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Chapter 2

The Chemistry of
Biology

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Atoms, Bonds, and Molecules


Matter - all materials that
occupy space and have
mass. Matter is composed of
atoms

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Nucleus

Atom - simplest form of


matter not divisible into
simpler substances
Protons:
(+) subatomic particles
Neutrons:
neutral subatomic
particles
Electrons:
(-) subatomic particles

1 proton
1 electron

Hydrogen

Shells

Nucleus

proton
Nucleus

6 protons
6 neutrons Carbon
6 electrons

neutron
electron

(b)

Different Types of Atoms


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All atoms share the


same fundamental
structure
Element - pure
substances with a
characteristic number
of protons, neutrons,
and electrons and
predictable chemical
behaviors

Nucleus

1 proton
Hydrogen
1 electron

Shells

Nucleus

proton
Nucleus

(b)

6 protons
6 neutrons Carbon
6 electrons

neutron
electron

The Major Elements of Life

Characteristics of Elements
Atomic number number of
protons
Mass number number of
protons and neutrons
Isotopes variant forms of the
same element that differ in the
number of neutrons
Atomic weight average
mass numbers of all isotopic
forms
Electron orbitals volumes of
space surrounding the atomic
nucleus where electrons are
likely to be found

Shell

Hydrogen

Shell 2
Shell 1

Carbon

Orbitals

(a)

Nucleus

1 proton
1 electron

Hydrogen

Shells

Nucleus

proton
Nucleus

(b)

6 protons
6 neutrons
6 electrons

Carbon

neutron
electron

Biologically Important Atoms


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Chemical symbol

H
HYDROGEN

Atomic number

NITROGEN

Chemical name

OXYGEN
7p

1p
Number
Of e in
Each
Energy
level

Mg

12

MAGNESIUM

6
25

11

12p
Li

Be

Na

Mg

11p

Na
281

Ca

Rb

Sr

AT. MASS 22.99

24

AT. MASS 24.30

AT. MASS 12.01

Ti

Ca

Cr

20

Mn

Fe

Co

Ni

Tc

Ru

Rh

Pd

Ba

Fr

Ne

AT. MASS 16.00

Al

Si

Cl

Ar

Cl

Cu

Re

Os

Ir

17

CHLORINE
Zn

Ga

Gs

As

Se

Br

Kr
17p

15

16
Cl

SULFUR

Pt

287

Ra

15p

20p

Ca
19p

AT. MASS 35.45

19

POTASSIUM

PHOSPHORUS

CALCIUM
Cs

282

Sc

P
SO
QN
26

6p

Mg

SODIUM

He

AT. MASS 14.00

AT. MASS 1.00

Na

8p

CARBON

16p

2882

285

AT. MASS 40.08

AT. MASS 30.97

286
AT. MASS 32.06

K
2881
AT. MASS 39.10

Concept Check:
If two atoms have the same number of protons and electrons
but different numbers of neutrons, they would be

A. Different elements
B. Isotopes of the same element
C. Ions of the same element
D. Orbitals of the same element
7

Bonds and Molecules


Molecule - a chemical substance that results from
the combination of two or more atoms
Compounds - molecules that are combinations of
two or more different elements
Formula/Mass weight - sum of all of the atomic
masses of the atoms a molecule contains
Chemical bonds - when 2 or more atoms share,
donate, or accept electrons to form molecules and
compounds
3 types: covalent, ionic, and hydrogen
8

3 Types of Chemical Bonds


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1. Covalent bonds
electrons are shared
among atoms

Polar covalent bonds


unequal sharing
Nonpolar covalent
bonds equal sharing

Covalent Bonds

Single

Double

Covalent Bonds
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H
e

H
e

1p

1p

Hydrogen atom

H2

1p

Hydrogen atom

H
Molecular oxygen (O2)
O O
Double bond

1p

H H

Single bond

1p+

H C H
H

8p+
8n

Hydrogen molecule

H
8p+
8n

1p+

6p+
6n

1p+

H
Methane (CH4)

