Chapter 03

Chapter 3: DNA Replication
1. Models of DNA replication: Meselson-Stahl Experiment
2. DNA synthesis and elongation
3. DNA polymerases
4. Origin and initiation of DNA replication
5. Prokaryote/eukaryote models (circular/linear chromosomes)
6. Telomere replication
7. Histone/chromatin assembly
Alternative models of DNA replication (Fig 3.1):
1958: Matthew Meselson & Frank Stahl’s Experiment
Equilibrium density gradient centrifugation (Box 3.1)

1958: Matthew Meselson & Frank Stahl’s Experiment
Semiconservative model of DNA replication (Fig. 3.2)

1955: Arthur Kornberg
Worked with E. coli.

Discovered the mechanisms of DNA synthesis.
Four components are required:
1. dNTPs: dATP, dTTP, dGTP, dCTP

(deoxyribonucleoside 5’-triphosphates)
(sugar-base + 3 phosphates)
2. DNA template
3. DNA polymerase (Kornberg enzyme)
4. Mg 2+
(optimizes DNA polymerase activity)
1959: Arthur Kornberg (Stanford University) & Severo Ochoa (NYU)

Three main features of the DNA synthesis reaction:
1. DNA polymerase I catalyzes formation of phosphodiester bond

between 3’-OH of the deoxyribose (on the last nucleotide) and
the 5’-phosphate of the dNTP.
• Energy for this reaction is derived from the release of two of the
three phosphates of the dNTP.
2. DNA polymerase “finds” the correct complementary dNTP at

each step in the lengthening process.
• rate ≤ 800 dNTPs/second

• low error rate
3. Direction of synthesis is 5’ to 3’
DNA polymerase
Image credit:
Protein Data Bank
DNA elongation (Fig. 3.3b):
DNA elongation (Fig. 3.3a):
In prokaryotes, there are three main types of DNA polymerase
Polymerase Polymerization (5’-3’) Exonuclease (3’-5’) Exonuclease (5’-3’) #Copies
I Yes Yes Yes 400
II Yes Yes No ?
III Yes Yes No 10-20
•3’ to 5’ exonuclease activity = ability to remove nucleotides from the

3’ end of the chain
•Important proofreading ability
•Without proofreading error rate (mutation rate) is 1 x 10 -6
•With proofreading error rate is 1 x 10-9 (1000-fold decrease)
•5’ to 3’ exonuclease activity functions in DNA replication & repair.

Eukaryotic enzymes:
Five common DNA polymerases from mammals.
• Polymerase  (alpha): nuclear, DNA replication, no proofreading
• Polymerase  (beta): nuclear, DNA repair, no proofreading
• Polymerase  (gamma): mitochondria, DNA repl., proofreading
• Polymerase  (delta): nuclear, DNA replication, proofreading
• Polymerase  (epsilon): nuclear, DNA repair (?), proofreading
1. Different polymerases for the nucleus and mtDNA
2. Some polymerases proofread; others do not.
3. Some polymerases used for replication; others for repair.
4. Polymerases vary by species.

Origin of replication (e.g., the prokaryote example):
 Begins with double-helix denaturing into single-strands thus

exposing the bases.
 Exposes a replication bubble from which replication proceeds in

both directions.
~245 bp in E. coli
Initiation of replication, major elements:
 Segments of single-stranded DNA are called template strands.
 Gyrase (a type of topoisomerase) relaxes the supercoiled DNA.
 Initiator proteins and DNA helicase binds to the DNA at the

replication fork and untwist the DNA using energy derived from
ATP (adenosine triphosphate).
(Hydrolysis of ATP causes a shape change in DNA helicase)
 DNA primase next binds to helicase producing a complex called

a primosome (primase is required for synthesis),
 Primase synthesizes a short RNA primer of 10-12 nucleotides,

to which DNA polymerase III adds nucleotides.
 Polymerase III adds nucleotides 5’ to 3’ on both strands

beginning at the RNA primer.
 The RNA primer is removed and replaced with DNA by

polymerase I, and the gap is sealed with DNA ligase.
 Single-stranded DNA-binding (SSB) proteins (>200) stabilize

the single-stranded template DNA during the process.
Model of replication in E. coli
DNA replication is continuous on the leading strand and
semidiscontinuous on the lagging strand:
Unwinding of any single DNA replication fork proceeds in one

direction.
The two DNA strands are of opposite polarity, and DNA polymerases
only synthesize DNA 5’ to 3’.
Solution: DNA is made in opposite directions on each template.
•Leading strand synthesized 5’ to 3’ in the direction of

the replication fork movement.
continuous
requires a single RNA primer
•Lagging strand synthesized 5’ to 3’ in the opposite

direction.
semidiscontinuous (i.e., not continuous)
requires many RNA primers , DNA is

synthesized in short fragments.
Supercoiled DNA relaxed by gyrase & unwound by helicase + proteins:
5’ SSB Proteins
Okazaki Fragments
1 ATP
Polymerase III 2
Helicase
Lagging strand 3 +
Initiator Proteins
3’
primase base pairs
Polymerase III 5’
RNA primer replaced by polymerase I

& gap is sealed by ligase
3’

5’
Leading strand
RNA Primer
3’
Fig. 3.8 Model of DNA Replication
DNA ligase seals the gaps between Okazaki fragments with a
phosphodiester bond (Fig. 3.7)
Fig. 3.5 - Model of DNA replication
Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
Fig. 3.5 - Model of DNA replication
Concepts and terms to understand:
Why are gyrase and helicase required?
The difference between a template and a primer?
The difference between primase and polymerase?
What is a replication fork and how many are there?
Why are single-stranded binding (SSB) proteins required?
How does synthesis differ on leading strand and lagging strand?
Which is continuous and semi-discontinuous?
What are Okazaki fragments?

