Biology

Sylvia S. Mader
Michael Windelspecht

Chapter 3
The Chemistry of
Organic Molecules
Lecture Outline

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

BACTERIA

common
ancestor ARCHAEA
(first cells)

Protists

Plants
cell with nucleus

EUKARYA
Fungi

Animals

Past Present
Time
 A Portion of the Periodic Table
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

I VIII
1 atomic number 2
1 H atomic symbol atomic mass He
1.008 II III IV V VI VII 4.003

3 4 5 6 7 8 9 10
2 Li Be B C N O F Ne
Periods

6.941 9.012 10.81 12.01 14.01 16.00 19.00 20.18

11 12 13 14 15 16 17 18
3 Na Mg Al Si P S Cl Ar
22.99 24.31 26.98 28.09 30.97 32.07 35.45 39.95

19 20 31 32 33 34 35 36
4 K Ca Ga Ge As Se Br Kr
39.10 40.08 69.72 72.59 74.92 78.96 79.90 83.60

Groups
4
How Do Atoms Interact to Form
Molecules?
Ionic bonds form among charged atoms
that are called ions - NaCl
Covalent bonds form between uncharged
atoms that share electrons
Hydrogen bonds are attractive forces
between polar molecules
 :
There are 3 types of chemical bonds

Bond
Description Example
Strength

Bonding of
Two atoms share
Covalent Strong Oxygen and
electrons.
Hydrogen in H2O

Oppositely charged Bond between

Ionic Moderate ions are attracted to Na+ and Cl- in
each other. salt.
Forms between
oppositely charges
Bonds between
Hydrogen Weak portions of covalently
water molecules.
bonded hydrogen
atoms.

6
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Biosphere
Regions of the Earths crust,
waters, and atmosphere
inhabited by living things

Ecosystem
A community plus
the physical environment

Community
Interacting populations in a
particular area

Population
Organisms of the same
species in a particular area

Organism elephant tree

An individual; complex
individuals contain organ systems

Organ System nervous shoot

Composed of several organs
working together
system system

Organ the brain leaves

Composed of tissues functioning
together for a specific task

Tissue
A group of cells with a common
structure and function

nervous tissue epidermal tissue

nerve cell
Cell plant cell
The structural and functional
unit of all living things

Molecule methane
Union of two or more atoms of
the same or different elements

Atom oxygen
Smallest unit of an element
composed of electrons, protons,
and neutrons
Learning Outcomes
3.1 Organic Molecules

1. Explain how the properties of carbon enable it to produce diverse organic molecules.
2. Describe how functional groups affect a carbon molecules chemical reactivity.
3. Compare what is added and what is produced during biomolecule synthesis and degradation reactions.
3.2 Carbohydrates

1. List several examples of important monosaccharides and polysaccharides.

2. Compare the energy and structural uses of starch, glycogen, and cellulose.
3.3 Lipids
1. Describe why lipids are essential to living organisms.
2. Explain where fats and oils are produced.
3. Contrast the structures of fats, phospholipids, and steroids.
4. Compare the functions of phospholipids and steroids in cells.
3.4 Proteins
1. Describe functions of proteins in cells.
2. Explain how a polypeptide is constructed from amino acids.
3. Compare the four levels of protein structure.
4. Analyze the factors that affect protein structure and function.
3.5 Nucleic Acids
1. Distinguish between a nucleotide and a nucleic acid.
2. Compare the structure and function of DNA and RNA nucleic acids.
3. Examine why purines and pyrimidines pair together.
4. Explain how ATP is able to store energy.

8
3.1 Organic Molecules
1. Explain how the properties of carbon
enable it to produce diverse organic
molecules.
2. Describe how functional groups
affect a carbon molecules chemical
reactivity.
3. Compare what is added and what is
produced during biomolecule synthesis
and degradation reactions.
 3.1 Organic Molecules
Organic molecules contain carbon and
hydrogen atoms.

