Mutagenesis, repair mechanisms and applications in strain improvement MCQs With Answer

Introduction:

Mutagenesis and DNA repair are central to understanding how genetic changes arise and how cells maintain genomic integrity. For M.Pharm students, mastering these concepts is crucial for rational strain improvement, optimizing drug-producing microbes and ensuring biosafety. This quiz set covers physical, chemical and biological mutagens, types of mutations, cellular repair pathways (like base excision, nucleotide excision, mismatch repair, photoreactivation and SOS response), and modern applications such as directed mutagenesis, CRISPR-based editing and screening strategies in industrial strain development. Questions emphasize mechanistic details, experimental approaches and practical implications for pharmaceutical biotechnology and microbial strain optimization.

Q1. Which mutagen is most likely to cause G:C → A:T transitions by alkylating guanine at the O6 position?

• Nitrosoguanidine (NTG)
• Ethyl methanesulfonate (EMS)
• 5-bromouracil
• Ultraviolet (UV) radiation

Correct Answer: Ethyl methanesulfonate (EMS)

Q2. Photoreactivation repairs which type of DNA lesion and which enzyme directly reverses it?

• Pyrimidine dimers repaired by photolyase
• O6-methylguanine repaired by O6-methylguanine-DNA methyltransferase
• Abasic sites repaired by AP endonuclease
• Double-strand breaks repaired by RecA

Correct Answer: Pyrimidine dimers repaired by photolyase

Q3. Which DNA repair pathway primarily removes bulky helix-distorting lesions such as thymine dimers in bacteria?

• Base excision repair (BER)
• Nucleotide excision repair (NER)
• Mismatch repair (MMR)
• Direct reversal by methyltransferase

Correct Answer: Nucleotide excision repair (NER)

Q4. In bacteria, a defect in MutS protein would most directly increase the frequency of which type of mutation?

• Large chromosomal deletions
• Frameshift mutations from intercalating agents
• Base substitution errors arising during replication
• Double-strand breaks from ionizing radiation

Correct Answer: Base substitution errors arising during replication

Q5. Which mutagenesis strategy is best described as introducing random genome-wide mutations followed by selection of desired phenotypes?

• Site-directed mutagenesis
• Directed evolution
• Random (classical) mutagenesis
• Homologous recombination-based editing

Correct Answer: Random (classical) mutagenesis

Q6. 5-bromouracil (5-BU) is a base analog that increases mutation frequency by doing which of the following?

• Intercalating between base pairs to cause frameshifts
• Causing single-strand nicks that lead to deletions
• Pairing ambiguously with adenine and guanine to cause transitions
• Crosslinking DNA strands to block replication

Correct Answer: Pairing ambiguously with adenine and guanine to cause transitions

Q7. Which enzyme removes uracil from DNA during base excision repair?

• Uracil-DNA glycosylase (UDG)
• AP endonuclease
• DNA photolyase
• DNA ligase

Correct Answer: Uracil-DNA glycosylase (UDG)

Q8. In strain improvement for antibiotic production, why might one deliberately use a mutator strain (defective in DNA repair)?

• To reduce the metabolic burden by eliminating repair proteins
• To increase mutation rate and accelerate generation of beneficial variants
• To ensure complete genomic stability during fermentation
• To selectively induce double-strand breaks for recombination

Correct Answer: To increase mutation rate and accelerate generation of beneficial variants

Q9. The Ames test measures mutagenicity by scoring revertants in auxotrophic strains. Which bacterial strain property is central to this assay?

• Presence of photolyase for repair
• Auxotrophy requiring a specific nutrient for growth
• Resistance to antibiotics used in selection
• High natural rate of homologous recombination

Correct Answer: Auxotrophy requiring a specific nutrient for growth

Q10. Which repair pathway is mainly responsible for repairing replication-associated single-base mismatches and small insertion-deletion loops?

