerals back into the blood.
Develop from monocytes. Structure:
Areas of the bone:
The epipheysis is the is one of the rounded
ends of the long bones of the body which
makes up a joint.
Metaphysis is the area of the bone which
grows during childhood
Below the metaphysis is the diaphysis, or
the shaft of the bone, which makes up the
main section of the bone.

Compact bone is highly organized, dense

bone that doesn't appear to have cavities from
the outside.
Osteoclasts burrow tunnels called Haversian canals throughout. They contain

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blood and lymph vessels and are connected by Volkmann's canals.

Osteoclasts are followed by osteoblasts, which lay down new matrix onto tunnel
walls, forming concentric rings called lamellae.
Osteocytes traped between the lamella in spaces called lacunae exchange
nutrients via canaliculi, small canals between the lacunae of bone.
An entire system of haversian canals and lamellae is called an osteon, or a
Haversian system.
Also filled with yellow bone marrow that contains adipose cells for fat storage.

Spongy (cancellous) bone is less dense and consists of an interconnecting lattice of

bony spicules called trabeculae. Filled with red bone marrow, which is the site of
RBC development.
Bone growth occurs at cartilaginous epiphyseal plates (occurs at the metaphysis)
that are replaced by bone in adulthood. Bone increases in length but also in diameter
along the diaphysis as well. When a person reaches full maturity, the new bone
slowly hardens and the plate turns into the epiphyseal line
Most of the Ca2+ in body is stored in bone matrix as hydroxyapatite.

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Bones can be made from a combination of compact and spongy bone.

Bone formation occurs during the fetal stage of development in a developing human.
Endochondral ossification is when existing cartilage is replaced by bone (long
bones, limbs, fingers, toes)
Intramembranous ossification is when undifferentiated connective tissue is
replaced by bone (flat bones, skull, sternum, mandible, clavicles)
Osteoporosis
Osteoporosis is characterized by low bone mass and structural deterioration of bone tissue.
The weakness emerges from an imbalance in the process of bone maintenancethe
destruction of bone material exceeds the rate of replacement.

Ways to prevent osteoporosis:

Weight-bearing exercise such as walking or running strengthens bones.
Strong bones also require an adequate intake of dietary calcium and enough vitamin D
which are both essential to bone replacement.
Estrogen the hormone can help maintain bone density.

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Functions of the skin
Functions
Thermoregulation: helps regulate body temperature
Protection: skin is a physical barrier to abrasion, bacteria, dehydration, many chemicals,
and UV radiation.
Environmental sensory input: skin gathers information about environment by sensing
temperature, pressure, pain and touch
Excretion: water and salts excreted through skin
Immunity: specialized cells of the epidermis are components of the immune system
Blood reservoir: Vessels in the dermis hold up to 10% of the blood in resting adult
Vitamin D synthesis: UV radiation on skin catalyzes the synthesis of vitamin D from a
precursor molecule
Structure of the skin
Epidermis
Epidermis is the superficial epithelial tissue.
It is avascular, meaning it has no blood vessels linking to it.
It depends on the dermis for oxygen and nutrients.
Layers from top to bottom:
Stratum corneum 25 to 30 layers of dead cells.
Filled with keratin (fibrous protein responsible for protective properties of the
epidermis) and surrounded by lipids.
Lamellar granulues makes it water repellent
Stratum lucidum 3-5 layers of clear, dead cell.
Only located in the palms, soles of feet, and finger tips
Stratum granulosum 3-5 layers of dying cells
lamellar bodies release hydrophobic lipids
the stratum granulosum is that layer containing granules which can easily strain
Stratum spinosum 8-10 layers of cells
Cells are held together by desmosomeskeratin involving adhesion proteins
Provides strength and flexibility
Stratum basale (germinativum) contains merkel cells and stem cells that divide to
produce keratinocytes; attached by basement membrane.

