Genomic and proteomic tools: DNA electrophoresis and PCR MCQs With Answer

Introduction

Genomic and proteomic tools: DNA electrophoresis and PCR MCQs With Answer provides M.Pharm students with a focused, exam-oriented collection of multiple-choice questions targeting the practical and theoretical principles of DNA separation and amplification. This set emphasizes core concepts such as gel matrix selection, resolution of fragments, staining methods, and advanced electrophoresis approaches, together with PCR fundamentals including reagent roles, thermal cycling parameters, variants like RT-, q-, nested- and multiplex-PCR, and troubleshooting common inhibitors and artifacts. Questions are designed to deepen understanding, reinforce laboratory decision-making, and prepare students for tests and research tasks by integrating conceptual knowledge with applied experimental considerations.

Q1. What is the primary factor that determines DNA fragment migration rate during agarose gel electrophoresis?

• Molecular charge of the DNA
• Length (size) of the DNA fragment
• Base composition (GC content) of the DNA
• Presence of dyes in the loading buffer

Correct Answer: Length (size) of the DNA fragment

Q2. In standard agarose gel electrophoresis, DNA migrates toward which electrode and why?

• Toward the cathode because DNA is positively charged in buffer
• Toward the anode because DNA carries a net negative charge
• Toward the cathode because smaller fragments are attracted there
• It remains stationary because agarose blocks movement

Correct Answer: Toward the anode because DNA carries a net negative charge

Q3. Which agarose concentration is most appropriate to resolve a 200 bp PCR product?

• 0.3% agarose
• 0.7% agarose
• 1.5–2.0% agarose
• 3.0% agarose

Correct Answer: 1.5–2.0% agarose

Q4. Which staining dye intercalates with DNA and is commonly visualized under UV light but is mutagenic?

• SYBR Safe
• Ethidium bromide
• Coomassie Brilliant Blue
• Silver stain

Correct Answer: Ethidium bromide

Q5. What is the main advantage of using TBE buffer over TAE buffer for DNA electrophoresis?

• TBE provides better buffering capacity and sharper resolution for small fragments
• TBE produces faster DNA migration for large fragments
• TBE is less inhibitory to downstream enzymatic reactions
• TBE is nonionic and does not conduct electricity

Correct Answer: TBE provides better buffering capacity and sharper resolution for small fragments

Q6. Pulsed-field gel electrophoresis (PFGE) is used primarily to separate which type of DNA?

• Small oligonucleotides below 50 bp
• Proteins with bound DNA
• Large genomic DNA fragments up to megabase range
• Single-stranded RNA molecules

Correct Answer: Large genomic DNA fragments up to megabase range

Q7. Which of the following best describes the role of magnesium ions (Mg2+) in PCR?

• Act as a fluorescent reporter
• Stabilize primer secondary structures to prevent annealing
• Serve as an essential cofactor for DNA polymerase activity
• Denature template DNA during the initial step

Correct Answer: Serve as an essential cofactor for DNA polymerase activity

Q8. Which property distinguishes Taq DNA polymerase from high-fidelity polymerases?

• Taq has 3’→5′ exonuclease proofreading activity
• Taq lacks 3’→5′ exonuclease proofreading activity and has higher error rate
• Taq cannot synthesize DNA at high temperatures
• Taq requires RNA primers rather than DNA primers

Correct Answer: Taq lacks 3’→5′ exonuclease proofreading activity and has higher error rate

Q9. In PCR, what is the purpose of the annealing step?

• To separate double-stranded DNA into single strands
• To synthesize new DNA from primers
• To allow primers to hybridize (bind) to complementary target sequences
• To inactivate DNA polymerase after cycling

Correct Answer: To allow primers to hybridize (bind) to complementary target sequences

Q10. Which PCR variant is specifically used to quantify nucleic acids in real time using fluorescence?

• Nested PCR
• Multiplex PCR
• qPCR (real-time PCR)
• Touchdown PCR

Correct Answer: qPCR (real-time PCR)

Q11. What is the main purpose of a DNA ladder (molecular weight marker) on a gel?

• To increase DNA migration speed
• To provide reference fragment sizes for estimating sample band sizes
• To stain the gel uniformly
• To denature proteins present in the sample

Correct Answer: To provide reference fragment sizes for estimating sample band sizes

Q12. Which of these is a common PCR inhibitor found in blood that can reduce amplification efficiency?

• Tris buffer
• EDTA
• Heme
• Polyethylene glycol

Correct Answer: Heme

Q13. Touchdown PCR improves specificity by which mechanism?

• Using lower annealing temperatures progressively to increase yield
• Starting with high annealing temperature and progressively lowering it to favor specific primer binding
• Doubling the primer concentration each cycle
• Including restriction enzymes during amplification

Correct Answer: Starting with high annealing temperature and progressively lowering it to favor specific primer binding

Q14. Which gel electrophoresis method provides higher resolving power for small DNA fragments (under ~100 bp)?

• Low percentage agarose gel (0.3%)
• Denaturing polyacrylamide gel electrophoresis (PAGE)
• Pulsed-field gel electrophoresis (PFGE)
• Standard horizontal agarose gel at high voltage

Correct Answer: Denaturing polyacrylamide gel electrophoresis (PAGE)

Q15. What does the term “hot-start PCR” refer to?

• Performing PCR at room temperature to save energy
• Using DNA polymerase that is inactive at lower temperatures and activated by heat to reduce non-specific amplification
• Manually heating tubes between every cycle
• Adding primers after the first 5 cycles

Correct Answer: Using DNA polymerase that is inactive at lower temperatures and activated by heat to reduce non-specific amplification

Q16. In agarose gel electrophoresis, what effect does increasing voltage have, assuming buffer and gel are suitable?

• Always improves resolution without any drawbacks
• Decreases run time but can reduce resolution and cause gel overheating
• Converts agarose to polyacrylamide
• Prevents DNA from binding staining dyes

Correct Answer: Decreases run time but can reduce resolution and cause gel overheating

Q17. Nested PCR is mainly used to:

• Increase throughput by amplifying multiple targets simultaneously
• Reduce contamination by using uracil-DNA glycosylase
• Increase specificity and sensitivity by using two sequential primer pairs
• Directly quantify RNA without reverse transcription

Correct Answer: Increase specificity and sensitivity by using two sequential primer pairs

Q18. Melt curve analysis in qPCR is used to:

• Separate RNA strands prior to reverse transcription
• Assess product specificity by distinguishing amplicons based on melting temperature
• Measure absolute quantity of template without standards
• Stain DNA with ethidium bromide during amplification

Correct Answer: Assess product specificity by distinguishing amplicons based on melting temperature

Q19. Which practice helps prevent PCR carryover contamination in a molecular biology lab?

• Sorting tubes by color only
• Using separate pre- and post-PCR work areas and aerosol-resistant tips
• Reusing pipette tips to avoid waste
• Amplifying all samples in one large batch without controls

Correct Answer: Using separate pre- and post-PCR work areas and aerosol-resistant tips

Q20. Alkaline agarose gel electrophoresis is used when you want to:

• Separate proteins based on charge
• Run RNA gels under neutral conditions
• Denature DNA to single strands for analysis of size or strand breaks
• Visualize DNA without any staining

Correct Answer: Denature DNA to single strands for analysis of size or strand breaks

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