DNA Replication, Repair, and Genome Stability
Replication fidelity
Mechanistic overview
DNA replication is semiconservative and highly coordinated. Replicative polymerases synthesize DNA with proofreading activity, while helicases, primases, ligases, and topoisomerases resolve topological and priming constraints. High fidelity results from nucleotide selectivity, proofreading, and postreplicative mismatch repair.
Why fidelity matters
Even low error rates matter across large genomes and many cell divisions; replication errors are a major source of somatic mutation and hereditary disease.
Which enzyme directly relieves torsional stress ahead of the replication fork?
Topoisomerases cut and rejoin DNA to reduce supercoiling during replication.
Correct answer: Topoisomerase
State the direction of DNA synthesis and why it matters mechanistically.
This constraint determines leading and lagging strand synthesis and the need for Okazaki fragments.
Correct answer: DNA is synthesized because polymerases add nucleotides to the 3' hydroxyl group.
Damage and repair
Repair pathways
Cells continuously repair base damage, deamination, oxidation, single- and double-strand breaks, and replication mismatches. Core pathways include base excision repair, nucleotide excision repair, mismatch repair, homologous recombination, and nonhomologous end joining. Defects in these pathways elevate mutation rates and genome instability.
Major repair pathways
Homologous recombination
- High fidelity
- Uses a homologous template during
Nonhomologous end joining
- Fast but error-prone
- Directly ligates broken ends
Which repair pathway is most closely associated with correcting replication mismatches?
Mismatch repair recognizes and corrects base-pairing errors that escape polymerase proofreading.
Correct answer: Mismatch repair
Why are homologous recombination defects especially dangerous during DNA replication?
Replication creates lesions that are best repaired using a sister chromatid as template.
Correct answer: Because replication-associated breaks and collapsed forks require accurate template-based repair to preserve genome integrity.
Common sources of mutational burden
| Source | Example | Consequence |
|---|---|---|
| Endogenous damage | Oxidative lesions | Base substitutions |
| Replication error | Polymerase misincorporation | Point mutation |
| Recombination defect | Unequal crossover | Copy-number variation |
| Telomere dysfunction | End-replication failure | Chromosome instability |