A research team engineers a bacterial strain in which the 3′-to-5′ proofreading exonuclease of DNA polymerase is inactivated. Compared to wild-type bacteria, what change in mutation rate would you expect?
ANo change — mismatch repair handles all errors independently of proofreading
BA modest increase, since proofreading catches only a small fraction of errors
CA large increase — roughly 100-fold — because proofreading corrects ~99% of polymerase errors before mismatch repair acts
DComplete genomic collapse, since all DNA polymerases require proofreading to proceed
Replication fidelity is multiplicative: polymerase selectivity (~10⁻⁵ error rate) × proofreading (~100-fold correction) × mismatch repair (~100-fold correction) = final rate ~10⁻⁹ to 10⁻¹⁰. Removing proofreading eliminates ~99% error correction at that stage, raising the pre-MMR error rate from ~10⁻⁷ to ~10⁻⁵. MMR still operates but now faces ~100× more substrate, so the final mutation rate rises roughly 100-fold. Option A misunderstands the multiplicative structure — MMR cannot fully compensate for lost proofreading. Option B understates proofreading's contribution.
Question 2 Multiple Choice
CpG dinucleotides are among the most mutation-prone sites in the human genome. What is the primary reason?
ACpG sites are in regions of open chromatin where DNA polymerase makes more errors
BThe cytosine in CpG is frequently methylated; methylated cytosine deaminates to thymine rather than uracil, making the lesion harder to detect and repair
CCpG sequences form secondary structures that block mismatch repair from operating
DCpG sites are prone to depurination, which removes guanine more frequently than at other sites
5-methylcytosine (the methylated form of cytosine at CpG sites) deaminates spontaneously to thymine — a normal DNA base. Unlike unmethylated cytosine deamination (which produces uracil, readily recognized and removed by uracil-DNA glycosylase), the resulting G:T mismatch is repaired less efficiently. This means CpG→TpG transitions escape repair more often, making CpG the most common mutational hotspot in the human genome. Option D confuses depurination (loss of purines from the backbone) with deamination, a distinct chemical reaction.
Question 3 True / False
The final spontaneous mutation rate in human cells (~10⁻⁹ to 10⁻¹⁰ per base per division) primarily reflects the accuracy of DNA polymerase itself.
TTrue
FFalse
Answer: False
DNA polymerase alone has an error rate of roughly 10⁻⁵ — far higher than the observed final rate. The final rate results from three multiplicative layers: polymerase selectivity (10⁻⁵), proofreading (~100-fold reduction to ~10⁻⁷), and mismatch repair (~100-fold further reduction to ~10⁻⁹). Cancers with MMR deficiency (e.g., Lynch syndrome) show dramatically elevated mutation rates, demonstrating that repair is not a minor contributor but a critical determinant of final fidelity.
Question 4 True / False
Spontaneous mutations from chemical decay of DNA — such as depurination and deamination — primarily become permanent mutations if the damage occurs during S phase of the cell cycle.
TTrue
FFalse
Answer: False
DNA damage from depurination and deamination can occur at any time throughout the cell cycle — and if not repaired before the next round of replication, the lesion becomes a permanent mutation. Repair pathways (base excision repair, mismatch repair) operate continuously, not only during S phase. The critical window is whether repair completes before DNA polymerase encounters the lesion. If an AP site or deaminated base is bypassed by polymerase before repair acts, it becomes fixed regardless of when in the cell cycle the damage originally occurred.
Question 5 Short Answer
Why does knocking out mismatch repair cause such a dramatic increase in mutation rate, even though DNA polymerase already has its own proofreading activity?
Think about your answer, then reveal below.
Model answer: Proofreading and mismatch repair are sequential, multiplicative layers. Proofreading corrects ~99% of polymerase errors immediately after incorporation, but the remaining ~1% reach the double-stranded DNA stage. Mismatch repair then corrects most of those residual mismatches, achieving the final ~10⁻⁹ rate. Without MMR, those residual errors go uncorrected, raising the mutation rate roughly 100-fold.
The layers are not redundant — they operate on different substrates at different stages. Proofreading acts co-replicatively on single-stranded/nascent-strand misincorporations; MMR acts post-replicatively on mismatches that survived proofreading. Together they account for most of the ~10⁵-fold improvement from raw polymerase fidelity to the final observed rate. This multiplicative architecture also explains why cancer cells with MMR deficiency become hypermutators, accumulating thousands of extra mutations per cell division.