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
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
Choice (c) is the correct answer. Choices (a) and (b) are false. Although choice (d) is a
correct statement, it is not the reason that DNA replication is called semiconservative.
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
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
(b) the reaction can occur at room temperature
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 polymera
Choice (d) is the correct answer. Bacteria have one origin of replication, and Drosophila has many. Choice (a) is incorrect because the Drosophila genome is bigger than the E. coli genome. Choice (b) is incorrect, because eukaryotic polymerases are not fa
Meselson and Stahl grew cells in media that contained different isotopes of nitrogen (15N and 14N) so that the DNA molecules produced from these different isotopes could be distinguished by mass.
A. Explain how "light" DNA was separated from "heavy" DNA i
A.
The DNA samples collected were placed into centrifuge tubes containing cesium chloride. After high-speed centrifugation for 2 days, the heavy and light DNA products were separated by density.
B. The three models were conservative, semiconservative, and
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 typica
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
toge
How many replication forks are formed when an origin of replication is opened?
(a) 1
(b) 2
(c) 3
(d) 4
(b) 2
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
o
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.
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
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
temp
(d) The replication forks formed at the origin move in opposite directions.
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�
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)
(a) hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi) + Pi
Use your knowledge of how a new strand of DNA is synthesized to explain why DNA replication must occur in the 5?-to-3? direction. In other words, what would be the consequences of 3?-to-5? strand elongation?
There would be several detrimental consequences to 3?-to-5? strand elongation. One of those most directly linked to the processes of DNA replication involves synthesis of the lagging strand. After the RNA primers are degraded, the DNA segments remaining w
Figure Q6-15 shows a replication bubble.
Figure Q6-15
A. On the figure, indicate where the origin of replication was located (use O).
B. Label the leading-strand template and the lagging-strand template of the right-hand fork [R] as X and Y, respectively.
See Figure A6-15.
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
You will probably add exogenous nucleoside triphosphates to serve as the building blocks needed to make new strands of DNA. Although these monomers will be present in the extracts, they will be present at lower concentrations than are normally found insid
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(b) Leading and lagging strands are synthesized bidirectionally from the replication origin, and are joined together by DNA ligase where the two replication forks meet at the termination site. Choice (a) is not correct, because this answer implies that th
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
Choice (a) is the best answer because DNA synthesis cannot begin without the initial primers. Choice (b) is a good answer because lagging-strand synthesis requires continual use of RNA primers for discontinuous replication to occur.
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(d) lagging-strand completion
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(a) Because helicase unwinds the two DNA template strands, replication of both strands
depends upon the activity of helicase at the time of initiation.
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(b) Okazaki fragment synthesis
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(d) lagging-strand completion
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
(d) Each newly synthesized strand in a daughter duplex was synthesized by a mixture of continuous and discontinuous DNA synthesis from multiple origins. Consider a single replication origin. The fork moving in one direction synthesizes a daughter strand c
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
(d) It will be more likely to generate mismatched base pairs.
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 responsi
Choice (d) is the correct answer. DNA from all organisms is chemically identical except for the sequence of nucleotides. The proteins listed in choices (a) to (c) can act on any DNA regardless of its sequence. In contrast, the initiator proteins recognize
Most cells in the body of an adult human lack the telomerase enzyme because its gene is turned off and is therefore not expressed. An important step in the conversion of a normal cell into a cancer cell, which circumvents normal growth control, is the res
In the absence of telomerase, the life-span of a cell and its progeny cells is limited. With each round of DNA replication, the length of telomeric DNA will shrink, until finally all the telomeric DNA has disappeared. Without telomeres capping the chromos
6-27 Which diagram accurately represents the directionality of DNA strands at one side of a replication fork?
d
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
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 synthe
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
___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
The synthesis of DNA in living systems occurs in the 5?-to-3? direction. However, scientists synthesize short DNA sequences needed for their experiments on an instrument dedicated to this task.
A. The chemical synthesis of DNA by this instrument proceeds
A. The actual chemical reaction in DNA synthesis is the same regardless of whether going in the 5?-to-3? or in the 3?-to-5? direction. The most important distinction between these two options is that if DNA is synthesized in the 3?-to-5? direction, the 5?
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?
(b) sliding clamp
Use the components in the list below to label the diagram of a replication fork in Figure Q6-32.
A. DNA polymerase
B. single-strand binding protein
C. Okazaki fragment
D. primase
E. sliding clamp
F. RNA primer
G. DNA helicase
See Figure A6-32.