Four classes of organic molecules

(biomolecules) exist in living organisms:
Carbohydrates
Lipids
Proteins
Nucleic Acids

10
Inorganic versus Organic Molecules

11
Fig. 3.1
13
Biology: Life on Earth, 9e Copyright 2011 Pearson Education Inc.
Biology: Life on Earth, 9e Copyright 2011 Pearson Education Inc.
 The Carbon Atom
The carbon quite small with 2 electrons in the first shell
and four electrons in the outer shell .
To complete it outer shell, it always share electrons with
CHNOPS
It shares electrons with as many of four other elements,
and produces a diverse molecules
More importantly, is the ability of carbon to share
electrons with other carbon atom
C- C bond is quite stable and allow the formation of long
carbon chains
Bonds can be single, double, triple
The diversity of organic molecules is further enhanced by
the presence of functional groups
16
 A Portion of the Periodic Table
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

I VIII
1 atomic number 2
1 H atomic symbol atomic mass He
1.008 II III IV V VI VII 4.003

3 4 5 6 7 8 9 10
2 Li Be B C N O F Ne
Periods

6.941 9.012 10.81 12.01 14.01 16.00 19.00 20.18

11 12 13 14 15 16 17 18
3 Na Mg Al Si P S Cl Ar
22.99 24.31 26.98 28.09 30.97 32.07 35.45 39.95

19 20 31 32 33 34 35 36
4 K Ca Ga Ge As Se Br Kr
39.10 40.08 69.72 72.59 74.92 78.96 79.90 83.60

Groups
17
18
 Table 2-3

Biology: Life on Earth, 9e Copyright 2011 Pearson Education Inc.

 Bohr Models of Atoms
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electron valence shell

electron shell C N
H nucleus

hydrogen carbon nitrogen

1H 12 C 14 N
1 6 7

P S
O

oxygen phosphorus sulfur

16 31 32
8
O 15 P 16S

20
Figure 3.1B
Length. Carbon skeletons vary in length.

Ethane Propane
Branching. Skeletons may be unbranched
or branched.

Butane Isobutane
Double bonds. Skeletons may have double bonds.

1-Butene 2-Butene
Rings. Skeletons may be arranged in rings.

Cyclohexane Benzene
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cyclohexane
 Page 39

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octane
 The Carbon Skeleton and Functional
Groups

The carbon chain of an organic molecule is

called its skeleton or backbone.
Diversity of organic molecules due to
attachment of different functional groups to the
carbon skeleton
Functional groups are clusters of specific
atoms bonded to the carbon skeleton with
characteristic structures and functions.
Determine the chemical reactivity and polarity
of organic molecules
25
 The Carbon Skeleton and Functional
Groups

The carbon chain of an organic molecule is

called its skeleton or backbone.
Functional groups are clusters of specific
atoms bonded to the carbon skeleton with
characteristic structures and functions.
Determine the chemical reactivity and polarity
of organic molecules

26
Table 3.2
 Isomers

Isomers are organic molecules that have

identical molecular formulas but a different
arrangement of atoms.
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glyceraldehyde dihydroxyacetone

H H O H O H

H C C C H H C C C H

OH OH OH OH

28
Fig. 3-6, p. 52
 Biomolecules
Carbohydrates, lipids, proteins, and nucleic
acids are called biomolecules.
Usually consist of many repeating units
Each repeating unit is called a monomer.
A molecule composed of monomers is
called a polymer (many parts).
Example: amino acids (monomer) are
joined together to form a protein
(polymer)

30
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Fig. 3.3

Biomolecules

Category Subunit(s) Polymer

Carbohydrates* Monosaccharide Polysaccharide

Lipids Glycerol and fatty acids Fat

Proteins* Amino acids Polypeptide

Nucleic acids* Nucleotide DNA,RNA

*Polymers
The McGraw Hill Companies, Inc./John Thoeming, photographer
 Synthesis and Degradation
A dehydration reaction is a chemical reaction
in which subunits are joined together by the
formation of a covalent bond and water is
produced during the reaction.
Used to connect monomers together to make
polymers
Example: formation of starch (polymer) from glucose
subunits (monomer)

