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2.1 Prokaryotic Replication β Test 1
Q1. 5'β3' exonuclease activity is exhibited by which DNA polymerase?β I
Q2. All DNA polymerases are template-dependent, EXCEPT:β Terminal transferase
Q3. In bacteria, which enzyme removes the RNA primer at the start of each Okazaki fragment?β DNA polymerase I
Q4. Which technique did Meselson and Stahl use to demonstrate semiconservative replication?β Density gradient (CsCl) centrifugation
Q5. Reducing PCR primers from 13-mer to 6-mer would most likely cause:β Several non-specific fragments are amplified
Q6. To amplify a product specific to cDNA (not contaminating genomic DNA), design primers:β Spanning an exon-exon boundary (exon junction)
Q7. A chaperone-type protein found in E. coli replication is:β DnaC
Q8. Which set of activities is present in DNA polymerase I?β 5'β3' polymerase and 3'β5' exonuclease (and 5'β3' exonuclease)
Q9. An expression vector does NOT necessarily contain:β Inverted repeats
Q10. If bidirectional replication of a chromosome takes 40 min, unidirectional replication would take:β 80 min
Q11. Copying errors during replication are corrected by the proofreading activity that recognizes incorrect bases:β At the 3' end of the growing chain, removed by 3'β5' exonuclease
Q12. Correct order of events on the lagging strand: (1) phosphodiester bond by DNA pol, (2) SSB binding, (3) helicase separation, (4) exonuclease processing, (5) RNA primer by primase.β 3,2,5,1,4
Q13. Which enzyme relaxes supercoiled DNA?β Type-I topoisomerase
Q14. DNA polymerase I of E. coli exhibits all the following EXCEPT:β 5'β3' RNA-dependent DNA polymerase
Q15. DNA polymerase is involved in:β DNA duplication (replication)
Q16. DNA replication in mitochondria is also known as:β D-loop replication
Q17. During DNA replication, the two strands are separated by:β DNA helicase
Q18. During replication, RNase H removes all of the RNA primer except the ribonucleotide directly linked to DNA because it:β Only cleaves bonds between two ribonucleotides
Q19. E. coli completes replication in 40 min; genome MW β 2.6Γ10βΉ (β4Γ10βΆ bp). The average fork rate (nucleotides/sec per fork) is about:β 7200
2.1 Prokaryotic Replication β Test 2
Q20. E. coli divides every ~20 min although replication takes 40 min because:β A second round of replication begins before the first finishes (multifork replication)
Q21. Regarding supercoiling removal at the fork, which statements are all correct? A) supercoils accumulate from helicase unwinding; C) topoisomerases remove supercoils by breaking one or both strands ahead of the fork; D) both topo I and topo II can remove positive supercoils.β A, C, D
Q22. For 5'-GGAACCTT......GATCGATC-3', a valid forward (FP) and reverse (RP) primer pair for PCR is:β FP: 5'-GGAACCTT and RP: 5'-GATCGATC
Q23. Match enzymes to functions β DNA pol I, primase, helicase, gyrase with: unzipping helix, supercoiling control, removing primer/closing gaps, synthesizing RNA primer.β Pol Iβremove primer/close gaps, primaseβRNA primer, helicaseβunzip, gyraseβsupercoiling
Q24. All T are labeled with Β³H and all C with Β³Β²P. The DNA is incubated with DNA polymerase I and only dTTP. What happens to Β³H and Β³Β²P?β Β³H reduces, Β³Β²P unchanged
Q25. In E. coli, which enzyme synthesizes the RNA primer for Okazaki fragments?β DnaG (primase)
Q26. In an in-vitro replication setup, which omissions block DNA synthesis? I. No ligase, II. No primase, III. only dNTPs (no NTPs), IV. no DNA polymerase.β II, III, IV
Q27. The Klenow fragment is derived from:β DNA polymerase I
Q28. Which stable isotope did Meselson and Stahl use to label DNA?β ΒΉβ΅N
