BIOL Ch. 6
6-8 How many replication forks are formed when an origin of replication is opened? (a) 1 (b) 2 (c) 3 (d) 4
(b) 2
6-60 In addition to the repair of DNA double-strand breaks, homologous recombination is a mechanism for generating genetic diversity by swapping segments of parental chromosomes. During which process does swapping occur? (a) DNA replication (b) DNA repair (c) meiosis (d) transposition
(c) meiosis
6-40 Even though DNA polymerase has a proofreading function, it still introduces errors in the newly synthesized strand at a rate of 1 per 107 nucleotides. To what degree does the mismatch repair system decrease the error rate arising from DNA replication? (a) 2-fold (b) 5-fold (c) 10-fold (d) 100-fold
(d) 100-fold
6-21 What part of the DNA replication process would be most directly affected if a strain of bacteria lacking single-strand binding protein were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion
(b) Okazaki fragment synthesis
6-35 Which of the following statements about sequence proofreading during DNA replication is false? (a) The exonuclease activity is in a different domain of the DNA polymerase. (b) The exonuclease activity cleaves DNA in the 5′-to-3′ direction. (c) The DNA proofreading activity occurs concomitantly with strand elongation. (d) If an incorrect base is added, it is "unpaired" before removal.
(b) The exonuclease activity cleaves DNA in the 5′-to-3′ direction
Which of the following statements is true with respect to this in vitro replication system? (a) There will be only one leading strand and one lagging strand produced using this template. (b) The leading and lagging strands compose one half of each newly synthesized DNA strand. (c) The DNA replication machinery can assemble at multiple places on this plasmid. (d) One daughter DNA molecule will be slightly shorter than the other.
(b) The leading and lagging strands compose one half of each newly synthesized DNA strand.
6-52 Which of the following statements is not an accurate statement about thymine dimers? (a) Thymine dimers can cause the DNA replication machinery to stall. (b) Thymine dimers are covalent links between thymidines on opposite DNA strands. (c) Prolonged exposure to sunlight causes thymine dimers to form. (d) Repair proteins recognize thymine dimers as a distortion in the DNA backbone.
(b) Thymine dimers are covalent links between thymidines on opposite DNA strands
6-51 Sometimes, chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the adenosine in the sequence TCAT is depurinated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication? (a) TCGT (b) TAT (c) TCT (d) TGTT
(c) TCT
6-43 Beside the distortion in the DNA backbone caused by a mismatched base pair, what additional mark is there on eukaryotic DNA to indicate which strand needs to be repaired? (a) a nick in the template strand (b) a chemical modification of the new strand (c) a nick in the new strand (d) a sequence gap in the new strand
(c) a nick in the new strand
6-54 Several members of the same family were diagnosed with the same kind of cancer when they were unusually young. Which one of the following is the most likely explanation for this phenomenon? It is possible that the individuals with the cancer have _______________________. (a) inherited a cancer-causing gene that suffered a mutation in an ancestor's somatic cells. (b) inherited a mutation in a gene required for DNA synthesis. (c) inherited a mutation in a gene required for mismatch repair. (d) inherited a mutation in a gene required for the synthesis of purine nucleotides.
(c) inherited a mutation in a gene required for mismatch repair.
6-1 The process of DNA replication requires that each of the parental DNA strands be used as a ___________________ to produce a duplicate of the opposing strand. (a) catalyst (b) competitor (c) template (d) copy
(c) template
6-57 Select the option that best completes the following statement: Nonhomologous end joining is a process by which a double-stranded DNA end is joined ___________________. (a) to a similar stretch of sequence on the complementary chromosome. (b) after repairing any mismatches. (c) to the nearest available double-stranded DNA end. (d) after filling in any lost nucleotides, helping to maintain the integrity of the DNA sequence.
(c) to the nearest available double-stranded DNA end.
6-10 How does the total number of replication origins in bacterial cells compare with the number of origins in human cells? (a) 1 versus 100 (b) 5 versus 500 (c) 10 versus 1000 (d) 1 versus 10,000
(d) 1 versus 10,000
6-5 If the genome of the bacterium E. coli requires about 20 minutes to replicate itself, how can the genome of the fruit fly Drosophila be replicated in only 3 minutes? (a) The Drosophila genome is smaller than the E. coli genome. (b) Eukaryotic DNA polymerase synthesizes DNA at a much faster rate than prokaryotic DNA polymerase. (c) The nuclear membrane keeps the Drosophila DNA concentrated in one place in the cell, which increases the rate of polymerization. (d) Drosophila DNA contains more origins of replication than E. coli DNA.
(d) Drosophila DNA contains more origins of replication than E. coli DNA.
