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REPLICATION

M.Prasad NaiduMSc Medical Biochemistry, Ph.D,.

Watson and crick

IntroductionBesides maintaining the integrity of DNA

sequences by DNA repair, all organisms must duplicate their DNA accurately before every cell division.

DNA replication occurs at polymerization rates of about 500 nucleotides per second in bacteria and about 50 nucleotides per second in mammals.

Clearly, the proteins that catalyze this process must be both accurate and fast.

Speed and accuracy are achieved by means of a multienzyme complex that guides the process and constitutes an elaborate "replication machine."

•Replication occurs in 5’ to 3’ direction only.

•Replication is simultaneous on both strands.•Replication is bidirectional. •Replication obeys base pair rule

•Replication results in 2 daughter DNA strands.• Each daughter DNA strand has one parent strand and one complementary strand synthesized newly. Hence this Replication is semi-conservative. Held by phospho-di-ester bonds and Hydrogen bonds

CELL - CYCLECell cycle is a sequence of events that

occur in a cell during cell division. It results in formation of 2 identical

daughter cells. Duration of cell cycle varies from cell to cell. It occurs in 4 phases G1 PHASE [ gap-1]

S PHASE [synthetic] G2 PHASE [gap-2]

M PHASE [ mitotic]

G0

CELL- CYCLE

G1 phase ; Preparative phase for DNA synthesis. All cellular components replicate except DNA . Cell size

increases. Any damage to DNA is detected. S phase ; DNA replication takes place. G2 phase ; Prepares for cell division and spindle formation. Any damage to DNA is detected.

M phase; Cell undergoes cell division . It includes prophase ,metaphase, anaphase ,and telophase.

After mitosis cell may continue cycle by re-entering into G1 or enter G0 and remain dormant or leads to cell

death

MODELS FOR DNA REPLICATIONThese are many hypothesis to explain the process of replication. They are

1. Conservative model 2. Semi conservative model3. Dispersive model

SEMI CONSERVATIVE MODEL OF REPLICATION

REPLICATION IS SEMICONSERVATIVE

SEMI CONSERVATIVE MODEL OF REPLICATION

DNA-REPLICATIONRequirements 1.Deoxyribonucleotides [ dATP, dGTP, dCTP, dTTP ] 2.Template DNA strand [parent strand] 3.RNA primer4.Enzymes DNA polymerase Primase Helicase DNA Ligase Topo-isomerases Single Strand Binding

Proteins.

Single strand binding protein (SSBP )

Binds to ssDNA Has two function 1. prevents reannealing , thus providing ss template

required by polymerases 2. protects ssDNA from nuclease activity

Show cooperative binding

Helicases Separate the ds DNA to ss DNA by dissolving the

hydrogen bonds holding the two strands togetherThese separates dsDNA at physiological

temperatureATP dependentAt least 9 helicases have been described in E coliOf which DNA binding protein A, B , C ( Dna A, Dna

B, Dna C ) are most importantInitial separation is by Dna AContinued further by Dna B ( major strand

separating protein acts bidirectionally )Dna C is required for loading Dna B at site of

replication

PRIMASE:

Primase is a specilised RNA polymerase It synthesis a short strech of RNA in 5’

3’ direction on a template running in 3’ 5’ direction.

An RNA primer, about 100-200 nucleotides long, is synthesized by the RNA primase.

The RNA primer is removed by DANP, using exonuclease activity and is replaced with deoxyribo nucleotides by DNAP

DNA Ligases

DNA ligases close nicks in the phosphodiester backbone of DNA.  Two of the most important biologically roles of DNA ligases are:

1. Joining of Okazaki fragments during replication.

2. Completing short-patch DNA synthesis occurring in DNA repair process. 

There are two classes of DNA ligases:

1. The first uses NAD+ as a cofactor and only found in bacteria. 

2. The second uses ATP as a cofactor and found in eukaryotes, viruses and bacteriophages. 

DNA LIGASE STRUCTURE

DNA Ligase Mechanism

The reaction occurs in three stages in all DNA ligases:

1.Formation of a covalent enzyme-AMP intermediate linked to a lysine side-chain in the enzyme.

