Exam 5: DNA Replication, Repair, and Recombination

Indicate whether each of the following DNA lesions is typically repaired via the base excision (B) or nucleotide excision (N) repair pathway? Your answer would be a four-letter string composed of letters B and N only, e.g. BBBB. 1. Deaminated cytosines 2. Depurinated residues 3. Thymine dimers 4. Bulky guanine adducts

Which of the following repair pathways can accurately repair a double-strand break?

What combination of the following events normally prevents the origins of replication in the yeast Saccharomyces cerevisiae from "firing" more than once during the cell cycle? Your answer is a two-letter string composed of letters A to E only, e.g. AB. Order the letters in your answer alphabetically.

Which of the following features is common between the replication origins in Escherichia coli and Saccharomyces cerevisiae?

DNA-only transposons …

What is the main source of the free energy for the mechanical work performed by DNA helicases during DNA replication in our cells?

Which of the following is NOT correct regarding homologous recombination and its regulation?

At the replication fork, the template for the lagging strand is thought to loop around. This looping would allow the lagging-strand polymerase to move along with the rest of the replication fork instead of in the opposite direction. The single-strand part of the loop is bound by the single-strand DNA-binding (SSB) proteins. As each Okazaki fragment is synthesized toward completion, how does the size of the loop change? What about the size of the SSB-bound part of the loop?

The telomerase enzyme in human cells …

Indicate true (T) and false (F) descriptions below regarding the nucleotide excision repair pathway. Your answer would be a four-letter string composed of letters T and F only, e.g. FFFF. ( ) It involves recognition of distortions in the DNA double helix rather than specific base changes. ( ) It involves endonucleolytic cleavage and helicase-mediated strand removal. ( ) It involves cleavage by the AP endonuclease. ( ) It is coupled to the DNA transcription machinery of the cell.

In cells that are exposed to sunlight, ultraviolet (UV) light can result in covalent linkage between two adjacent DNA bases. If not repaired in time, such dimers can lead to inheritable mutations. Consider the sequence 5?-GGTATGATCATTATAA-3? in the chromosome of a cell that is exposed to intense sunlight. How many possible dimers can form in the region of DNA double helix corresponding to this sequence?

Indicate whether each of the following mobile elements in Drosophila is a DNA-only transposon (D), a retroviral-like retrotransposon (R), or a nonretroviral retrotransposon (N). Your answer would be a four-letter string composed of letters D, R, and N only, e.g. RRRR. ( ) P elements; these have inverted terminal repeats and move with the help of a transposase enzyme. ( ) Copia elements; these have directly repeated long terminal repeats and move with the help of a reverse transcriptase and an integrase. ( ) F elements; these are long interspersed nuclear elements (LINEs). ( ) Mariner elements; these move via a DNA intermediate.

This protein is present at every replication fork and prevents DNA polymerase from dissociating, but does not impede the rapid movement of the enzyme. Which of the following is true regarding this protein?

Examples of two general types of DNA damage are shown in the following drawing. Which type of damage (1 or 2) is more common in our cells?

The mutation rate in bacteria is about 3 nucleotide changes per 10 billion nucleotides per cell generation. Under laboratory conditions, bacteria such as Escherichia coli can divide and double in number about every 40 minutes. If a single Escherichia coli cell is allowed to exponentially divide for 10 hours in this manner, how many mutations would you expect to observe on average in the genome (4.5 million nucleotide pairs) of each of the resulting bacteria compared to the original cell? Assume all mutations are neutral; that is, they do not affect the cell-division time.

Which of the following is correct regarding the mutation rate of genomic DNA in different organisms?

During DNA replication in the cell, DNA primase makes short primers that are then extended by the replicative DNA polymerases. These primers …

On average, errors occur in DNA synthesis only once in every ten billion nucleotides incorporated. Which of the following does NOT contribute to this high fidelity of DNA synthesis?

Which of the following is NOT correct regarding long and short interspersed nuclear elements?

Fill in the gap in the following paragraph using what you know about the activities of the proteins involved in DNA replication. "Mitochondrial DNA replication requires a set of proteins similar to those used for the replication of the nuclear genome. However, mitochondria lack a dedicated DNA ... and use the mitochondrial RNA polymerase instead."