Lecture Notebook

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W. H. Freeman and Company

Copyright 2012 Sinauer Associates, Inc. Cover photograph Fred Bavendam/Minden Pictures.
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Nucleic Acids,
Proteins, and Enzymes
The base may be either
a pyrimidine or a purine.

Base

Base
P

Base

Ribose or
deoxyribose

Nucleoside

Phosphate

Nucleotide

Pyrimidines
O

NH2
HC

H3C

HC

C
O
N
H
Cytosine (C)

Purines

O
NH

C
O
N
H
Thymine ( T )

NH

HC

C
O
N
H
Uracil (U)

HC

NH2
N

HC

N
HC

CH
C
N
N
H
Adenine (A)

NH

C
C
N
NH2
N
H
Guanine (G)

FIGURE 3.1 Nucleotides Have Three Components (Page 35)

TABLE 3.1 Distinguishing RNA from DNA

Nucleic Acid

Sugar

Bases

Strands

RNA

Ribose

Adenine

Single

Cytosine

Guanine

Uracil

DNA

Deoxyribose

Adenine

Cytosine

Guanine

Thymine

(Page 35)

Double

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Chapter 3|Nucleic Acids, Proteins, and Enzymes

Rest of polymer

Rest of polymer

O
O

Pyrimidine base

5 CH2

5 CH2

Pyrimidine base

5 CH2

1
2

O
5 CH2

OH

Formation of the bond

between nucleotides
always occurs by adding
the 5-phosphate end of
the new nucleotide to
the 3-OH end of the
nucleic acid.

OH

The numbering
5
of ribose carbons
4
is the basis for
identification of 5 3
and 3 ends of DNA
and RNA strands.

Condensation reaction
3

OH

OH

OH

OH
O

O Phosphodiester bond +

H2O

Purine base

5 CH2

5 CH2

1
3

2
OH

OH

OH

OH

FIGURE 3.2 Linking Nucleotides Together (Page 36)

Thymine

Adenine
Hydrogen bond

H3C
C
O

HC

HN
C

NH
N

C
O

POL Hillis
Sinauer Associates
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Figure 03.02 Date 06-22-10

A
Guanine

HC

NH

HC

N
C

HN

CH

HN

Polar bonds

O
C

N
N

Cytosine

CH
C

HC

N
C

N
O

IN-TEXT ART (Page 36)

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

(A)

(B)
RNA (single-stranded)

Double-stranded
segments form when
sequences of RNA
nucleotides pair with
one another.

O
OH
3

H2C 5 O

Phosphate

3 end

U NH

Folding brings together

distant base sequences.

G NH

Ribose

NH

H2C

3
NH

A N
H2C

O
NH

C N
5

H2C

O
5 end

In RNA, the bases are attached to ribose. The bases

in RNA are the purines adenine (A) and guanine (G)
and the pyrimidines cytosine (C) and uracil (U).

FIGURE 3.3 RNA (Page 37)

DNA can replicate.

DNA

Transcription

RNA

Information
POL
Hillis coded in the
sequence
of nucleotide bases
Sinauer
Associates
in DNAStudio
is passed to a sequence
Morales
of nucleotide
RNA.
Figure
03.03 bases
Date in
06-22-10

Translation

Polypeptide

Information in RNA is passed

to polypeptides, but never
the reverse (polypeptides to
nucleic acids).

IN-TEXT ART (Page 37)

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

(A)

5
(B)

DNA (double-stranded)

Pyrimidine base
Deoxyribose

Purine base

O
OH

3 end

H2C

HN

T NH

N C

HN T

NH

C N
5

H2C

5 end
P

C
A

CH2

T
C

CH2

NH

A N
H 2C

NH

HN

G NH
H2C

P
Phosphate

O 5 CH2

N A

5 end

O
HN G
HN

CH2

O
3

3 end

OH

Hydrogen
bond

5
3

In DNA, the bases are attached to deoxyribose, and the base

thymine (T) is found instead of uracil. Hydrogen bonds between
purines and pyrimidines hold the two strands of DNA together.

FIGURE 3.4 DNA (Page 38)

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Figure 03.04 Date 07-23-10

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

(A)

DNA

During replication, two complete

copies of the DNA molecule are made.

DNA

DNA

(B)

DNA
RNA for
protein 2

RNA for
protein 1

DNA sequences that encode specific

proteins are transcribed into RNA.