2.Transfer of the AMP nucleotide to the 5’-phosphate of the nicked DNA strand.

3.Attack on the AMP-DNA bond by the 3’-OH of the nicked DNA sealing the phosphate backbone and resealing AMP. 

SUPERCOILSAs two strands unwind ,they result in the

formation of positive supercoils ( super twists ) in the region of DNA ahead of replication fork.

Accumulation of these supercoils interfere with further unwinding of ds DNA.

This problem is solved by the enzyme Topoisomerases.

These catalyze the interconvertion of topoisomers of DNA

Catalyze in a three step process 1. cleavage of one or both strands of DNA

2. passage of a segment of DNA through this break

3. resealing of the DNA

Two types of topoisomerases are presentDNA which different in the linking numer Linking number = (Twist +Wreth) 3 dimentional

-type I topoisomerases -type II topoisomerases

Topoisomerases IReversibly cut one strand of double helix

Have both nuclease ( strand cutting ) & ligase ( strand resealing )

Donot require ATP ,rather use the energy released by phosphodiester bond cleavage to reseal the nick

Removes only negative super coilsEx : bacteria

Topoisomerases II ( DNA gyrase )

Heterodimer with 2 swivelase & 2 ATPase subunits

Swivelase subunit catalyzes trans esterification reaction that breaks & reforms the phosphodiester backbone

ATPase subunit hydrolyzes ATP to trigger conformational changes that allow a double helix to pass through the transient gap

Possitive super coiled

DNA POLYMERASES

These are the enzymes responsible for the polymerisation of deoxy ribo nucleosides, triphosphates on a DNA template strand to form a new complementary DNA strand.

In prokaryotes based on site and conditions of action. They are divided into 3 types: I II III.

Common properties: 1. All polymerases can synthesis a new

strand of DNA in 5’ to 3” direction. On a template strand which is running in 3’to 5’ direction.

2. They also show Exo nuclease activity ( it cleaves the end terminals of DNA) in 3’to 5’ direction.

3. All DNA polymerases cannot initiate the process of replication on their own. This is the basic defect of DNAP synthesis of new strand .

COMPARISON OF PROKARYOTIC & EUKARYOTIC DNA POLYMERASE

Prokaryotic Eukaryotic FUNCTION

l α Gap filling &synthesis of lagging strand

ll ε DNA proofreading & repair

β DNA repairgamma Mitochondrial DNA

synthesislll δ leading strand

synthesis

REPLICATION

There are three phases of replication

1. Initiation 2. Elongation 3. Termination

STEPS IN DNA-REPLICATION

1.Recognition of origin of replication and Un- winding of double stranded DNA

2.Formation of replication bubbles with

2 replication forks for each replication bubble.

3.Initiation and elongation of DNA

strand.

4.Termination and Reconstitution of chromatin structure.

UNWINDING OF DS DNA

INITIATION OF DNA-REPLICATION

1.Identification of the origins of replication. The origin of replication [oriC locus] rich in AT pairs is identified. A specific protein [Dna A] binds to the oriC and

results in unwinding of ds DNA. Un winding of DNA results in formation of

replication bubble with 2 replication forks. Ss binding proteins binds to DNA to each strand to prevent re-annealing of DNA. Helicases continues the process of un winding. Topoisomerases relieve the super coils formed

during unwinding.

Topo-isomerases

DNA-REPLICATION2.Fomation of replication fork replication fork has 4 components 1.helicase [unwinds ds DNA] 2.primase [synthesizes RNA primer] 3.DNApolymerase[synthesizes DNA] 4.ss binding proteins [stabilizes the

strand]

2.ELONGATION OF DNA

Requires RNA primer, DNA template , DNAP enzyme

and deoxyribonucleotides [dATP,dGTP ,dCTP, dTTP]

DNA polymerase catalyze the stepwise addition of deoxyribonucleotides to 31 end of template

strand and thus copies the information from the template

DNA. DNAP requires RNA primer to start elongation. DNAP copies the information from DNA template

2.ELONGATION OF DNA

1.continous synthesis occurs towards the replication fork [leading strand] by DNA polymerase.

