In Escherichia coli DNA repair, which DNA polymerase primarily fills short gaps during nucleotide-excision repair and Okazaki fragment processing because it has 5'→3' exonuclease activity?

Difficulty: Medium

Correct Answer: DNA polymerase I

Explanation:


Introduction / Context:
E. coli encodes several DNA polymerases with distinct roles. Understanding which enzyme participates in repair versus replication is crucial for interpreting mutant phenotypes and biochemical assays.


Given Data / Assumptions:

  • Bacterial system (E. coli), not eukaryotes.
  • Short single-stranded gaps arise after primer removal and during excision repair.
  • An enzyme with both polymerase activity and 5'→3' exonuclease is advantageous for removing RNA primers and damaged nucleotides ahead of synthesis.


Concept / Approach:
DNA polymerase I possesses 5'→3' exonuclease activity that can remove RNA primers and excised oligonucleotides while simultaneously filling the gap with DNA. Polymerase III is the main replicative polymerase but lacks prominent 5'→3' exonuclease; Pol II is involved in repair under stress but is not the primary enzyme for primer removal.


Step-by-Step Solution:

1) Identify the task: remove a stretch of nucleotides ahead of the polymerase and replace them with DNA.2) Select the enzyme that combines 5'→3' exonuclease with polymerase activity.3) DNA polymerase I meets these criteria and is well known for nick translation and primer removal.4) Conclude that Pol I primarily fills the gaps in excision repair and Okazaki processing.


Verification / Alternative check:
Classic experiments with Pol I mutants (polA) and biochemical nick-translation assays demonstrate its 5'→3' exonuclease and repair roles, while Pol III functions as the high-processivity replicase.


Why Other Options Are Wrong:

  • DNA polymerase II: Participates in repair and restart but lacks the principal 5'→3' exonuclease-driven nick translation function.
  • DNA polymerase III holoenzyme: Main replicative polymerase; high processivity but not specialized for primer removal.
  • None of these: Incorrect because Pol I fits the described function.
  • Telomerase: Eukaryotic enzyme for telomere extension, absent in E. coli.


Common Pitfalls:
Assuming the major replicative polymerase also performs most repair gap-filling, or confusing 3'→5' proofreading with 5'→3' exonuclease used in nick translation.


Final Answer:
DNA polymerase I.

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