1p+
10

Polarity
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()

()
H

8p+

H
O

1p+

(+)
(a)

1p+

(+)

(+)

(+)

(b)

11

3 Types of Chemical Bonds


Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

2. Ionic bonds
electrons are
transferred to one
atom forming
positively charged
cations and
negatively charged
anions

Ionic Bond

(+)

()

12

Ionic Bonding
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Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

2
1

Na

17p
18n

11p
12n

Cl
1
2

NaCl crystals
(a)

(b)

Sodium atom (Na)

Na Cl

Chlorine atom (Cl)

[Na]+ [Cl]
Na
1
Sodium

Na
Cl

Chloride
1

Na

Cl

(d)

Kathy Park Talaro

Na
Cl

2
1

11p

Cl

Na

Na

Cl

Na

Cl2

(c)

Cl

Cl
Cl

Na

17p

Sodium ion (Na1)

Chlorine atom (Cl2)

(cation)

(anion)

13

3 Types of Chemical Bonds


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3. Hydrogen bonds weak


bonds between hydrogen
and other atoms

Hydrogen Bond
Molecule A

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Water molecule

O
2

Hydrogen bonds

H
1
1

H
O
2

(+)
()

O
or
N

H
1

Molecule B

14
14

Concept Check:
Molecules where atoms share electrons contain

A. Covalent Bonds
B. Ionic Bonds
C. Hydrogen Bonds

15

Oxidation-Reduction Reactions
Energy exchange in cells is a result of the movement
of electrons from one molecule to another.
Oxidation the loss of electrons
Reduction the gaining of electrons
Redox reactions
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1
Na

28 1

Reducing agent
gives up electrons.

Cl

28 7

Oxidizing agent
accepts electrons.

Na

28

Oxidized cation

2
Cl

28 8

Reduced anion
16

Chemical Shorthand
Reactants - molecules starting a reaction
Products - substances left by a reaction
Synthesis reaction - the reactants bond together in a
manner that produces an entirely new molecule

S + O2

SO2

Decomposition reaction - the bonds on a single reactant


molecule are broken to release two or more products

2H2O2

2H2O + O2

Exchange reaction - the reactants trade portions between


each other and release products that are combinations of
the two

HCl + NaOH

NaCl + H2O

17

Solutions
Solution a mixture of one or more substances called
solutes, dispersed in a dissolving medium called a
solvent
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2
1

1
2

NaCl crystals

Solutes Na & Cl
+

Na

Na
Cl

Na

Cl

Na
1

Cl

Cl
Cl

2
1

Solvent H2O

H
O

Na

Na

Cl

Na

Cl

11p

Cl

Cl

Na

17p

2
18

Sodium ion (Na1)


(cation)

Chlorine atom (Cl2)


(anion)

Aqueous Solutions
Hydrophilic molecules - dissolve in water
Hydrophobic molecules - repel water
Amphipathic molecules - have both hydrophilic
and hydrophobic properties
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Hydrogen
Oxygen

Water molecules

Na

Cl

19

Acidity, Alkalinity, and the pH Scale


Ionization of H2O releases hydrogen ions [H+]
and hydroxyl ions [OH ]
pH scale ranges from 0 to 14, expresses the
concentration of H+ ions
pH is the negative logarithm of the concentration of H+

0.
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pH

Acidic

[H+]

Increasing
acidity

Neutral

10

[OH]

11

12

13

14

Basic
(alkaline)

Increasing
basicity

20

pH and Ion Concentration

21

Concept Check:
If solution A has a pH of 2 and solution B has a pH of 4,
which of the following is true?

