DNA Replication: Enzymes, Topology, and Okazaki Fragments

What is the primary function of DNA polymerase I?

DNA repair and replication.

Which DNA polymerase is the principal enzyme for DNA replication?

DNA polymerase III.

What direction do all DNA polymerases synthesize DNA?

From 5' to 3'.

What is the purpose of using temperature-sensitive mutants in studying DNA replication?

To determine the importance of specific proteins by switching them on or off with temperature changes.

What is the difference between quick stop mutants and slow stop mutants?

Quick stop mutants cause immediate replication stoppage, while slow stop mutants allow the current round of replication to finish before stopping new rounds.

What problem does DNA topology present during replication?

DNA strands are coiled and need to be unwound for replication.

How do helicases contribute to DNA replication?

They separate and unwind the DNA duplex using ATP hydrolysis.

What is the equation that describes the linking number (Lk) in circular DNA?

Lk = T + W, where T is twist and W is writhe.

What happens when the linking number (Lk) is greater than Lk0?

Positive supercoiling occurs, which can resist replication fork movement.

What is the role of topoisomerases in DNA replication?

They change the linking number (Lk) to relieve torsional strain during replication.

Describe the mechanism of Type I topoisomerases.

They cleave the backbone of one DNA strand, allowing it to rotate and relieve supercoiling before resealing the backbone.

What is unique about bacterial Type II topoisomerase?

It can introduce negative supercoils, which is vital for replication progression.

What are Okazaki fragments and why are they important?

They are short DNA segments synthesized on the lagging strand, allowing for 5' to 3' synthesis despite the antiparallel nature of DNA.

What is the process of synthesizing Okazaki fragments?

Helicase opens the fork, primase lays down RNA primers, and DNA polymerase extends from these primers.

Why can't DNA be synthesized in the 3' to 5' direction?

It would not allow for proofreading, leading to unstable chains and error correction issues.

What is the role of DNA ligase in DNA replication?

It joins Okazaki fragments into a continuous DNA strand.

What is the relaxed form of DNA where W = 0 called?

Lk0.

What occurs if Lk is less than Lk0?

Negative supercoiling occurs, which aids in unwinding for transcription and replication.

What is the significance of the superhelical density (sigma) in relaxed DNA?

In relaxed DNA, sigma equals 0.

What is the main challenge posed by antiparallel strands during DNA replication?

It requires two polymerases, one for each direction, complicating the replication process.

What is the primary function of DNA polymerase II?

DNA repair.

What is the primary function of DNA polymerase IV?

DNA repair.

What is the primary function of DNA polymerase V?

DNA repair.

topoisomerase type II mechanism

both strands are cleaved and a section of the duplex is passed through the gap. gap is resealed, ATP dependent

name of unique bacterial type II topoisomerase

DNA gyrase