Chapter 11

DNA Replication and Recombination

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Copyright Education,
2009 Pearson Inc.
Education, Inc.
 Concept 16.2: Many proteins work
together in DNA replication and repair

• The relationship between structure and function is

manifest in the double helix
• Watson and Crick noted that the specific base
pairing suggested a possible copying mechanism
for genetic material

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 The Basic Principle: Base Pairing to
• aSince
Template Strand
the two strands of DNA are complementary,
each strand acts as a template for building a new
strand in replication
• In DNA replication, the parent molecule unwinds,
and two new daughter strands are built based on
base-pairing rules

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 Animation: DNA Replication Overview
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 Figure 16.9-1

A T
C G
T A
A T
G C

(a) Parent molecule

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 Figure 16.9-2

A T A T
C G C G
T A T A
A T A T
G C G C

(a) Parent molecule (b) Separation of

strands

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 Concept 16.2: Many proteins work
together in DNA replication and repair

• The relationship between structure and function is

manifest in the double helix
• Watson and Crick noted that the specific base
pairing suggested a possible copying mechanism
for genetic material

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 The Basic Principle: Base Pairing to
a Template Strand
• Since the two strands of DNA are complementary,
each strand acts as a template for building a new
strand in replication
• In DNA replication, the parent molecule unwinds,
and two new daughter strands are built based on
base-pairing rules

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 Animation: DNA Replication Overview
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 Figure 16.9-1

A T
C G
T A
A T
G C

(a) Parent molecule

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 Figure 16.9-3

A T A T A T A T
C G C G C G C G
T A T A T A T A
A T A T A T A T
G C G C G C G C

(a) Parent molecule (b) Separation of (c) “Daughter” DNA molecules,

strands each consisting of one
parental strand and one
new strand

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 • Watson and Crick’s semiconservative model of
replication predicts that when a double helix
replicates, each daughter molecule will have one
old strand (derived or “conserved” from the parent
molecule) and one newly made strand
• Competing models were the conservative model
(the two parent strands rejoin) and the dispersive
model (each strand is a mix of old and new)

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 Figure 16.10
Parent First Second
cell replication replication

(a) Conservative
model

(b) Semiconservative
model

(c) Dispersive model

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 • Experiments by Matthew Meselson and Franklin
Stahl supported the semiconservative model
• They labeled the nucleotides of the old strands
with a heavy isotope of nitrogen, while any new
nucleotides were labeled with a lighter isotope

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 • The first replication produced a band of hybrid
DNA, eliminating the conservative model
• A second replication produced both light and
hybrid DNA, eliminating the dispersive model and
supporting the semiconservative model

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 Does DNA replication follow the conservative, semiconservative,
or dispersive model?

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 Figure 16.11 EXPERIMENT
1 Bacteria 2 Bacteria
cultured in transferred to
medium with medium with
15N (heavy 14N (lighter
isotope) isotope)

RESULTS
3 DNA sample 4 DNA sample Less
centrifuged centrifuged dense
after first after second
replication replication More
dense
CONCLUSION
Predictions: First replication Second replication

Conservative
model

Semiconservative
model

Dispersive
model

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 Figure 16.11a

EXPERIMENT
1 Bacteria 2 Bacteria
cultured in transferred to
medium with medium with
15N (heavy 14N (lighter

isotope) isotope)

RESULTS
3 DNA sample 4 DNA sample Less
centrifuged centrifuged dense
after first after second
replication replication More
dense

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 Figure 16.11b

CONCLUSION
Predictions: First replication Second replication

Conservative
model

Semiconservative
model

Dispersive
model

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 DNA Replication: A Closer Look
• The copying of DNA is remarkable in its speed
and accuracy
• More than a dozen enzymes and other proteins
participate in DNA replication

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 Getting Started
• Replication begins at particular sites called
origins of replication, where the two DNA
strands are separated, opening up a replication
“bubble”
• A eukaryotic chromosome may have hundreds or
even thousands of origins of replication
• Replication proceeds in both directions from each
origin, until the entire molecule is copied