A hydrolysis reaction is a chemical reaction in

which a water molecule is added to break a
covalent bond.
Used to breakdown polymers into monomers
Example: digestion of starch into glucose monomers
32
Synthesis and Degradation of Biomolecules

monomer OH
monomer OH +
monomer OH + H monomer
monomer OH + H monomer

H2O
 monomer OH + H monomer

Dehydration H 2O
reaction

monomer monomer

a. Synthesis of a biomolecule
monomer monomer
 H2O

monomer monomer
Dehydration H 2O
reaction

monomer monomer
 monomer OH H monomer

Hydrolysis
reaction H 2O

monomer monomer

b. Degradation of a biomolecule
 monomer OH H monomer

dehydration H2O
reaction

monomer monomer

a. Synthesis of a biomolecule

monomer OH H monomer

hydration
reaction H2O

monomer monomer

b. Degradation of a biomolecule
43
 Synthesis and Degradation

Enzymes are required for cells to carry out

dehydration synthesis and hydrolysis reactions.

An enzyme is a molecule that speeds up a

chemical reaction.
Enzymes are not consumed in the reaction.
Enzymes are not changed by the reaction.

44
Check Your Progress 3.1
1. Describe the properties of a carbon
that makes it ideally suited to
produce carbon skeleton.
2. Explain the substitution of carboxyl
group for a hydroxyl group in
biomolecule would change the
molecule function.
3. Explain why water is needed for the
breakdown of a biomolecule.
3.2 Carbohydrates
1. Summarize the role of carbohydrates in a cell.
2. Distinguish among the forms of
carbohydrates.
3. Compare the energy and structural uses of
starch, glycogen, and cellulose.

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 3.2 Carbohydrates
Functions:
Immediate energy source
Provide building material (structural role)

Contain carbon, hydrogen and oxygen in a 1:2:1

ratio. CH2O

Varieties: monosaccharides, disaccharides, and

polysaccharides

Subunit called monosaccharides

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Fig. 3.5

b. Shell contains chitin.

a. Cell walls contain cellulose. c. Cell walls contain peptidoglycan.

a: Brand X Pictures/PunchStock; b: Ingram Publishing/Alamy; c: H. Pol/CNRI/SPL/Photo Researchers, Inc.
49
 Monosaccharides

A monosaccharide is a single sugar molecule.

Also called simple sugars, CH2O
Have a backbone of 3 to 7 carbon atoms
Examples:
Glucose (blood), fructose (fruit) and galactose
Hexoses - six carbon atoms, C6H12O6
Ribose and deoxyribose (in nucleotides)
Pentoses five carbon atoms, C5H10O5

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Glucose
Fig. 3.6

6 CH2OH
CH2OH
5C O O
H H H H
H H
C C1
4 OH H OH H
HO C OH HO OH
3
C
2
a. b.
H OH H OH

C6H12O6

O O

c. d.
Steve Bloom/Taxi/Getty
Fig. 3-6, p. 52
53
 Disaccharides

A disaccharide contains two

monosaccharides joined together by
dehydration synthesis.
Examples:
Lactose (milk sugar) is composed of galactose
and glucose.
Sucrose (table sugar) is composed of glucose
and fructose.
Maltose is composed of two glucose molecules.
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Figure 3.4A
Synthesis and Degradation of Maltose

CH2OH CH2OH
O H H O

+
OH HO

glucose C6H12O6 glucose C6H12O6

CH2OH CH2OH
O O
H H dehydration reaction
+
OH HO

glucose C6H12O6 glucose C6H12O6

CH2OH CH2OH CH2OH CH2OH
O O O O
H H dehydration reaction
+ O + H2O
OH HO

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

 CH2OH CH2OH CH2OH CH2OH
O O O O
H H dehydration reaction
+ O + H2O
OH HO

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

monosaccharide + monosaccharide disaccharide + water

CH2OH CH2OH
O O

maltose C12H22O11
CH2OH CH2OH
O O

O + H2O

maltose C12H22O11 water

 CH2OH CH2OH
O O

O + H2O
hydrolysis reaction

maltose C12H22O11 water

CH2OH CH2OH CH2OH CH2OH
O O O O
H H

+ O + H2O
OH HO hydrolysis reaction

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

 CH2OH CH2OH CH2OH CH2OH
O O O O
H H

+ O + H2O
OH HO hydrolysis reaction

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

monosaccharide + monosaccharide disaccharide + water

 dehydration reaction

hydrolysis reaction

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

monosaccharide + monosaccharide disaccharide + water

 Page 42

CH2OH CH2OH
O O

glucose O fructose

sucrose CH2OH
Fig. 3-6, p. 52
 Polysaccharides

A polysaccharide is a polymer of monosaccharides.