Researchers have isolated a mutant strain of E. coli that carries a temperature- sensitive variant of the enzyme DNA ligase. At the permissive temperature, the mutant cells grow just as well as the wild-type cells. At the nonpermissive temperature, all of
DNA ligase has an important role in DNA replication. After Okazaki fragments are synthesized, they must be ligated (covalently connected) to each other so that they finally form one continuous strand. At the nonpermissive temperature this does not happen,
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 si
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
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 pro
(b) The exonuclease activity cleaves DNA in the 5?-to-3? direction.
The sliding clamp complex encircles the DNA template and binds to DNA polymerase. This helps the polymerase synthesize much longer stretches of DNA without dissociating. While the loading of the clamp only occurs once on the leading strand, it must happen
The cell employs an additional protein in order to make the constant reloading of the sliding clamp on the lagging strand much more efficient. The protein, called the clamp loader, harnesses energy from ATP hydrolysis to lock a sliding clamp complex aroun
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
(b) Topoisomerases break the covalent bonds of the backbone allowing the local unwinding of DNA ahead of the replication fork
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 rep
(d) The leading strand doubles back on itself to form a primer for the lagging
strand.
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 ?-globin gene. What is the nature of the change?
(a) chromosome loss
(b) base
(b) base-pair change
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)
(d) 100-fold
Which of the choices below represents the correct way to repair the mismatch shown in Figure Q6-41?
Figure Q6-41
a
A mismatched base pair causes a distortion in the DNA backbone. If this were the only indication of an error in replication, the overall rate of mutation would be much higher. Explain why.
The distortion in the DNA backbone is insufficient information for the mismatch repair system to identify which base is incorrect and which was originally part of the chromosome when replication began. Without additional marks that identify the difference
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)
c
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 t
Choices (a) or (d) are correct. Choice (b) cannot account for these results because a mutation in the original mouse's germ cells would have no effect on the fetuses she was already carrying. Neither can choice (c), because mutations in the germ cells of
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
(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.
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 individu
(d) ultraviolet irradiation damage
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 tha
(d) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.
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
(b) 1/4
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
(a) TTAT
During DNA replication in a bacterium, a C is accidentally incorporated instead of an A into one newly synthesized DNA strand. Imagine that this error was not corrected and that it has no effect on the ability of the progeny to grow and reproduce.
A. Afte
a. One-half, or 50%. DNA replication in the original bacterium will create two new DNA molecules, one of which will now carry a mismatched C-T base pair. So one daughter cell of that cell division will carry a completely normal DNA molecule; the other cel
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 a
(c) TCT
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 expos
(b) Thymine dimers are covalent links between thymidines on opposite DNA
strands.
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 ba
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 cons
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 ________
Choice (c) is the correct answer. In fact, affected individuals in some families with a history of early-onset colon cancer have been found to carry mutations in mismatch repair genes. Mutations arising in somatic cells are not inherited, so choice (a) is
You have made a collection of mutant fruit flies that are defective in various aspects of DNA repair. You test each mutant for its hypersensitivity to three DNA-damaging agents: sunlight, nitrous acid (which causes deamination of cytosine), and formic aci
A. Mr Self-destruct is more likely than the other mutants to be defective in the DNA repair polymerase because Mr Self-destruct is defective in the repair of all three kinds of DNA damage. The repair pathways for all three kinds of damage are similar in t
The deamination of cytosine generates a uracil base. This is a naturally occurring nucleic acid base, and so does not represent a DNA lesion caused by damage due to chemicals or irradiation. Why is this base recognized as "foreign" and why is it important
Uracil is an RNA base and it is recognized as a mutational lesion because, as it is formed from the deamination of cytosine, it will be paired with a guanine in the context of the DNA duplex. Uracil pairs by forming two hydrogen bonds, similar to thymine,
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 repairi
(c) to the nearest available double-stranded DNA end.
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
(a) the recovery of lost nucleotides on a damaged DNA strand
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 occ
(b) 5? DNA strand overhangs
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)
(c) meiosis
Recombination has occurred between the chromosome segments shown in Figure Q6-61. The genes A and B, and the recessive alleles a and b, are used as markers
on the maternal and paternal chromosomes, respectively. After alignment and homologous recombinatio
(d) aB and Ab
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 follo
(d) E, F, B, C, D, A
Homologous recombination is initiated by double-strand breaks (DSBs) in a chromosome. DSBs arise from DNA damage caused by harmful chemicals or by radiation (for example, X-rays). During meiosis, the specialized cell division that produces gametes (sperm
A. Neither. The copy of Chromosome 3 you received from your mother is a hybrid of the ones she received from her mother and her father.
B. See Figure A6-43. The correct answers include any chromosome in which a
portion matches the information from the pat
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 u
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 recombina
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
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
Choice (c) is the correct answer. Choices (a) and (b) are false. Although choice (d) is a
correct statement, it is not the reason that DNA replication is called semiconservative.
