Exam 6: DNA Replication and Repair

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?

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?

DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand.What prevents this enzyme from catalyzing the reverse reaction?

Figure 6-63 shows a replication bubble. Figure 6-63 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. C.Indicate by arrows the direction in which the newly made DNA strands (indicated by dark lines) were synthesized. D.Number the Okazaki fragments on each strand as 1, 2, and 3 in the order in which they were synthesized. E.Indicate where the most recent DNA synthesis has occurred (use S). F.Indicate the direction of movement of the replication forks with arrows.

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?

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?

The chromatin structure in eukaryotic cells is much more complicated than that observed in prokaryotic cells.This is thought to be the reason why DNA replication occurs much faster in prokaryotes.How much faster is it?

The classic experiments conducted by Meselson and Stahl used isotopes of which element to distinguish newly synthesized DNA from parental DNA?

The sliding clamp complex must be reloaded for the synthesis of each Okazaki fragment on the lagging strand, while on the leading strand the clamp complex remains assembled over much longer stretches of DNA.Considering this information, explain how the cell is able to replicate the leading and lagging strands at the same rate.

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?

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.After this original bacterium has divided once, what proportion of its progeny would you expect to contain the mutation? B.What proportion of its progeny would you expect to contain the mutation after three more rounds of DNA replication and cell division?

Which of the following statements is NOT an accurate statement about thymine dimers?

Nonhomologous end joining can result in all but which of the following?

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) with a single origin of replication and a single replication termination site.The termination site is on the opposite side of the plasmid from the origin. Figure 6-11 Which of the following statements is TRUE with respect to this in vitro replication system?

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?

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?

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) with a single origin of replication and a single replication termination site.The termination site is on the opposite side of the plasmid from the origin. Figure 6-11A In addition to the extracts and the plasmid DNA, are there any additional materials you should add to this in vitro replication system? Explain your answer.

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?