Examples:
Starch provides energy storage in plants.
Glycogen provides energy storage in animals.
Cellulose is found in the cell walls of plants.
Chitin is found in the cell walls of fungi and
exoskeleton of some animals.
Peptidoglycan is found in the cell walls of bacteria.
 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Fig. 3.5

b. Shell contains chitin.

a. Cell walls contain cellulose. c. Cell walls contain peptidoglycan.

a: Brand X Pictures/PunchStock; b: Ingram Publishing/Alamy; c: H. Pol/CNRI/SPL/Photo Researchers, Inc.
 Amylose:
nonbranched

starch
granule

Amylopectin:
branched

a. Starch 250 m

glycogen
granule

b . Glycogen 150 nm

a: Jeremy Burgess/SPL/Photo Researchers, Inc.; b: Don W. Fawcett/Photo Researchers, Inc.

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

cellulose fiber
Fig. 3.9

microfibrils
plant
cell wall

cellulose fibers 5,000 m

CH2OH H OH
CH2OH H OH
O O
H H H
H O OH H H O OH H
O OH H H O OH H H O
H H O H H
O
H OH CH2OH H OH CH2OH

CH2OH H OH CH2OH H OH
O O glucose molecules
H H H
H O OH H H O OH H
O OH H H O OH H H O
H H H H
O O
H OH CH2OH H OH CH2OH
hydrogen bonds
CH2OH H OH CH2OH H OH
H O H H O
H O OHH H H O OH H
O OH H H O OH H H O
H H H H
O O
H OH CH2OH H OH CH2OH

Science VU
Figure 3.7

Starch granules
in potato tuber cells Starch

Glucose
monomer
Glycogen granules
in muscle
tissue Glycogen

Cellulose microfibrils Cellulose

in a plant cell wall

Hydrogen bonds

Cellulose
molecules
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76
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78
Figure 3-11 Chitin structure and function

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 Chitin: A Unique Polysaccharide

Fig. 3-10

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82
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85
Check Your Progress 3.2
1. Summarize the general
characteristics of carbohydrates and
their roles in living organisms.
2. Describe how monosaccharides are
combined to form disaccharides.
3. Explain why human cannot utilize
the glucose in cellulose as a nutrient
source.
3.3 Lipids
1. Describe why lipids are essential to living
organisms.
2. Distinguish between saturated and unsaturated
fatty acids.
3. Contrast the structures of fats, phospholipids,
and steroids.
4. Compare the functions of phospholipids and
steroids in cells.

87
 3.3 Lipids
Lipids are varied in structure.
Large nonpolar molecules that are insoluble in water
Functions:
Fat - Long-term energy storage and insulator
Structural components
Cell communication and regulation
Protection

Varieties: fats, oils, phospholipids, steroids, waxes

Figure 3.8A
91
 Triglycerides: Long-Term
Energy Storage
Also called fats and oils
Functions: long-term energy storage and
insulation
Consist of one glycerol molecule linked to
three fatty acids by dehydration synthesis
 H

H C OH

H C OH

H C OH

glycerol
a. Formation of a fat
 H H H H H
H O
C C C C C C H
H C OH HO
H H H H H

H H H H H H H
O
+ C C C C C C C C H
H C OH HO
H H H H H H H

H H H
O H
H
C C C C C
H C OH HO C
H H H
H H
kink

glycerol 3 fatty acids

a. Formation of a fat
 H H H H H
H O 3 H2O
C C C C C C H
H C OH HO
H H H H H

H H H H H H H
O
+ C C C C C C C C H
H C OH HO
H H H H H H H

H H H
O H
H
C C C C C 3 H2O
H C OH HO C
H H H
H H
in

glycerol 3 fatty acids 3 water

a. Formation of a fat molecules
 H H H H H H H O H H H H H
O 3 H2O
C C C C C C H H C O C C C C C C H
H C OH HO
H H H H H H H H H H

