Q.1 What is the primary enzyme that adds nucleotides during DNA replication?
DNA ligase
DNA helicase
DNA polymerase
RNA polymerase
Explanation - DNA polymerase catalyzes the formation of phosphodiester bonds by adding nucleotides to the growing DNA strand.
Correct answer is: DNA polymerase
Q.2 Which of the following creates the short DNA fragments on the lagging strand?
Okazaki fragments
Telomeres
Origins of replication
Replication forks
Explanation - Okazaki fragments are discontinuous DNA pieces synthesized on the lagging strand, later joined by DNA ligase.
Correct answer is: Okazaki fragments
Q.3 During DNA replication, which protein unwinds the double helix?
Topoisomerase
DNA polymerase
Helicase
Primase
Explanation - Helicase breaks the hydrogen bonds between base pairs, separating the two DNA strands to form replication forks.
Correct answer is: Helicase
Q.4 What short RNA segment provides a primer for DNA synthesis?
tRNA
mRNA
rRNA
RNA primer
Explanation - Primase synthesizes a short RNA primer that gives DNA polymerase a free 3'‑OH group to begin DNA synthesis.
Correct answer is: RNA primer
Q.5 Which enzyme removes RNA primers and fills the gaps with DNA?
DNA ligase
DNA polymerase I
Helicase
Topoisomerase
Explanation - In prokaryotes, DNA polymerase I has 5'→3' exonuclease activity to remove RNA primers and 5'→3' polymerase activity to replace them with DNA.
Correct answer is: DNA polymerase I
Q.6 Which of the following best describes the direction of synthesis on the leading strand?
5' → 3' continuously
3' → 5' continuously
5' → 3' discontinuously
3' → 5' discontinuously
Explanation - The leading strand is synthesized continuously in the 5' to 3' direction as the replication fork progresses.
Correct answer is: 5' → 3' continuously
Q.7 What is the function of DNA ligase in replication?
Unwinds DNA
Synthesizes RNA primers
Seals nicks between adjacent DNA fragments
Proofreads newly synthesized DNA
Explanation - DNA ligase forms phosphodiester bonds between adjacent Okazaki fragments, completing the lagging strand.
Correct answer is: Seals nicks between adjacent DNA fragments
Q.8 Which statement about the antiparallel nature of DNA is true?
Both strands run 5'→3' in the same direction.
One strand runs 5'→3' while the complementary strand runs 3'→5'.
Both strands run 3'→5' in opposite directions.
The strands are parallel but not antiparallel.
Explanation - DNA strands are antiparallel; one strand's 5' end aligns with the other's 3' end, which is essential for replication.
Correct answer is: One strand runs 5'→3' while the complementary strand runs 3'→5'.
Q.9 What is the role of topoisomerase (DNA gyrase) during replication?
Synthesizes new DNA strands
Relieves supercoiling ahead of the replication fork
Adds RNA primers
Joins Okazaki fragments
Explanation - Topoisomerase cuts and re‑joins DNA to prevent excessive torsional strain caused by unwinding.
Correct answer is: Relieves supercoiling ahead of the replication fork
Q.10 In eukaryotes, replication begins at:
A single origin of replication
Multiple origins of replication
The telomere only
The centromere only
Explanation - Eukaryotic chromosomes are large, so they contain many origins to ensure timely replication.
Correct answer is: Multiple origins of replication
Q.11 Which of the following enzymes possesses 3'→5' exonuclease activity for proofreading?
DNA polymerase I
DNA polymerase δ
DNA helicase
RNA polymerase
Explanation - DNA polymerase δ (in eukaryotes) has a 3'→5' exonuclease domain that removes misincorporated nucleotides.
Correct answer is: DNA polymerase δ
Q.12 The term 'semiconservative replication' means:
Both daughter DNA molecules are entirely new.
Each daughter DNA contains one original strand and one new strand.
One daughter DNA is old, the other is new.
The parental DNA is conserved, and a new copy is made separately.
Explanation - Semiconservative replication conserves one parental strand in each daughter helix, pairing it with a newly synthesized strand.
Correct answer is: Each daughter DNA contains one original strand and one new strand.
Q.13 Which of the following best explains why DNA polymerase cannot start a new strand de novo?
It requires a 3'‑OH group to add nucleotides.
It needs ATP hydrolysis to function.
It can only synthesize RNA.
It needs a double‑stranded template.
Explanation - DNA polymerase can only extend an existing nucleic acid chain; primase supplies the initial RNA primer with a 3'‑OH.
Correct answer is: It requires a 3'‑OH group to add nucleotides.
Q.14 Which of these nucleotides is NOT found in DNA?