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 Animation: Origins of Replication
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 Figure 16.12
(a) Origin of replication in an E. coli cell (b) Origins of replication in a eukaryotic cell
Origin of Double-stranded
Parental (template) strand Origin of replication DNA molecule
replication
Daughter (new)
strand Parental (template) Daughter (new)
strand strand
Replication
Double- fork
stranded
DNA molecule Replication
bubble
Bubble Replication fork

Two daughter
DNA molecules

Two daughter DNA molecules

0.25 m
0.5 m

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 Figure 16.12a

(a) Origin of replication in an E. coli cell

Origin of
replication Parental (template) strand

Daughter (new) strand

Double-
stranded Replication fork
DNA molecule Replication
bubble

Two
daughter
DNA molecules

0.5 m

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 Figure 16.12b

(b) Origins of replication in a eukaryotic cell

Double-stranded
Origin of replication DNA molecule

Parental (template) Daughter (new)

strand strand

Bubble Replication fork

Two daughter DNA molecules

0.25 m

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 Figure 16.12c

0.5 m
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 • At the end of each replication bubble is a
replication fork, a Y-shaped region where new
DNA strands are elongating
• Helicases are enzymes that untwist the double
helix at the replication forks
• Single-strand binding proteins bind to and
stabilize single-stranded DNA
• Topoisomerase corrects “overwinding” ahead of
replication forks by breaking, swiveling, and
rejoining DNA strands

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 Figure 16.13
Some of the proteins involved in the initiation of
DNA replication.
Primase

3
Topoisomerase
5 RNA
3 primer
5
3

Helicase

5
Single-strand binding
proteins

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 • DNA polymerases cannot initiate synthesis of a
polynucleotide; they can only add nucleotides to
the 3 end
• The initial nucleotide strand is a short RNA
primer

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 • An enzyme called primase can start an RNA
chain from scratch and adds RNA nucleotides one
at a time using the parental DNA as a template
• The primer is short (5–10 nucleotides long), and
the 3 end serves as the starting point for the new
DNA strand

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 Synthesizing a New DNA Strand
• Enzymes called DNA polymerases catalyze the
elongation of new DNA at a replication fork
• Most DNA polymerases require a primer and a
DNA template strand
• The rate of elongation is about 500 nucleotides
per second in bacteria and 50 per second in
human cells

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 • Each nucleotide that is added to a growing DNA
strand is a nucleoside triphosphate
• dATP supplies adenine to DNA and is similar to
the ATP of energy metabolism
• The difference is in their sugars: dATP has
deoxyribose while ATP has ribose
• As each monomer of dATP joins the DNA strand,
it loses two phosphate groups as a molecule of
pyrophosphate

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 Incorporation of a nucleotide into a DNA strand.
New strand Template strand
5 3 5 3

Sugar A T A T
Phosphate Base

C G C G

G C G C
DNA
OH
polymerase
3 A T A
P Pi OH
C Pyrophosphate 3 C

Nucleoside 2 Pi
triphosphate 5 5

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 Antiparallel Elongation
• The antiparallel structure of the double helix
affects replication
• DNA polymerases add nucleotides only to the free
3end of a growing strand; therefore, a new DNA
strand can elongate only in the 5to3direction

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 • Along one template strand of DNA, the DNA
polymerase synthesizes a leading strand
continuously, moving toward the replication fork

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 Animation: Leading Strand
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 Synthesis of the leading strand during DNA replication
Overview
Leading
Origin of replication Lagging
strand
strand

Primer

Lagging Leading
strand strand Origin of
Overall directions replication
of replication

3
5

5 RNA primer
3
3 Sliding clamp

DNA pol III

Parental DNA 5
3
5

5
3
3

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5
 Overview
Leading
strand Origin of replication Lagging
strand

Primer

Lagging Leading
strand strand
Overall directions
of replication

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 Origin of
replication

3
5

5 RNA primer
3
3 Sliding clamp

DNA pol III

Parental DNA 5
3
5

5
3
3

5
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 • To elongate the other new strand, called the
lagging strand, DNA polymerase must work in the
direction away from the replication fork
• The lagging strand is synthesized as a series of
segments called Okazaki fragments, which are
joined together by DNA ligase

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 Animation: Lagging Strand
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 3
Overview
5 3 Leading Origin of replication Lagging
Template
strand strand strand
RNA primer 5
for fragment 1 Lagging strand
3
2
1
5 Leading
1 3 strand
Overall directions
5 of replication

