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13. DNA, RNA, and DNA Replication — Practice Questions
This chapter introduces the structure and functions of nucleic acids and the process of DNA replication.
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(Multiple Choice — Click to Reveal Answer)
1. The genome of a newly discovered virus contains 22% guanine, 16% cytosine, 34% adenine, and 28% uracil. What is the most likely nature of this genome?
(A) single-stranded DNA
(B) double-stranded DNA
(C) single-stranded RNA
(D) double-stranded RNA
Answer
(C) — The presence of uracil and uneven base pairing suggests a single-stranded RNA genome.
2. Prokaryotic genomes are found in what form and cellular location?
(A) circular; nucleoid region
(B) circular; nucleus
(C) linear; nucleoid region
(D) linear; nucleus
Answer
(A) — Prokaryotic DNA is circular and located in the nucleoid, not the nucleus.
3. Which base composition would require the least energy to separate the DNA strands?
(A) 20% G, 20% C, 30% A, 30% T
(B) 30% G, 30% C, 20% A, 20% T
(C) 15% A, 15% T, 35% G, 35% C
(D) 25% G, 25% C, 25% A, 25% T
Answer
(A) — Fewer G–C pairs (which form three hydrogen bonds) reduce energy requirements to separate strands.
4. What is a structural difference between DNA and RNA?
(A) DNA has a five-carbon sugar; RNA has a four-carbon sugar.
(B) DNA has thymine; RNA has uracil.
(C) DNA has adenine; RNA has cytosine.
(D) DNA is typically single-stranded; RNA is typically double-stranded.
Answer
(B) — Thymine is found only in DNA, while uracil replaces it in RNA.
5. After one round of DNA replication, what result supports the semiconservative model?
(A) All DNA has one N-14 strand and one N-15 strand.
(B) 50% N-14 only; 50% N-15 only.
(C) All N-15 only.
(D) All N-14 only.
Answer
(A) — Semiconservative replication results in hybrid molecules with one old and one new strand.
6. After two rounds of replication, which result supports semiconservative replication?
(A) All hybrids
(B) 50% N-14 only; 50% N-15 only
(C) All N-15 only
(D) 50% N-14 only; 50% hybrids
Answer
(D) — Half are hybrids (N-15/N-14) and half are entirely N-14 after two cycles.
7. Why is replication continuous on one strand and discontinuous on the other?
(A) Thymine and uracil difference
(B) A–T vs G–C pairing
(C) RNA polymerase directionality
(D) DNA polymerase only adds nucleotides 5′ to 3′
Answer
(D) — DNA polymerase only works in the 5′ to 3′ direction, necessitating different mechanisms for each strand.
8. Which enzymes are correctly paired with their functions?
(A) helicase; topoisomerase
(B) DNA polymerase; topoisomerase
(C) DNA polymerase; ligase
(D) helicase; ligase
Answer
(A) — Helicase unwinds DNA; topoisomerase relieves supercoiling.
9. What enzymes add new nucleotides and join lagging strands?
(A) helicase; topoisomerase
(B) DNA polymerase; topoisomerase
(C) DNA polymerase; ligase
(D) helicase; ligase
Answer
(C) — DNA polymerase adds bases; ligase joins Okazaki fragments.
10. What are small circular DNA molecules outside the nucleus called?
(A) Okazaki fragments
(B) RNA primers
(C) plasmids
(D) linear chromosomes
Answer
(C) — Plasmids are small, circular DNA found outside of chromosomal DNA.
11. Which of the following enzymes initiates DNA replication by synthesizing a short RNA segment?
(A) DNA polymerase
(B) RNA polymerase
(C) ligase
(D) topoisomerase
Answer
(B) — RNA polymerase creates the primer needed for DNA polymerase to start synthesis.
12. What is the role of ligase in DNA replication?
(A) Adds nucleotides to the growing strand
(B) Synthesizes RNA primers
(C) Joins Okazaki fragments
(D) Unwinds DNA strands
Answer
(C) — Ligase seals nicks between Okazaki fragments on the lagging strand.
13. Which of the following best describes the directionality of DNA synthesis?
(A) 3′ to 5′
(B) 5′ to 3′
(C) Both 5′ to 3′ and 3′ to 5′
(D) No specific direction
Answer
(B) — DNA polymerase adds nucleotides in the 5′ to 3′ direction.
14. What does it mean that DNA replication is “semiconservative”?
(A) Each new DNA molecule has two new strands.