Adenine
Cytosine
Uracil
Guanine
Explanation - Uracil replaces thymine in RNA; DNA contains adenine, thymine, cytosine, and guanine.
Correct answer is: Uracil
Q.15 In prokaryotes, the origin of replication is called:
OriC
Centromere
Telomere
Replication bubble
Explanation - OriC is the specific DNA sequence where replication initiates in bacterial chromosomes.
Correct answer is: OriC
Q.16 Which of the following best describes the function of the sliding clamp (PCNA) in eukaryotes?
It unwinds the DNA double helix.
It holds DNA polymerase onto DNA, increasing processivity.
It synthesizes RNA primers.
It removes RNA primers.
Explanation - PCNA (proliferating cell nuclear antigen) forms a ring around DNA, allowing DNA polymerase to synthesize long stretches without dissociating.
Correct answer is: It holds DNA polymerase onto DNA, increasing processivity.
Q.17 What is the typical length of an Okazaki fragment in eukaryotic cells?
10–20 nucleotides
100–200 nucleotides
1,000–2,000 nucleotides
10,000–20,000 nucleotides
Explanation - Eukaryotic Okazaki fragments are generally 100–200 nucleotides long, shorter than the ~1,000 nucleotides in prokaryotes.
Correct answer is: 100–200 nucleotides
Q.18 Which protein complex recognizes the origin of replication in eukaryotes and assembles the pre‑replication complex?
ORC (Origin Recognition Complex)
RNA polymerase II
Ribosome
Spliceosome
Explanation - ORC binds to replication origins during G1 phase and recruits other factors to form the pre‑replication complex.
Correct answer is: ORC (Origin Recognition Complex)
Q.19 During replication, what is the term for the point where the two replication forks move away from each other?
Replication bubble
Replication fork
Replisome
Origin of replication
Explanation - The replication bubble is the region of unwound DNA containing two forks moving outward from the origin.
Correct answer is: Replication bubble
Q.20 Which of the following is a common cause of replication errors that can lead to mutations?
Misincorporation of nucleotides
Correct base pairing
High fidelity of DNA polymerase
Efficient proofreading
Explanation - If a wrong nucleotide is added and not corrected, it can become a permanent mutation after the next round of replication.
Correct answer is: Misincorporation of nucleotides
Q.21 The enzyme that joins DNA fragments by forming phosphodiester bonds is:
DNA polymerase
DNA helicase
DNA ligase
RNA polymerase
Explanation - DNA ligase catalyzes the formation of phosphodiester bonds, sealing nicks in the DNA backbone.
Correct answer is: DNA ligase
Q.22 What is the effect of telomerase on the ends of linear chromosomes?
It shortens telomeres each division.
It adds repetitive DNA sequences to prevent shortening.
It removes telomeric DNA.
It converts telomeric DNA to RNA.
Explanation - Telomerase extends telomeres using an RNA template, counteracting the end‑replication problem.
Correct answer is: It adds repetitive DNA sequences to prevent shortening.
Q.23 Which of the following statements is true about the leading and lagging strands?
Both are synthesized continuously.
Both are synthesized discontinuously.
Only the lagging strand is synthesized discontinuously.
Only the leading strand is synthesized discontinuously.
Explanation - The lagging strand is synthesized in short Okazaki fragments, while the leading strand is continuous.
Correct answer is: Only the lagging strand is synthesized discontinuously.
Q.24 Which of these proteins is NOT part of the bacterial replisome?
DnaB helicase
DNA polymerase III
RNA polymerase
Primase (DnaG)
Explanation - RNA polymerase synthesizes RNA transcripts, not DNA replication components, whereas the others are core replisome proteins.
Correct answer is: RNA polymerase
Q.25 In which phase of the cell cycle does DNA replication occur?
G1 phase
S phase
G2 phase
M phase
Explanation - S (synthesis) phase is dedicated to DNA replication before the cell proceeds to G2 and mitosis.
Correct answer is: S phase
Q.26 What is the main difference between DNA polymerase I and DNA polymerase III in prokaryotes?
Pol I synthesizes the bulk of DNA; Pol III removes RNA primers.
Pol I removes RNA primers; Pol III performs most DNA synthesis.
Both have identical functions.
Pol III only works on the lagging strand.
Explanation - Pol III is the primary replicative polymerase, while Pol I replaces RNA primers with DNA.
Correct answer is: Pol I removes RNA primers; Pol III performs most DNA synthesis.
Q.27 Which of the following best explains why DNA replication is described as 'bidirectional'?
It proceeds only in one direction from the origin.
Two replication forks move away from each origin in opposite directions.
