Chapter 10. DNA Replication

DNA replication requires:• Deoxyribonucleoside triphosphates: the fou

r dNTPs (dATP, dGTP, dCTP, dTTP).• DNA template• RNA primer• Enzymes, accessory proteins, and other fact

ors such as Mg2+.

DNA replication in prokaryotes is different from that in eukaryotes:

1)The templates: prokaryotic DNA is a double- stranded, closed circle, while eukaryotic DNA is a linear, double stranded structure.

2)Location: prokaryotic DNA replication is located in cytosol while that of eukaryotes occurs in the nucleus.

3)Starting origin: prokaryotic DNA replication starts at a single origin while that of eukaryotes starts at multiple origins.

4)Polymerase: E. coli contains three DNA polymerases, named polymerase I, II, and III; animal cells have at least five different DNA polymerases, designated , , , , and .

1. Important terms of DNA replication

• Semiconservative replication: after DNA replication, one strand of a parent duplex is associated with a newly synthesized strand in the daughter DNA duplex.

• Origin: the initiation site on a DNA strand for replication.

• Replication fork: a Y-shaped structure formed by the newly synthesized DNA duplexes and the parent DNA during DNA replication.

• RNA primer: a short RNA sequence synthesized by primase, from which DNA polymerases initiate DNA biosynthesis. The RNA primer is later degraded and replaced with DNA.

2. Enzymes of replication 1) DNA polymerases: using parent DNA sin

gle strand as a template, catalyze the reactions that extend the polydeoxyribo-nucleotide strands.

DNA polymerase(DNA)n residues + dNTP (DNA)n+1 residues + PPi

DNA polymerase catalyzed reaction

TO

CH2A

H

H

H

OH

O

CH2

H

H

H

OH

O

P O

HO

OPOP-OO

O- O-

O

G

5' 3'

5'

5'

3'5'

COCH2

G

H

H

H

OH

O

P O

O

CH2A

H

H

H

O

-O

T

C

PPi

2Pi

DNA polymerase

PyrophosphataseH2O

DNA polymerases of E. coli

Functions Polymerases Pol I Pol II Pol III5’3’ polymerization + + +3’5’ proofreading exonuclease + + +5’3’ repair exonuclease + - -

Human DNA polymerases

Location N N M N NReplication + - + + -Repair - + - - +Associated functions 5’3’ polymerase + + + + + 3’5’ exonuclease- - + + + 5’3’ exonuclease - - - - -Primase + - - - -N: nucleus M: mitochondrion +: yes -: no

2) DNA ligase: catalyzes the formation of a phosphodiester bond between a free 3’-OH and 5’-PO3

2- in DNA.

OH O -O-P-O

O-

O O P O

O-

5’

5’ 3’

3’

Ligase

DNA

DNA DNA

DNA

3) DNA topoisomerases: enzymes that catalyze the interconversion of topological isomers of DNA (Topology refers to the degree and nature of supercoiling). There two classes of topoisomerase, named I and II.

A) Topoisomerase I: makes a nick in only one strand and allows the intact strand to pass through the nick, which is then closed.

B) Topoisomerase II: makes a transient break in two strands and allows a duplex segment of DNA to pass through the “gate”, which is then closed by the enzyme.

Nalidixic acid inhibits bacterial topoisomerase II (gyrase). This drug is usually used to treat urinary tract infections.

N N

O

C2H5

COOH

CH3

3. DNA replication in E. coli1) The bacterial DNA replication starts at a s

ingle origin. Both DNA strands serve as template and the replication proceeds bi-directionally.

2) The process of DNA replication in E.coliA) Fork formation: helicase binds at the origi

n and opens the helix with ATP hydrolysis, forming a replication fork. This is followed by binding of single- strand binding (SSB) proteins to the single strands, stabilizing the single strand state.

helicase SSBDNA helix

B) Synthesis of primer: primase catalyzes formation of a short RNA sequence at the origin, using the parent DNA as template.

3’

5’

5’

3’

3’

5’

5’

3’

Primer

C) Synthesis of the leading strand and Okazaki fragments by polymerase III

3’

5’

5’

3’

New DNA sequence

3’

5’

5’

3’

Leading strandOkazaki fragments

Polymerase III

dNTP

D) Removal of RNA primers and formation of intact new DNA strands

Leading strand

New DNAParent DNARNA primer

Removal of RNA primer

Pol I fill up the gap, the ends joined by ligase

Okazaki fragments

New DNAParent DNARNA primer

Removal of RNA primer

Pol I fill up the gap, fragments joined by ligase

Okazaki fragment

E) Synthesis of both RNA primers and DNA sequence (leading strand and Okazaki fragments) is in a 5’3’ direction.

During DNA synthesis, the replication complex (polymerase III, SSB, etc.) moves in both directions. The topoisomerase I ahead of the replication fork makes a break to allow the DNA to rotate so that the DNA strands are ready for replication.

F) Topoisomerase II separates the interlocked daughter DNA molecules by causing a transient double strand break.

Topoisomerase II Double-stranded DNA

4. DNA replication in humans1) Cell cycle: the cell cycle of eukaryotes co

nsists of G1, S, G2, and M phases.

S(Synthesis, 7h)

G2(prepare for Mitosis, 4 h)

G1(growth, 11h)

M(Mitosis, 1-2h)G0(quiescent)

In human cells in culture, G1, S, and G2 make up interphase, which lasts for about 23 hours. The mitosis occurs in 1-2 hours. DNA replication occurs only in the S phase.

2) The replication process: similar to that in E. coli, it also needs topoisomerases, helicase, SSB, DNA polymerases, and ligase.

A) Initiation: DNA polymerase and are responsible for replication of chromosomal DNA. Polymerase has the primase activity and initiates the replication by synthesizing the RNA primers.