3
Okazaki
fragment 1
5
RNA primer
1
3
Synthesis of the lagging strand.
for fragment 2 5
5 Okazaki
3 fragment 2
2

1 3
5 5
3

2
1 3
5
5
3

2
1 3
5
Overall direction of replication
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 Figure 16.16a

Overview
Leading Origin of replication Lagging
strand strand

Lagging strand
2
1
Leading
strand
Overall directions
of replication

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 Figure 16.16b-1
3
5 3
Template
strand 5

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 Figure 16.16b-2
3
5 3
Template
strand 5
3 RNA primer
for fragment 1
5
1 3
5

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 Figure 16.16b-3
3
5 3
Template
strand 5
3 RNA primer
for fragment 1
5
1 3
5

3 Okazaki
fragment 1
5
1
3
5

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 Figure 16.16b-4
3
5 3
Template
strand 5
3 RNA primer
for fragment 1
5
1 3
5

3 Okazaki
fragment 1
5
1
RNA primer 3
for fragment 2 5
5
3
2
Okazaki
fragment 2 1 3
5

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 Figure 16.16b-5
3
5 3
Template
strand 5
3 RNA primer
for fragment 1
5
1 3
5

3 Okazaki
fragment 1
5
1
RNA primer 3
for fragment 2 5
5
3
2
Okazaki
fragment 2 1 3
5
5
3

2
1 3
5 5
3

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 Figure 16.16b-6
3
5 3
Template
strand 5
3 RNA primer
for fragment 1
5
1 3
5

3 Okazaki
fragment 1
5
1
RNA primer 3
for fragment 2 5
5
3
2
Okazaki
fragment 2 1 3
5
5
3

2
1 3
5 5
3
2
1 3
5
Overall direction of replication
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 Figure 16.17

Overview
Leading Origin of
replication Lagging
strand strand

Leading
Lagging strand
strand Overall directions
Leading strand of replication

5 DNA pol III

3 Primer
Primase
3 5
3
Parental DNA pol III Lagging strand
DNA 5
4 DNA pol I DNA ligase
35
3 2 1 3

5

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 Figure 16.17a
Overview
Leading Origin of
replication Lagging
strand strand

Leading
Lagging strand
strand Overall directions
of replication

Leading strand

5 DNA pol III

3 Primer
Primase
3 5
3
Parental
DNA

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 Figure 16.17b
Overview
Leading Origin of
replication Lagging
strand strand

Leading
Lagging strand
strand Overall directions
Leading strand of replication

Primer

DNA pol III Lagging strand

5
4 DNA pol I DNA ligase
3 5
3 3 2 1 3

5
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 The DNA Replication Complex
• The proteins that participate in DNA replication form a
large complex, a “DNA replication machine”
• The DNA replication machine may be stationary during
the replication process
• Recent studies support a model in which DNA
polymerase molecules “reel in” parental DNA and
“extrude” newly made daughter DNA molecules

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 Animation: DNA Replication Review
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 A current model of the DNA replication complex.

DNA pol III

Parental DNA Leading strand
5
5 3 3

3
3 5 5

Connecting Helicase
protein

3 5 Lagging
DNA strand
3 Lagging strand template
pol III 5

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 Proofreading and Repairing DNA
• DNA polymerases proofread newly made DNA,
replacing any incorrect nucleotides
• In mismatch repair of DNA, repair enzymes
correct errors in base pairing
• DNA can be damaged by exposure to harmful
chemical or physical agents such as cigarette
smoke and X-rays; it can also undergo
spontaneous changes
• In nucleotide excision repair, a nuclease cuts
out and replaces damaged stretches of DNA

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 Figure 16.19
5 3
Nucleotide excision 3 5
repair of DNA
Nuclease
damage

5 3

3 5

DNA
polymerase

5 3

3 5
DNA
ligase

5 3

3 5
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 Evolutionary Significance of Altered DNA
Nucleotides

• Error rate after proofreading repair is low but not

zero
• Sequence changes may become permanent and
can be passed on to the next generation
• These changes (mutations) are the source of the
genetic variation upon which natural selection
operates