Replication occurs only on the leading strand.
DNA polymerase can synthesize both 5'→3' and 3'→5' strands.
Explanation - From each origin, two forks are formed, each traveling in opposite directions, enabling rapid duplication of the genome.
Correct answer is: Two replication forks move away from each origin in opposite directions.
Q.28 Which type of mutation is most likely to result from a failure to proofread during DNA replication?
Frameshift mutation
Point mutation (base substitution)
Chromosomal translocation
Gene duplication
Explanation - Proofreading primarily corrects misincorporated bases; its failure often leads to single‑base substitutions.
Correct answer is: Point mutation (base substitution)
Q.29 The enzyme that synthesizes the RNA primer during replication is:
DNA polymerase
Primase
Ligase
Topoisomerase
Explanation - Primase is an RNA polymerase that creates a short RNA primer for DNA polymerase to extend.
Correct answer is: Primase
Q.30 Which of the following is true about the fidelity of DNA replication in eukaryotes?
Error rate is about 1 in 10 nucleotides.
Proofreading reduces errors to ~1 in 10⁴, and mismatch repair lowers it further to ~1 in 10⁹.
DNA polymerases have no proofreading activity.
Mismatch repair works before DNA polymerase adds nucleotides.
Explanation - Combined proofreading and mismatch repair provide high replication accuracy, roughly one mistake per billion nucleotides added.
Correct answer is: Proofreading reduces errors to ~1 in 10⁴, and mismatch repair lowers it further to ~1 in 10⁹.
Q.31 Which of the following nucleic acid structures is formed temporarily during lagging‑strand synthesis?
RNA–DNA hybrid (Okazaki fragment junction)
Triple helix
DNA–RNA hybrid telomere
G‑quadruplex
Explanation - When an RNA primer is attached to a new Okazaki fragment, a short RNA‑DNA hybrid region exists until the primer is removed.
Correct answer is: RNA–DNA hybrid (Okazaki fragment junction)
Q.32 Which of the following best describes the term 'origin of replication' in eukaryotes?
A single site per chromosome.
Multiple sites where DNA synthesis initiates.
The telomeric region only.
A protein complex that degrades DNA.
Explanation - Eukaryotic chromosomes contain many origins to ensure complete replication within a reasonable time.
Correct answer is: Multiple sites where DNA synthesis initiates.
Q.33 In the context of DNA replication, what does the term 'processivity' refer to?
The speed at which DNA unwinds.
The number of nucleotides added before the polymerase dissociates.
The accuracy of base pairing.
The ability to proofread mismatches.
Explanation - High processivity means a polymerase can synthesize long stretches of DNA without falling off the template.
Correct answer is: The number of nucleotides added before the polymerase dissociates.
Q.34 Which of the following DNA polymerases is primarily responsible for DNA repair rather than replication?
DNA polymerase α
DNA polymerase β
DNA polymerase δ
DNA polymerase ε
Explanation - Pol β participates mainly in base excision repair pathways, filling short gaps left after damaged bases are removed.
Correct answer is: DNA polymerase β
Q.35 What is the 'end‑replication problem' and how is it resolved?
DNA polymerase cannot replicate the leading strand; solved by helicase.
RNA primers cannot be placed at the very end of chromosomes; solved by telomerase.
Topoisomerase cannot relieve supercoiling at telomeres; solved by ligase.
Replication forks cannot form at telomeres; solved by origins of replication.
Explanation - Because DNA polymerase needs a primer, the extreme 3' end would be lost each division; telomerase extends telomeres to prevent loss.
Correct answer is: RNA primers cannot be placed at the very end of chromosomes; solved by telomerase.
Q.36 Which of the following statements about DNA replication timing is correct?
All origins fire simultaneously.
Origins fire at random times throughout S phase.
Origins fire in a regulated, sequential manner, with early‑replicating regions often being gene‑rich.
Replication timing is not regulated.
Explanation - Replication timing is developmentally regulated; early‑firing origins tend to be in transcriptionally active regions.
Correct answer is: Origins fire in a regulated, sequential manner, with early‑replicating regions often being gene‑rich.
Q.37 Which of the following is NOT a typical feature of a prokaryotic replication origin (oriC)?
AT‑rich region
DnaA binding sites
Multiple replication forks
Single circular DNA molecule
Explanation - Bacterial oriC typically initiates a single bidirectional replication; multiple forks arise later as the replication proceeds.
Correct answer is: Multiple replication forks
Q.38 During replication, the 'lagging strand template' runs in which direction relative to the replication fork movement?
5'→3'
3'→5'
Both directions simultaneously
It does not have a defined direction.