6-62 The events listed below are all necessary for homologous recombination to occur properly: A. Holliday junction cut and ligated B. strand invasion C. DNA synthesis D. DNA ligation E. double-strand break F. nucleases create uneven strands. Which of the following is the correct order of events during homologous recombination? (a) E, B, F, D, C, A (b) B, E, F, D, C, A (c) C, E, F, B, D, A (d) E, F, B, C, D, A
(d) E, F, B, C, D, A
6-25 A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but fails to replicate with the yeast DNA. Where do you think the block to replication arises? Choose the protein or protein complex below that is most probably responsible for the failure to replicate bacterial DNA. Give an explanation for your answer. (a) primase (b) helicase (c) DNA polymerase (d) initiator proteins
(d) initiator proteins
6-19 What part of the DNA replication process would be most directly affected if a strain of bacteria lacking the exonuclease activity of DNA polymerase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion
(d) lagging-strand completion
6-22 What part of the DNA replication process would be most directly affected if a strain of bacteria lacking DNA ligase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion
(d) lagging-strand completion
6-46 Human beings with the inherited disease xeroderma pigmentosum have serious problems with lesions on their skin and often develop skin cancer with repeated exposure to sunlight. What type of DNA damage is not being recognized in the cells of these individuals? (a) chemical damage (b) X-ray irradiation damage (c) mismatched bases (d) ultraviolet irradiation damage
(d) ultraviolet irradiation damage
6-9 Answer the following questions about DNA replication. A. On a DNA strand that is being synthesized, which end is growing—the 3′ end, the 5′ end, or both ends? Explain your answer. B. On a DNA strand that is being used as a template, where is the copying occurring relative to the replication origin—3′ of the origin, 5′, or both?
A. The 3′ end. DNA polymerase can add nucleotides only to the 3′-OH end of a nucleic acid chain. B. Both, as a result of the bidirectional nature of chromosomal replication.
6-45 The repair of mismatched base pairs or damaged nucleotides in a DNA strand requires a multistep process. Which choice below describes the known sequence of events in this process? (a) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by repair proteins, the gap is filled by DNA polymerase, and the strand is sealed by DNA ligase. (b) DNA repair polymerase simultaneously removes bases ahead of it and polymerizes the correct sequence behind it as it moves along the template. DNA ligase seals the nicks in the repaired strand. (c) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by an exonuclease, and the gap is repaired by DNA ligase. (d) A nick in the DNA is recognized, DNA repair proteins switch out the wrong base and insert the correct base, and DNA ligase seals the nick.
(a) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by repair proteins, the gap is filled by DNA polymerase, and the strand is sealed by DNA ligase
6-44 A pregnant mouse is exposed to high levels of a chemical. Many of the mice in her litter are deformed, but when they are interbred with each other, all their offspring are normal. Which two of the following statements could explain these results? (a) In the deformed mice, somatic cells but not germ cells were mutated. (b) The original mouse's germ cells were mutated. (c) In the deformed mice, germ cells but not somatic cells were mutated. (d) The toxic chemical affects development but is not mutagenic.
(a) In the deformed mice, somatic cells but not germ cells were mutated (d) The toxic chemical affects development but is not mutagenic.
6-49 Sometimes, chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the cytosine in the sequence TCAT is deaminated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication? (a) TTAT (b) TUAT (c) TGAT (d) TAAT
(a) TTAT
6-13 DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand. What prevents this enzyme from catalyzing the reverse reaction? (a) hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi) + Pi (b) release of PPi from the nucleotide (c) hybridization of the new strand to the template (d) loss of ATP as an energy source
(a) hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi) + Pi
6-20 What part of the DNA replication process would be most directly affected if a strain of bacteria lacking helicase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion
(a) initiation of DNA synthesis
You decide to use different bacterial strains (each having one protein of the replication machinery mutated) in order to examine the role of individual proteins in the normal process of DNA replication. 6-18 What part of the DNA replication process would be most directly affected if a strain of bacteria lacking primase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion
(a) initiation of DNA synthesis
6-58 Nonhomologous end joining can result in all but which of the following? (a) the recovery of lost nucleotides on a damaged DNA strand (b) the interruption of gene expression (c) loss of nucleotides at the site of repair (d) translocations of DNA fragments to an entirely different chromosome
(a) the recovery of lost nucleotides on a damaged DNA strand
6-48 In somatic cells, if a base is mismatched in one new daughter strand during DNA replication, and is not repaired, what fraction of the DNA duplexes will have a permanent change in the DNA sequence after the second round of DNA replication? (a) 1/2 (b) 1/4 (c) 1/8 (d) 1/16
(b) 1/4
6-59 Homologous recombination is an important mechanism in which organisms use a "backup" copy of the DNA as a template to fix double-strand breaks without loss of genetic information. Which of the following is not necessary for homologous recombination to occur? (a) 3′ DNA strand overhangs (b) 5′ DNA strand overhangs (c) a long stretch of sequence similarity (d) nucleases
(b) 5′ DNA strand overhangs
The DNA duplex consists of two long covalent polymers wrapped around each other many times over their entire length. The separation of the DNA strands for replication causes the strands to be "overwound" in front of the replication fork. How does the cell relieve the torsional stress created along the DNA duplex during replication? (a) Nothing needs to be done because the two strands will be separated after replication is complete. (b) Topoisomerases break the covalent bonds of the backbone allowing the local unwinding of DNA ahead of the replication fork. (c) Helicase unwinds the DNA and rewinds it after replication is complete. (d) DNA repair enzymes remove torsional stress as they replace incorrectly paired bases.
