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Biochemistry and Molecular Biology

DNA Structure and Replication Practice Questions

20 free DNA Structure and Replication practice questions for the USMLE Step 1. Tap an option to answer — you get instant feedback, the correct answer, and a detailed explanation for every question.

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Question 1 of 20 Medium

The Meselson and Stahl experiment provided evidence for which model of DNA replication?

  1. A Conservative replication
  2. B Dispersive replication
  3. C Semiconservative replication
  4. D Random fragmentary strand replication

Correct answer: Semiconservative replication

Meselson and Stahl grew E. coli in heavy nitrogen-15 and then shifted the culture to nitrogen-14. After one round of replication every molecule was of intermediate density, which ruled out conservative replication; after two rounds, light and intermediate bands appeared, which ruled out dispersive replication. Each daughter duplex therefore keeps one parental strand and one newly synthesized strand — semiconservative replication.

Question 2 of 20 Medium

Which enzyme is responsible for unwinding the DNA double helix at the replication fork by breaking hydrogen bonds between base pairs?

  1. A DNA polymerase
  2. B RNA primase
  3. C DNA helicase
  4. D DNA ligase

Correct answer: DNA helicase

DNA helicase unwinds the double helix by breaking hydrogen bonds between complementary base-pairs, creating single-stranded template DNA for replication to proceed.

Question 3 of 20 Medium

Why must DNA replication be initiated with a primer rather than directly by DNA polymerase?

  1. A Leading strand runs 3′→5′ while the lagging strand runs 5′→3′
  2. B Leading strand is continuous; lagging strand is made in Okazaki fragments
  3. C The lagging strand is built from RNA while the leading strand is DNA
  4. D The lagging strand, unlike the leading strand, needs no ligase

Correct answer: Leading strand is continuous; lagging strand is made in Okazaki fragments

DNA polymerases require a free 3′-OH group to add new nucleotides, so an RNA primer (made by primase) provides this starting point before DNA synthesis can proceed.

Question 4 of 20 Medium

What distinguishes leading-strand synthesis from lagging-strand synthesis during DNA replication?

  1. A Leading strand is made 3′→5′ while lagging is made 5′→3′
  2. B Leading strand is continuous; lagging is discontinuous
  3. C Lagging strand is copied from an RNA template
  4. D Lagging strand synthesis does not require DNA ligase

Correct answer: Leading strand is continuous; lagging is discontinuous

Both strands are synthesised 5′→3′, because DNA polymerase can only add nucleotides to a free 3′ hydroxyl. The leading strand runs continuously toward the fork; the lagging strand template runs the wrong way, so it is copied backwards in short Okazaki fragments that are later joined by DNA ligase. Both strands are primed by RNA.

Question 5 of 20 Medium

Which enzyme joins Okazaki fragments on the lagging strand to create a continuous DNA strand?

  1. A DNA polymerase I
  2. B DNA polymerase III
  3. C DNA ligase
  4. D Topoisomerase

Correct answer: DNA ligase

DNA ligase seals the sugar–phosphate backbone by forming phosphodiester bonds between adjacent Okazaki fragments, producing a continuous lagging strand.

Question 6 of 20 Medium

Which of the following proteins stabilize single-stranded DNA during replication to prevent re-annealing or degradation?

  1. A Topoisomerase relaxing supercoils
  2. B Single-strand binding proteins (SSBs)
  3. C The DNA polymerase III holoenzyme
  4. D RNA primase synthesizing primers

Correct answer: Single-strand binding proteins (SSBs)

Single-strand binding proteins (SSBs) bind to unwound single-stranded DNA at the replication fork, preventing the strands from re-forming a duplex or forming secondary structures.

Question 7 of 20 Medium

What is the role of topoisomerase (or DNA gyrase in prokaryotes) during DNA replication?

  1. A To synthesize the RNA primer for replication
  2. B To unwind the duplex DNA at replication origins
  3. C To relieve torsional strain ahead of the fork
  4. D To ligate adjacent Okazaki fragments together

Correct answer: To relieve torsional strain ahead of the fork

As helicase unwinds the double helix, overwinding ahead of the fork causes torsional strain; topoisomerase relieves this by introducing transient breaks and resealing DNA, allowing replication to proceed smoothly.

Question 8 of 20 Medium

Which DNA polymerase performs the bulk of leading-strand synthesis in prokaryotes during replication?

  1. A DNA polymerase I
  2. B DNA polymerase II
  3. C DNA polymerase III
  4. D DNA polymerase IV

Correct answer: DNA polymerase III

In prokaryotes, DNA polymerase III is the main enzyme that synthesizes new DNA strands (both leading and lagging) during replication.

Question 9 of 20 Medium

Which of the following correctly describes the directionality of new DNA strand synthesis by DNA polymerase?

  1. A 5′ to 3′
  2. B 3′ to 5′
  3. C Either direction depending on strand
  4. D Direction changes after RNA primer removal

Correct answer: 5′ to 3′

DNA polymerases catalyze synthesis in the 5′→3′ direction, adding new nucleotides to the 3′-OH end of the growing strand.

Question 10 of 20 Medium

Why are Okazaki fragments necessary on the lagging strand during DNA replication?

  1. A Because the lagging strand template is read in the 3′→5′ direction by polymerase
  2. B Because DNA polymerase cannot synthesize continuously on the lagging template
  3. C Because the lagging strand lacks a primer for polymerase to extend
  4. D Because topoisomerase is unable to act on the lagging strand template

Correct answer: Because DNA polymerase cannot synthesize continuously on the lagging template

Because DNA polymerase synthesizes only in 5′→3′ direction, the antiparallel orientation of the lagging template means replication must proceed in short discontinuous fragments (Okazaki fragments) rather than continuously.

