Question 1

How does long-patch base excision repair differ from short-patch BER?

Accepted Answer

Long-patch BER repairs multiple nucleotides rather than a single damaged base. DNA polymerase δ/ε adds several nucleotides that displace original ones, creating a flap structure containing the damaged base. Flap Endonuclease (FEN) removes this flap before DNA ligase seals the nick. This contrasts with short-patch BER, which removes and replaces only one nucleotide.

Question 2

What role does PCNA play in long-patch base excision repair?

Accepted Answer

PCNA (proliferating cell nuclear antigen) acts as the lynchpin of long-patch BER. It serves as a scaffold to anchor DNA polymerase at the damaged site and binds to FEN-1 to facilitate its nuclease activity. Replication factor C (RF-C) loads PCNA onto DNA, enabling the coordinated action of repair proteins.

Question 3

Why is long-patch BER preferred during ATP shortage?

Accepted Answer

Under ATP shortage, cells shift preference toward long-patch BER because poly(ADP-ribose) serves as a unique ATP source during the ligation step. Under normal physiological conditions, short-patch BER predominates. This metabolic flexibility allows cells to continue DNA repair even when ATP availability is limited.

Question 4

How does the type of DNA glycosylase determine which BER pathway is used?

Accepted Answer

The specific DNA glycosylase recruited to a damaged site depends on lesion type. Monofunctional glycosylases favor long-patch repair events through their sequential action, while bifunctional glycosylases drive short-patch BER. This lesion-dependent recruitment ensures the appropriate pathway selection for efficient DNA repair.

Question 5

What is a flap structure in long-patch base excision repair?

Accepted Answer

A flap is an overhang of oligonucleotides created when DNA polymerase δ/ε adds multiple nucleotides that displace the original strand. This flap contains the damaged base and is recognized and removed by Flap Endonuclease (FEN) in the presence of PCNA, allowing DNA ligase to complete the repair.

Question 6

Why is long-patch BER particularly effective for ionizing radiation damage?

Accepted Answer

Long-patch BER repairs a patch of several nucleotides rather than single bases, making it effective for complex lesions caused by ionizing radiation. The mechanism's ability to remove and replace multiple damaged nucleotides simultaneously addresses the extensive DNA damage characteristic of radiation exposure.

Question 7

How does the cell cycle state influence the choice between long-patch and short-patch BER?

Accepted Answer

Long-patch BER uses proteins required during DNA replication, including PCNA, RF-C, and FEN1, suggesting it repairs damage in replicating DNA. Short-patch BER is used for repairing resting DNA. This distinction allows cells to coordinate repair pathway selection with their replication status.

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