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
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
(b) the reaction can occur at room temperature
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 polymera
Choice (d) is the correct answer. Bacteria have one origin of replication, and Drosophila has many. Choice (a) is incorrect because the Drosophila genome is bigger than the E. coli genome. Choice (b) is incorrect, because eukaryotic polymerases are not fa
Meselson and Stahl grew cells in media that contained different isotopes of nitrogen (15N and 14N) so that the DNA molecules produced from these different isotopes could be distinguished by mass.
A. Explain how "light" DNA was separated from "heavy" DNA i
A.
The DNA samples collected were placed into centrifuge tubes containing cesium chloride. After high-speed centrifugation for 2 days, the heavy and light DNA products were separated by density.
B. The three models were conservative, semiconservative, and
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 typica
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
toge
How many replication forks are formed when an origin of replication is opened?
(a) 1
(b) 2
(c) 3
(d) 4
(b) 2
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
o
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.
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
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
temp
(d) The replication forks formed at the origin move in opposite directions.
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�
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)
(a) hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi) + Pi
Use your knowledge of how a new strand of DNA is synthesized to explain why DNA replication must occur in the 5?-to-3? direction. In other words, what would be the consequences of 3?-to-5? strand elongation?
There would be several detrimental consequences to 3?-to-5? strand elongation. One of those most directly linked to the processes of DNA replication involves synthesis of the lagging strand. After the RNA primers are degraded, the DNA segments remaining w
Figure Q6-15 shows a replication bubble.
Figure Q6-15
A. On the figure, indicate where the origin of replication was located (use O).
B. Label the leading-strand template and the lagging-strand template of the right-hand fork [R] as X and Y, respectively.
See Figure A6-15.
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
You will probably add exogenous nucleoside triphosphates to serve as the building blocks needed to make new strands of DNA. Although these monomers will be present in the extracts, they will be present at lower concentrations than are normally found insid
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(b) Leading and lagging strands are synthesized bidirectionally from the replication origin, and are joined together by DNA ligase where the two replication forks meet at the termination site. Choice (a) is not correct, because this answer implies that th
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
Choice (a) is the best answer because DNA synthesis cannot begin without the initial primers. Choice (b) is a good answer because lagging-strand synthesis requires continual use of RNA primers for discontinuous replication to occur.
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(d) lagging-strand completion
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(a) Because helicase unwinds the two DNA template strands, replication of both strands
depends upon the activity of helicase at the time of initiation.
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(b) Okazaki fragment synthesis
You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation. These extracts provide the proteins required for DNA replication. Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) wit
(d) lagging-strand completion
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
(d) Each newly synthesized strand in a daughter duplex was synthesized by a mixture of continuous and discontinuous DNA synthesis from multiple origins. Consider a single replication origin. The fork moving in one direction synthesizes a daughter strand c
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
(d) It will be more likely to generate mismatched base pairs.
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 responsi
Choice (d) is the correct answer. DNA from all organisms is chemically identical except for the sequence of nucleotides. The proteins listed in choices (a) to (c) can act on any DNA regardless of its sequence. In contrast, the initiator proteins recognize
Most cells in the body of an adult human lack the telomerase enzyme because its gene is turned off and is therefore not expressed. An important step in the conversion of a normal cell into a cancer cell, which circumvents normal growth control, is the res
In the absence of telomerase, the life-span of a cell and its progeny cells is limited. With each round of DNA replication, the length of telomeric DNA will shrink, until finally all the telomeric DNA has disappeared. Without telomeres capping the chromos
6-27 Which diagram accurately represents the directionality of DNA strands at one side of a replication fork?
d
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
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 synthe
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
___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
The synthesis of DNA in living systems occurs in the 5?-to-3? direction. However, scientists synthesize short DNA sequences needed for their experiments on an instrument dedicated to this task.
A. The chemical synthesis of DNA by this instrument proceeds
A. The actual chemical reaction in DNA synthesis is the same regardless of whether going in the 5?-to-3? or in the 3?-to-5? direction. The most important distinction between these two options is that if DNA is synthesized in the 3?-to-5? direction, the 5?
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?
(b) sliding clamp
Use the components in the list below to label the diagram of a replication fork in Figure Q6-32.
A. DNA polymerase
B. single-strand binding protein
C. Okazaki fragment
D. primase
E. sliding clamp
F. RNA primer
G. DNA helicase
See Figure A6-32.