Question 11 of 20 Medium

Which component forms the “replisome” complex at the replication fork in prokaryotes?

  1. A Helicase + primase + DNA Pol III holoenzyme
  2. B DNA Pol I + ligase + topoisomerase + SSB
  3. C SSB + RNA polymerase + helicase + ligase
  4. D Ligase + primase + topoisomerase + SSB

Correct answer: Helicase + primase + DNA Pol III holoenzyme

The replisome in prokaryotes comprises helicase, primase, and the DNA Pol III holoenzyme working together at each replication fork to coordinate unwinding, primer synthesis, and DNA elongation.

Question 12 of 20 Medium

Which statement correctly describes the number of origins of replication in prokaryotic versus eukaryotic chromosomes?

  1. A Prokaryotes have multiple origins; eukaryotes have a single origin
  2. B Both have a single origin
  3. C Prokaryotes have a single origin; eukaryotes have multiple origins
  4. D Both have multiple origins

Correct answer: Prokaryotes have a single origin; eukaryotes have multiple origins

Prokaryotes (with circular chromosomes) typically replicate from a single origin of replication, whereas eukaryotic linear chromosomes use multiple origins to replicate large genomes efficiently.

Question 13 of 20 Medium

Which of the following polymerases is primarily responsible for lagging-strand elongation in eukaryotic cells?

  1. A DNA polymerase α
  2. B DNA polymerase β
  3. C DNA polymerase δ
  4. D DNA polymerase ε

Correct answer: DNA polymerase δ

In eukaryotes, DNA polymerase δ is the main polymerase responsible for lagging-strand synthesis, while polymerase ε largely handles leading-strand synthesis.

Question 14 of 20 Medium

What problem at the ends of linear eukaryotic chromosomes is addressed by the enzyme telomerase during replication?

  1. A Accumulation of mismatched base pairs in the duplex
  2. B Excessive supercoiling stress ahead of the fork
  3. C Loss of terminal DNA after RNA primer removal
  4. D Formation of stable hairpin loops at chromosome ends

Correct answer: Loss of terminal DNA after RNA primer removal

Because removal of the RNA primer at the ends would leave a gap, telomerase extends the 3′ end of linear chromosomes, preventing progressive shortening (end-replication problem).

Question 15 of 20 Medium

What is the role of single-stranded DNA binding proteins (SSBs) during replication?

  1. A They synthesize the RNA primers used by polymerase
  2. B They prevent re-annealing of unwound parental strands
  3. C They remove RNA primers from the lagging strand
  4. D They seal the nicks left in the sugar-phosphate backbone

Correct answer: They prevent re-annealing of unwound parental strands

SSBs coat the separated single strands at the replication fork, preventing them from re-forming a double helix or forming secondary structures, thus enabling polymerases to access the templates.

Question 16 of 20 Medium

During DNA replication, which enzyme replaces RNA primers on the lagging strand with DNA in prokaryotes?

  1. A DNA polymerase III
  2. B DNA polymerase I
  3. C DNA ligase
  4. D RNA primase

Correct answer: DNA polymerase I

In prokaryotes, DNA polymerase I has exonuclease activity to remove RNA primer segments and fills in the corresponding gaps with DNA prior to ligation.

Question 17 of 20 Medium

Which of the following is NOT required for formation of the replication fork during DNA replication?

  1. A DNA helicase
  2. B DNA ligase
  3. C Single-strand binding proteins (SSBs)
  4. D Topoisomerase

Correct answer: DNA ligase

DNA ligase is used later to join Okazaki fragments; it is not required for formation of the replication fork itself, which needs helicase to unwind DNA, SSB to stabilize strands, and topoisomerase to relieve torsional stress.

Question 18 of 20 Medium

Which feature of DNA’s structure provides the chemical basis for the semiconservative replication mechanism?

  1. A Presence of short RNA primers on each strand
  2. B Right-handed coiling of the double helix
  3. C Antiparallel strands with complementary base-pairing
  4. D Tight packaging of DNA around histone proteins

Correct answer: Antiparallel strands with complementary base-pairing

DNA’s antiparallel strands and complementary A–T and G–C base-pairing allow each parental strand to serve as a template — enabling semiconservative replication.

Question 19 of 20 Medium

If a toxin specifically inhibited DNA primase, which process would be directly impaired during DNA replication?

  1. A Unwinding of the parental DNA double helix
  2. B Removal of RNA primers from the new strands
  3. C Synthesis of RNA primers to initiate DNA synthesis
  4. D Ligation of adjacent Okazaki fragments together

Correct answer: Synthesis of RNA primers to initiate DNA synthesis

Primase synthesizes the short RNA primers needed to provide a 3′-OH starting point for DNA polymerase; without primase, no DNA synthesis can begin on either strand.

Question 20 of 20 Medium

Which statement correctly describes how replication forks proceed on circular prokaryotic chromosomes?

  1. A Replication proceeds unidirectionally from a single origin
  2. B Replication begins at multiple origins spaced around the chromosome
  3. C Replication proceeds bidirectionally from a single origin
  4. D Replication uses telomerase to replicate ends

Correct answer: Replication proceeds bidirectionally from a single origin

In prokaryotes, replication starts at a single origin of replication and proceeds bidirectionally, creating two replication forks that copy the circular chromosome until completion.

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