A. Solution A has 2 times more H+ ions than solution B


B. Solution B has 2 times more H+ ions than solution A
C. Solution A has 10 times more H+ ions than solution B
D. Solution B has 10 times more H+ ions than solution A
E. Solution A has 100 times more H+ ions than solution B
22

The Chemistry of Carbon and


Organic Compounds
Organic chemicals compounds containing
carbon bonded to hydrogens
Carbon is the fundamental element of life
Contains 4 atoms in its outer orbital
Can form single, double, or triple covalent bonds
Can form linear, branched, or ringed molecules

23

The Versatility of Bonding in Carbon


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Linear
C
C

C 1 H

C H
Branched

C 1 O

C 1 N

C N

C 1 C

C C

C
(a)

C 1 C

C 1 N

C
Ringed

C
C

N
(b)

C
C

C
C

24

Functional Groups of Organic


Compounds
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Accessory molecules
that bind to organic
compounds

TABLE 2.3 Representative Functional Groups and


Organic Compounds That Contain Them
Formula of
Functional Group

Name

Can Be Found in

R*

Hydroxyl

Alcohols,
carbohydrates

Carboxyl

Fatty acids, proteins,


organic acids

Amino

Proteins, nucleic acids

Ester

Lipids

Sulfhydryl

Cysteine (amino acid),


proteins

Carbonyl,
terminal end

Aldehydes,
polysaccharides

Carbonyl,
internal

Ketones,
polysaccharides

Phosphate

DNA, RNA, ATP

H
O

C
OH
H

Confer unique
reactive properties on
the whole molecule

NH2

H
O
R

C
O

H
R

SH

H
O
R

C
H
O

C
O

P
OH

OH

25

Macromolecules
Biochemicals are organic compounds produced
by living things
Macromolecules: large compounds assembled
from smaller subunits
Monomer: a repeating subunit
Polymer: a chain of monomers
4 Biological Macromolecules: Carbohydrates,
Lipids, Proteins, Nucleic Acids
26

Biological Macromolecules
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27

Carbohydrates
Sugars and polysaccharides
General formula (CH2O)n
Aldehydes and ketones
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Aldehyde group

O
C1

C2

OH

CH2OH

HO

C3

C4

OH

C5

OH

C6

HO OH

OH

O
C1

H
2

OH

OH

C2

OH

HO

C3

HO

C4

C5

OH

C6

CH2OH
O
5
H
HO
H
4

OH

OH

H OH

OH

Glucose

C1

C2

HO

C3

C4

OH

C5

OH

C6

OH

Ketone group

HOCH2

OH

H
4

OH

HO CH
2OH
1
3

Galactose

Fructose

28

Carbohydrates
Saccharide: simple carbohydrate
Monosaccharide: 3-7 carbons
Disaccharide: two monosaccharides
Polysaccharide: five or more monosaccharides
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O
O

Monosaccharide
O

Disaccharide

O
O

CH2

O
O

CH 2

Polysaccharide

29

Carbohydrates
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Subunits linked by
glycosidic bonds

C
C
C

H OH
C 1 C
OH H
C
C

O
C

H2 O
O H
C

C
H C

O
C
C

(a)
6

Dehydration
synthesis: loss of
water in a
polymerization
reaction

H
C4
HO

CH2OH
O
C
5
H
H
H
1C 1 C 4
H
O
OH HO
2
3
C
C
H
OH
Glucose

CH2OH
O
C
5
H
H
1C
OH
H
OH
2
3
C
C
H
OH

CH2OH
C5
O
H
H
H
H
1C
C4
C4
OH
H
O
HO
2
3
C
C
H
OH

Glucose

CH2OH
O
C
5
H
OH
H
2
3
C
C

H
1C

H2 O

H2 O

CH2OH
O
C
5
OH
H
1(b) C 1
OH
H
H
3
2
C
C
H
OH

H2 O

OH

OH

Maltose

(b)
6

CH2OH
C
O

5
H
H
4
C
OH
HO
3
C
H

H
C4
HO

(c)

CH2OH
6
O
C
CH2OH O
5
H
H
1 C 1 C5
H
OH
H
2
3
OH H
4
C
C
C
OH
H
OH

Glucose

HO
C4
H

(d)