Explanation - The lagging strand template is oriented 3'→5' relative to fork progression, requiring synthesis of short fragments in the opposite direction.
Correct answer is: 3'→5'
Q.39 Which of the following best describes a 'replication fork barrier' (RFB)?
A sequence that enhances helicase activity.
A protein complex that blocks fork progression to regulate replication timing.
A region where DNA polymerase initiates synthesis.
A telomeric DNA repeat.
Explanation - RFBs are used in certain organisms (e.g., yeast rDNA) to prevent collisions between replication and transcription machinery.
Correct answer is: A protein complex that blocks fork progression to regulate replication timing.
Q.40 What is the role of the MCM complex in eukaryotic DNA replication?
It synthesizes RNA primers.
It serves as the replicative helicase, unwinding DNA.
It ligates Okazaki fragments.
It removes mismatched bases.
Explanation - The MCM (Mini‑Chromosome Maintenance) complex forms the core helicase that unwinds DNA at replication forks.
Correct answer is: It serves as the replicative helicase, unwinding DNA.
Q.41 Which of the following statements about DNA polymerase fidelity is FALSE?
Proofreading occurs via a 3'→5' exonuclease activity.
Polymerases have an intrinsic error rate of about 1 in 10⁴ without proofreading.
DNA polymerase can add nucleotides without a template strand.
Mismatch repair further reduces replication errors.
Explanation - DNA polymerases require a complementary template; template‑independent synthesis is characteristic of terminal transferases, not replicative polymerases.
Correct answer is: DNA polymerase can add nucleotides without a template strand.
Q.42 In eukaryotes, which DNA polymerase is primarily responsible for initiating synthesis on both leading and lagging strands?
DNA polymerase α
DNA polymerase β
DNA polymerase δ
DNA polymerase ε
Explanation - Pol α, in complex with primase, synthesizes a short RNA‑DNA primer on both strands before handing off to Pol δ (lagging) or Pol ε (leading).
Correct answer is: DNA polymerase α
Q.43 What is the function of the protein RPA (Replication Protein A) during DNA replication?
It ligates DNA fragments.
It stabilizes single‑stranded DNA.
It synthesizes RNA primers.
It removes RNA primers.
Explanation - RPA binds to and protects ssDNA generated by helicase, preventing secondary structures and nucleolytic degradation.
Correct answer is: It stabilizes single‑stranded DNA.
Q.44 Which of the following best explains why DNA replication is faster in prokaryotes than in eukaryotes?
Prokaryotes have multiple origins of replication.
Prokaryotes lack histones and thus have less chromatin compaction.
Eukaryotic DNA polymerases are slower.
Prokaryotes replicate only one strand.
Explanation - The lack of nucleosomes in bacteria allows helicase and polymerases to access DNA more readily, speeding replication.
Correct answer is: Prokaryotes lack histones and thus have less chromatin compaction.
Q.45 During the S phase checkpoint, which kinase primarily monitors replication stress and halts cell cycle progression if needed?
Cyclin‑dependent kinase 1 (CDK1)
ATM kinase
ATR kinase
Chk2 kinase
Explanation - ATR detects single‑stranded DNA at stalled forks and activates downstream effectors to pause replication.
Correct answer is: ATR kinase
Q.46 Which of these mechanisms helps to resolve the supercoiling that builds up ahead of the replication fork?
DNA polymerase activity
Helicase activity
Topoisomerase activity
Ligase activity
Explanation - Topoisomerases cut one or both DNA strands, allow rotation to relieve supercoils, and then reseal the DNA.
Correct answer is: Topoisomerase activity
Q.47 In the bacterial replisome, which protein is responsible for coordinating the synthesis of the leading and lagging strands?
DnaB helicase
Tau subunit of DNA polymerase III
Primase (DnaG)
DNA ligase
Explanation - The τ subunit bridges the polymerase cores for leading and lagging strand synthesis, synchronizing their activity.
Correct answer is: Tau subunit of DNA polymerase III
Q.48 Which of the following best describes the 'mismatch repair' (MMR) system?
It corrects errors made during transcription.
It removes and replaces misincorporated nucleotides after DNA replication.
It adds telomeric repeats to chromosome ends.
It joins Okazaki fragments.
Explanation - MMR detects base mismatches and small insertion/deletion loops, excising the erroneous segment and filling it correctly.
Correct answer is: It removes and replaces misincorporated nucleotides after DNA replication.
Q.49 What is the main reason that DNA polymerases synthesize DNA only in the 5'→3' direction?
The phosphodiester bond formation requires a 3'‑OH group on the primer.
The 5'‑phosphate group is more reactive.
DNA strands are inherently 5'→3' only.