H H H H H H H O H H H H H H H
O

H C OH
+ C C C C C C C C H H C H C C C C C C C C H
HO
H H H H H H H H H H H H H H

H H H O H H H
O H H
H O H
C C C C 3 H2O H C C C C C
C C
H C OH HO C C
H H H H H H H
H H H
in in

glycerol 3 fatty acids 3 water fat molecule

a. Formation of a fat molecules
Triglycerides: Long-Term Energy Storage
Fatty acids are either unsaturated or saturated.
Unsaturated - one or more double bonds between
carbons
Tend to be liquid at room temperature
Example: plant oils

Saturated - no double bonds between carbons

Tend to be solid at room temperature
Examples: butter, lard

97
 H H H H H H H O H H H H H
O 3 H2O
C C C C C C H H C O C C C C C C H
H C OH HO

Fig. 3.10
H H H H H H H H H H

H H H H H H H O H H H H H H H
O
+ C C C C C C C C H H C H C C C C C C C C H
H C OH HO
H H H H H H H H H H H H H H

H H H O H H H
O H H
C C C C H H C O C C C C H
C 3 H2O C
H C OH HO C C
H H H H H H H
H H H
in in

glycerol 3 fatty acids 3 water fat molecule

molecules
a. Formation of a fat

corn corn oil

H H H H H H H H H H H H H H H
O
C C C C C C C C C C C C C C C C C C H
HO
H H H H H H H H H H H H H

unsaturated fatty acid with double bonds (yellow)

unsaturated fat

mil butter

H H H H H H H H H H H H H H H
O
C C C C C C C C C C C C C C C C H
HO
H H H H H H H H H H H H H H H

saturated fatty acid with no double bonds saturated fat

b. Types of fatty acids c. Types of fats
Figure E5-2 Caribou legs are adapted to cold

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 Phospholipids: Membrane Components
Structure is similar to triglycerides
Consist of one glycerol molecule linked to two fatty
acids and a modified phosphate group
The fatty acids are nonpolar and hydrophobic.
The modified phosphate group is polar and
hydrophilic.
Function: form plasma membranes
In water, phospholipids aggregate to form a lipid
bilayer.
Polar phosphate heads are oriented towards the
water.
Nonpolar fatty acid tails are oriented away from water.
Nonpolar fatty acid tails form a hydrophobic core.

100
101
Phospholipids Form
Membranes
glycerol
O
CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH
CH CH2 CH2 2 CH2 CH3
Polar 1
CH2 O
C 2

Head 2
fatty acids
O CH2 O
3
R O P O CH2 C CH2 CH
2 CH2 CH2 CH2 CH2 CH2 CH

O
Nonpolar Tails
phosphate
a. Phospholipid structure

outside cell
inside cell

b.. Plasma membrane of a cell

Figure 3-15 Phospholipids

variable
functional phosphate
group group

polar head glycerol fatty acid tails

backbone
(hydrophilic) (hydrophobic)

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 Steroids: Four Fused Carbon Rings

Composed of four fused carbon rings

Various functional groups attached to the carbon
skeleton

Functions: component of animal cell

membrane, regulation
Examples: cholesterol, testosterone, estrogen
Cholesterol provide stability to membrane,
also the precursor molecule for several other
steroids (testosterone and estrogen).
104
3.4 What Are Lipids?

Steroids contain four fused carbon rings

Steroids are composed of four carbon rings fused
together with various functional groups protruding
from them
Examples of steroids include cholesterol
Found in the membranes of animal cells
Component of male and female sex hormones
Makes up 2% of human brain
Excessive cholesterol contributes to cardiovascular
disease
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106
 Steroid Diversity
OH
CH3

CH3

O
b. Testosterone

CH3

HC CH3

(CH2)3
OH
HC CH3 CH3
CH3

CH3

HO

HO c. Estrogen
a. Cholesterol
Ernest A. Janes/Bruce Coleman/Photoshot
Figure 3-16 Steroids

Estrogen

Cholesterol Testosterone
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 Waxes
Long-chain fatty acid bonded to a long-chain
alcohol
Solid at room temperature
Waterproof
Resistant to degradation
Function: protection
Examples: earwax, plant cuticle, beeswax

109
3.4 What Are Lipids?

