Quiz 9 (L8 CH 9) - Dr. Kudus This is the answer sheet to the multiple choice questions. Many have PDF

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Dr. Kudus
This is the answer sheet to the multiple choice questions. Many have been repeated each year, and it gives an explanation as to why the correct answer is correct. These can be brought into the test and many test questions may be similar to the MCI's. These have been filled in by st...

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Quiz 9 (L8 CH 9) ANSWERS (Mark other answer if there is a discrepancy, please leave a comment for your discrepancy) 1. Which of the following is necessary for DNA replication in test tubes (i.e. by PCR)? A. Topoisomerase B. Helicase C. Primase D. Primers E. SSB 2. Which of the following are necessary for DNA replication regardless of the system? A. dNTPs B. Primers C. A DDDP D. DNA template E. All these items 3. Which of the following is the actual substrate of a DNA-dependent DNA polymerase (DDDP)? A. ssDNA hybridized to a primer with an open 3'OH B. RNA primers attached to dsDNA C. ssDNA covered by SSB D. dsDNA E. NTPs 4. What appears to be the actual function of the cellular DNA polymerases involved in chromosome replication? A. Ensure that RNA primers are used and not DNA primers B. Ensure that DNA is replicated from replication origins and not elsewhere C. Ensure that dNTPs and not NTPs are used in copying DNA templates (and not RNA templates) D. Ensure that cellular chromosomes are replicated (not the genomes of DNA viruses or other invaders) 5. Which of the following is a RNA-dependent DNA polymerase (RDDP)? A. E. coli DNA polymerase III B. Human DNA polymerase delta C. E. coli RNA polymerase or human RNA polymerase II D. Reverse transcriptase of human immunodeficiency viruses 6. If you want to incorporate a radiolabeled phosphate atom in to DNA through DNA replication, which of the phosphate atoms of a dNTP (say dGTP) must be radiolabeled? A. alpha phosphate B. beta phosphate C. gamma phosphate D. any of these phosphates 7. The cellular DNA polymerases have a structure of a human right hand with the following regions. The correct functions of the each of the regions are shown below except _________, which is incorrect. A. Thumbs: binds dNTPs and binds newly synthesized DNA B. Palm: Binds primers and template DNA, and catalyzes DNA synthesis C. Fingers: Keep the template ssDNA away from the reaction center except one nucleotide and also

stabilize dNTP D. Wrist: Moves DNA with mis-incorporated nucleotide and removes the nucleotide by 3’ to 5’ exonuclease activity 8. Wrong dNTPs are usually not incorporated to the primer because of all the following reasons except ___________. A. The wrong dNTP would not properly base pair with the template DNA B. The wrong dNTP would not be stabilized by the O-helix of the finger region C. The 3'OH of the primer would be too far from the alpha PO4 of a non-base-paired (wrong) dNTP D. The wrong dNTP will be promptly removed by the exonuclease activity of palm region of the enzyme 9. Why NTPs are not incorporated to DNA although NTPs may base pair with the template more stably than dNTPs, and NTPs are present at much higher concentrations in the cell compared to dNTP? A. The discriminator amino acid of the palm will not allow a NTP to enter and stay in the reaction center B. The palm pocket does not fit NTPs propely C. The thumb does not bind NTPs D. Because of all these options 10. Which of the following DNA polymerase is more processive? A. DNA polymerase III: May replicates one full chromosome without falling down B. Taq DNA polymerase: Falls down after copying about 100-4,000 bp DNA C. E. coli DNA polymerase I: Falls down after copying 1-100 bp of DNA 11. After each nucleotide is copied, the DNA polymerase must move DNA by one nucleotide. At this point any DNA polymerase may fall down from the template. How DNA polymerases generally avoid such a fall? A. The thumb domain remains attached to the DNA template B. The finger domain remains attached to the DNA template C. The palm remain attached to the DNA template 12. The highly processive DNA polymerases such as bacterial DNA pol III or eukaryotic DNA pol delta have __________ activities. A. 5’ to 3’ exonuclease activity for removing RNA primer B. 5’ to 3’ polymerase or primer extension activity C. 3’ to 5’ exonuclease activity for proof reading D. two of these activities E. all these activities 13. The proofreading function of DNA polymerases contributes to each of the following but not necessarily _______. A. reduces the rate of mutation B. slows down replication rate C. increases the replication accuracy D. increases the overall processivity 14. A replication bubble initiated at a replication origin in a cellular chromosome would have ___________. A. one replication fork, one leading strand and one lagging strand B. two replication forks, one leading strand and one lagging strand