RNA primers are only 5'‑phosphorylated.
Explanation - DNA polymerases add nucleotides to the free 3'‑OH of the growing strand, dictating 5'→3' synthesis.
Correct answer is: The phosphodiester bond formation requires a 3'‑OH group on the primer.
Q.50 During replication, the term 'replication fork stalling' most often results from:
Excessive helicase activity.
DNA lesions such as thymine dimers.
Abundant dNTPs.
High processivity of DNA polymerase.
Explanation - DNA damage can block polymerase progression, causing the fork to stall and requiring repair pathways.
Correct answer is: DNA lesions such as thymine dimers.
Q.51 Which of the following statements about the 'sliding clamp' is correct?
It hydrolyzes ATP to unwind DNA.
It forms a closed ring around DNA to increase polymerase processivity.
It removes RNA primers.
It initiates the formation of replication origins.
Explanation - The sliding clamp (β‑clamp in bacteria, PCNA in eukaryotes) encircles DNA, allowing polymerase to remain attached during synthesis.
Correct answer is: It forms a closed ring around DNA to increase polymerase processivity.
Q.52 In which cellular organelle does mitochondrial DNA replication occur?
Nucleus
Mitochondrion
Chloroplast
Endoplasmic reticulum
Explanation - Mitochondria contain their own circular genome that replicates independently of nuclear DNA.
Correct answer is: Mitochondrion
Q.53 What is the primary difference between leading‑strand DNA polymerase and lagging‑strand DNA polymerase in prokaryotes?
Leading‑strand polymerase has 5'→3' activity; lagging has 3'→5' activity.
They are the same enzyme (DNA polymerase III) but function in different contexts.
Leading‑strand polymerase synthesizes RNA; lagging synthesizes DNA.
Lagging‑strand polymerase also acts as helicase.
Explanation - DNA polymerase III performs synthesis on both strands; its behavior differs due to the orientation of the template.
Correct answer is: They are the same enzyme (DNA polymerase III) but function in different contexts.
Q.54 Which of the following statements accurately describes the role of DNA polymerase ε (epsilon) in eukaryotes?
It initiates DNA synthesis on the lagging strand.
It is the primary polymerase for leading‑strand synthesis.
It removes RNA primers.
It repairs double‑strand breaks.
Explanation - Pol ε works mainly on the leading strand after the primer is laid down by Pol α.
Correct answer is: It is the primary polymerase for leading‑strand synthesis.
Q.55 The 'origin recognition complex' (ORC) binds to DNA during which phase of the cell cycle?
M phase
G1 phase
S phase
G2 phase
Explanation - ORC binds origins in G1, licensing them for activation in S phase.
Correct answer is: G1 phase
Q.56 Which of the following is NOT a typical feature of eukaryotic DNA replication origins?
AT‑rich sequences
Presence of ORC binding sites
Single origin per chromosome
Association with nucleosome‑free regions
Explanation - Eukaryotic chromosomes possess many origins to ensure timely replication.
Correct answer is: Single origin per chromosome
Q.57 During DNA replication, what is a 'replication bubble'?
A region where DNA is tightly coiled.
A double‑stranded region awaiting transcription.
A locally unwound region containing two replication forks.
A protein complex that synthesizes RNA primers.
Explanation - The bubble forms as helicase unwinds DNA, allowing synthesis to occur bidirectionally.
Correct answer is: A locally unwound region containing two replication forks.
Q.58 In the context of DNA replication fidelity, what does the term 'mutational hot‑spot' refer to?
A region where DNA polymerase cannot bind.
A DNA sequence that is prone to frequent mutations.
A location where DNA is never replicated.
A site where telomerase is most active.
Explanation - Hot‑spots are often repetitive or have secondary structures that increase replication errors.
Correct answer is: A DNA sequence that is prone to frequent mutations.
Q.59 Which enzyme is primarily responsible for sealing nicks after RNA primer removal on the lagging strand in eukaryotes?
DNA polymerase δ
DNA ligase I
DNA helicase
Primase
Explanation - Ligase I joins the newly synthesized DNA fragments, completing the lagging strand.
Correct answer is: DNA ligase I
Q.60 What distinguishes the 'replicative helicase' in eukaryotes from that in prokaryotes?
Eukaryotic helicase is a single protein; prokaryotic helicase is a complex.
Eukaryotic helicase (MCM2‑7) is a hexameric ring; bacterial DnaB is a hexameric helicase but functions differently.
Prokaryotic helicase requires ATP; eukaryotic helicase does not.
Both helicases are identical in structure and function.
Explanation - While both are hexameric, the eukaryotic MCM complex has additional regulatory subunits and interacts with Cdc45 and GINS to form the CMG helicase.