• Nucleotide excision repair (NER)
• Mismatch repair (MMR)
• Non-homologous end joining (NHEJ)
• Base excision repair (BER)

Correct Answer: Mismatch repair (MMR)

Q11. Which physical mutagen primarily induces double-strand breaks and large deletions useful for creating gene knockouts but requires careful handling due to high penetrance?

• Ultraviolet (UV-C) radiation
• Gamma rays / ionizing radiation
• Visible light with photosensitizers
• Xanthine oxidase-generated ROS

Correct Answer: Gamma rays / ionizing radiation

Q12. Site-directed mutagenesis using oligonucleotide primers primarily relies on which cellular or enzymatic process to incorporate the desired change?

• Translesion synthesis by error-prone polymerases
• Template-directed DNA synthesis by DNA polymerase during replication or PCR
• Non-homologous end joining after double-strand break
• Photoreactivation to reverse mismatches

Correct Answer: Template-directed DNA synthesis by DNA polymerase during replication or PCR

Q13. In the bacterial SOS response, which protein mediates induction of error-prone polymerases leading to increased mutagenesis?

• LexA cleavage causing RecA-mediated de-repression
• MutS activation leading to mismatch repair
• Photolyase activation by light
• Dam methylase overexpression

Correct Answer: LexA cleavage causing RecA-mediated de-repression

Q14. Which of the following is a common strategy to screen for secondary metabolite overproducers after mutagenesis?

• Whole-genome shotgun sequencing of all mutants
• High-throughput phenotypic screening using indicator plates or HPLC assays
• Selection for antibiotic sensitivity
• Measuring mutation frequency by fluctuation test only

Correct Answer: High-throughput phenotypic screening using indicator plates or HPLC assays

Q15. O6-methylguanine-DNA methyltransferase (MGMT) repairs which damage and how does it act?

• Removes thymine dimers by photoreversal using light energy
• Transfers a methyl group from O6-methylguanine to a cysteine on the enzyme (suicide reaction)
• Excises oxidized bases and replaces them via BER
• Performs error-prone synthesis across abasic sites

Correct Answer: Transfers a methyl group from O6-methylguanine to a cysteine on the enzyme (suicide reaction)

Q16. Which mutagenic agent acts primarily as an intercalator and is most associated with frameshift mutations?

• 5-bromouracil
• Acridine orange
• Ethyl methanesulfonate (EMS)
• UV-B radiation

Correct Answer: Acridine orange

Q17. CRISPR-Cas9 can be used in strain improvement. Which advantage does CRISPR-mediated editing have over classical random mutagenesis?

• Generates large numbers of random mutations quickly
• Enables precise, targeted edits with minimal off-target genomic disruption
• Always avoids requirement for selection or screening
• Relies solely on error-prone polymerases to create diversity

Correct Answer: Enables precise, targeted edits with minimal off-target genomic disruption

Q18. During base excision repair (BER), after a DNA glycosylase removes the damaged base, what is the next immediate enzymatic step?

• DNA ligase seals the nick
• AP endonuclease cleaves the phosphodiester backbone at the abasic site
• DNA helicase unwinds the surrounding DNA
• Photolyase reverses the lesion

Correct Answer: AP endonuclease cleaves the phosphodiester backbone at the abasic site

Q19. Which selection strategy is most appropriate when you aim to isolate mutants with overexpression of a secreted enzyme?

• Replica plating for auxotrophy
• Screening colonies on substrate-containing indicator plates that produce a halo
• Using rifampicin resistance selection
• Measuring DNA repair enzyme activities

Correct Answer: Screening colonies on substrate-containing indicator plates that produce a halo

Q20. In microbial strain improvement, what is the main regulatory/ethical concern associated with using high mutation rates or mutator strains?

• Mutator strains cannot produce metabolites
• Increased genomic instability may create unintended pathogenic traits or unpredictable behavior
• High mutation rates completely eliminate the need for screening
• Mutator strains are universally more robust in industrial fermenters

Correct Answer: Increased genomic instability may create unintended pathogenic traits or unpredictable behavior

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