CH2OH
O
C
5
H
H
H
1C 1 C4
OH
H
CH HO
3
2
C
C
H
OH
Galactose

OH
C
OH
CH OH
3
C 1 2
H
2

C5
H
H
4
C
OH

H
C
OH O

2C
OH
2OH
C CH
1
H

Sucrose

Glucose

CH2OH O

Fructose

CH2OH
O
C
5
H
H
1C
OH
H
OH
3
2
C
C
H
OH

1C

HO
C4
H

CH2OH
O
C
5
H
H
1(b) C O C 4
OH
H
H
3
2
C
C
H
OH
Lactose

30

Carbohydrates
Functions cell structure, adhesion, and
metabolism
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CH2OH
H
OH
CH2OH
H
OH
O
O
H
H
H H
H1
H 1H
4
1 O 4 OH
4H
1 O 4 OH
OH
H
H
OH
H
H
O
O
O
H H
H H
O
O
H
OH
CH2OH
H
OH
CH2OH

CH2OH
CH2OH
CH2OH
5
5
5
O
O
O
H H H
H H H
H
H H
4
1
4
1
4
1
O
O
O
O
OH H
OH H
OH H
3

OH

OH

OH

CH2OH
5
O
H
H H
4
1
OH H
Branch O
Branch
2
3
point
H O O
H 6 C OH
5
O
H
H H
4
1
O
OH H

H
bonds

(a) Cellulose

(b) Starch

OH

31

Lipids
Long or complex, hydrophobic, C - H chains
Triglycerides, phospholipids in membranes,
steroids like cholesterol
Functions
Triglycerides energy storage
Phospholipid major cell membrane component
Steroids cell membrane component

32

Triglycerides: 3 fatty acids bound to glycerol


Triglycerides are used for energy storage
Could be saturated or unsaturated
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Fatty acids
1
O
C
HO

Triglycerides

Palmitic acid, a saturated fatty acid


2
O
C
HO

Linolenic acid, an unsaturated fatty acid

33

Phospholipids: glycerol with 2 fatty


acids and a phosphate group
Bilayers of phospholipids form membranes
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Variable alcohol group
R
O
O P O2
O
HCH H

Phosphate

HC
O
O C

CH

Charged
head

Polar lipid molecule

Glycerol

Polar head
Nonpolar
tails

O
O C

HCH HCH
HCH HCH

Tail
Double
bond
Creates
a kink.

HCH HCH
HCH HCH
HCH HCH
HCH HCH

HCH
HC
HC
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
H

HCH
HCH
HCH
HCH
HCH
HCH

1 Phospholipids in single layer

HCH
HCH
HCH
HCH
HCH

Fatty acids
(a)

Water

Water

Water

2 Phospholipid bilayer
(b)

34

Membrane Lipids
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Glycolipid

Phospholipids

Cholesterol is
inserted into the
phospholipid bilayer

Cell
membrane

Protein
Site for
ester bond
with a fatty
acid
Cholesterol

Cholesterol

HO
H C

Globular protein

CH2

CH2 H2C
C

CH3
H2
HC
C
CH2CH H2C

CH

CH

CH3

C
HC

CH2C
H2

CHCH3

CH2
CH2
CH2

CH
CH3 CH3

35

Concept Check:
Triglycerides that have double bonds in their fatty acids are
best described as

A. Saturated
B. Unsaturated
C. Phospholipids
D. Cholesterol
36

Proteins

Predominant molecules in cells


Monomer amino acids 20
Polymer peptide, polypeptide, protein
Subunits linked by peptide bonds
Fold into very specific 3-D shapes
Functions support, enzymes, transport,
defense, movement

37

Amino Acids
Amino acids are
the monomers that
make up a protein
polymer

38

Formation of a Peptide Bond


Amino acids are attached through peptide bonds to form
proteins
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Bond forming
H

H
N
H

C
C
R1

C
R1

R2

H
N

OH

H
H

N
H

C
H

N
O

R2

OH

N
O

C
R3

N
H

N
OH

R4

R4

R3

C
H

C
H

OH
C
O

H
+ 3H2O

C
O

39

Protein Structure
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Primary
Structure
Secondary
Structure
Tertiary
Structure

Amino acids

1 The primary structure is a series of


amino acids bound in a chain.
Amino acids display small charged
functional groups (red symbols).