Correct answer is: Eukaryotic helicase (MCM2‑7) is a hexameric ring; bacterial DnaB is a hexameric helicase but functions differently.
Q.61 Which of the following best explains why DNA replication is highly coordinated with transcription in eukaryotic cells?
Both processes use the same polymerase.
Replication forks are blocked by active transcription units to avoid collisions.
Transcription occurs only after replication is complete.
DNA replication does not interact with transcription.
Explanation - Cells employ mechanisms (e.g., R-loop resolution, replication fork barriers) to prevent interference between replication and transcription machinery.
Correct answer is: Replication forks are blocked by active transcription units to avoid collisions.
Q.62 In which of the following scenarios would you expect an increased usage of translesion synthesis (TLS) polymerases?
During normal, error‑free DNA replication.
When the replication fork encounters DNA damage that blocks high‑fidelity polymerases.
During telomere elongation by telomerase.
During RNA transcription.
Explanation - TLS polymerases can synthesize past lesions but are error‑prone, acting as a backup when normal polymerases stall.
Correct answer is: When the replication fork encounters DNA damage that blocks high‑fidelity polymerases.
Q.63 Which of the following proteins is essential for loading the sliding clamp onto DNA in eukaryotes?
RFC (Replication Factor C)
PCNA
RPA
MCM
Explanation - RFC acts as a clamp loader, opening PCNA and placing it around DNA.
Correct answer is: RFC (Replication Factor C)
Q.64 What is the primary source of deoxyribonucleotide triphosphates (dNTPs) for DNA synthesis?
Ribonucleotide reductase converting ribonucleotides to deoxyribonucleotides.
RNA polymerase synthesizing dNTPs.
DNA ligase breaking down nucleotides.
Telomerase extending telomeres.
Explanation - RNR reduces ribonucleoside diphosphates to deoxyribonucleoside diphosphates, which are then phosphorylated to dNTPs.
Correct answer is: Ribonucleotide reductase converting ribonucleotides to deoxyribonucleotides.
Q.65 Which of the following best describes the 'replication fork reversal' mechanism?
The fork splits into two separate forks.
The fork collapses and the DNA is degraded.
The newly synthesized strands anneal, forming a four‑way junction to protect the fork.
The replication machinery moves backward.
Explanation - Fork reversal creates a chicken‑foot structure, allowing repair proteins to access lesions and stabilize the replication machinery.
Correct answer is: The newly synthesized strands anneal, forming a four‑way junction to protect the fork.
Q.66 Which of the following is a key difference between bacterial and eukaryotic DNA replication speed?
Bacteria replicate at ~1000 nucleotides per second; eukaryotes at ~50 nucleotides per second.
Eukaryotes replicate faster due to multiple origins.
Bacteria replicate slower because they have a single origin.
Both replicate at the same speed.
Explanation - Prokaryotic polymerases operate at a higher rate, but eukaryotes compensate with many origins.
Correct answer is: Bacteria replicate at ~1000 nucleotides per second; eukaryotes at ~50 nucleotides per second.
Q.67 What is the function of the protein 'Cdc45' in the eukaryotic replication complex?
It acts as a helicase.
It loads the sliding clamp.
It forms part of the CMG helicase complex, helping to unwind DNA.
It removes RNA primers.
Explanation - Cdc45 associates with MCM and GINS to create the active helicase complex (CMG).
Correct answer is: It forms part of the CMG helicase complex, helping to unwind DNA.
Q.68 Which of the following best explains why the leading strand does not require Okazaki fragments?
It is synthesized in the 3'→5' direction.
It is synthesized continuously because the DNA polymerase can follow the replication fork.
It does not need a primer.
It is synthesized by RNA polymerase.
Explanation - The leading strand template runs 3'→5' toward the fork, allowing continuous synthesis in the 5'→3' direction.
Correct answer is: It is synthesized continuously because the DNA polymerase can follow the replication fork.
Q.69 During DNA replication, what is the significance of the 'origin recognition complex' (ORC) being bound to chromatin throughout the cell cycle?
It constantly synthesizes DNA.
It ensures that origins are licensed only once per cell cycle.
It degrades dNTPs.
It acts as a transcription factor.
Explanation - Persistent ORC binding helps prevent re‑licensing of origins, maintaining genomic stability.
Correct answer is: It ensures that origins are licensed only once per cell cycle.
Q.70 Which of the following enzymes is primarily responsible for extending the RNA primer with DNA nucleotides on the lagging strand in eukaryotes?