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Melanocytes are most likely found in the stratum germinativum

The keratinocytes are pushed from this layer to the stratum corneum. As they rise,
they accumulate keratin and die. When they die, they lose cytoplasm, nucleus, and
other organelles. At the outermost layer of the skin, they slough off the body.
Cells of the epidermis
Keratinocytes produce the protein keratin that helps waterproof the skin
Melanocytes transfer skin pigment melanin to keratinocytes
Melanin protects the cell nucleus from the destructive effects of UV radiation.
Individual and racial differences in skin coloring are probably due to differences in
melanocyte activity.
Langerhans cells interact with helper T-cells of the immune system. They are
macrophages.
Merkel cells attach to sensory neurons and function in touch sensation
Dermis
Dermis is the primary connective tissue of the skin.
Contains collagen and elastic fibers
Contains hair follicles, glands, nerves, and blood vessels
Layers of the dermis
Papillary region makes up the top 20% of the dermis
Reticular region is the dense connective tissue that is made up of collagen and elastic
fibers
Provides strength and elasticity (stretch marks are dermal tears!)
Packed with oil glands, sweat gland ducts, fat, and hair follicles
Hypodermis (subcutaneous)
The hypodermis is not part of the skin. It is the innermost and the thickest layer.
Mainly composed of adipocytes, cells that are specialized in accumulating and storing
fats. These cells are grouped together in lobules separated by connective tissue. Acts as
energy reserve and as a thermoregulatory insulator.
Has pressure sensing nerve endings
Passage for blood vessels

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Glands of the skin

Sebaceous (oil) glands are connected to hair follicles except on the palms and soles.
Secrete an oily secretion called sebum.
Sebum is usually ducted into a hair follicle where it softens and lubricates the hair and
skin and has a bactericidal action.
Ceruminous glands secrete ear wax
Mammary glands secrete milk
Sudoriferous glands are sweat glands. Two types:
Eccrine glands are on most of the body. They regulate temperature through perspiration
and eliminate urea.
Apocrine glands are on the armpits, pubic region, and nipples. They secrete viscous
secretions with an unknown function. Activated by the sympathetic nervous system.

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Signaling
Intracellular communication
In endocrine signaling, hormones secreted into extracellular fluid by endocrine cells reach
target cells via the bloodstream or hemolymph.
Local regulators are molecules that act over short distances and reach their target cells
solely by diffusion.
In paracrine signaling, the local regulator targets cells that lie near the secreting cell.
In autocrine signaling, the local regulator targets the secreting cell itself.
In synaptic signaling, neurons form specialized junctions called synapses with target cells,
such as other neurons and muscle cells.
At most synapses, neurons secrete neurotransmitters.
In neuroendocrine signaling, specialized neurons called neurosecretory cells secrete
neurohormones, which diffuse from nerve cell endings into the bloodstream.
Members of a particular animal species sometimes communicate with each other via
pheromones, chemicals that are released into the external environment.
Types of local regulators
Prostaglandins are local regulators that promote inflammation and the sensation of pain
in response to injury. They are modified fatty acids.
Cytokines and growth factors are typically local regulators.
Nitrous oxide (NO) is a gas that functions as a local regulator and a neurotransmitter.
When the level of oxygen in the blood falls, endothelial cells in blood vessel walls
synthesize and release NO.
NO causes vasodilation, which increases blood flow to the tissues.
Classes of hormones
Hormones are transported throughout the body in blood. A small amount generates a large
impact. They tend to have slower effects.
Many hormones elicit more than one type of response in the body.
These molecules bind to receptors that are highly specific to their structure.
Some hormones have receptors on almost all cells, some have receptors only on specific
tissues.
Peptide hormones are synthesized in the rough ER as a larger preprohormone (precursor
to one or more prohormones), cleaved in the ER lumen to a prohormone (committed
precursor of a single hormone) and then cleaved again (and possibly modified with carbs) in
the golgi body to the final form.
Includes: FSH, LH, ACTH, HGH, TSH, prolactin, ADH, oxytocin, PTH, glucagon and
insulin
They are water-soluble hormones, so they cannot diffuse through the plasma membrane.
They attach to a membrane receptor and initiate signal transduction pathways.
Secondary messengers are created along the pathways; which create the actual effects.
This is indirect stimulation.
Steroid hormones are synthesized from cholesterol in the smooth ER.
Includes: glucocorticoids, mineralocorticoids, cortisol, aldosterone, esterogen,
progesterone, and testosterone.
They are lipid-soluble hormones, so they are able to diffuse through the plasma
membrane.
Steroid hormones attaches to a receptor in the cytoplasm or the nucleus. The
hormone+receptor binds to an active portion of DNA and alters the transcription rate.
This is an example of direct stimulation since the hormone itself is generating the