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 Replicating the Ends of DNA Molecules

• Limitations of DNA polymerase create problems

for the linear DNA of eukaryotic chromosomes
• The usual replication machinery provides no way
to complete the 5 ends, so repeated rounds of
replication produce shorter DNA molecules with
uneven ends
• This is not a problem for prokaryotes, most of
which have circular chromosomes

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 Shortening of the ends of linear DNA molecules.
5
Ends of parental Leading strand
DNA strands Lagging strand
3

Last fragment Next-to-last fragment

Lagging strand RNA primer

5
3
Parental strand
Removal of primers and
replacement with DNA
where a 3 end is available
5
3
Second round
of replication

5
New leading strand 3
New lagging strand 5
3
Further rounds
of replication

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 5
Ends of parental Leading strand
DNA strands Lagging strand
3

Last fragment Next-to-last fragment

Lagging strand RNA primer

5
3
Parental strand
Removal of primers and
replacement with DNA
where a 3 end is available
5
3

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 5
3
Second round
of replication

5
New leading strand 3
New lagging strand 5
3
Further rounds
of replication

Shorter and shorter daughter molecules

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 • Eukaryotic chromosomal DNA molecules have
special nucleotide sequences at their ends called
telomeres
• Telomeres do not prevent the shortening of DNA
molecules, but they do postpone the erosion of
genes near the ends of DNA molecules
• It has been proposed that the shortening of
telomeres is connected to aging

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 Figure 16.21

Telomeres

1 m

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 • If chromosomes of germ cells became shorter in
every cell cycle, essential genes would eventually
be missing from the gametes they produce
• An enzyme called telomerase catalyzes the
lengthening of telomeres in germ cells

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 • The shortening of telomeres might protect cells
from cancerous growth by limiting the number of
cell divisions
• There is evidence of telomerase activity in cancer
cells, which may allow cancer cells to persist

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 Let’s Review

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 Figure 16.UN03

DNA pol III synthesizes

leading strand continuously 3
5
Parental
DNA DNA pol III starts DNA
synthesis at 3 end of primer, Origin of
5 continues in 5  3 direction replication
3
5 Lagging strand synthesized
in short Okazaki fragments,
Helicase later joined by DNA ligase

Primase synthesizes 3
a short RNA primer 5
DNA pol I replaces the RNA
primer with DNA nucleotides

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 Chapter 11
DNA Replication and Recombination

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Copyright Education,
2009 Pearson Inc.
Education, Inc.
Learning Objectives

11.1 DNA Is Reproduced by Semiconservative

Replication
11.2 DNA Synthesis in Bacteria Involves Five
Polymerases, as well as Other Enzymes
11.3 Many Complex Tasks Must Be Performed
during DNA Replication
11.4 A Summary of DNA Replication in
Prokaryotes
11.5 Replication in Prokaryotes Is Controlled by a
Variety of Genes
Continued
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11.6 Eukaryotic DNA Synthesis Is Similar to
Synthesis in Prokaryotes, but More Complex
11.7 Telomeres Provide Structural Integrity at
Chromosome Ends but are Problematic to
Replicate

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 11.1 DNA Is Reproduced by
Semiconservative Replication

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Section 11.1

• The complementarity of DNA strands

allows each strand to serve as a template
for synthesis of the other (Figure 11.1).

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Copyright © 2009 Pearson Education, Inc. Figure 11.1
Section 11.1

• Three possible modes of DNA replication

are possible:
• conservative
• semiconservative
• dispersive
(Figure 11.2)

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Copyright © 2009 Pearson Education, Inc. Figure 11.2
Section 11.1

• The Meselson-Stahl experiment

demonstrated that:
• DNA replication is semiconservative
• each new DNA molecule consists of one old
strand and one newly synthesized strand
(Figure 11.3 and Figure 11.4)

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Copyright © 2009 Pearson Education, Inc. Figure 11.3
Copyright © 2009 Pearson Education, Inc. Figure 11.4
Section 11.1

• DNA replication begins at the origin of

replication and is bidirectional rather than
unidirectional (Figure 11.6).

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Copyright © 2009 Pearson Education, Inc. Figure 11.6
Section 11.1

• A replicon is the length of DNA that is

replicated following one initiation event at
a single origin.