DNA polymerase α
DNA polymerase δ
DNA polymerase ε
DNA ligase I
Explanation - Pol δ extends the RNA primer synthesized by Pol α, performing bulk synthesis of the lagging strand.
Correct answer is: DNA polymerase δ
Q.71 What is the main purpose of the 'GINS' complex in eukaryotic DNA replication?
To synthesize RNA primers.
To load the sliding clamp.
To stabilize the CMG helicase and aid its activity.
To ligate DNA fragments.
Explanation - GINS (Go-Ichi-Ni-San) partners with MCM and Cdc45, forming the active helicase complex.
Correct answer is: To stabilize the CMG helicase and aid its activity.
Q.72 Which of the following best describes the role of the 'single‑strand binding protein' (SSB) in bacteria?
It synthesizes DNA.
It prevents the re‑annealing of separated DNA strands.
It joins Okazaki fragments.
It removes RNA primers.
Explanation - SSB binds ssDNA, protecting it from nucleases and secondary structures during replication.
Correct answer is: It prevents the re‑annealing of separated DNA strands.
Q.73 In eukaryotic cells, which checkpoint kinase is directly activated by the accumulation of single‑stranded DNA at stalled forks?
Chk1
Chk2
ATR
ATM
Explanation - ATR responds to ssDNA coated with RPA, phosphorylating downstream effectors to halt cell‑cycle progression.
Correct answer is: ATR
Q.74 Which of the following processes can generate a 'DNA hairpin' structure that hinders replication?
High GC content causing stable secondary structures.
Presence of telomeric repeats.
Transcription of non‑coding RNAs.
All of the above.
Explanation - Sequences rich in GC or repetitive motifs can fold into hairpins, creating obstacles for polymerases.
Correct answer is: All of the above.
Q.75 What is the main advantage of having multiple origins of replication in eukaryotic chromosomes?
It allows simultaneous transcription and replication.
It reduces the time required to replicate the entire genome.
It prevents telomere shortening.
It eliminates the need for DNA ligase.
Explanation - Multiple origins enable concurrent replication forks, shortening S‑phase duration.
Correct answer is: It reduces the time required to replicate the entire genome.
Q.76 During DNA replication, what is the functional consequence of a mutation that disables the 3'→5' exonuclease activity of DNA polymerase?
Increased replication speed.
Higher error rate due to loss of proofreading.
Inability to add nucleotides.
Complete halt of replication.
Explanation - The exonuclease activity removes misincorporated nucleotides; its loss leads to more mutations.
Correct answer is: Higher error rate due to loss of proofreading.
Q.77 Which enzyme fills in the gaps after RNA primer removal on the lagging strand in prokaryotes?
DNA polymerase I
DNA polymerase III
DNA ligase
Primase
Explanation - Pol I has 5'→3' exonuclease activity to remove primers and polymerase activity to replace them with DNA.
Correct answer is: DNA polymerase I
Q.78 What does the term 'replication licensing' refer to?
The process of adding telomeres.
The loading of MCM helicase onto origins during G1 phase.
The synthesis of RNA primers.
The removal of DNA polymerase after replication.
Explanation - Licensing ensures that each origin fires only once per cell cycle, preventing re‑replication.
Correct answer is: The loading of MCM helicase onto origins during G1 phase.
Q.79 In which cellular compartment does DNA replication of the chloroplast genome occur?
Nucleus
Mitochondria
Chloroplast stroma
Cytoplasm
Explanation - Chloroplasts contain their own circular DNA that replicates within the stromal matrix.
Correct answer is: Chloroplast stroma
Q.80 Which of the following proteins is directly responsible for the removal of RNA primers during eukaryotic lagging‑strand synthesis?
DNA polymerase α
DNA polymerase ε
Flap endonuclease 1 (FEN1)
DNA ligase I
Explanation - FEN1 cuts off the RNA‑DNA flap generated when DNA polymerase δ displaces the RNA primer, allowing ligation.
Correct answer is: Flap endonuclease 1 (FEN1)
Q.81 What is the primary cause of the 'lagging‑strand synthesis problem'?
The antiparallel nature of DNA.
Lack of DNA polymerase.
Absence of ATP.
Overabundance of dNTPs.
Explanation - Because DNA polymerase can only synthesize 5'→3', the lagging strand must be made in short fragments that are later joined.
Correct answer is: The antiparallel nature of DNA.
Q.82 Which of the following best describes a 'replication fork barrier' (RFB) in yeast rDNA?
A DNA sequence that accelerates fork progression.
A protein complex that halts fork movement to prevent collisions with transcription machinery.
A telomeric repeat that blocks replication.
A site where DNA polymerase initiates synthesis.
