DNA Repair
High-Yield Summary
- Replisome setup: helicase unwinds DNA at the origin of replication (1/chromosome in prokaryotes, multiple in eukaryotes), single-stranded DNA-binding proteins stabilize exposed strands, primase lays RNA primers, topoisomerase (DNA gyrase in prokaryotes) relieves supercoiling ahead of the fork.
- Leading strand: template runs 3'→5' toward fork, synthesized continuously (Pol ε in eukaryotes, one primer). Lagging strand: template runs 5'→3' toward fork, synthesized discontinuously as Okazaki fragments (Pol α primes, Pol δ extends, repeated primers) — DNA ligase seals the nicks.
- RNA primer removal: prokaryotes use Pol I's 5'→3' exonuclease activity; eukaryotes use Pol δ strand-displacement (creates a flap) + FEN1 (cuts flap), assisted by RNase H2.
- Telomerase extends linear chromosome ends using its own RNA template — eukaryotes only (prokaryotic chromosomes are circular, no ends to lose).
- Replication is semiconservative: each daughter molecule has one original strand + one new strand, produced by the multi-protein replisome.
- Oncogenes = mutated, overactive proto-oncogenes (gain of function). Tumor suppressor genes (p53, Rb; a.k.a. anti-oncogenes) halt cell cycle/trigger repair — cancer risk rises when they lose function.
- Four repair pathways: proofreading and mismatch repair (MSH2/MLH1, mainly S phase) fix replication errors; nucleotide excision repair (bulky lesions, e.g. thymine dimers) and base excision repair (small damage, e.g. deaminated cytosine) fix environmental/chemical damage.
Key Terms
- Origin of replication
- Specific DNA site where replication begins; one per chromosome in prokaryotes, multiple in eukaryotes.
- Okazaki fragment
- Short DNA fragment synthesized discontinuously on the lagging strand.
- Semiconservative replication
- Each daughter DNA molecule retains one original (template) strand and one newly synthesized strand.
- Proto-oncogene / Oncogene
- Normal growth-regulating gene / its mutated, overactive cancer-driving form.
- Tumor suppressor gene
- Gene (e.g. p53, Rb) that halts the cell cycle or triggers repair; loss of function removes this safeguard.
- AP site
- Sugar-phosphate backbone left after a glycosylase removes a damaged base in base excision repair.
Leading vs. Lagging Strand
| Feature | Leading vs. Lagging Strand |
|---|---|
| Template orientation toward fork | 3'→5' / 5'→3' |
| Synthesis pattern | Continuous / Discontinuous (Okazaki fragments) |
| Primary eukaryotic polymerase | Pol ε / Pol δ (extending Pol α-laid primers) |
| Primer requirement | One, at the origin / Repeated, one per fragment |
Four DNA Repair Pathways
- 1Proofreading (replication error): DNA polymerase detects a mismatch during synthesis, excises and replaces it immediately.
- 2Mismatch repair (replication error): scans for errors that escaped proofreading, mainly during S phase; MSH2 (MutS homolog) recognizes the mismatch, MLH1 (MutL homolog) coordinates repair.
- 3Nucleotide excision repair (damaged base, bulky lesions e.g. thymine dimers): excision endonuclease cuts both sides of the lesion, DNA polymerase fills the gap, ligase seals it.
- 4Base excision repair (damaged base, small lesions e.g. deaminated cytosine): glycosylase removes the damaged base leaving an AP site, AP endonuclease cuts the backbone there, polymerase and ligase fill/seal.
Common MCAT Trap
- Proofreading happens during synthesis; mismatch repair happens after, largely during S phase, using methylation to distinguish new strand from template — don't merge these into one step.
- Nucleotide excision repair = bulky lesions (thymine dimers); base excision repair = small, non-bulky damage (deaminated cytosine). Matching pathway to damage type is a common question angle.
- Cancer arises from a gain of function in a proto-oncogene (→ oncogene) OR a loss of function in a tumor suppressor gene — two opposite directions of mutation effect, same disease outcome.
Quick Recall
Which eukaryotic polymerase primarily synthesizes the leading strand, and which extends Okazaki fragments?
Why don't prokaryotes need telomerase?
What are MSH2 and MLH1 the human homologs of?
What enzyme removes a damaged base in base excision repair, and what structure does that leave behind?