(b) Topoisomerases break the covalent bonds of the backbone allowing the local unwinding of DNA ahead of the replication fork
6-39 Sickle-cell anemia is an example of an inherited disease. Individuals with this disorder have misshapen (sickle-shaped) red blood cells caused by a change in the sequence of the β-globin gene. What is the nature of the change? (a) chromosome loss (b) base-pair change (c) gene duplication (d) base-pair insertion
(b) base-pair change
6-2 DNA replication is considered semiconservative because ____________________________. (a) after many rounds of DNA replication, the original DNA double helix is still intact. (b) each daughter DNA molecule consists of two new strands copied from the parent DNA molecule. (c) each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand. (d) new DNA strands must be copied from a DNA template.
(b) each daughter DNA molecule consists of two new strands copied from the parent DNA molecule
6-3 The classic experiments conducted by Meselson and Stahl demonstrated that DNA replication is accomplished by employing a ________________ mechanism. (a) continuous (b) semiconservative (c) dispersive (d) conservative
(b) semiconservative
6-31 DNA polymerases are processive, which means that they remain tightly associated with the template strand while moving rapidly and adding nucleotides to the growing daughter strand. Which piece of the replication machinery accounts for this characteristic? (a) helicase (b) sliding clamp (c) single-strand binding protein (d) primase
(b) sliding clamp
6-4 Initiator proteins bind to replication origins and disrupt hydrogen bonds between the two DNA strands being copied. Which of the factors below does not contribute to the relative ease of strand separation by initiator proteins? (a) replication origins are rich in A-T base pairs (b) the reaction can occur at room temperature (c) they only separate a few base pairs at a time (d) once opened, other proteins of the DNA replication machinery bind to the origin
(b) the reaction can occur at room temperature
6-12 The chromatin structure in eukaryotic cells is much more complicated than that observed in prokaryotic cells. This is thought to be the reason that DNA replication occurs much faster in prokaryotes. How much faster is it? (a) 2× (b) 5× (c) 10× (d) 100×
(c) 10×
6-23 Which of the following statements about the newly synthesized strand of a human chromosome is true? (a) It was synthesized from a single origin solely by continuous DNA synthesis. (b) It was synthesized from a single origin by a mixture of continuous and discontinuous DNA synthesis. (c) It was synthesized from multiple origins solely by discontinuous DNA synthesis. (d) It was synthesized from multiple origins by a mixture of continuous and discontinuous DNA synthesis.
(d) It was synthesized from multiple origins by a mixture of continuous and discontinuous DNA synthesis.
6-24 You have discovered an "Exo-" mutant form of DNA polymerase in which the 3′to-5′ exonuclease function has been destroyed but the ability to join nucleotides together is unchanged. Which of the following properties do you expect the mutant polymerase to have? (a) It will polymerize in both the 5′-to-3′ direction and the 3′-to-5′ direction. (b) It will polymerize more slowly than the normal Exo+ polymerase. (c) It will fall off the template more frequently than the normal Exo+ polymerase. (d) It will be more likely to generate mismatched base pairs.
(d) It will be more likely to generate mismatched base pairs.
6-47 You are examining the DNA sequences that code for the enzyme phosphofructokinase in skinks and Komodo dragons. You notice that the coding sequence that actually directs the sequence of amino acids in the enzyme is very similar in the two organisms but that the surrounding sequences vary quite a bit. What is the most likely explanation for this? (a) Coding sequences are repaired more efficiently. (b) Coding sequences are replicated more accurately. (c) Coding sequences are packaged more tightly in the chromosomes to protect them from DNA damage. (d) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.
(d) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.
6-38 Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not true regarding the replication of telomeric sequences? (a) The lagging-strand telomeres are not completely replicated by DNA polymerase. (b) Telomeres are made of repeating sequences. (c) Additional repeated sequences are added to the template strand. (d) The leading strand doubles back on itself to form a primer for the lagging strand.
(d) The leading strand doubles back on itself to form a primer for the lagging strand.
6-11 Which of the following statements correctly explains what it means for DNA replication to be bidirectional? (a) The replication fork can open or close, depending on the conditions. (b) The DNA replication machinery can move in either direction on the template strand. (c) Replication-fork movement can switch directions when the fork converges on another replication fork. (d) The replication forks formed at the origin move in opposite directions.
