Chem 114C DNA replication

What is the overall organization of prokaryotic (e.coli) replication?

Simpler replisome centered on DNA polymerase III as the main replicative polymerase

What is the function of helicase in prokaryotic DNA replication?

ATP-dependent helices unwinds duplex DNA at the fork

How does ssDNA stabilization work in prokaryotes?

SSB binds exposed single-stranded DNA and keeps it open

What is the main replicative polymerase in prokaryote DNA replication?

Polymerase III

What is the starter polymerase in prokaryote DNA replication?

No pol a-like stage

What does leading strand elongation look like in prokaryote DNA replication?

Usually folded into the general role of Pol III

What does lagging strand elongation look like in prokaryote DNA replication?

Pol III repeatedly re-initiates on Okazaki fragments

What does the sliding clamp in prokaryote DNA replication do?

B clamp increases processivity by keeping polymerase associated with DNA

What does the clamp loader do in prokaryote DNA replication?

Places the sliding clamp onto the DNA

How does proofreading in prokarytote DNA replication work?

Pol III has 3’ to 5’ exonuclease proofreading; Pol I has exonuclease activity for cleanup

Describe RNA primer removal in prokaryote DNA replication.

Pol I removes primers through nick translation, with RNase H used in cleanup

How are the gaps filled in prokaryote DNA replication after the primer is removed?

Pol I fills in DNA

How does ligation in prokary DNA replication work?

DNA ligase seals the remaining nick

What do the leading and lagging strand look like in prokaryote DNA replication?

Trombone model coordinates continuous leading strand and discontinuous lagging strand synthesis

What is the overall organization of Eukaryote DNA replication?

More elaborate with multiple specialized polymerases and additional coordination demands

What is the function of helicase in eukaryotic DNA replication?

ATP-dependent helicase unwinds DNA

How is ssDNA stabilized in eukaryote DNA replication?

Analogous single stranded binding factors stabilize exposed ssDNA

What is the main replicative polymerase in eukaryote DNA replication?

Pol E handles the leading stand and Pol delta handles the lagging strand

What follows eukaryotic priming in DNA replication?

a starter polymerase stage

What is the starter polymerase and how does it work in eukaryote DNA replication?

Pol a extends the RNA primer with about 10-15 nt of DNA before handoff

What is the main polymerase in leading stand elongation in eukaryote DNA replication?

Pol epsilon

What is the main polymerase in lagging stand elongation in eukaryote DNA replication?

Pol delta, it is processive and proofreading competent

What is the sliding clamp in eukaryote DNA replication?

PCNA

What does the clamp loader do in eukaryote DNA replication?

Places PCNA onto DNA

What does proofreading look like in eukaryote DNA replication?

pol alpha lacks 3’ to 5’ exonuclease proofreading and pol delta has proofreading activity

How are RNA primers removed in eukaryote DNA replication?

RNase H and FEN1 remove the primers because eukaryotic polymerase do not solve this with pol I

What is the function of FEN1 in eukaryote DNA replication?

cleaves a 5’ ribonucleotide/flap during Okazaki fragment maturation

What fills in the gaps after primer removal in eukaryote DNA replication?

Pol delta

What is the function of DNA ligase in eukaryote DNA replication?

seals the remaining nicks

What model is used to describe eukaryote DNA replication?

Trombone model

What major issue does eukaryotic replication face

Linear chromosome ends create an end replication problem

after primer removal at chromosome termini

Describe telomerase maintenance in eukaryote DNA replication.

Telomerase extends chromosome ends using its own RNA template so termini are not progressively lost