Oils, fats, and waxes are lipids containing only

carbon, hydrogen, and oxygen (continued)
Waxes are highly saturated and solid at room
temperature
Waxes form waterproof coatings such as on
Leaves and stems in plants
Fur in mammals
Insect exoskeletons
Waxes are also used to build honeycomb structures

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 Waxes

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a. b.

a: Das Fotoarchiv/Peter Arnold, Inc.; b: Martha Cooper/Peter Arnold, Inc.

111
Figure 3-13b Wax

Wax

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113
Check Your Progress 3.3
1. List the functions of triglycerides,
phospholipid, steroids, and waxes.
2. Contrast the structure of a saturated
fatty acid with that of an
unsaturated fatty acid. .
3. Explain why phospholipids form a
bilayer in water.
3.4 Proteins
1. Describe functions of proteins in cells.
2. Explain how a polypeptide is
constructed from amino acids.
3. Compare the four levels of protein
structure.
4. Understand the factors that affect
protein structure and function.

115
 3.4 Proteins
Proteins are polymers of amino acids linked
together by peptide bonds.
A peptide bond is a covalent bond between amino
acids.

Two or more amino acids joined together are

called peptides.
Long chains of amino acids joined together are
called polypeptides.

A protein is a polypeptide that has folded into

a particular shape and has function.

116
 Functions of Proteins
Metabolism
Most enzymes are proteins that act as catalysts to accelerate
chemical reactions within cells.
Support
Keratin and collagen
Transport
Hemoglobin and membrane proteins
Defense
Antibodies
Regulation
Hormones are regulatory proteins that influence the metabolism of
cells.
Motion
Muscle proteins and microtubules
117
 Amino Acids: Protein Monomers
There are 20 different common amino acids.
Amino acids differ by their R groups.

amino acidic
group group
H

H2N C COOH

R
R = rest of molecule
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Sample Amino Acids with Nonpolar (Hydrophobic) R Groups

H O H H O
O
H H3N+ C C H3N+ C C H3N+ C C H
O O
O O
H3N+ CH2 O CH2 H2 N+ C C
C C (CH2)2
O
O CH H2C CH2
CH S
CH3 CH3 CH3 CH2
H3C CH3
valine (Val) methionine (Met) phenylalanine (Phe) leucine (Leu) proline (Pro)

Sample Amino Acids with Polar (Hydrophilic) R Groups

H O H O H O H O
H3N+ C C H3N+ C C H3N+ C C H3N+ C C
O O O (CH2)2 O
CH2 CH CH2
SH OH C
cysteine (Cys) serine (Ser)
H O NH2 O
H3N+ C H OH glutamine (Gln)
C O
tyrosine (Tyr)
O H3N+ C C
CH2
CH O
C
NH2 O OH CH3
asparagine (Asn) threonine (Thr)

Sample Amino Acids with Ionized R Groups

H O H O
H O H3N+ C C H3N+ C C H O
H O
H3N+ C O (CH2)3 O C
C CH2 H3N+ C H3N+ C
C
O CH2 O
CH2 CH2 O NH
CH2
CH2 NH
CH2 C C N+ H2
COO- N+ H 3 O O NH2 N+H
glutamicacid (Glu) lysine (Lys) aspartic acid (Asp) arginine (Arg) histidine (His)
Synthesis and Degradation of a Peptide
amino group

amino acid
amino group acidic group

amino acid amino acid

amino group acidic group

dehydration reaction

amino acid amino acid

amino group acidic group peptide bond

dehydration reaction

amino acid amino acid water

dipeptide
amino group acidic group peptide bond

dehydration reaction

hydrolysis reaction

amino acid amino acid water

dipeptide
 Page 50

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peptide bond
 Levels of Protein Structure

Proteins cannot function properly unless they

fold into their proper shape.
When a protein loses it proper shape, it said to be
denatured.
Exposure of proteins to certain chemicals, a
change in pH, or high temperature can disrupt
protein structure.

