DNA DNA RReplicationeplication-II-II

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OverviewI. General Features of Replication• Semi-Conservative• Starts at Origin• Bidirectional• Semi-Discontinuous

II. Identifying Proteins and Enzymes of ReplicationIII. Detailed Examination of the Mechanism of

Replication• Initiation• Priming• Elongation• Proofreading and Termination

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Mechanism of DNA replication

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DNA replication system

• Template: Double stranded DNA

• Substrate: dNTP

• Primer: Short RNA fragment with a free 3´-OH end

• Enzyme: DNA-dependent DNA polymerase (DDDP), other enzymes,

protein factor.

Overview of bacterial DNA replication

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DNA Polymerases Elongate DNA in the 5′→3′ Direction

First, all DNA polymerases require a template strand that guides the polymerization reaction according to the Watson-Crick base-pairing rules.

Second, DNA polymerases require a primer strand that is complementary to the template and contains a free 3′-OH group to which a nucleotide can be added.

Most primers are oligonucleotides of RNA rather than DNA, and specialized enzymes (primases) synthesize primers when and where they are required.

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DNA polymerases can only add nucleotides to a preexisting strand ;

they cannot synthesize DNA starting from only a template strand .

Many different DNA polymerases have been studied from various types of bacteria, archaea, and eukaryotes, and mitochondria from many different species. All known DNA polymerases use the mechanism.

The 3′-hydroxyl group of the primer strand, (dNMP)n, is activated to attack the α phosphorus of the incoming dNTP, resulting in attachment of a dNMP to the primer 3′ terminus and release of pyrophosphate (PPi).

The DNA polymerase active site must have at least two sites:

i. The template nucleotide that pairs with the incoming dNTP is positioned

in the insertion site. i. The primer 3′-terminal base pair is positioned in the

postinsertion site.

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Most DNA Polymerases Contain DNA Exonuclease Activity

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DNA nucleasesclass of enzymes that

degrade DNA

Exonucleases Shorten DNA from

the ends

Endonucleases Cut DNA at internal

positions

Exonucleases degrades DNA

in the 3′→5′ direction

Exonucleases degrades DNA

in the 5′→3′ direction

Do you think the two DNA exonucleases of Pol I have the same active sites?

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The 3′→5′ proofreading exonuclease of DNA polymerases .

The 3′→5′ Exonuclease:

When an incorrect dNMP is incorporated, the 3′→5′ exonuclease removes the mismatched nucleotide, giving the polymerase a second chance at incorporating the correct one. This activity, known as proofreading, is not the reverse of the polymerization reaction- pyrophosphate is not involved, and the mismatched nucleotide is released as a dNMP, not a dNTP. Also, proofreading by the 3′→5′ exonuclease occurs at a separate active site from polymerization.

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Most DNA polymerases contain this proofreading exonuclease activity, although some do not and thus become more capable of bypassing a DNA lesion.

The 5′→3′ Exonuclease: Pol I also contains a second

exonuclease that degrades DNA in the 5′→3′ direction, the same direction as DNA synthesis.

The 5′→3′ exonuclease is unique to Pol I and reflects the enzyme’s role in DNA repair.

The 5′→3′ exonuclease is capable of functioning at the same time as the polymerase, because the two activities act in the same direction.

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Nick translation by Pol I. DNA polymerase I (Pol I) is organized into three major domains: DNA polymerase, 3′→5′ proofreading exonuclease, and 5′→3′ exonuclease. At a nick, the gap between lagging-strand fragments—Pol I degrades the RNA primer in the 5′→3′ direction, releasing NMPs, and simultaneously extends the 3′ terminus with dNTPs in the same direction. The net result is movement of the nick in the 5′→3′ direction along the DNA until all RNA is removed.

Five E. coli DNA Polymerases Function in DNA Replication and Repair

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DNA polymerases require a primed template and extend the 3′ terminus of the primer strand by reaction with dNTPs.

A dNTP that correctly base-pairs to the template strand is incorporated into the primer strand with the release of pyrophosphate. Pyrophosphate is hydrolyzed by pyrophosphatase, which reduces the concentration of pyrophosphate in the cell and makes the reverse reaction extremely unlikely.

DNA polymerases are inherently very accurate, and are made even more accurate by a proofreading 3′→5′ exonuclease.

Pol I also contains a 5′→3′ exonuclease that degrades DNA while, at the same time, the polymerase synthesizes DNA, in the process of nick translation.

E. coli has five DNA polymerases. Pol III is responsible for chromosome replication, and Pol I is used to remove RNA primers and fill in the resulting gaps with DNA. The other three (II, IV, and V) are involved in DNA repair and in moving replication forks past sites of DNA damage.

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