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effects.
Tyrosine derivatives are formed by enzymes in the cytosol or on the rough ER.
Includes: catecholamines, T3, T4
They are either water-soluble or lipid-soluble.
Feedback regulation and coordination with the nervous system
Simple pathways
In a simple endocrine pathway, endocrine cells respond directly to an internal or
environmental stimulus by a secreting a particular hormone. The hormone will travel in the
bloodstream to the target cells, where it will elicit the appropriate responses.
In a simple neuroendocrine pathway, the stimulus is received by a sensory neuron, which
stimulates a neurosecretory cell. The neurosecretory cell then secretes a neurohormone,
which will diffuse into the bloodstream and travel to target cells.
Feedback regulation
Regulation often involves negative feedback, in which the response reduces the initial
stimulus.
Positive feedback reinforces a stimulus, leading to an even greater response.

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Organs of the endocrine system
Endocrine glands vs. exocrine glands
Endocrine glands synthesizes and secretes hormones into the bloodstream.
Exocrine glands secrete substances by way of a duct to the exterior of the body.
Hypothalamus
The hypothalamus monitors the external environment and internal conditions of the body.
Contains neurosecretory cells that link the hypothalamus to the pituitary gland.
Synthesizes ADH (vasopressin) and oxytcin to be stored in the posterior pituitary.
Synthesizes releasing and inhibiting hormones to regulate the anterior pituitary.
Synthesizes gonadotropin releasing hormone (GnRH) from neurons, which stimulates the
anterior pituitary to secretes FSH and LH.
Anterior pituitary
The anterior pituitary mainly regulates hormone production by other grands.
The anterior pituitary is regulated by the hypothalamus.
Releasing hormones are produced by neurosecretory cells in the hypothalamus and are
secreted into the blood. This blood flows directly into the anterior pituitary, where the
releasing hormones stimulate the release of tropic or direct hormones produced/stored and
secreted in the anterior pituitary.
Direct hormones directly stimulate target organs. Types of direct hormones
produced/stored in the anterior pituitary:
Somatotropin (HGH), which stimulates bone and muscle growth.
Prolactin stimulates milk production in females.
Endorphins inhibit perception of pain (technically a neurohormone).
Tropic hormones stimulate other endocrine glands. Types of tropic hormones
produced/stored in the anterior pituitary:
Adrenocrticotrophic hormone (ACTH) stimulates the adrenal cortex to release
glucocorticoids, which are involved in regulation of metabolism of glucose.
Thyroid-stimulating hormone (TSH) stimulates the thyroid gland (increases size
and cell number) to release thyroid hormone.
Lutenizing hormone (LH) in females stimluates the formation of the corpus
luteum. In males, leutinzing hormone stimulates leydig cells of the testes to produce
testosterone.
Follicle-stimulating hormone (FSH) in females stimulates maturation of ovarian
follices to secrete estrogen. In males, FSH stimulates sertoli cells to help mature
sperm cells.
Posterior pituitary
The posterior pituitary does not synthesize hormones, it stores hormones produced by the
hypothalamus. Hormones that it stores/secretes:
Antidiuretic hormone (ADH/vasopressin) increases the reabsorption of water by
increasing the amount of aquaporins in the epithelium cells in the collecting duct.
Coffee and alcohol blocks ADH.
Oxytocin is secreted during childbirth. It increases the strength of uterine contractions
and stimulates milk ejection.
Pineal gland
Pineal gland secretes melatonin, a hormone that participates in regulation of biological
rhythms.

