DNA Repair and Replication

These flashcards cover key concepts and details regarding DNA repair and the processes involved in DNA replication, as discussed in the lecture.

What are the roles of DNA polymerases I, II, IV, and V?

They are involved in various aspects of DNA repair and repair DNA damaged by external forces such as UV light.

What is the active form of DNA polymerase III called?

The holoenzyme.

What is the function of the sliding clamp in DNA replication?

It tethers DNA polymerase to the DNA template to prevent dissociation and allows for high-speed replication.

What key issues must be resolved during DNA replication?

Unwinding the helix, reducing coiling, synthesizing primers, discontinuous synthesis of the second strand, removing RNA primers, joining DNA fragments, and proofreading.

What protein initiates DNA unwinding?

DnaA.

What components are required for the function of DNA helicase?

It requires energy supplied by the hydrolysis of ATP to denature hydrogen bonds and stabilize the double helix.

What do single-stranded binding proteins (SSBPs) do?

They stabilize the open conformation of the helix and bind specifically to single strands of DNA.

What is the role of DNA gyrase?

It relieves coiled tension from unwinding the helix by making cuts and is a member of the DNA topoisomerases.

What does primase do during DNA replication?

Primase synthesizes the RNA primer needed for DNA polymerase III to start elongation.

What happens to RNA primers on the lagging strand?

DNA polymerase I removes the RNA primers and replaces them with DNA.

What are Okazaki fragments?

Short segments of DNA synthesized on the lagging strand, each with an RNA primer.

What defines continuous and discontinuous DNA synthesis?

Continuous synthesis occurs on the leading strand and discontinuous synthesis occurs on the lagging strand.

What type of mutation can interrupt aspects of DNA replication?

Lethal mutations, such as ligase-deficient or proofreading-deficient mutations.

What is a temperature-sensitive mutation?

A conditional mutation that may not be expressed at certain permissive temperatures but shows a mutant phenotype under restrictive temperatures.

At what rate does DNA polymerase III synthesize base pairs?

Around 1000 nucleotides per second.

How does proofreading occur during DNA replication?

DNA polymerase uses its exonuclease activity to excise misinserted nucleotides.

What initial challenge must be overcome to begin DNA synthesis from a double helix?

The double helix must be unwound, a process initiated by DnaA protein and carried out by DNA helicase, which denatures hydrogen bonds.

What issue arises due to DNA unwinding, and what enzyme resolves it?

Unwinding the helix causes supercoiling ahead of the replication fork. This coiled tension is relieved by DNA gyrase, a member of the DNA topoisomerases.

Why is it necessary to synthesize primers during DNA replication?

DNA polymerase cannot initiate DNA synthesis on its own; it requires a pre-existing 3'-OH group. Primase synthesizes short RNA primers to provide this starting point for DNA polymerase III.

Explain the concept of discontinuous synthesis in DNA replication.

Due to the antiparallel nature of DNA and the 5' to 3' synthesis direction of DNA polymerase, the lagging strand must be synthesized in short fragments (Okazaki fragments), opposite to the overall direction of the replication fork.

What happens to the RNA primers after DNA synthesis has begun?

The RNA primers must be removed from the newly synthesized DNA strands, a function primarily performed by DNA polymerase I, which also replaces them with DNA nucleotides.

What is the final step required to connect newly synthesized DNA segments?

After RNA primers are removed and replaced with DNA, nicks remain between the DNA fragments (e.g., Okazaki fragments). These nicks are sealed by DNA ligase to create a continuous DNA strand.

What is the final mechanism that ensures accuracy and resolves errors during DNA replication?

Proofreading, where DNA polymerase uses its exonuclease activity to excise misinserted nucleotides.