Why is strand discrimination the most critical step in mismatch repair — the step without which the entire pathway could cause net harm?
ABecause mismatches only occur on the newly synthesized strand, so only one strand needs to be scanned
BBecause without knowing which strand contains the error, the repair system might correct the template strand, converting the replication mistake into a permanent mutation
CBecause strand discrimination determines which exonuclease is recruited to remove the mismatch
DBecause discrimination prevents the repair machinery from processing legitimate base modifications as mismatches
A mismatch is structurally ambiguous — both strands look normal except for the non-Watson-Crick pairing. The system cannot tell from the mismatch alone which base is wrong. If it corrects the template strand (the correct one), it converts the correct sequence to the error — a permanent mutation worse than the original replication mistake. Strand discrimination (hemimethylation in bacteria, strand discontinuities in eukaryotes) is what allows consistent targeting of the newly synthesized strand, achieving the 100- to 1000-fold fidelity improvement.
Question 2 Multiple Choice
A patient with Lynch syndrome has a germline mutation inactivating one copy of MLH1. Decades later they develop colorectal cancer with microsatellite instability (MSI). What sequence of molecular events best explains this?
AThe single inherited MLH1 mutation directly activates oncogenes, initiating cancer immediately
BLoss of the second MLH1 allele somatically (two-hit model) eliminates MMR, creating a mutator phenotype that accelerates mutation accumulation in tumor suppressors and oncogenes
CMSI caused by the inherited mutation directly kills normal cells, allowing cancer cells to proliferate unopposed
DMicrosatellite instability in Lynch syndrome is present in all cells from birth and gradually causes cancer
Lynch syndrome follows the two-hit model: the inherited MLH1 mutation is heterozygous — the second allele still provides sufficient MMR function. When the second allele is somatically inactivated (the 'second hit'), MMR is completely eliminated in that cell lineage. Polymerase slippage at microsatellites goes uncorrected (producing MSI), and the mutator phenotype dramatically accelerates accumulation of mutations throughout the genome, including in tumor suppressor genes, driving cancer development.
Question 3 True / False
A mismatch repair system that cannot distinguish the new strand from the template strand would be approximately as likely to cause permanent mutations as to prevent them.
TTrue
FFalse
Answer: True
If the system randomly selects which strand to correct, it will fix the template strand in ~50% of cases — replacing the correct base with the error, permanently embedding the replication mistake as a heritable mutation. Proper strand discrimination ensures the system corrects the new strand in every case, achieving its full fidelity improvement. Without discrimination, the repair system would be no more useful than random mutagenesis, undermining its entire biological purpose.
Question 4 True / False
Eukaryotic mismatch repair uses the same GATC hemimethylation mechanism as bacteria to identify the newly synthesized strand.
TTrue
FFalse
Answer: False
This is a critical mechanistic difference. Bacteria use GATC methylation: the parental strand is methylated at GATC sites; the newly synthesized strand is transiently unmethylated, allowing MutH to nick the new strand specifically. Eukaryotes lack MutH and do not use methylation for strand discrimination. Instead, they exploit structural features of ongoing replication — nicks at Okazaki fragment junctions on the lagging strand, the 3' terminus on the leading strand, and the orientation of the PCNA sliding clamp — to identify the new strand.
Question 5 Short Answer
Why are microsatellite sequences (short tandem repeats like CACACACA) particularly vulnerable when mismatch repair is defective, and why is microsatellite instability (MSI) used as a diagnostic marker for MMR dysfunction?
Think about your answer, then reveal below.
Model answer: DNA polymerase slips frequently on repetitive sequences — the template or new strand can loop out during synthesis, creating insertion/deletion loops of one or more repeat units. MMR normally corrects these loops before they are permanently incorporated. Without MMR, each slippage event changes the repeat count in that cell, producing measurable length variation at microsatellite loci across the genome. Since slippage at microsatellites is frequent and the length changes accumulate in every cell division, MMR-deficient tumors show MSI at multiple loci simultaneously. Comparing tumor DNA to matched normal DNA from the same patient detects this variation, making MSI a sensitive and specific diagnostic marker for MMR dysfunction.
MSI testing is used both to screen for Lynch syndrome (where inherited MMR gene mutations predispose to colorectal and other cancers) and to identify sporadic MMR-deficient cancers. The latter are clinically important because MMR-deficient tumors accumulate many mutations throughout the genome, generating neoantigens that make them highly responsive to immune checkpoint blockade therapy — a major advance in cancer treatment that depends on this molecular distinction.