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 11.2 DNA Synthesis in Bacteria Involves
Five Polymerases, as well as Other
Enzymes

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Section 11.2

• DNA polymerase catalyzes DNA

synthesis and requires a DNA template
and all four dNTPs (Figure 11.7).

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The chemical reaction catalyzed by DNA polymerase I. During
each step, a single nucleotide is added to the growing complement of
the DNA template, using a nucleoside triphosphate as the substrate.
The release of inorganic pyrophosphate drives the reaction
energetically.

Copyright © 2009 Pearson Education, Inc. Figure 11.7

Section 11.2

• Chain elongation occurs in the 5' to 3'

direction by addition of one nucleotide at a
time to the 3' end (Figure 11.8).
• As the nucleotide is added, the two
terminal phosphates are cleaved off.

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 Demonstration of synthesis of DNA

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Section 11.2

• DNA polymerases I, II, and III can

elongate an existing DNA strand (called a
primer) but cannot initiate DNA synthesis
(Table 11.2).
• All three possess 3' to 5' exonuclease
activity.
• But only DNA polymerase I demonstrates
5' to 3' exonuclease activity.

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Copyright © 2009 Pearson Education, Inc. Table 11.2
Section 11.2

• DNA polymerase III is the enzyme

responsible for the 5' to 3' polymerization
essential in vivo.
• Its 3' to 5' exonuclease activity allows
proofreading.

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Section 11.2

• Polymerase I is believed to be responsible

for:
• removing the primer
• the synthesis that fills gaps produced during
synthesis

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Section 11.2

• DNA polymerases I, II, IV, and V are

involved in various aspects of repair of
damaged DNA.

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Section 11.2

• DNA polymerase III has 10 subunits

whose functions are shown in Table 11.3.

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Copyright © 2009 Pearson Education, Inc. Table 11.3
 11.3 Many Complex Tasks Must Be
Performed during DNA Replication

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Section 11.3

• There are seven key issues that must be

resolved during DNA replication:
• unwinding of the helix
• reducing increased coiling generated during
unwinding
• synthesis of a primer for initiation
• discontinuous synthesis of the second strand
continued

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Section 11.3

continued
• removal of the RNA primers
• joining of the gap-filling DNA to the adjacent
strand
• proofreading

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Section 11.3

• DnaA binds to the origin of replication and

is responsible for the initial steps in
unwinding the helix (Figure 11.9).

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Copyright © 2009 Pearson Education, Inc. Figure 11.9
Section 11.3

• Subsequent binding of DnaB and DnaC further

opens and destabilizes the helix.
• Single-stranded binding proteins (SSBPs)
stabilize the open conformation.
• Proteins such as these, which require the energy
normally supplied by the hydrolysis of ATP to
break hydrogen bonds and denature the double
helix, are called helicases.

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Section 11.3

• Unwinding produces supercoiling that is

relieved by DNA gyrase, a member of a
larger group of enzymes referred to as
DNA topoisomerases.

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Section 11.3

• To elongate a polynucleotide chain, DNA

polymerase III requires a primer with a
free 3'-hydroxyl group.

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Section 11.3

• The enzyme primase synthesizes an RNA

primer that provides the free 3'-hydroxyl
required by DNA polymerase III (Figure
11.10).

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Copyright © 2009 Pearson Education, Inc. Figure 11.10
Section 11.3

• As the replication fork moves, only one

strand can serve as a template for
continuous DNA synthesis—the leading
strand.
• The opposite lagging strand undergoes
discontinuous DNA synthesis (Figure
11.11).

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 •Opposite polarity of DNA synthesis along the
two strands, is necessary because the two strands
of DNA run antiparallel to one another and DNA
polymerase III synthesizes only in one direction (
to ).
•On the lagging strand, synthesis must be
discontinuous, resulting in the production of
Okazaki fragments.
•On the leading strand, synthesis is continuous.
RNA primers are used to initiate synthesis on
both strands
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Copyright © 2009 Pearson Education, Inc. Figure 11.11
Section 11.3

• The lagging strand is synthesized as

Okazaki fragments, each with an RNA
primer.