Explanation - RFBs protect highly transcribed regions by temporarily stopping replication forks.
Correct answer is: A protein complex that halts fork movement to prevent collisions with transcription machinery.
Q.83 During S phase, which cyclin‑dependent kinase (CDK) activity is essential for the activation of replication origins?
CDK1/Cyclin B
CDK2/Cyclin E
CDK4/Cyclin D
CDK9/Cyclin T
Explanation - CDK2/Cyclin E phosphorylates components of the pre‑replication complex, triggering origin firing.
Correct answer is: CDK2/Cyclin E
Q.84 Which of the following statements about DNA replication in viruses is true?
All viruses use host DNA polymerase.
RNA viruses never replicate their genomes using DNA intermediates.
Some DNA viruses encode their own DNA polymerases.
Viral genomes are always double‑stranded.
Explanation - Large DNA viruses (e.g., poxviruses) carry genes for their own replication machinery.
Correct answer is: Some DNA viruses encode their own DNA polymerases.
Q.85 Which of the following best explains why the mitochondrial DNA polymerase (Pol γ) has a higher error rate than nuclear DNA polymerases?
Pol γ lacks proofreading activity.
Mitochondrial DNA lacks histones, exposing it to damage.
The mitochondrial environment has higher ROS levels leading to damage.
Pol γ is more processive, causing more errors.
Explanation - The absence of protective nucleosomes and higher oxidative stress increase mutation rates in mitochondrial DNA.
Correct answer is: Mitochondrial DNA lacks histones, exposing it to damage.
Q.86 What is the primary function of the 'primase' component of DNA polymerase α in eukaryotes?
It adds DNA nucleotides to the primer.
It synthesizes a short RNA primer (~10 nucleotides).
It removes RNA primers.
It ligates DNA fragments.
Explanation - Primase part of Pol α makes the RNA primer that DNA polymerases δ and ε extend.
Correct answer is: It synthesizes a short RNA primer (~10 nucleotides).
Q.87 Which of the following best describes the 'end‑replication problem'?
DNA polymerase cannot replicate the leading strand.
RNA primers cannot be placed at the very ends of linear chromosomes.
Topoisomerases cannot relieve supercoiling at telomeres.
Replication forks cannot be formed at telomeres.
Explanation - Because DNA polymerase needs a primer, the extreme 3' end would be lost each division; telomerase restores these ends.
Correct answer is: RNA primers cannot be placed at the very ends of linear chromosomes.
Q.88 Which of the following enzymes is responsible for adding nucleotides to the 3' end of a growing DNA strand?
DNA helicase
DNA polymerase
RNA polymerase
DNA ligase
Explanation - DNA polymerase catalyzes the addition of deoxynucleotides to the 3'‑OH of the primer or nascent strand.
Correct answer is: DNA polymerase
Q.89 What does the term 'semiconservative' refer to in DNA replication?
Both daughter DNA molecules are completely new.
Each daughter molecule retains one original strand and receives one new strand.
One daughter DNA is old, the other is new.
DNA replication conserves the parental DNA without change.
Explanation - Semiconservative replication preserves one parental strand in each daughter helix.
Correct answer is: Each daughter molecule retains one original strand and receives one new strand.
Q.90 Which of the following proteins directly binds to the origin of replication in eukaryotic cells?
RNA polymerase II
Origin Recognition Complex (ORC)
DNA ligase
Topoisomerase II
Explanation - ORC recognizes specific DNA sequences at origins and recruits other replication factors.
Correct answer is: Origin Recognition Complex (ORC)
Q.91 During DNA replication, the lagging strand is synthesized in a direction opposite to the movement of the replication fork. This is achieved by:
Continuous synthesis by DNA polymerase.
Synthesis of short Okazaki fragments that are later joined.
Using RNA polymerase instead of DNA polymerase.
Reverse transcription.
Explanation - Okazaki fragments allow synthesis opposite to fork progression; DNA ligase later joins them.
Correct answer is: Synthesis of short Okazaki fragments that are later joined.
Q.92 Which of the following enzymes has both polymerase and 5'→3' exonuclease activities in prokaryotes?
DNA polymerase I
DNA polymerase III
DNA helicase
DNA ligase
Explanation - Pol I can add nucleotides and remove RNA primers via its 5'→3' exonuclease activity.
Correct answer is: DNA polymerase I
Q.93 The presence of which DNA secondary structure can stall replication forks and lead to genome instability?
Z‑DNA
G‑quadruplexes
A‑DNA
B‑DNA
Explanation - G‑quadruplexes formed by guanine‑rich sequences can impede polymerases and need specialized helicases to resolve.
Correct answer is: G‑quadruplexes