C. two replication forks, two leading strands and two lagging strands D. two replication forks, one leading strand and multiple lagging strands 15. Technically, the lagging or leading strands are the _________ strands of a particular location of a replication fork. A. template DNA B. top and the bottom C. newly synthesized DNA 16. Okazaki fragments are about 1,000bp in length, and part of the lagging strand. Okazaki fragments are__________ molecules till they are repaired and ligated. A. DNA B. RNA C. partly RNA, partly DNA D. partly single-stranded and partly double-stranded 17. All the primers used in cellular DNA replication are RNA but chromosomal DNA found in the interphase cell lacks RNA altogether. This is because the primer sequences are removed by _______. A. Bacterial DNA polymerase III or eukaryotic pol delta B. bacterial DNA polymerase I C. RNaseH and exonucleases D. two of these enzymes E. any these enzymes 18. The Okazaki fragments are ligated together by __________ as the RNA primers are removed and replaced. A. DNA polymerase I, III or delta. B. RNase H or exonuclease C. DNA ligases D. topisomearses 19. DNA helicases bind dsDNA or ssDNA, and open dsDNA to create ssDNA by removing hydrogen bonds using energy from ATP hydrolysis. DNA helicases have some structural similarity with______ and they open DNA ______ direction. A. wedges/ 3’ to 5’ B. human left hand/ 5’ to 3’ C. rings/ 5’ to 3’ or 3’ to 5’ 20. At physiological pH and salt concentration, DNA would stay double-stranded, not single-stranded molecules. How is DNA kept single-stranded during DNA replication? A. Single strand binding protein (SSB) binds, coats and stabilizes ssDNA B. DNA polymerases keep the ssDNA strands separate from each other. C. DNA helicase keep the ssDNA strands separate from each other. 21. There are five identical ssDNA molecules but sufficient SSBs to completely cover only one piece of the ssDNA molecules in a test tube. How the SSBs will react at this situation? A. They will bind each of the five ssDNA molecules partly covering each of the five molecules B. They will bind only one molecule of ssDNA until it is completely covered

22. Which of the following is incorrect about the cellular primases? A. They may initiate RNA synthesis without a primer B. They may synthesize DNA using dNTPs C. They may synthesize RNA using NTPs D. They are accurate and processive 23. Helicases cause severe under-twisting of DNA at the replication fork but induce severe positive superhelix formation downstream in the dsDNA. How the DNA polymerase and the helicase enzyme pass through the superhelices? A. DNA polymerases push through the kinks B. DNA helicases use energy of ATP and move through the kinks C. DNA topoisomerases cut and ligate DNA to remove the superhelical knots. D. All these solve the problem of the removal of superhelices and progress of the replication fork. 24. The activities of topoisomerases are shown below. Which of the items is described incorrectly? A. Topo Is cut and ligate ssDNA B. Topo IIs cut and ligate dsDNA C. All Topoisomerases require ATP for biological activities D. Some cancer and antimicrobial drugs inactivate topoisomerases 25. Which of the following enzymes/proteins are not considered a regular part of the replication fork? A. Ligases and RNase H B. Primases and SSB C. DNA polymerases D. Topoisomerases E. Helicases 26. Cells always have multiple DNA polymerases, some for chromosome replication, and some for DNA repair under various situations. The DNA polymerases that replicate chromosomal DNA are generally __________. A. made of one polypeptide chain, making it simple and precise B. unique (one enzyme for the cell) to avoid confusions in enzyme choice C. made of multiple polypeptide chains, making them multifunctional and processive 27. Even the highly processive DNA polymerase III or delta would fall of DNA template if there were no______. A. DNA helicase bound to ssDNA B. SSB protein bound to ssDNA C. sliding clamp or PCNA ringed on DNA D. topoisomerase I and/or II bound to chromosomal DNA 28. The sliding clamp and PCNA are structurally somewhat similar to __________ because both _________. A. DNA helicase/ bind ssDNA in the central hole B. SSB or RNaseH/ stay away from the replication fork C. Primases/ interact with DNA and DNA polymerases D. DNA topoisomerase/ need ATP hydrolysis for enzyme activity 29. Which of the following eukaryotic proteins may not interact with the sliding clamp or PCNA?

A. The clamp loader B. The helicase loader C. The histone chaperones D. DNA delta, epsilon, etc. E. The DNA repair and methylase enzymes 30. Every time an Okazaki fragment is initiated on the template of the lagging strand, the following also are performed but not _________. A. new sliding clamp is loaded on to DNA B. DNA repair and modification enzymes are loaded to the sliding clamp C. DNA polymerase III or DNA polymerase delta is attached to the sliding clamp 31. Bacterial DNA polymerase III holoenzyme contains all the following items except ___________. A. a primase B. a sliding clamp C. a clamp loader D. as much as three molecules of DNA polymerases III E. three tau subunits, each bound to a DNA polymerase 32. Which of the following is defined incorrectly? A. Replisome: all proteins/enzymes associated with a replication fork B. Initiators: The origin-binding proteins (i.e. replicator-binding proteins) C. Replicon: all the enzymes needed for replication initiation and completion D. Replicator: Is DNA sequence that is recognized/bound to by the initiator proteins 33. If the 245bp replicator is removed from the E. coli chromosome (the chromosome is made of 4.6x106 bp of DNA), the chromosome will _______, if a replicator of a human chromosome it removed, the chromosome will _______. A. not be replicated/ not be replicated B. not be replicated/ be replicated C. be replicated/ not be replicated D. be replicated/ be replicated 34. The replicators are unique and essential for DNA replication because of each of these reasons except _________. A. have sepcfic DNA sequence to be recognized by the initiators B. have repeat DNA and AT-rich DNA for portein binding and easeful melting of DNA, respectively C. are made of ministallites that can be distinguished from other DNA because of the repeat DNA sequences 35. The events that take place during DNA replication initiation in E. coli are: Q. Helicases are loaded on ssDNA; R. SSB binds and stabilizes ssDNA; S. A DNA holoenzyme loads sliding clamps; T. Initiators bind replicators and open up dsDNA making a stretch of ssDNA; U. A primase makes a primer and then falls off. The events are organized in a haphazardly manner. A correct sequence of the events is ________. A. QRSTU B. TRQUS C. SQTRU D. RTSQU