Q29. Which activity is NOT performed by bacterial DNA polymerase I?β 3'β5' polymerase
Q30. Order of proteins added during prokaryotic replication-initiation complex formation: P=DnaB, Q=primase, R=Pol III, S=SSB, T=DnaA.β T-P-S-Q-R
Q31. The origin of replication (oriC) is characterized by:β AT-rich sequences
Q32. Primase is best described as:β DNA-dependent RNA polymerase
Q33. The proofreading activity of DNA polymerase is:β 3'β5' exonuclease activity
Q34. Which protein(s) have BOTH polymerase and nuclease activities? i) Pol III, ii) RNA polymerase, iii) ribozymes, iv) Pol I.β i and iv only
Q35. Reaction essential for proofreading during replication by DNA polymerase III:β 3'β5' exonuclease
Q36. Which statements are true for bacterial DNA replication?β RNA primer required to initiate synthesis
Q37. Terminal deoxynucleotidyl transferase (TdT) catalyses:β Addition of nucleotides to the 3' terminus of DNA
2.1 Prokaryotic Replication β Test 3
Q38. Terminal transferase catalyses the addition of:β Deoxynucleotide to the 3'-OH end
Q39. The enzyme Sequenase used in DNA sequencing has:β High processivity (modified T7 DNA polymerase, no 3'β5' exo)
Q40. The enzyme that synthesizes DNA from an mRNA template is:β Reverse transcriptase
Q41. The Klenow fragment is derived from E. coli DNA polymerase:β I
Q42. The lagging strand is synthesized in short pieces because:β DNA polymerase synthesizes only 5'β3'
Q43. Okazaki fragments of the lagging strand are joined by:β DNA ligase
Q44. The primary mechanism by which DNA polymerase ensures replication fidelity is:β Complementary base pairing plus 3'β5' proofreading
Q45. The RNA primers used to initiate replication in E. coli are:β Removed by DNA polymerase I via nick translation
Q46. The substrate(s) for primase is/are:β NTPs (ribonucleotides)
Q47. Two DNA fragments can be covalently joined by:β DNA ligase
Q48. The function of DNA gyrase is to:β Reduce torsional strain (supercoiling) ahead of the fork
Q49. If the dideoxynucleotide concentration is too high in chain-termination sequencing:β Very short molecules dominate; little long-range sequence
Q50. When PCR amplifies the region OUTSIDE the primers (around a circularized template) it is called:β Inverse PCR
Q51. Which enzyme forms the covalent bond between two restriction fragments?β DNA ligase
Q52. Which isotope labeled DNA in the proof of semiconservative replication?β ΒΉβ΅N
Q53. Which activities are present in DNA polymerase I (select the complete set)?β 5'β3' polymerase, 3'β5' exonuclease, 5'β3' exonuclease
Q54. Which feature is NOT correct for a typical plasmid vector?β Can express very high-molecular-weight proteins / carry very large inserts
Q55. Which statement is NOT applicable to DNA topoisomerase?β Its active-site tyrosine is phosphorylated during catalysis
Q56. Which is NOT involved in lagging-strand synthesis?β RNase A
2.1 Prokaryotic Replication β Test 4
Q57. Which component is NOT required for PCR?β Dideoxy-dNTPs (ddNTPs)
Q58. Which reaction mixture gives the desired PCR product?β Primers, dNTPs, template, Taq DNA polymerase
Q59. Which reaction is required for proofreading by DNA polymerase III?β 3'β5' exonuclease
Q60. Which stable isotope was used to show DNA replicates semiconservatively?β ΒΉβ΅N
Q61. Which statements about DNA replication are true? (best single answer)β 5'β3' exonuclease of DNA polymerase removes the RNA primer; helicases unwind DNA
Q62. Which statements about the E. coli chromosome are correct? I) single replicon, II) replication begins at oriC, III) replication can start anywhere, IV) a single fork moves around.β I and II
Q63. Which technique maps the transcription start site of a gene?β Primer extension