(B) DNA is partially conserved and partially degraded.
(C) Each new DNA molecule has one old and one new strand.
(D) One strand is copied, and one is discarded.
Answer
(C) — Semiconservative replication retains one original strand in each new DNA molecule.
15. Okazaki fragments are found on which strand?
(A) Leading strand
(B) Lagging strand
(C) Both strands
(D) Neither strand
Answer
(B) — The lagging strand is synthesized in fragments called Okazaki fragments.
16. What type of bond connects nitrogenous bases in DNA?
(A) Ionic bonds
(B) Peptide bonds
(C) Hydrogen bonds
(D) Covalent bonds
Answer
(C) — Hydrogen bonds hold base pairs together across the DNA double helix.
17. Which sugar is present in DNA?
(A) Glucose
(B) Ribose
(C) Fructose
(D) Deoxyribose
Answer
(D) — DNA contains deoxyribose, which lacks an oxygen atom compared to ribose.
18. Which base is found in RNA but not in DNA?
(A) Adenine
(B) Cytosine
(C) Uracil
(D) Thymine
Answer
(C) — Uracil replaces thymine in RNA.
19. Which enzyme relieves supercoiling during DNA replication?
(A) Ligase
(B) Helicase
(C) Topoisomerase
(D) RNA polymerase
Answer
(C) — Topoisomerase cuts and reattaches DNA to relieve tension caused by unwinding.
20. Why is DNA more stable than RNA?
(A) DNA is single-stranded
(B) DNA contains uracil
(C) DNA lacks a 2′ hydroxyl group
(D) DNA is smaller than RNA
Answer
(C) — The absence of the 2′ OH group in DNA makes it more chemically stable than RNA.
21. Which base pairs form three hydrogen bonds?
(A) A–T
(B) A–U
(C) G–C
(D) T–A
Answer
(C) — G–C pairs form three hydrogen bonds, making them more stable than A–T pairs.
22. What is the function of RNA primers in DNA replication?
(A) They bind Okazaki fragments.
(B) They initiate DNA synthesis by providing a 3′ end.
(C) They replicate the leading strand.
(D) They unwind DNA strands.
Answer
(B) — DNA polymerase requires a primer with a 3′ hydroxyl group to begin synthesis.
23. What defines the antiparallel nature of DNA?
(A) Base pair orientation
(B) Phosphate group presence
(C) Opposing 5′ to 3′ directionality
(D) Hydrogen bonding differences
Answer
(C) — One DNA strand runs 5′ to 3′, the other runs 3′ to 5′, making them antiparallel.
24. Which of the following contains the base thymine?
(A) DNA only
(B) RNA only
(C) Both DNA and RNA
(D) Neither
Answer
(A) — Thymine is found in DNA, while uracil is its counterpart in RNA.
25. Which best describes plasmids?
(A) Linear chromosomes
(B) Short RNA fragments
(C) Circular extranuclear DNA
(D) Repeating sequences of proteins
Answer
(C) — Plasmids are circular, non-chromosomal DNA found in both prokaryotes and some eukaryotes.
26. A retrovirus with reverse transcriptase has a higher mutation rate than typical DNA viruses. What is the reason for this?
(A) Reverse transcriptase lacks proofreading ability
(B) DNA viruses replicate slower
(C) RNA viruses use DNA ligase
(D) Reverse transcriptase causes deletions only
Answer
(A) — Reverse transcriptase lacks proofreading function, increasing mutation rate.
27. Which of the following would occur if topoisomerase failed to function during DNA replication?
(A) RNA primers wouldn’t be synthesized
(B) DNA strands would not unwind
(C) Supercoiling would prevent replication
(D) Ligase would fail to join fragments
Answer
(C) — Without topoisomerase, supercoiling would build up and halt replication.
28. In the Meselson-Stahl experiment, what was observed after two rounds of DNA replication to support the semiconservative model?
(A) All DNA was heavy
(B) Half hybrid, half light DNA
(C) All DNA was light
(D) Half DNA had two heavy strands
Answer
(B) — One hybrid strand and one fully N-14 strand support semiconservative replication.
29. Why does DNA polymerase require a primer to begin synthesis?
(A) It cannot synthesize de novo
(B) It needs ligase activation
(C) It binds only to ribose
(D) It cannot bind DNA
Answer
(A) — DNA polymerase needs an existing 3′ OH group to add nucleotides.