Replication of circular DNA in
E. coli (3.10):
1. Two replication forks result in

a theta-like () structure.
2. As strands separate, positive

supercoils form elsewhere in
the molecule.
3. Topoisomerases relieve
tensions in the supercoils,
allowing the DNA to continue
to separate.
Rolling circle model of DNA
replication (3.11):
1. Common in several
bacteriophages including .
2. Begins with a nick at the

origin of replication.
3. 5’ end of the molecule is

displaced and acts as primer
for DNA synthesis.
4. Can result in a DNA molecule

many multiples of the genome
length (and make multiple
copies quickly).
5. During viral assembly the

DNA is cut into individual viral
chromosomes.
DNA replication in eukaryotes:
Copying each eukaryotic chromosome during the S phase of the cell

cycle presents some challenges:
Major checkpoints in the system
1. Cells must be large enough, and the environment favorable.
2. Cell will not enter the mitotic phase unless all the DNA has
replicated.
3. Chromosomes also must be attached to the mitotic spindle for

mitosis to complete.
4. Checkpoints in the system include proteins call cyclins and

enzymes called cyclin-dependent kinases (Cdks).
• Each eukaryotic chromosome is one linear DNA double helix
• Average ~108 base pairs long
• With a replication rate of 2 kb/minute, replicating one human

chromosome would require ~35 days.
• Solution ---> DNA replication initiates at many different sites

simultaneously.
Rates are cell

specific!
Fig. 3.14
Fig. 3.13 - Replication forks visible in Drosophila
What about the ends (or telomeres) of linear chromosomes?
DNA polymerase/ligase cannot fill gap at end of chromosome after

RNA primer is removed. If this gap is not filled, chromosomes
would become shorter each round of replication!
Solution:
1. Eukaryotes have tandemly repeated sequences at the ends of

their chromosomes.
2. Telomerase (composed of protein and RNA complementary to

the telomere repeat) binds to the terminal telomere repeat and
catalyzes the addition of of new repeats.
3. Compensates by lengthening the chromosome.
4. Absence or mutation of telomerase activity results in

chromosome shortening and limited cell division.
Fig. 3.16 Synthesis of telomeric DNA by telomerase
Final Step - Assembly into Nucleosomes:
• As DNA unwinds, nucleosomes must disassemble.
• Histones and the associated chromatin proteins must be

duplicated by new protein synthesis.
• Newly replicated DNA is assembled into nucleosomes almost

immediately.
• Histone chaperone proteins control the assembly.
Fig. 3.17

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Chapter 3: DNA Replication

1. Models of DNA replication: Meselson-Stahl Experiment

2. DNA synthesis and elongation

4. Origin and initiation of DNA replication

5. Prokaryote/eukaryote models (circular/linear chromosomes)

Equilibrium density gradient centrifugation (Box 3.1)

Semiconservative model of DNA replication (Fig. 3.2)

Worked with E. coli.

Four components are required:

1. dNTPs: dATP, dTTP, dGTP, dCTP

3. DNA polymerase (Kornberg enzyme)

1959: Arthur Kornberg (Stanford University) & Severo Ochoa (NYU)

1. DNA polymerase I catalyzes formation of phosphodiester bond

2. DNA polymerase “finds” the correct complementary dNTP at

• rate ≤ 800 dNTPs/second

Polymerase Polymerization (5’-3’) Exonuclease (3’-5’) Exonuclease (5’-3’) #Copies

I Yes Yes Yes 400

III Yes Yes No 10-20

•3’ to 5’ exonuclease activity = ability to remove nucleotides from the

•Important proofreading ability

•Without proofreading error rate (mutation rate) is 1 x 10 -6

•With proofreading error rate is 1 x 10-9 (1000-fold decrease)

•5’ to 3’ exonuclease activity functions in DNA replication & repair.

Five common DNA polymerases from mammals.

• Polymerase  (alpha): nuclear, DNA replication, no proofreading

• Polymerase  (beta): nuclear, DNA repair, no proofreading

• Polymerase  (gamma): mitochondria, DNA repl., proofreading

• Polymerase  (delta): nuclear, DNA replication, proofreading

• Polymerase  (epsilon): nuclear, DNA repair (?), proofreading

1. Different polymerases for the nucleus and mtDNA

2. Some polymerases proofread; others do not.

3. Some polymerases used for replication; others for repair.

4. Polymerases vary by species.

 Begins with double-helix denaturing into single-strands thus

 Exposes a replication bubble from which replication proceeds in

 Segments of single-stranded DNA are called template strands.

 Gyrase (a type of topoisomerase) relaxes the supercoiled DNA.

 Initiator proteins and DNA helicase binds to the DNA at the

 DNA primase next binds to helicase producing a complex called

 Primase synthesizes a short RNA primer of 10-12 nucleotides,

 Polymerase III adds nucleotides 5’ to 3’ on both strands

 The RNA primer is removed and replaced with DNA by

 Single-stranded DNA-binding (SSB) proteins (>200) stabilize

Unwinding of any single DNA replication fork proceeds in one

Solution: DNA is made in opposite directions on each template.

•Leading strand synthesized 5’ to 3’ in the direction of

requires a single RNA primer

•Lagging strand synthesized 5’ to 3’ in the opposite

semidiscontinuous (i.e., not continuous)

requires many RNA primers , DNA is

RNA primer replaced by polymerase I

Why are gyrase and helicase required?

The difference between a template and a primer?

The difference between primase and polymerase?

What is a replication fork and how many are there?

Why are single-stranded binding (SSB) proteins required?

How does synthesis differ on leading strand and lagging strand?

Which is continuous and semi-discontinuous?

What are Okazaki fragments?

1. Two replication forks result in