Chapter 16

DNA Structure

DNA Replication
PowerPoint Lectures for
Biology, Seventh Edition
Neil Campbell and Jane Reece

Lectures by Chris Romero

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 • Overview: Life’s Operating Instructions

• In 1953, James Watson and Francis Crick

shook the world
– With an elegant double-helical model for the
structure of deoxyribonucleic acid, or DNA

Figure 16.1
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 • DNA, the substance of inheritance
– Is the most celebrated molecule of our time

• Hereditary information
– Is encoded in the chemical language of DNA
and reproduced in all the cells of your body

• It is the DNA program

– That directs the development of many different
types of traits

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 • Concept 16.1: DNA is the genetic material

• Early in the 20th century

– The identification of the molecules of
inheritance loomed as a major challenge to
biologists

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 The Search for the Genetic Material: Scientific Inquiry
• The role of DNA in heredity
– Was first worked out by studying bacteria and
the viruses that infect them

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 Additional Evidence That DNA Is the Genetic Materia
• Prior to the 1950s, it was already known that DNA

– Is a polymer of nucleotides, each consisting of

three components: a nitrogenous base, a
sugar, and a phosphate group
Sugar-phosphate Nitrogenous
backbone bases
5 end CH3
O– 5
O P O CH2 H O
O 1
O– 4 H H N N
H H H
3 2 O
H Thymine (T)
O
H H
O P O CH2 O N
N
O– H H N H
H H N
H N
H
Adenine (A)
O H H
O P O CH2 O H N H
O– H H N N
H H
H O
Cytosine (C)
O 5
O P O CH2 H N
O 1 O
O– 4 H H N
PhosphateH H
3 2 N H
N DNA nucleotide
OH H
Sugar (deoxyribose) N H
H
Figure 16.5 3 end Guanine (G)

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 Building a Structural Model of DNA: Scientific Inquiry
• Once most biologists were convinced that DNA
was the genetic material
– The challenge was to determine how the
structure of DNA could account for its role in
inheritance

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 • Maurice Wilkins and Rosalind Franklin
– Were using a technique called X-ray
crystallography to study molecular structure

• Rosalind Franklin
– Produced a picture of the DNA molecule using
this technique

(a) Rosalind Franklin (b) Franklin’s X-ray diffraction

Figure 16.6 a, b Photograph of DNA
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 • Watson and Crick deduced that DNA was a
double helix
– Through observations of the X-ray
crystallographic images of DNA
G C
A T
T A

1 nm

G C
3.4 nm
C G
A T
C G

T A

T A
A T

A T

G C
0.34 nm
A T

Figure 16.7a, c (a) Key features of DNA structure (c) Space-filling model

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 • Franklin had concluded that DNA
– Was composed of two antiparallel sugar-
phosphate backbones, with the nitrogenous
bases paired in the molecule’s interior

• The nitrogenous bases

– Are paired in specific combinations: adenine
with thymine, and cytosine with guanine

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 5 end

O
OH
P Hydrogen bond
–
O 3 end
O
OH
O
T A

O O CH2
O
P
–
O O
O O–
P
H2C O
O O
G C

O O CH2
O
P
–
O O
O–
O
P
H2 C O
O O
C G

O O CH2
O
P O
–
O O–
O P
H 2C O
O O
A T

O CH2
OH
3 end O
O–
P
O
O
(b) Partial chemical structure
Figure 16.7b 5 end

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 • Watson and Crick reasoned that there must be
additional specificity of pairing
– Dictated by the structure of the bases

• Each base pair forms a different number of

hydrogen bonds
– Adenine and thymine form two bonds,
cytosine and guanine form three bonds

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 H

N N H O CH3

N N
N H
Sugar N N

O Sugar
Adenine (A) Thymine (T)

N O H N

N
N H N
Sugar N
N

N H O Sugar
H
Figure 16.8 Guanine (G) Cytosine (C)

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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

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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