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Thyroid
Thryoid glands are located on the ventral surface of the trachea. Hormones that it
produces/secretes:
Achondroplasia is dwarfism of the thyroid.
Progeria is premature aging of the thyroid.
Thyroxine (T4) and Triiodothyronine (T3) are necessary for the growth and
neurological development in children and increase basal metabolic rate in body.
Provide a negative feedback on TSH, meaning high amounts of T3 and T4 will
decrease production of TSH.
Hypothyroidism means undersecretion of T3 and T4; results in low heart and
respiratory rate.
Hyperthryoidism means oversecretion of T3 and T4; results in increased metabolic
rate and sweating.
Hypo- and hyperthyroidism lead to goiter, the abnormal enlargement of the thyroid
gland.
Calcitonin tones down Ca2+ in blood.
It decreases plasma Ca2+ by inhibiting its release from bone
Decreases osteoclast activity and number.
Parathyroid
The Parathyroid is four pea-shaped structures attached to the back of thyroid. Hormones
that it produces/secretes:
Parathyroid hormone (PTH) is antagonistic to calcitonin.
Raises Ca2+ concentrations in the blood by stimulating release from bone.
Increases osteocyte absorption of Ca + P from bone; stimulates osteoclast
proliferation
Increases renal Ca absorption
Thymus
Thymus is involved in the immune response. Hormones that it produces/secretes:
Thymosins stimulate lymphocytes (WBCs) to become T-cells
Adrenal gland
Adrenal gland is located on the top of kidneys and consists of two main parts:
Adrenal cortex secretes only steroid hormones. Hormones that it produces/secretes:
Glucocorticoids (cortisol and cortisone) raise blood glucose levels (stimulates
gluconeogenesis in liver); affect fat and protein metabolism; stress hormones
Mineralocorticoids (aldosterone) increaes reabsorption of Na+ and secretion of K+.
Causes passive reabsorption of water in the nephron, which will cause a rise in blood
volume/pressure.
Androgenic steroids these hormones are converted elsewhere in the body to form
estrogens and androgens; however, these steroid hormones are produced in much
larger amounts by the gonads.
Adrenal medulla. Hormones that it produces/secretes:
Epinephrine and norepinephrine fight or flight hormones.
These hormones are catecholamines they are water soluble, bind to receptors
on target tissue membranes, and mainly act via a second messenger.
Glycogen glucose, vasoconstrictor to internal organs and skin but vasodilator
to skeletal muscle, increased heartbeat.

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Pancreas
Pancreas (exocrine and endocrine) has bundles of cells called islets of Landerhans which
contains two cell types:
Alpha cells secrete glucagon: catabolic, released when energy charge low; raises blood
glucose levels. Stimulates liver to break down glycogen into glucose.
Beta cells secrete insulin: anabolic, released when energy charge is high; lower blood
glucose levels. Stimulates liver and most other body cells to absorb glucose. Provokes
liver and muscles to turn glucose into glycogen and fat cells to turn glucose into fat.
Somatostatin is released by delta cells of pancreas; inhibits both insulin and glucagon.
Possibly increases nutrient absorption time
Testis and Ovaries
Testis produces and secretes testosterone, a hormone that induces spermatogenesis and
secondary male sex characteristics.
Ovaries produces and secretes estrogen and progesterone:
Estrogen is involved in the menstrual cycle and produces secondary female sex
characteristics.
Progesterone is involved in the menstrual cycle and pregnancy.
Gastrointestinal hormones
Gastrin secretes stimulation of HCl when food is in the stomach.
Secretin, secreted from the small intestine, neutralizes the acidity of chyme by enhancing
the secretion of alkaline bicarbonate.
Cholecystokinin, secreted from the small intestine, causes the contraction of the gallbladder
to release bile in the presence of high fatty food.