30. What would be the immediate effect of a ligase inhibitor on DNA replication?
(A) Failure to initiate replication
(B) Incomplete lagging strand synthesis
(C) Disruption of transcription
(D) Misfolding of the replication fork
Answer
(B) — Ligase is essential for joining Okazaki fragments on the lagging strand.
31. Which of the following statements is FALSE regarding DNA replication enzymes?
(A) Helicase unwinds DNA
(B) DNA polymerase synthesizes new DNA
(C) Ligase creates RNA primers
(D) Topoisomerase prevents DNA overwinding
Answer
(C) — RNA polymerase, not ligase, creates RNA primers.
32. Why does RNA contain uracil instead of thymine?
(A) Uracil binds to guanine
(B) RNA uses a different sugar
(C) Uracil is more energy-efficient
(D) Uracil replaces thymine in RNA
Answer
(D) — Uracil serves as the RNA counterpart to thymine in DNA.
33. What part of the nucleotide links to the phosphate group of the next nucleotide in a DNA strand?
(A) 5′ phosphate
(B) 3′ hydroxyl
(C) Nitrogenous base
(D) Ribose sugar
Answer
(B) — The 3′ hydroxyl of one nucleotide bonds to the 5′ phosphate of the next.
34. Which strand serves as a continuous template for DNA polymerase during replication?
(A) Lagging strand
(B) RNA strand
(C) Leading strand
(D) Template strand
Answer
(C) — The leading strand is synthesized continuously in the 5′ to 3′ direction.
35. Which of the following mutations would most likely result from a faulty reverse transcriptase?
(A) Increased thymine dimers
(B) Deletion of exons
(C) Higher point mutation frequency
(D) Loss of topoisomerase activity
Answer
(C) — Faulty reverse transcriptase increases point mutations due to lack of error checking.
36. What type of nucleotides would you expect to find in the genome of a virus that uses reverse transcriptase?
Answer
RNA viruses contain adenine, cytosine, guanine, and uracil — thymine is not found in RNA.
37. Why do reverse transcriptase inhibitors typically have few side effects in eukaryotic cells?
Answer
Eukaryotic cells do not normally use reverse transcriptase, so inhibiting it does not interfere with normal cell processes.
38. Predict the mutation rate of a retrovirus compared to that of a DNA virus.
Answer
Retroviruses have a higher mutation rate than DNA viruses.
39. Justify why the mutation rate is higher in retroviruses than in DNA viruses.
Answer
Reverse transcriptase lacks proofreading capability, resulting in more replication errors than DNA polymerase.
40. Describe the role of ligase during DNA replication.
Answer
Ligase joins the Okazaki fragments on the lagging strand by forming covalent bonds in the sugar-phosphate backbone.
41. Identify an appropriate control in an experiment testing a ligase inhibitor.
Answer
The control would be DNA replication under the same conditions but without the ligase inhibitor.
42. Predict which DNA strand would be most affected by a ligase inhibitor.
Answer
The lagging strand would be most affected because it is synthesized in fragments that require ligase for joining.
43. Justify your answer to the previous question.
Answer
The lagging strand forms Okazaki fragments that must be joined by ligase; inhibition prevents completion of the strand.
44. Why is a primer necessary during PCR amplification?
Answer
DNA polymerase needs a primer with a free 3′ hydroxyl group to initiate synthesis of the new DNA strand.
45. Describe the relationship between the number of PCR cycles and DNA copies generated.
Answer
The number of DNA copies doubles with each PCR cycle — an exponential relationship.
46. Predict the number of PCR cycles needed to generate at least 1,000 copies of DNA.
Answer
10 cycles are needed to exceed 1,000 copies, producing 1,024 copies.
47. Justify your answer to the previous question.
Answer
Each cycle doubles the number of DNA molecules: 2⁰ = 1, 2¹ = 2, ..., 2¹⁰ = 1,024 copies.
48. Explain the role of topoisomerase during DNA replication.
Answer
Topoisomerase prevents DNA from supercoiling by making temporary cuts and resealing the sugar-phosphate backbone.
49. Define the antiparallel structure of DNA.
Answer
DNA strands run in opposite directions — one strand 5′ to 3′ and the other 3′ to 5′.
50. Why is it important that purines pair with pyrimidines in DNA?
Answer
Pairing a purine with a pyrimidine maintains a constant width in the DNA double helix structure.