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 • In DNA replication
– The parent molecule unwinds, and two new
daughter strands are built based on base-
pairing rules
T
A T A T A A T A T A T
C G C G C G C G C G C G
T A T A T A T A T A T A
A T A T A T A T A T A T
G C G C G C C G C G C
G

(a) The parent molecule has two
complementary strands of DNA.
Each base is paired by hydrogen
bonding with its specific partner,
A with T and G with C.
(b) The first step in replication is
separation of the two DNA
strands.
(c) Each parental strand now
serves as a template that
determines the order of
nucleotides along a new,
complementary strand.
(d) The nucleotides are connected
to form the sugar-phosphate
backbones of the new strands.
Each “daughter” DNA
molecule consists of one parental
strand and one new strand.

Figure 16.9 a–d

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 • DNA replication is semiconservative
– Each of the two new daughter molecules will
have one old strand, derived from the parent
molecule, and one newly made strand First Second
Parent cell replication replication
(a) Conservative
model. The two
parental strands
reassociate
after acting as
templates for
new strands,
thus restoring
the parental
double helix.

(b) Semiconservative
model. The two
strands of the
parental molecule
separate,
and each functions
as a template
for synthesis of
a new, comple-
mentary strand.

(c) Dispersive
model. Each
strand of both
daughter mol-
ecules contains
a mixture of
old and newly
synthesized
DNA.
Figure 16.10 a–c
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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: Origins of Replication
• The replication of a DNA molecule
– Begins at special sites called origins of
replication, where the two strands are
separated

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 • A eukaryotic chromosome
– May have hundreds or even thousands of
replication origins
Origin of replication Parental (template) strand
0.25 µm
Daughter (new) strand

1 Replication begins at specific sites

where the two parental strands
separate and form replication
bubbles. Bubble Replication fork

2 The bubbles expand laterally, as

DNA replication proceeds in both
directions.

3 Eventually, the replication

bubbles fuse, and synthesis of
the daughter strands is
complete. Two daughter DNA molecules

(a) In eukaryotes, DNA replication begins at many sites along the giant (b) In this micrograph, three replication
DNA molecule of each chromosome. bubbles are visible along the DNA of
Figure 16.12 a, b a cultured Chinese hamster cell (TEM).

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 Elongating a New DNA Strand
• Elongation of new DNA at a replication fork
– Is catalyzed by enzymes called DNA
polymerases, which add nucleotides to the 3
end of a growing strand
New strand Template strand
5 end 3 end 5 end 3 end

Sugar A T A T
Phosphate Base

C G C G

G C G C

A T A
T OH
P P P
P
P C Pyrophosphate3 end C
OH
2 P
Nucleoside
Figure 16.13 triphosphate 5 end 5 end

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 Antiparallel Elongation
• How does the antiparallel structure of the
double helix affect replication?

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 • DNA polymerases add nucleotides
– Only to the free 3end of a growing strand

• Along one template strand of DNA, the leading

strand
– DNA polymerase III can synthesize a
complementary strand continuously, moving
toward the replication fork

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 • To elongate the other new strand of DNA, the
lagging strand
– DNA polymerase III 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 then joined
together by DNA ligase

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 • Synthesis of leading and lagging strands
during DNA replication
1 DNA pol Ill elongates
DNA strands only in the
5 3 direction.3 2 One new strand, the leading strand,
Parental DNA 5 can elongate continuously 5 3
as the replication fork progresses.
5
3 Okazaki
3 The other new strand, the
fragments
lagging strand must grow in an overall
2 3 5 direction by addition of short
1 3 segments, Okazaki fragments, that grow
5 5 3 (numbered here in the order
DNA pol III they were made).