FIGURE 3.5 DNA Replication and Transcription (Page 39)

Carboxyl
group
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COO
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AminoFigure 03.05 Date 06-21-10
Side chain
R
group

carbon

IN-TEXT ART (Page 39)

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

TABLE 3.2 The Twenty Amino Acids in Proteins

A. Amino acids with electrically charged hydrophilic side chains
Positive +
Amino acids have
both three-letter
and single-letter
abbreviations.

Arginine
(Arg; R)

Histidine
(His; H)

Lysine
(Lys; K)

H
+

H3N

COO

H3N

CH2

COO

H3N

CH2

CH2

NH

CH2

COO

H
COO

H 3N

but each
has a different
side chain.

COO

H3N

CH2

CH2

COO

CH2
COO

CH2

Glutamic acid
(Glu; E)

CH2

NH

HC

H
+

CH2

CH

Aspartic acid
(Asp; D)

The general
structure of all
amino acids is
the same

CH2
+

NH

Negative

NH2

+NH
3

NH2

B. Amino acids with polar but uncharged side chains (hydrophilic)

Threonine
(Thr; T)

Serine
(Ser; S)
H
+

H3N

Asparagine
(Asn; N)

H
+

COO H3N

CH2OH

C
C

H
+

OH

CH2

CH2

CH2

COO H3N

H2N

Cysteine
(Cys; C)

H
+

COO H3N

CH3

C. Special cases
Tyrosine
(Tyr; Y)

Glutamine
(Gln; Q)

COO H3N

Glycine
(Gly; G)

H
COO

H3N

CH2

Proline
(Pro; P)

H
COO

H3N

CH2

C
H

H
+

COO

H2N

H2C

COO

CH2
CH2

SH

C
H 2N

OH

D. Amino acids with nonpolar hydrophobic side chains

Alanine
(Ala; A)
H
+

H3N

C
CH3

Leucine
(Leu; L)

Isoleucine
(Ile; I)
H
COO

H3N

COO

CH3

H3N

H3N

C
CH2
CH2

CH
H3C

Phenylalanine
(Phe; F)

H
COO

CH2

CH2
CH3

Methionine
(Met; M)

CH3

Tryptophan
(Trp; W)

H
COO

H3N

C
CH2

Valine
(Val; V)
H

H
COO

H3N

COO

H 3N

COO

CH

CH2
C CH

H3C

CH3

NH

CH3

(Page 40)

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Table 03.02 Date 07-8-10

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

Cysteine molecules
in polypeptide chain
Side chains

C
H

CH2

SH SH

N
H

CH2

C
2H
C

CH2

CH2
S

Disulfide bridge

IN-TEXT ART (Page 41)

H
H

+
N

+
N

O
C

Amino group

Carboxyl group
The amino group of
one amino acid reacts
with the carboxyl group
of another to form a
peptide linkage.
A molecule of water is
lost (condensation) as
each linkage forms.

H2O

LIFE 8/E Purves/Sadava/Orians/Heller/Hillis

Sinauer Associates
Elizabeth Morales Illustration Services
Figure LIFE 9/E 03.05.eps
Date 04/24/09

Peptide linkage

H
H

+
N

H
N

O
C

H
R

N terminus
(H3N+)

Polypeptide
grows in this
direction.

C terminus
(COO)

Repetition of this reaction,

by addition to the C terminus,
links many amino acids
together into a polypeptide.

FIGURE 3.6 Formation of a Peptide Linkage (Page 41)

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

(A)
Primary structure
Amino acid monomers are joined,
forming polypeptide chains.

H
C
R

Amino acid monomers

(B)

Peptide bond

O
H
C

N
H

(C)

Secondary structure
Polypeptide chains may form
helices or pleated sheets.

Helix

Pleated sheet

Hydrogen bond

Hydrogen bond
(D)
Tertiary structure
Polypeptides fold, forming specific shapes.
Folds are stabilized by bonds, including
hydrogen bonds and disulfide bridges.

(E)
Quaternary structure
Two or more polypeptides assemble to form larger
protein molecules. The hypothetical molecule here
is a tetramer, made up of four polypeptide subunits.

Pleated sheet

Subunit 1

Subunit 2

Subunit 3

Subunit 4

Hydrogen bond

Helix

Disulfide bridge

FIGURE 3.7 The Four Levels of Protein Structure (Page 42)

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Figure 03.07 Date 07-05-10

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Chapter 3|Nucleic Acids, Proteins, and Enzymes

Protein 1

COO

10

Protein 2
H3N+

Ionic interactions occur

between charged R groups.

Two nonpolar groups

interact hydrophobically.

OH

Hydrogen bonds form

between two polar groups.

