DNA Damage and Replication Overview

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Questions and Answers

What is the immediate consequence when a DNA replication fork encounters a lesion in the DNA template, and it bypasses it?

  • Replication stalls until the lesion is repaired.
  • Translesion synthesis occurs with aid of a specific DNA polymerase.
  • A single-strand gap is formed, and replication continues downstream. (correct)
  • The replication fork collapses due to a double strand break.

Which of the following describes a scenario where a lesion in the template strand does not necessarily stall the replication fork?

  • When an O-meG base is present, which pairs with thymine. (correct)
  • When the lesion is a base that causes a significant DNA distortion.
  • When the lesion is undergoing nucleotide excision repair.
  • When a translesion DNA polymerase is used.

What is the most frequent immediate outcome when the replisome encounters a lesion in the DNA template before repair?

  • The replication fork collapses resulting in a double-strand break.
  • The replisome continues to synthesise over the lesion, using a specialised DNA polymerase.
  • The replication fork stalls, waiting for damage repair. (correct)
  • The replisome bypasses the lesion, leading to a downstream gap.

What directly leads to the collapse of the replication fork, creating a double strand break?

<p>The replication fork encountering a lesion that is undergoing repair. (A)</p> Signup and view all the answers

How does translesion synthesis (TLS) differ from normal DNA replication?

<p>TLS utilizes specialized DNA polymerase that can synthesize over lesions. (A)</p> Signup and view all the answers

What is the significance of an O-meG base in the template strand for DNA replication?

<p>It can result in a C to T transition mutation due to mispairing with thymine. (B)</p> Signup and view all the answers

Which process is required to restore an undamaged replication fork following a double-strand break resulting from a stalled replication fork?

<p>Recombinational DNA repair. (A)</p> Signup and view all the answers

Why is damage to DNA considered to be highly deleterious?

<p>The consequences can cause mutations upon DNA replication. (C)</p> Signup and view all the answers

What is the immediate consequence of a DNA lesion that blocks the replication machinery but allows it to resume further downstream?

<p>A single-strand gap with no complementary strand at the location of the lesion (C)</p> Signup and view all the answers

Why is a lesion in the lagging strand more easily bypassed by the replication machinery?

<p>The mechanism for initiating Okazaki fragments allows for continuation downstream (B)</p> Signup and view all the answers

What is the initial step in the recombinational repair of a double-strand break (DSB)?

<p>Degradation of 5' ends to create 3' single-stranded overhangs (A)</p> Signup and view all the answers

What is the role of the homologous DNA molecule in double-strand break (DSB) repair?

<p>It serves as a template for restoring genetic information (C)</p> Signup and view all the answers

What is the key characteristic of the strand invasion process during homologous recombination?

<p>The displacement and base-pairing of a 3' single-stranded extension with a homologous strand (A)</p> Signup and view all the answers

What is the significance of using the 3' ends for single strand invasion?

<p>They can act directly as primers for DNA synthesis (C)</p> Signup and view all the answers

What is a 'D-loop' in the context of recombinational DNA repair?

<p>A temporary structure formed by strand invasion of a 3' single-stranded extension (A)</p> Signup and view all the answers

What is the main difference between how DNA polymerase works in synthesis dependent strand annealing (SDSA), and general replication?

<p>In SDSA, the invasion strand is used as a primer for synthesis, while generally, primers are RNA. (D)</p> Signup and view all the answers

In synthesis-dependent strand annealing (SDSA), what happens to the lengthened invading strands after extension by the DNA polymerase?

<p>They are displaced by helicases and anneal to each other (C)</p> Signup and view all the answers

Which of the following enzymes is NOT directly involved in the early stages of recombinational DNA repair of a double strand break?

<p>DNA Ligases (A)</p> Signup and view all the answers

Flashcards

DNA damage

Alterations in DNA structure that can impair function.

Translesion synthesis (TLS)

A mechanism that allows DNA replication to continue over a lesion.

Lesion

A site of damage or alteration in DNA.

Replication fork

The Y-shaped structure that forms during DNA replication.

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Double-strand break

A critical form of DNA damage where both strands are severed.

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Nucleotide excision repair (NER)

A DNA repair mechanism that removes damaged bases.

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Base excision repair (BER)

A DNA repair process that fixes small base damage in DNA.

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Stalled replication fork

A halted replication process due to a DNA lesion.

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Lesion bypass plus restart

A replication process that continues after a DNA lesion is left as a gap.

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Single-strand gap

A gap left in DNA where there is no complementary strand to guide repair.

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Okazaki fragments

Short DNA strands synthesized on the lagging strand during replication.

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Recombinational DNA repair

A repair pathway that utilizes homologous DNA to fix breaks.

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Double-strand breaks (DSBs)

A severe type of DNA damage where both strands are broken.

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Homologous recombination

A process where damaged DNA uses a homologous sequence for repair.

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D-loop

A structure formed when a single-stranded DNA invades a double-stranded DNA.

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Strand invasion

The process where a 3' extension of single-stranded DNA invades homologous DNA.

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Synthesis-dependent strand annealing (SDSA)

A pathway for DSB repair where elongated strands anneal to each other.

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DNA polymerase

An enzyme that synthesizes new DNA strands during replication and repair.

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Study Notes

DNA Damage and Replication

  • DNA damage is common and harmful. Consequences appear during replication.
  • Replication can continue over a lesion (translesion synthesis, TLS). Specialized polymerases aid TLS.
  • Normally, only specialized polymerases perform TLS. Regular polymerases might replicate some lesions without significant distortion.
  • A lesion can also stop replication, requiring repair before continuing or restart replication further downstream.
  • Replication can halt if a repair process is happening when a lesion is encountered. This can lead to a replication fork collapse and double-strand breaks.
  • Recombinational DNA repair restores the replication fork structure and allows replication to restart.
  • Most lesions cause the replication fork to stall. Replication ceases until repaired.
  • The replication machinery may bypass the lesion and resume downstream of the lesion.
  • This bypass plus restart phenomenon is frequent when the lesion is in the lagging strand.

Double-Strand Breaks (DSBs)

  • DSBs occur due to oxidative DNA damage, oxygen-rich environments, or ionizing radiation.
  • DSBs are destructive and usually lethal if not repaired.
  • DSBs can arise from a broken template strand encountered by a replication fork during repair.
  • Recombination repairs DSBs. Repair requires a homologous, undamaged DNA molecule.
  • The repair DNA guides restoration of information lost at the break.
  • Repair initiation involves three enzymatic reactions:
    • Processing broken ends to create single-stranded extensions (overhangs)
    • Strand invasion of the homologous chromosome.
    • Replicative extension of the invading strand.

Recombinational DNA Repair Process

  • Enzymes process broken DNA ends into 3' single-stranded extensions (overhangs).
  • Recombinase enzymes facilitate strand invasion of the homologous chromosome.
  • The invading strands are extended by DNA polymerases.
  • Several pathways resolve the "double crossover" intermediate, one of which is synthesis-dependent strand annealing (SDSA).

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