A yeast chromosome contains about 400 initiation sites for DNA replication. These origins are called ARS for “autonomous replication sequence”, insertion of which into a bacterial plasmid may cause autonomous replication of DNA.

ARS is recognized by “origin recognition complex (8 proteins)” which initiates replication.

B) Extension: DNA polymerase is responsible for the lagging strand biosynthesis and for the leading strand biosynthesis. DNA polymerase is also responsible for proof-reading.

Leading strand: in DNA replication the extending strand that can be continuously synthesized.

Legging strand: refers to the strand that is discontinuously synthesized via Okazaki fragments.

C) Termination: DNA fragments synthesized during replication are linked via phosphodiester bonds catalyzed by ligase to form an intact DNA strand.

3’

5’

5’3’

Lagging strand

Leading strand

Replication of eukaryotic DNA

+

The synthesis of the chromosomal ends: the enzyme that replicates the chromosomal ends (telomeres) is called “telomerase”, which carries a short RNA sequence serving as a template for the end replication.

The human telomerase consists of three components: human telomerase RNA (hTR), human telomerase associated protein 1 (hTP1), and human telomerase reverse transcriptase (hTRT).

Replication of telomeric DNA

GGGTTGGGGTTG-3’5’

GGGTTGGGGTTG5’

GGGTTGGGGTTGGGGTTG5’

GGGTTGGGGTTGGGGTTGGGGTTG-3’5’ CCCAAC-5’

Telomerase

hTRACCCCAAC

ACCCCAAC

5. Reverse transcription: a way of DNA biosynthesis using RNA as template. Reverse transcriptase is responsible for this type of DNA synthesis, and it is essential for reproduction of RNA viruses, which are called “retroviruses”, such as human immunodeficiency virus (HIV) and RNA tumor viruses.

RNA tumor virus DNA provirus RNA tumor virus

Mechanism of reverse transcription:

R | U5 | B | | U3 | R

R | U5 | B | | U3 | R R | U5

B | | U3 | R R | U5

tRNA

DNA synthesis

RNA degradation

B | | U3 | R R | U5

B | | U3 | R B | | U3 | R | U5

B | | U3 | R | U5

B | |U3 | R | U5 U3 | R | U5 | B

First jump

DNA extension

RNA degradation

2nd DNA synthesis

B | |U3 | R | U5 U3 | R | U5 | B

B | |U3 | R | U5 U3 | R | U5 | B

U3 | R | U5 | B | |U3 | R | U5 U3 | R | U5 | B | |U3 | R | U5

RNA degradation

Second jump

2nd DNA extension

Double-stranded proviral DNA

Significance of reverse transcription: the synthesized proviral DNA is integrated into the host cell DNA, from which the viral RNAs can be synthesized in the host cell.

+

Host DNA

Retroviral DNA

Integrated proviral DNA

Integration

6. Mutations and lesions in DNA

A) Mutation: A heritable change in DNA due to an alteration in the base sequence.

Types of mutation: substitution, deletion, and insertion.

(1) Substitution of one base pair for another is the most common type of mutation. This type includes: transition and transversion.

Transition: replacement of one purine by the other.

Transversion: replacement of a purine by a pyrimidine, or a pyrimidine by a purine.

A T T A A T T A

G C C G C G G C Transitions transversions

(2) Deletion or insertion of one or more base pairs in DNA may alter the reading frame in translation, unless an integral multiple of three base pairs is inserted or deleted. This reading-frame alteration is called “frame-shift mutation”.

e.g. ACT GGC AGT TCA AGC

ACT AGG CAG TTC AAG C

B) Lesions and repairs: DNA is damaged by many chemical and physical agents, and cells possess mechanisms for repair.

Ionizing radiation, ultraviolet light, and some chemicals may cause base alteration or deletion, breakdown of phosphodiester bonds, covalently cross-link of DNA strands, etc. Many of these DNA damages can be repaired by the cell, some damages may cause mutation, and some may cause death of the cell.

Pyrimidine dimer formation: adjacent pyrimidine residues on a DNA strand can become covalently linked when the DNA is exposed to ultraviolet light.

A C C G C A T—T C A G T G

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

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

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

5’

3’

3’

5’

5’

3’

3’

5’

UV

HN

CN

C

CC

R

OCH3

OH

C

CN

C

NHC

O

R

CH3

O

H

HN

CN

C

CC

R

OCH3

OH

NH

CN

C

CC

R

OH3C

OH

UV Repair

Formation and recovery of T-T dimer

Once the pyrimidine dimer is formed, it can not fit into the DNA double helix and therefore, the DNA replication and gene expression are blocked until the lesion is removed.

Repair of DNA damage: includes light repair, excision repair, and SOS repair, etc.

(1) Light repair (photolyase repair): a mechanism for removal of thymine dimers. Nearly all cells contain a photoreactivating enzyme called DNA photolyase, which cleaves the dimer into its normal bases when the enzyme is excited by photons.

(2) Excision repair: a mechanism involving hydrolytic removal of the damaged DNA fragment, synthesis of a new one to repair the gap.

Mechanism of excision repair

Endonuclease cleavage

Exonuclease removal

Polymerase synthesis

Ligase linking

Damaged segment

(3) SOS repair (SOS response): when DNA molecules are severely damaged, single- stranded DNA (ssDNA) binds to recA protein. The ssDNA-recA complex activates the SOS genes that encode mRNAs for repair proteins. The repair proteins increase by hundred folds to mediate the repair of damaged DNA molecules.

ssDNA-recA DNA damages

activated lexA

SOS genes

lexA

SOS genes

autoproteolysis

Activated genes

Repair proteins

Inactive genes

Degraded lexA fragments

Note: lexA is a repressor of SOS genes