2 The secondary structure


develops when CO and NH
groups on adjacent amino
acids form hydrogen bonds.
This action folds the chain
into local configurations called
the helix and -pleated
sheet. Most proteins have
both types of secondary
structures.

Primary structure

helix

-pleated sheet

Secondary structure

N H

O C

C O

H N

N
C
C O

Detail of hydrogen bond

Disulfide bond

3 The tertiary structure forms when


portions of the secondary structure
further interact by forming covalent
disulfide bonds and additional
interactions. From this emerges a
stable three-dimensional molecule.
Depending on the protein, this may be
the final functional state.

S S

Tertiary structure

Quaternary
Structure

O C

Projected 3-dimensional
shape (note grooves and
projections)

4 The quaternary structure exists only in


proteins that consist of more than one
polypeptide chain. Shown here is a
model of the cholera toxin, composed
of five separate polypeptides, each
one shown in a different color.

Image courtesy RCSB Protein Data Bank, www.pdp.org

Quaternary structure

40

Nucleic Acids

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DNA and RNA


Nucleotide monomer
DNA deoxyribonucleic
acid
A,T,C,G nitrogen bases
Double helix
Function hereditary
material

RNA ribonucleic acid


A,U,C,G nitrogen bases
Function organize protein
synthesis

N base
Pentose sugar
Phosphate
(a) A nucleotide, composed of a phosphate, a pentose
sugar, and a nitrogen base (either A,T,C,G, or U) is
the monomer of both DNA and RNA.

Backbone

Backbone
P

DNA
D

P
D

P
A

P
D

P
C

P
D

P
G

P
D

P
C

P
D

RNA

H bonds

(b) In DNA, the polymer is composed of


alternating deoxyribose (D) and
phosphate (P) with nitrogen bases (A,T,C,G)
attached to the deoxyribose. DNA almost
always exists in pairs of strands, oriented
so that the bases are paired across the
central axis of the molecule.

P
A

R
P

(c) In RNA, the polymer


is composed of
alternating ribose (R)
and phosphate (P)
attached to nitrogen
41
bases (A,U,C,G), but
it is usually a single strand.

Nucleotide Components
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HOCH2 O

DNA Nucleotides:
Deoxyribose
C, G, A or T

HOCH2 O

OH
H

OH OH

Deoxyribose

Ribose

(a) Pentose sugars


H

Ribose
C, G, A or U

OH H

RNA Nucleotides:

OH

O
N

H
N

H
N

H
N

N
H

Guanine (G)

(b) Purine bases

Adenine (A)

H3C

H
N

O
H

N
N

H
N

Thymine (T)

Cytosine (C)

Uracil (U)

(c) Pyrimidine bases

42

Double Helix of DNA


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DNA is formed by
two very long
polynucleotide
strands linked along
their length by
hydrogen bonds

Backbone
strands

Base pairs

D
Hydrogen
O bonds
P

O
O

P
D

G
O

43

DNA Passing on the Genetic


Message
Each strand is copied
Replication is guided
by base pairing
End result is two
separate double
strands

Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Cells
Events in Cell Division

Events in DNA Replication


A

H-bonding severed
G

New
bases

Two single strands


T
C

Two double strands


A

44

ATP: The Energy Molecule of Cells


Adenosine triphosphate
Nucleotide - adenine, ribose, three phosphates

Function - transfer and storage of energy


Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

NH2

O
O

P
O

O
O

P
O

O
O

N
7

9
N

4 3
N

CH2 O

1
2

O
OH

OH
Adenosine

Adenosine diphosphate (ADP)


Adenosine triphosphate (ATP)

45

Concept Check:
Which of the following is TRUE about RNA?

A. It is a double stranded molecule


B. It contains the sugar deoxyribose
C. It contains the nitrogenous base Uracil
D. It holds the genetic information
E. All of the above are true
46