36. The eukaryotic initiator is a six-protein complex named origin recognition complex or ORC. ORC binds DNA in a _________, initially during the ________ phase of the cell cycle. A. ATP-dependent manner/ G1 B. sequence specific manner/G1 or S C. sequence specific and ATP-dependent manner/S, G2 or M D. sequence specific but ATP-independent manner/G1, S, G2 or M 37. If a portion of a chromosome is replicated more than once per cell cycle, __________; if a portion of a chromosome is replicated less than once per cell cycle, ___________. A. there will be a gene amplification event/ the chromosome will break during metaphase B. the chromosome will break during metaphase/ there will be a gene amplification event C. the cell will transform to a tumor cell/ there will be an apoptotic cell death D. there will be apoptotic cell death/ the cell will transform to a tumor cell 38. Eukaryotic helicase Mcm2-7 binds DNA through interacting with all the following but not directly with _______ and it initially binds ________. A. Cdt1/ssDNA B. CDK/ dsDNA C. ORC/ melted repeat DNA of the replicator D. Cdc6/ melted AT-rich DNA of the replicator 39. Helicase is activated during the S, G2 or M phase. Activation of helicase ultimately means _______. A. shifting from dsDNA to ssDNA B. interacting with CDK, DDK and other cell cycle regulating proteins C. interacting with cdc45, GINS and other cell cycle regulating proteins D. interacting with the primase (i.e. DNA polymerase alpha) and the processive DNA polymerases 40. CDK protein levels are low during _______ phase and this is the time helicases are loaded on ORCDNA complex, CDK level is high in ________ phase, this is the time when helicases are activated. A. G1/ S B. S/ G2 C. G/ M D. M/ G1 41. Helicases are loaded and activated at different growth phases of the cell cycle. This is done this way to_______. A. prevent DNA synthesis during G1 phase B. allow DNA synthesis only during the S phase C. ensure DNA replication is limited to no more than once per cell cycle D. partition resources and allocate resources to different stages of the cell cycle 42. The replisome of bacteria and eukaryotes differ in many ways, particularly the latter lacks the ________. A. homologues of the sliding clamp loader and the sliding clamp B. the RNA primer removing enzymes and DNA ligases C. the holoenzyme D. primases E. SSB

43. Bacteria prevent continuous (i.e. the Mary go-round) DNA replication of the circular chromosome by having ________ proteins that bind the replication terminator regions (the ter sites). The newly synthesized DNA molecules remain catenated, and the two DNA catenae are separated from each other by the enzyme ________. A. dnaA/ helicase B. tus / resolvase C. recA/ recBCD 44. The telomeres of the eukaryotic somatic cells are shortened by about 10 bp every time DNA is replicated but the stem cells keep the telomere size intact. The telomere of the somatic cells shortens because of all the following but not because ________. A. the RNA primer at the extreme 5’ ends of the chromosomes are removed by RNaseH or exonucleases B. the RNA primer at the extreme 5’ ends removed by RNaseH cannot be replaced by any DNA polymerases C. Okazaki fragments of the extreme 5’ ends of the lagging strand are not ligated to the next Okazaki fragment D. the shortened chromosome gets replicated next time and makes the shortness permanent and the process goes on 45. The somatic cells of humans die after about 60 duplications, most likely because of ________. (Only the most obvious answer will be scored). A. mutations in the telomerase gene B. accumulated toxins inside the cells C. accumulated DNA point mutations D. accumulated protein and lipid oxidation E. accumulated shortening of the telomeres 46. The telomerase enzyme is somewhat comparable to _______ because it __________. A. reverse transcriptase/ uses a RNA template but synthesizes DNA B. bacterial DNA polymerase I/ extends a DNA primer and destroys RNA C. eukaryotic DNA polymerase alpha/ can synthesize RNA as well as DNA D. RNA polymerase/ uses RNA as the template and polymerizes nucleotides 47. Large rodents (such as capybaras) only retain telomerase activity in the stem cells and shut down the telomerase activity in the somatic cells. Small rodents (such as mice) retain telomerase activity both in the stem cells and somatic cells. Which of the following hypothesis would explain this paradox most accurately? A. Large bodied animals do not require telomerase activity to maintain telomere length. B. Large-bodied animals bear higher lifetime risk of cancers, so they shut down telomerase in somatic cells C. Small-bodied animals seldom if ever get cancers, so telomerase inactivation is irrelevant for these animals D. The telomerase enzymes of large animals and small animals are different in terms of structures and functions...