Proteins can have up to four levels of structure:

Primary
Secondary
Tertiary
Quaternary

126
 Four Levels of Protein Structure
Primary
The sequence of amino acids
Secondary
Characterized by the presence of alpha helices and
beta (pleated) sheets held in place with hydrogen
bonds
Tertiary
Final overall three-dimensional shape of a
polypeptide
Stabilized by the presence of hydrophobic
interactions, hydrogen bonding, ionic bonding, and
covalent bonding
Quaternary
Consists of more than one polypeptide
127
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H3N+

Primary Structure
This level of structure amino acid
is determined by the peptide bond COO
sequence of amino
acids coded by a
gene that joins to
form a polypeptide.

C
O
CH C hydrogen bond
O C N O
R C C
CH
C H N H H C
N R hydrogen bond R C O O
CH O C C
H R C
R C C N
O H R C H
O N H N
CH N
C N R H C O
C R C O
CH O O H
C C R N
N R H
O C N H N H C
H R C O C O R
Secondary Structure CH C
O C N R C
Hydrogen bonding CH R C O N
C H N H R C
between amino acids N N
R
causes the polypeptide CH C
C O
to form an alpha helix O H
or a pleated sheet. N
alpha) helix (beta) sheet = pleated sheet

Tertiary Structure
Interactions of amino
acid side chains with
water, covalent bonding
between R groups, and
other chemical interactions
determine the folded
three-dimensional shape disulfide bond
of a protein.
Quaternary Structure

This level of structure

occurs when two or more
folded polypeptides interact
to perform a biological function.
Fig. 3-21, p. 66
 Examples of Fibrous Proteins

a. b. c.
a: Gregory Pace/Corbis; b: Ronald Siemoneit/Corbis Sygma; c: Kjell Sandved/Visuals Unlimited

130
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 Protein-Folding Diseases

Chaperone proteins help proteins fold into their

normal shape.
Defects in chaperone proteins may play a role in
several human diseases such as Alzheimer disease
and cystic fibrosis.

Prions are misfolded proteins that have been

implicated in a group of fatal brain diseases
known as TSEs.
Mad cow disease is one example of a TSE disease.

132
 Check Your Progress 3.4
1. List the roles of proteins in living
organisms.
2. Describe how two amino acids are
combined to form a polypeptide.
3. Summarize the difference among
primary, secondary, tertiary, and
quarternary structure.
4. Describe the consequence of
incorrect protein folding.
5.
3.5 Nucleic Acids
1. Distinguish between a nucleotide and
a nucleic acid.
2. Compare the structure and function of
DNA and RNA nucleic acids.
3. Explain how ATP is able to store
energy.

134
 3.5 Nucleic Acids
Nucleic acids are polymers of nucleotides.

Two varieties of nucleic acids:

DNA (deoxyribonucleic acid)
Genetic material that stores information for its own
replication and for the sequence of amino acids in
proteins.
RNA (ribonucleic acid)
Perform a wide range of functions within cells
which include protein synthesis and regulation of
gene expression; mRNA, tRNA, rRNA
135
 DNA

Nucleus

Nucleolus

Nucleophore
Rough ER with ribosomes

Cytoplasm

How does genetic information stored in DNA get to the cytoplasm? And once
the information is there, how is that message read and used to construct the
corresponding protein?

require participation of mRNA

 Structure of a Nucleotide
Each nucleotide is composed of three parts:
A phosphate group
A pentose sugar
A nitrogen-containing (nitrogenous) base
There are five types of nucleotides found in nucleic
acids.
DNA contains adenine, guanine, cytosine, and thymine.
RNA contains adenine, guanine, cytosine, and uracil.
Nucleotides are joined together by a series of
dehydration synthesis reactions to form a linear
molecule called a strand.

137
 Nucleotides

phosphate nitrogen-
P C containing
base
5' O

4' S 1'
3' 2'
pentose sugar
 O
nitrogen-
O phosphate P C containing
P O
base
O 5' O

4' S 1'
3' 2'
pentose sugar
a. Nucleotide structure
 O
nitrogen- CH2OH
O phosphate P C containing
P O OH
base O
O 5' O C H H C

S H C C H
4' 1'

3' 2' OH H
pentose sugar deoxyribose (in DNA)
a. Nucleotide structure b. Deoxyribose versus ribose
 O
nitrogen- CH2OH CH2OH
phosphate P C containing
O P O OH OH
base O O
O 5' O C H H C C H H C