Q64. Which enzyme is used for 5'-end labeling of DNA with Ξ³-Β³Β²P-ATP?β T4 polynucleotide kinase
Q65. Which isotope was used to label DNA in the proof of semiconservative replication (repeat context)?β ΒΉβ΅N
Q66. Which reaction is essential for proofreading during replication by DNA polymerase III (variant)?β 3'β5' exonuclease
Q67. Which reaction is required during DNA replication by DNA polymerase III for synthesis?β 5'β3' polymerase
Q68. Order of proteins in the prokaryotic replication-initiation complex (variant): P=DnaB, Q=primase, R=Pol III, S=SSB, T=DnaA.β T-P-S-Q-R
Q69. Which protein separates the two interlinked daughter chromosomes when E. coli replication terminates?β Topoisomerase IV
Q70. Which statement about the E. coli chromosome is correct (variant)? I) single replicon, II) begins at oriC, III) any-point start, IV) single fork.β I and II
Q71. Which statement regarding DNA replication is correct?β Leading strand requires one RNA primer
Q72. Who established that DNA, not protein, is the genetic material (using Β³Β²P/Β³β΅S-labeled phage)?β Hershey and Chase
Q73. An E. coli mutant polymerase shows an error rate of 10β»Β³ instead of 10β»βΆ. Which activity is it most likely missing?β 3'β5' exonuclease (proofreading)
Q74. The drug that selectively inhibits eukaryotic replicative DNA polymerases and blocks DNA synthesis is:β Aphidicolin
2.1 Prokaryotic Replication β Test 5
Q75. The optimum temperature for Taq DNA polymerase in PCR is about:β 72Β°C
Q76. Selective degradation of single-stranded DNA is carried out by:β S1 nuclease
Q77. The E. coli DNA polymerase with the highest fidelity replicative role and 3'β5' exonuclease used as the main replicase is:β DNA polymerase III
Q78. Why are ribonucleotides (rNTPs) incorporated into DNA at a much lower rate than dNTPs by DNA polymerase?β The nucleotide-binding pocket discriminates against the 2'-OH (steric/sugar selectivity)
Q79. When the nucleus of a non-dividing frog red blood cell is transplanted into an enucleated frog egg, the egg divides. Best interpretation:β The egg cytoplasm controls/reactivates nuclear DNA synthesis
Q80. Mechanism of gene regulation does NOT include:β Rate of DNA replication
Q81. Gene regulation excludes which of the following?β DNA replication
Q82. The Hershey-Chase experiment proved that:β DNA is the genetic material of the virus
Q83. In the lysogenic state of phage Ξ»:β CI (repressor) is on while Cro is off
Q84. Regarding the screw sense (handedness) of A-, B- and Z-DNA:β A and B are both right-handed
Q85. Selective inhibition by aphidicolin targets which process, helping define replicative polymerases?β Replicative DNA synthesis (Pol Ξ±/Ξ΄/Ξ΅)
Q86. A drug that blocks DNA polymerase activity would directly interfere with:β Continued replicative DNA synthesis
Q87. DNA gyrase introduces which kind of supercoils, aiding replication and compaction?β Negative supercoils (ATP-dependent)
Q88. The Ξ²-clamp (sliding clamp) of E. coli Pol III functions to:β Increase processivity by tethering the polymerase to DNA
Q89. SSB (single-strand binding protein) functions during replication to:β Coat and stabilize exposed single strands, preventing reannealing/secondary structure
Q90. In E. coli, the initiator protein that binds oriC and triggers origin melting is:β DnaA
Q91. The leading strand differs from the lagging strand in that it is:β Synthesized continuously in the direction of fork movement
Q92. Nick translation, used to label DNA probes, exploits which two activities of DNA polymerase I?β 5'β3' exonuclease and 5'β3' polymerase
Q93. Which best describes the role of DnaB in E. coli replication?β Replicative helicase that unwinds DNA at the fork