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Section 11.3

• DNA polymerase I removes the primers on

the lagging strand and the fragments are
joined by DNA ligase.

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Section 11.3

• Both DNA strands are synthesized

concurrently by looping the lagging strand
to invert the physical but not biological
direction of synthesis (Figure 11.12).

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•Illustration of how concurrent DNA synthesis may be achieved on
both the leading and lagging strands at a single replication fork.

•The lagging template strand is “looped” in order to invert the

physical direction of synthesis, but not the biochemical direction.
The enzyme functions as a dimer, with each core enzyme achieving
synthesis on one or the other strand.

Copyright © 2009 Pearson Education, Inc. Figure 11.12

Section 11.3

• The -subunit clamp prevents the core

enzyme from falling off the template during
DNA synthesis.

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Section 11.3

• Proofreading and error correction are

an integral part of DNA replication.

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Section 11.3

• All of the DNA polymerases have 3' to 5'

exonuclease activity that allows
proofreading.

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Section 11.3

• DNA synthesis at a single replication fork

involves:
• DNA polymerase III
• single-stranded binding proteins
• DNA gyrase
• DNA helicase
• RNA primers
(Figure 11.13)

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 11.4 A Summary of DNA Replication
in Prokaryotes

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Copyright © 2009 Pearson Education, Inc. Figure 11.13
 11.5 Replication in Prokaryotes Is
Controlled by a Variety of Genes

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Section 11.5

• A number of genes involved in DNA

replication have been identified by
conditional mutations (Table 11.4).

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Copyright © 2009 Pearson Education, Inc. Table 11.4
 11.6 Eukaryotic DNA Synthesis Is Similar to
Synthesis in Prokaryotes, but More
Complex

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Section 11.6

• In eukaryotic cells:
• there is more DNA than prokaryotic cells
• the chromosomes are linear
• the DNA is complexed with proteins
• This makes DNA replication more complex
in eukaryotes than in bacteria.

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Section 11.6

• Eukaryotic chromosomes contain multiple

origins of replication to allow the genome
to be replicated in a few hours (Figure
11.14).

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 Multiple origins of replication along a eukaryotic chromosome

Copyright © 2009 Pearson Education, Inc. Figure 11.14

Section 11.6

• Three DNA polymerases are involved in

replication of nuclear DNA.
• One involves mitochondrial DNA
replication.
• Others are involved in repair processes
(Table 11.5).

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Copyright © 2009 Pearson Education, Inc. Table 11.5
Section 11.6

• Pol  and  are the major forms of the

enzyme involved in initiation and
elongation.
• Pol  possesses low processivity, a term
that reflects the length of DNA that is
synthesized by an enzyme before it
dissociates from the template.

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Section 11.6

• Pol  functions in synthesis of the RNA

primers during initiation on the leading and
lagging strands.
• Polymerase switching occurs, and Pol 
is replaced by Pol  for elongation.

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 11.7 Telomeres Provide Structural Integrity
at Chromosome Ends but Are
Problematic to Replicate

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Section 11.7

• Telomeres at the ends of linear

chromosomes consist of long stretches of
short repeating sequences and preserve
the integrity and stability of chromosomes.

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Section 11.7

• Lagging strand synthesis at the end of the

chromosome is a problem because once
the RNA primer is removed, there is no
free 3'-hydroxyl group from which to
elongate (Figure 11.16).

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The difficulty
encountered during the
replication of the ends of
linear chromosomes. A
gap (- -b- -) is left
following synthesis on
the lagging strand.

Copyright © 2009 Pearson Education, Inc. Figure 11.16

Section 11.7

• Telomerase directs synthesis of the

telomere repeat sequence to fill the gap
(Figure 11.17).
• This enzyme is a ribonucleoprotein with an
RNA that serves as the template for the
synthesis of its DNA complement.

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•The predicted solution to the
problem posed in Figure 11–16.
The enzyme telomerase directs
synthesis of the TTGGGG
sequences, resulting in the
formation of a hairpin structure.

•The gap can now be filled, and,

following cleavage of the hairpin
structure, the process averts the
creation of a gap during replication
of the ends of linear chromosomes.

Copyright © 2009 Pearson Education, Inc. Figure 11.17

 THE END

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