FIGURE 3.8 Noncovalent Interactions between Proteins

and Other Molecules (Page 43)

POL Hillis
Sinauer Associates
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Figure 03.08
Date 07-23-10

Beta pleated
sheets are part
of the secondary
structure.

Folds in the tertiary

structure create
a surface for
interaction with
other molecules.

Alpha helical regions

are part of the
secondary structure.

FIGURE 3.9 The Structure of a Protein (Page 43)

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

11

INVESTIGATION
FIGURE 3.10 Primary Structure Specifies Tertiary Structure Using the protein ribonuclease, Christian Anfinsen showed that
proteins spontaneously fold into a functionally correct three-dimensional configuration. As long as the primary structure is not
disrupted, the information for correct folding under the right conditions is retained.
HYPOTHESIS
Under controlled conditions that simulate normal cellular environment in the laboratory, the primary structure
of a denatured protein can reestablish the proteins three-dimensional structure.
METHOD

Chemically denature functional ribonuclease, disrupting disulfide bridges

and other intramolecular interactions that maintain the proteins shape, so
that only primary structure (i.e., the amino acid sequence) remains. Once
denaturation is complete, remove the disruptive chemicals.

RESULTS

When the disruptive agents are

removed, three-dimensional
structure is restored and the
protein once again is functional.

helix
2 Add chemicals that

1 Extract and

disrupt hydrogen and

ionic bonds (urea)
and disulfide bridges
(mercaptoethanol).

purify a
functional
protein,
ribonuclease,
from tissue.

3 Slowly remove the

chemical agents

Disulfide
bridge

Denatured
protein

pleated
sheet

CONCLUSION
In normal cellular conditions, the primary structure of a protein specifies how it folds into a
functional, three-dimensional structure.
ANALYZE THE DATA

A. At what time did disulfide bonds begin to form?

B. At what time did enzyme activity begin to appear?
C. Explain the difference between your answers for the times
of (A) and (B).

100
Percentage recovery of activity

Initially, disulfide bonds (SS) in RNase A were eliminated

because the sulfur atoms in cysteine were reduced (SH). At
time 0, reoxidation began and at various times, the amount of
disulfide bond re-formation (blue circles) and the function of
ribonuclease (enzyme activity; red circles) were measured by
chemical methods. Here are the data:

80

Disulfide bond
formation

60
40

Ribonuclease
activity

20

For more, go to Working with Data 3.1 at yourBioPortal.com.

100

200
300
400
500
Time of reoxidation (min)

600

700

Go to yourBioPortal.com for original citations, discussions, and relevant links for all INVESTIGATION figures.
(Page 44)

POL Hillis
Sinauer Associates

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

12

subunits

Heme
(see Table 3.3)

subunits

IN-TEXT ART (Page 44)

(A)

Free energy

Energy
barrier
Reactants
(stable)

Transition state
intermediate (unstable)
Ea

G for the
reaction is not
affected by Ea.

Products
Ea is the activation

Time course of reaction

energy required for

a reaction to begin.

ava/Orians/Heller/Hillis
(B)
ation Services
ps
Date 4/24/09
Free energy

The ball needs a push ( Ea ) to

get it out of the depression.

Stable
state

Free energy

Less stable
state (transition state)
A ball that has received an
input of activation energy can
roll downhill spontaneously,
releasing free energy.

Time course of reaction

FIGURE 3.11 Activation Energy Initiates Reactions (Page 46)

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Chapter 3|Nucleic Acids, Proteins, and Enzymes

Free energy

Ea

13

An uncatalyzed
reaction has
greater activation
energy than does a
catalyzed reaction.

Uncatalyzed
reaction

Ea
Reactants
There is no difference
in free energy between
catalyzed and
uncatalyzed reactions.

Catalyzed
reaction

Products
Time course of reaction

FIGURE 3.12 Enzymes Lower the Energy Barrier (Page 47)

1 Enzyme is available with

empty activity site.

Sucrose

Active site

2 Substrate binds to

enzyme, forming the

enzyme-substrate
complex.

Enzyme
(sucrase)

O
O

Glucose
O

Water

Fructose

4 Products are

released.
3 Substrate is converted
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FIGURE
3.13
Action (Page 47)
Figure
03.12Enzyme
Date 06-21-10

Enzyme
Substrate

The enzyme strains the substrate.

IN-TEXT ART (Page 47)

2012 Sinauer Associates, Inc.

POL Hillis

Chapter 3|Nucleic Acids, Proteins, and Enzymes

14

When the substrates bind to the active

site, the two halves of the enzyme move
together, changing the shape of the
enzyme so that catalysis can take place.