S H C C H H C C H
4' 1'

3' 2' OH H OH OH
pentose sugar deoxyribose (in DNA) ribose (in RNA)
a. Nucleotide structure b. Deoxyribose versus ribose
 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Pyrimidines Purines
NH2 O O
NH2 O
C C CH3 C
N CH HN C CH C N C N
HN N C C
C T U HN
CH CH C CH A CH G CH
HC C
O N O N N N C N
O N H2N N
H H H H H
cytosine thymine in DNA uracil in RNA adenine guanine
c. Pyrimidines versus purines
 O
nitrogen- CH2OH CH2OH
phosphate P C containing
O P O OH OH
base O O
O 5' O C H H C C H H C

S H C C H H C C H
4' 1'

3' 2' OH H OH OH
pentose sugar deoxyribose (in DNA) ribose (in RNA)
a. Nucleotide structure b. Deoxyribose versus ribose

Pyrimidines Purines
NH2 O O
NH2 O
C C CH3 C
N CH HN C CH C N C N
HN C C
C T U N HN
CH CH C CH A CH G CH
HC C
O N O N N N C N
O N H2N N
H H H H H
cytosine thymine in DNA uracil in RNA adenine guanine
c. Pyrimidines versus purines
 Structure of DNA and RNA
The backbone of the nucleic acid strand is composed
of alternating sugar-phosphate molecules.
RNA is predominately a single-stranded molecule.
DNA is a double-stranded molecule.
DNA is composed of two strands held together by
hydrogen bonds between the nitrogen-containing
bases. The two strands twist around each other to
form a double helix.
Adenine hydrogen bonds with thymine
Cytosine hydrogen bonds with guanine
The bonding between the nucleotides in DNA is
referred to as complementary base pairing.

144
Fig. 3-6, p. 52
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Fig. 3.19
RNA Structure
N O
N
G N
P
N
NH2
S
H Nitrogen-containing
bases
O N O
P U
N
CH3
S

Backbone
N NH2
P
N A N
S N
C Cytosine S Ribose
G Guanine A Adenine
O N NH2
P Phosphate U Uracil
P C
N
S
 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

DNA Structure
T A

C G

A T

G C

C CCytosine S Sugar
GGGuanine A AAdenine
P Phosphate T TThymine

a. Space-filling model b. Double helix

H

N H O N

Complementary N
N H

N
N
N

sugar
O H N

Base Pairing in sugar H

cytosine (C) guanine (G)

DNA N
H
N

H O
C
CH3

N
N H N
suga r N N
O
sugar
adenine (A) thymine (T)
c. Complementary base pairing

Photodisk Red/Getty RF
Figure 3-25 Deoxyribonucleic acid

hydrogen
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bond
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 A Special Nucleotide: ATP

ATP (adenosine triphosphate) is composed of adenine,

ribose, and three phosphates.
ATP is a high-energy molecule due to the presence of
the last two unstable phosphate bonds.
Hydrolysis of the terminal phosphate bond yields:
The molecule ADP (adenosine diphosphate)
An inorganic phosphate
Energy to do cellular work
ATP is called the energy currency of the cell.

151
 ATP
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a. adenosine triphosphate c.

NH2 NH2

N N H2O N N

N N P P P N N P P + P + ENERGY

adenosine triphosphate adenosine diphosphate phosphate

b. ATP ADP
c: Jennifer Loomis / Animals Animals / Earth Scenes
Figure 3-24 The energy-carrier molecule adenosine triphosphate (ATP)

2014 Pearson Education, Inc.

 Table 3-2 (1 of 2)

Biology: Life on Earth, 9e Copyright 2011 Pearson Education Inc.

 Table 3-2 (2 of 2)

Biology: Life on Earth, 9e Copyright 2011 Pearson Education Inc.

 Check Your Progress 3.5
1. Examine how a nucleic acid stores
information.
2. Describe the three components of a
nucleotide.
3. Evaluate the properties of ATP that
make it an ideal carrier of energy.
4.
157
Fig. 3-19, p. 64
Fig. 3-20, p. 65
Fig. 3-22a, p. 67
Table 3-2

2014 Pearson Education, Inc.

Fig. 3-CO, p. 46