Template
strand

4 DNA ligase joins Okazaki

fragments by forming a bond between
Leading strand their free ends. This results in a
Lagging strand
3 continuous strand.
2 1

Template
strand DNA ligase
Figure 16.14 Overall direction of replication
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 Priming DNA Synthesis
• DNA polymerases cannot initiate the synthesis
of a polynucleotide
– They can only add nucleotides to the 3 end

• The initial nucleotide strand

– Is an RNA or DNA primer

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 • Only one primer is needed for synthesis of the
leading strand
– But for synthesis of the lagging strand, each
Okazaki fragment must be primed separately

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 1 Primase joins RNA nucleotides
into a primer. 3
5

5 3

Template
strand 2 DNA pol III adds DNA nucleotides to the
primer, forming an Okazaki fragment.
3 RNA primer 3 5
1
5

3 After reaching the next

RNA primer (not shown),
DNA pol III falls off.
Okazaki 3
3 fragment
5
1
5
4 After the second fragment is
primed. DNA pol III adds DNA
nucleotides until it reaches the
first primer and falls off. 5
3
3 2
1
5

5 DNA pol 1 replaces the

RNA with DNA, adding to
the 3 end of fragment 2.
5 3
3
2 5
1

6 DNA ligase forms a bond 7 The lagging strand

between the newest DNA in this region is now
and the adjacent DNA of complete.
fragment 1. 5 3
3 2 5
1

Figure 16.15 Overall direction of replication

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 Other Proteins That Assist DNA Replication
• Helicase, topoisomerase, single-strand binding
protein
– Are all proteins that assist DNA replication

Table 16.1
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 • A summary of DNA replication
Overall direction of replication Lagging
Leading
1 Helicase unwinds the strand Origin of replication strand
parental double helix.
2 Molecules of single- 3 The leading strand is
strand binding protein synthesized continuously in the
stabilize the unwound 5 3 direction by DNA pol III. Lagging Leading
template strands.
strand OVERVIEW strand
DNA pol III

Leading
strand

5 Replication fork
DNA pol I DNA ligase
3
Primase 2
Parental DNA DNA pol III Lagging 1
Primer strand 3
4 Primase begins synthesis
3 5
of RNA primer for fifth 4
Okazaki fragment.

5 DNA pol III is completing synthesis of 6 DNA pol I removes the primer from the 5 end 7 DNA ligase bonds
the fourth fragment, when it reaches the of the second fragment, replacing it with DNA the 3 end of the
RNA primer on the third fragment, it will nucleotides that it adds one by one to the 3 end second fragment to
dissociate, move to the replication fork, of the third fragment. The replacement of the the 5 end of the first
and add DNA nucleotides to the 3 end last RNA nucleotide with DNA leaves the sugar- fragment.
of the fifth fragment primer. phosphate backbone with a free 3 end.
Figure 16.16
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 The DNA Replication Machine as a Stationary Complex
• The various proteins that participate in DNA
replication
– Form a single large complex, a DNA
replication “machine”

• The DNA replication machine

– Is probably stationary during the replication
process

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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

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 • In nucleotide excision repair
– Enzymes cut out and replace damaged
stretches of DNA
1 A thymine dimer
distorts the DNA molecule.
2 A nuclease enzyme cuts
the damaged DNA strand
at two points and the
damaged section is
removed.
Nuclease

DNA 3 Repair synthesis by

polymerase a DNA polymerase
fills in the missing
nucleotides.

DNA
ligase 4 DNA ligase seals the
Free end of the new DNA
To the old DNA, making the
strand complete.
Figure 16.17

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 Replicating the Ends of DNA Molecules
• The ends of eukaryotic chromosomal DNA
– Get shorter with each round of replication
5
End of parental Leading strand
DNA strands Lagging strand
3

Last fragment Previous fragment

RNA primer
5
Lagging strand
3
Primer removed but Removal of primers and
cannot be replaced replacement with DNA
with DNA because where a 3 end is available
no 3 end available
for DNA polymerase 5
3
Second round
of replication

5
New leading strand3
New lagging strand 5
3
Further rounds
of replication
Shorter and shorter
Figure 16.18 daughter molecules

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 • Eukaryotic chromosomal DNA molecules
– Have at their ends nucleotide sequences,
called telomeres, that postpone the erosion of
genes near the ends of DNA molecules

Figure 16.19 1 µm
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 • If the 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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