2.discontinuous synthesis occurs

away from the replication fork in pieces called as okazaki fragments which are ligated by DNA ligase [lagging strand]. It requires multiple RNAprimers.

Okazaki fragments

First demonstrated by Reiji Okazaki

Short fragments of DNA present on the lagging strand resulted by retrograde synthesis.

Okazaki fragments in human cells average about 130 - 200 nucleotide in length

In E coli they are about ten times this.

REPLICATION

RNA primer is removed by DNAP with exonuclease activity. Again the gap is filled

by DNAP. The two Okazaki pieces are later joined by DNA ligase.

ROLE OF TELOMERS IN EUKARYOTIC REPLICATION A small portion of 31 end of parent strand

is not replicated and length of chromosome reduces.

Telomeres play a crucial role in eukaryotic replication.

Telomeres contain the repeat sequence of [TTAGGG]n . They prevent the shorting of chromosome

with each cell division by an enzyme telomerase.

Telomerase enzyme synthesizes and maintains the telomeric DNA.

Telomerase adds repeats to 31end of DNA

3.TERMINATION OF DNA REPLICATION

In prokaryotes the process of replication is terminated when the two replication forks moving in opposite directions from the origin meet.

In E.coli replication of circular DNA takes about 30 minutes.

In eukaryotes replication is terminated

when entire DNA is duplicated in S phase of cell cycle.

INHIBITORS OF REPLICATION

1.Inhibitors of DNA; Prevents un-winding of DNA.

E.g. actinomycin, mitomycin

2.Inhibitors of deoxy-ribonucleotides; E.g. Anti-folates [ inhibits

Purine\ Pyrimidine synthesis] 3.Inhibitors of replicative enzymes; E.g. norflox [inhibit DNA

gyrase] ciploflox

Replication in Eukaryotic cells More complex than prokaryotic replication

Semicoservative ,occurs bidirectional from many oigins forming multiple replication bubbles

Eg:- replication of Drosophilia chromosomes

single Ori C ---16 days to replicate

multiple Ori C ---3 min ( 6000 replication forks )

Sequence functionally similar to Ori C have been identified in yeast & are called ARS ( autonomously replicating sequence )

ARS –span about 300bp ( conserved sequence )

There are about 400 ARS elements in yeast

Eukaryotic DNA polymerases

Type Location Major role

α Nucleus Replication of nuclear DNAGap filling & synthesis of lagging strand

β Nucleus Proof reading & Repair of nuclear DNA

γ Mitochondrial

Replication of mitochondrial DNA

δ Nucleus Replication of nuclear DNALeading strand synthesis

ε Nucleus Repair of nuclear DNA

Replication in linear genome

Problem arise with replication of ends of linear genome

( Telomers )

Removal of RNA primer on the lagging strand produces a daughter DNA with an incomplete 5’ end

If not synthesized shorter and shorter daughter DNA would result from successive rounds of replication

This problem is solved by the enzyme TELOMERASE

Telomers Ends of the eukaryotic linear chromosomes

Contains thousands of hexameric repeats ( TTAGGG )

Some shortening of this telomer is not a problem as they donot encode for proteins

Cell is no longer able to divide & is said tobe senescent if shortening occurs beyond some critical length

In germ cells ,stem cells as well as in cancer cells ,telomers

donot shorten & the cells do not senesce.( due to the presence of Telomerase enzyme )

Telomerase

Ribonucleoprotein enzyme ( reverse transcriptase ) catalyzing the elongation of the 3’ ending strand

Contains a RNA molecule that serves as the template for the elongation of the telomeric end

Highly processive –hundreds of nucleotides are added before it dissociates

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