DNA Replication

purpose of dna replication

copy genetic material before cell divides, occurs in S phase

three models of dna replication

semiconservation - each parent strand serves as a template for daughter strand (one old, one new)

conservation - new molecule made of new strands

dispersive - old and new dna, mixed in each strand

replication process

innitation - helicase unwinds double helix and creates replicatin fork

• one replication fork in prokaryotes

• multiple replication forks in eukarytoes

elongation - leading and lagging strand synthesis

1. Helicase unwins double helix, SSBPs attach to hold strands apart, toipomerase relieves torsional stress

2. Primase adds RNA primers to 5’ end

3. DNA polymerase synthesizes the strands

Lagging strand synthesis

• each okazaki fragment needs a rna primer

• ligase seals any nicks in sugar phosphate backbone

DNA polymerase structure

DNA poly I - removes RNA primers to add DNA

DNA poly III - adds nucleotides to template strand

Structure:

Palm - active site where OH group attacks alpha phosphate

• nucleotide can only be added if correct complementary base pair and is dntp (deoxyribose, nitrogenous base, triphosphate)

Bottom of palm - exonuclease clips of mismatched bases

How do the replication enzymes know where to begin replicating? What is this area called?

Area - origin of replication

Enzymes recognize specific dna sequences at origin sites

Explain why DNA replication only proceeds in the 5’ to 3’ direction. Be able to draw out the polymerization reaction. What drives this reaction forward?

Because DNA polymerase can only add nucleotides at the 3 prime OH group of the growing DNA strand . That OH group attacks the alpha phosphate of an incoming dNTP, forming a phosphodiester bond

PPi is released

Why is there a leading and lagging strand?

There is a leading and ladding strand because DNA polymerase can only add nucleotides in the 5 to 3 prime direction, but the two strands run in opposite directions so the leading strand is synthesized continously while the lagging strand is syntheiszed in fragements.

Where does the energy for replication come from (specifically, the energy for the addition of each nucleotide)

the incoming dNTPs

What are primers and why are they important for synthesis?

RNA primers provide a starting point with a free 3 prime OH for new nucleotides that will be added by DNA polymerase

Describe the structure of DNA polymerases. What does each region of the “right hand” do?

Structure of a hand

Palm - active site where OH group attacks alpha phosphate

Bottom of palm - exonuclease activity that cuts off mismatched bases

Fingers - postion incoming dNTPS

End replication problem

When RNA primers are removed after lagging strand synthesis, it leaves a gap that can’t be filled with DNA. So the telomere extends the 3 prime end using an rna template to make dna. (reverse transcriptase activity)

Telomeres Mechanism

Telomere - buffer zone that prevent important dna from being lost as strand shortens

telomerase - enzyme with reverse transcriptase activity

Mechanism - extends 3' end, ends up with overhang