(d) The replication forks formed at the origin move in opposite directions.
6-64 Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Homologous recombination cannot occur in prokaryotic cells, because they are haploid, and therefore have no extra copy of the chromosome to use as a template for repair. B. The first step in repair requires a nuclease to remove a stretch of base pairs from the 5′ end of each strand at the site of the break. C. The 3′ overhang "invades" the homologous DNA duplex, which can be used as a primer for the repair DNA polymerase. D. The DNA template used to repair the broken strand is the homologous chromosome inherited from the other parent.
A. False. Homologous recombination also occurs in prokaryotic cells, and typically occurs very shortly after DNA replication, when the newly replicated duplexes are in close proximity. B. True. C. True. D. False. Although it is called homologous recombination, this is not a process that depends on the proximity of parental homologs. When used as a mechanism for DNA repair, homologous recombination uses the sister chromatids in an undamaged, newly replicated (homologous) DNA helix as a template.
6-34 Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. The repair polymerase is the enzyme that proofreads the newly synthesized strands to ensure the accuracy of DNA replication. B. There is a single enzyme that degrades the RNA primers and lays down the corresponding DNA sequence behind it. C. DNA ligase is required to seal the sugar-phosphate backbone between all the DNA fragments on the lagging strand. D. The repair polymerase does not require the aid of the sliding clamp, because it is only synthesizing DNA over very short stretches.
A. False. The repair polymerase is used to fill in the spaces left vacant after the RNA primers are degraded. B. False. This is a two-step process that requires two different enzymes. First, a nuclease removes the RNA primers. Then, the repair polymerase fills in the complementary DNA sequence. C. True. D. True.
6-7 Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate. B. DNA replication origins are typically rich in G-C base pairs. C. Meselson and Stahl ruled out the dispersive model for DNA replication. D. DNA replication is a bidirectional process that is initiated at multiple locations along chromosomes in eukaryotic cells.
A. False. The two strands do need to separate for replication to occur, but this is accomplished by the binding of initiator proteins at the origin of replication. B. False. DNA replication origins are typically rich in A-T base pairs, which are held together by only two hydrogen bonds (instead of three for C-G base pairs), making it easier to separate the strands at these sites. C. True. D. True.
6-53 Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Ionizing radiation and oxidative damage can cause DNA double-strand breaks. B. After damaged DNA has been repaired, nicks in the phosphate backbone are maintained as a way to identify the strand that was repaired. C. Depurination of DNA is a rare event that is caused by ultraviolet irradiation. D. Nonhomologous end joining is a mechanism that ensures that DNA double-strand breaks are repaired with a high degree of fidelity to the original DNA sequence.
A. True. B. False. It is believed that the nicks are generated during DNA replication as a means of easy identification of the newly synthesized strand but are sealed by DNA ligase shortly after replication is completed. C. False. Depurination occurs constantly in our cells through spontaneous hydrolysis of the bond linking the DNA base to the deoxyribose sugar. D. False. Homologous recombination can repair double-strand breaks without any change in DNA sequence, but nonhomologous end joining always involves a loss of genetic information because the ends are degraded by nucleases before they can be ligated back together.
6-28 Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Primase is needed to initiate DNA replication on both the leading strand and the lagging strand. B. The sliding clamp is loaded once on each DNA strand, where it remains associated until replication is complete. C. Telomerase is a DNA polymerase that carries its own RNA molecule to use as a primer at the end of the lagging strand. D. Primase requires a proofreading function that ensures there are no errors in the RNA primers used for DNA replication.
A. True. B. False. Although the sliding clamp is only loaded once on the leading strand, the lagging strand needs to unload the clamp once the polymerase reaches the RNA primer from the previous segment and then reload it where a new primer has been synthesized. C. True. D. False. Primase does not have a proofreading function, nor does it need one because the RNA primers are not a permanent part of the DNA. The primers are removed, and a DNA polymerase that does have a proofreading function fills in the remaining gaps.
6-29 Because all DNA polymerases synthesize DNA in the 5′-to-3′ direction, and the parental strands are antiparallel, DNA replication is accomplished with the use of two mechanisms: continuous and discontinuous replication. Indicate whether the following items relate to (1) continuous replication, (2) discontinuous replication, or (3) both modes of replication. ______ primase ______ single-strand binding protein ______ sliding clamp ______ RNA primers ______ leading strand ______ lagging strand ______ Okazaki fragments ______ DNA helicase ______ DNA ligase
___3___ primase ___2___ single-strand binding protein ___3___ sliding clamp ___3___ RNA primers ___1___ leading strand ___2___ lagging strand ___2___ Okazaki fragments ___3___ DNA helicase ___2___ DNA ligase