Researchers have isolated a mutant strain of E. coli that carries a temperature- sensitive variant of the enzyme DNA ligase. At the permissive temperature, the mutant cells grow just as well as the wild-type cells. At the nonpermissive temperature, all of
DNA ligase has an important role in DNA replication. After Okazaki fragments are synthesized, they must be ligated (covalently connected) to each other so that they finally form one continuous strand. At the nonpermissive temperature this does not happen,
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 si
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
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 pro
(b) The exonuclease activity cleaves DNA in the 5?-to-3? direction.
The sliding clamp complex encircles the DNA template and binds to DNA polymerase. This helps the polymerase synthesize much longer stretches of DNA without dissociating. While the loading of the clamp only occurs once on the leading strand, it must happen
The cell employs an additional protein in order to make the constant reloading of the sliding clamp on the lagging strand much more efficient. The protein, called the clamp loader, harnesses energy from ATP hydrolysis to lock a sliding clamp complex aroun
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
(b) Topoisomerases break the covalent bonds of the backbone allowing the local unwinding of DNA ahead of the replication fork
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 rep
(d) The leading strand doubles back on itself to form a primer for the lagging
strand.
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 ?-globin gene. What is the nature of the change?
(a) chromosome loss
(b) base
(b) base-pair change
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)
(d) 100-fold
Which of the choices below represents the correct way to repair the mismatch shown in Figure Q6-41?
Figure Q6-41
a
A mismatched base pair causes a distortion in the DNA backbone. If this were the only indication of an error in replication, the overall rate of mutation would be much higher. Explain why.
The distortion in the DNA backbone is insufficient information for the mismatch repair system to identify which base is incorrect and which was originally part of the chromosome when replication began. Without additional marks that identify the difference
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)
c
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 t
Choices (a) or (d) are correct. Choice (b) cannot account for these results because a mutation in the original mouse's germ cells would have no effect on the fetuses she was already carrying. Neither can choice (c), because mutations in the germ cells of
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
(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.
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 individu
(d) ultraviolet irradiation damage
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 tha
(d) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.
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
(b) 1/4
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
(a) TTAT
During DNA replication in a bacterium, a C is accidentally incorporated instead of an A into one newly synthesized DNA strand. Imagine that this error was not corrected and that it has no effect on the ability of the progeny to grow and reproduce.
A. Afte
a. One-half, or 50%. DNA replication in the original bacterium will create two new DNA molecules, one of which will now carry a mismatched C-T base pair. So one daughter cell of that cell division will carry a completely normal DNA molecule; the other cel
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 a
(c) TCT
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 expos
(b) Thymine dimers are covalent links between thymidines on opposite DNA
strands.
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 ba
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 cons
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 ________
Choice (c) is the correct answer. In fact, affected individuals in some families with a history of early-onset colon cancer have been found to carry mutations in mismatch repair genes. Mutations arising in somatic cells are not inherited, so choice (a) is
You have made a collection of mutant fruit flies that are defective in various aspects of DNA repair. You test each mutant for its hypersensitivity to three DNA-damaging agents: sunlight, nitrous acid (which causes deamination of cytosine), and formic aci
A. Mr Self-destruct is more likely than the other mutants to be defective in the DNA repair polymerase because Mr Self-destruct is defective in the repair of all three kinds of DNA damage. The repair pathways for all three kinds of damage are similar in t
The deamination of cytosine generates a uracil base. This is a naturally occurring nucleic acid base, and so does not represent a DNA lesion caused by damage due to chemicals or irradiation. Why is this base recognized as "foreign" and why is it important
Uracil is an RNA base and it is recognized as a mutational lesion because, as it is formed from the deamination of cytosine, it will be paired with a guanine in the context of the DNA duplex. Uracil pairs by forming two hydrogen bonds, similar to thymine,
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 repairi
(c) to the nearest available double-stranded DNA end.
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
(a) the recovery of lost nucleotides on a damaged DNA strand
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 occ
(b) 5? DNA strand overhangs
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)
(c) meiosis
Recombination has occurred between the chromosome segments shown in Figure Q6-61. The genes A and B, and the recessive alleles a and b, are used as markers
on the maternal and paternal chromosomes, respectively. After alignment and homologous recombinatio
(d) aB and Ab
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 follo
(d) E, F, B, C, D, A
Homologous recombination is initiated by double-strand breaks (DSBs) in a chromosome. DSBs arise from DNA damage caused by harmful chemicals or by radiation (for example, X-rays). During meiosis, the specialized cell division that produces gametes (sperm
A. Neither. The copy of Chromosome 3 you received from your mother is a hybrid of the ones she received from her mother and her father.
B. See Figure A6-43. The correct answers include any chromosome in which a
portion matches the information from the pat
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 u
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 recombina