Cell and Molc Chapter 6
The 3′ overhang "invades" the homologous DNA duplex, which can be used as a primer for the repair DNA polymerase.
True.
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.
True.
True or False. DNA replication is a bidirectional process that is initiated at multiple locations along chromosomes in eukaryotic cells.
True.
True or False. Meselson and Stahl ruled out the dispersive model for DNA replication.
True.
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?
initiation of DNA synthesis; Because helicase unwinds the two DNA template strands, replication of both strands depends upon the activity of helicase at the time of initiation.
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.
initiator proteins
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?
lagging-strand completion
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?
lagging-strand completion
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?
meiosis
Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not true regarding the replication of telomeric sequences?
The leading strand doubles back on itself to form a primer for the lagging strand.
Which of the following statements is not an accurate statement about thymine dimers?
Thymine dimers are covalent links between thymidines on opposite DNA strands.
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?
Topoisomerases break the covalent bonds of the backbone allowing the local unwinding of DNA ahead of the replication fork.
Ionizing radiation and oxidative damage can cause DNA double-strand breaks.
True.
True or False? Primase is needed to initiate DNA replication on both the leading strand and the lagging strand.
True.
True or False? Telomerase is a DNA polymerase that carries its own RNA molecule to use as a primer at the end of the lagging strand.
True.
The classic experiments conducted by Meselson and Stahl demonstrated that DNA replication is accomplished by employing a ________________ mechanism.
semiconservative
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?
sliding clamp
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.
template
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?
the reaction can occur at room temperature
Nonhomologous end joining can result in all but which of the following?
the recovery of lost nucleotides on a damaged DNA strand
Select the option that best completes the following statement: Nonhomologous end joining is a process by which a double-stranded DNA end is joined ___________________.
to the nearest available double-stranded DNA end.
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?
ultraviolet irradiation damage
How does the total number of replication origins in bacterial cells compare with the number of origins in human cells?
1 versus 10,000
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?
1/4
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?
100-fold
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?
10×
How many replication forks are formed when an origin of replication is opened?
2
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?
5′ DNA strand overhangs
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?
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.
True or False? The sliding clamp is loaded once on each DNA strand, where it remains associated until replication is complete.
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.
True or False. DNA replication origins are typically rich in G-C base pairs.
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.
Depurination of DNA is a rare event that is caused by ultraviolet irradiation.
False. Depurination occurs constantly in our cells through spontaneous hydrolysis of the bond linking the DNA base to the deoxyribose sugar.
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.
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.
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.
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.
After damaged DNA has been repaired, nicks in the phosphate backbone are maintained as a way to identify the strand that was repaired.
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.
True or False? Primase requires a proofreading function that ensures there are no errors in the RNA primers used for DNA replication.
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.
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?
Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.
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?
Okazaki fragment synthesis
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?
TCT
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?
TTAT
On a DNA strand that is being synthesized, which end is growing—the 3′ end, the 5′ end, or both ends? Explain your answer.
The 3′ end. DNA polymerase can add nucleotides only to the 3′-OH end of a nucleic acid chain.
The DNA template used to repair the broken strand is the homologous chromosome inherited from the other parent.
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.
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?
Drosophila DNA contains more origins of replication than E. coli DNA.
True or False. When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate.
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.
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 resumption of telomerase expression. Explain why telomerase might be necessary for the ability of cancer cells to divide over and over again.
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 chromosome ends, the ends might be treated like breaks arising from DNA damage, or crucial genetic information might be lost. Cells whose DNA lacks telomeres will stop dividing or die. However, if telomerase is provided to cells, they may be able to divide indefinitely because their telomeres will remain a constant length despite repeated rounds of DNA replication.
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?
In the deformed mice, somatic cells but not germ cells were mutated; The toxic chemical affects development but is not mutagenic.
Which of the following statements about the newly synthesized strand of a human chromosome is true?
It was synthesized from multiple origins by a mixture of continuous and discontinuous DNA synthesis.
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?
It will be more likely to generate mismatched base pairs.
Which of the following statements correctly explains what it means for DNA replication to be bidirectional?
The replication forks formed at the origin move in opposite directions.
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 between the newly synthesized strand and the template strand, the repair would be corrected only 50% of the time by random chance. The error rate (and therefore the mutation rate) would still be less than in a system that lacked the mismatch repair enzymes (1 mistake per 107 base pairs), but greater than the error rate in a system that accurately identifies the newly synthesized strand (1 mistake per 109 base pairs).
Which of the following statements about sequence proofreading during DNA replication is false?
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?
The leading and lagging strands compose one half of each newly synthesized DNA strand.
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 will have 5′ ends with a single phosphate group. The incoming nucleotide will have a 3′-OH group. Without the energy provided by the release of PPi from the 5′ end, the process of elongation would no longer be energetically favorable.
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 for cells to have a mechanism to recognize and remove uracil when it is found in the DNA duplex?
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, and is thus a poor partner for guanine, which forms three hydrogen bonds with cytosine. The mismatch causes a distortion of the DNA backbone, allowing the repair machinery to recognize the uracil as a lesion. Because uracil pairs preferably with adenine (its partner in double-stranded RNA), the deamination of cytosine to uracil is highly mutagenic. If unrepaired, it can result in the transition of a C-G base pair to a T-A base pair.
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 nick in the new 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 β-globin gene. What is the nature of the change?
base-pair change
DNA replication is considered semiconservative because ____________________________.
each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand.
DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand. What prevents this enzyme from catalyzing the reverse reaction?
hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi) + Pi
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 _______________________.
inherited a mutation in a gene required for mismatch repair.
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?
initiation of DNA synthesis