Empty
active site

FIGURE 3.14 Some Enzymes Change Shape When Substrate

Binds to Them (Page 48)

TABLE 3.3

Some Examples of Nonprotein

Partners of Enzymes

Type of molecule

Role in Catalyzed reactions

Cofactors
Iron (Fe2+ or Fe3+)

Oxidation/reduction

Copper (Cu or Cu )

Oxidation/reduction

Zinc (Zn2+)

Helps bind NAD

2+

Coenzymes
Biotin

Carries COO

Coenzyme A

Carries COCH3

NAD

Carries electrons

FAD

Carries electrons

ATP

Provides/extracts energy

Prosthetic groups
Heme
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Binds ions, O2, and electrons;

contains iron cofactor

Flavin
Figure 03.14 Date 06-21-10Binds electrons
Retinal
Converts light energy
(Page 48)

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

At low substrate concentration, the
presence of an enzyme greatly
increases the reaction rate.

15

At high substrate concentration, the

maximum rate is reached when all
enzyme molecules are occupied with
substrate molecules.

Reaction rate

Maximum rate

Reaction
with enzyme

With no enzyme present, the

reaction rate increases steadily as
substrate concentration increases.

Reaction without
enzyme
Concentration of substrate

FIGURE 3.15 Catalyzed Reactions Reach a Maximum Rate

(Page 49)

Acetylcholinesterase

Active
site
DIPF

The hydroxyl group is

on the side chain of
serine in the active site.

DIPF, an irreversible
inhibitor, reacts with the
hydroxyl group of serine.

Covalent attachment of DIPF

to the active site prevents
substrate from entering.

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CH
H
Figure 03.15 Date 06-21-10 3

CH3
CH3

O
Ser

Active site
serine

OH

F
O
H

O
Ser

P
O
CH3
CH3

O
O
H

P
O
CH3
CH3

FIGURE 3.16 Irreversible Inhibition (Page 50)

2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

16

(A) Competitive inhibition

Competitive
inhibitor

Active site

Substrate
Inhibitor and substrate
compete; only one
at a time can bind to
the active site.

(B) Noncompetitive inhibition

Substrate
Active site

An inhibitor may
bind to a site away
from the active site,
changing the
enzymes shape so
that the substrate
no longer fits.

Noncompetitive
inhibitor

FIGURE 3.17 Reversible Inhibition (Page 50)

The active site is
not exposed;
enzyme is inactive.

Phosphorylation
site

Regulatory
site

Inactive
enzyme

HO
Pi

Phosphate
is added
covalently.

Activator

Protein
kinase

Active site open

Active site open

POL Hillis
Sinauer Associates
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Figure 03.17 Date 07-23-10

Active
enzyme

HO

An activator
binds to the
regulatory site
noncovalently.

Active
enzyme

Substrate

Substrate

Substrate binds
at the open
active site.

Active
enzyme

HO

Active
enzyme

Product

FIGURE 3.18 Allosteric Regulation of Enzyme Activity (Page 51)

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Chapter 3|Nucleic Acids, Proteins, and Enzymes

1 The first reaction is

17

2 Each of these reactions is catalyzed by

a different enzyme, and each forms a
different intermediate product.

the commitment
step.

NH3
+

NH3

COO

CH3

COO

OH

CH2

CH2

CH3

CH3

CH3

COO

a-ketobutyrate
(intermediate product)

Threonine
(starting material)

Isoleucine
(end product)

3 Buildup of the end product allosterically inhibits

the enzyme catalyzing the commitment step, thus

shutting down its own production.

FIGURE 3.19 Feedback Inhibition of Metabolic Pathways (Page 52)

(A)

Chymotrypsin

Reaction rate

Pepsin

1
Acidic

Arginase

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7
pH

10

11

12
Basic

(B)

Reaction rate

Maximum
rate

Optimal
temperature
Temperature

FIGURE 3.20 Enzyme Activity Is Affected by the Environment

(Page 52)
2012 Sinauer Associates, Inc.

Chapter 3|Nucleic Acids, Proteins, and Enzymes

18

COOH

Arachidonic acid
2 O2
Aspirin

Cyclooxygenase

COOH

O
Prostaglandin H2

FIGURE 3.21 Aspirin: An Enzyme Inhibitor (Page 53)

An acetyl group is transferred

from aspirin to an amino acid
in the active site.

Acetyl group

Modified active site

Aspirin

Cyclooxygenase with aspirin in active site

FIGURE 3.22 Inhibition by Covalent Modification (Page 54)

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Figure 03 21 Date 06-22-10

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