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Exam 5: DNA Replication, Repair, and Recombination

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Question 1

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Which of the following is true regarding retroviral-like retrotransposons?

A) They encode both a reverse transcriptase and an RNA polymerase.
B) They have directly repeated long terminal repeats at their two ends when integrated into chromosomal DNA.
C) Their genomic RNA can be translated to produce viral coat proteins.
D) They leave double-strand breaks in the original donor DNA.
E) The Alu element in our genome is an example of retroviral-like retrotransposons.

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Question 2

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In Escherichia coli, replication of DNA can occur throughout the cell cycle while the cell is also actively transcribing its genes. This means collisions between replication forks and RNA polymerases are inevitable. Depending on the orientation of the genes, collisions can be rear-end (when both machines are traveling in the same direction) or head-on (when they are traveling in opposite directions). In the following paragraph, match each of the letters (A to D) to one appropriate number below. Do not use a number more than once. Your answer would be a four-digit number composed of digits 1 to 5 only, e.g. 1253. "Typically, in a rear-end collision, the (A) of RNA polymerase collides with the (B) in the replication fork. In contrast, in a head-on collision, the (C) of RNA polymerase hits the (D) in the fork." 1. front edge (of RNA polymerase) 2. rear edge (of RNA polymerase) 3. DNA helicase 4. leading-strand DNA polymerase 5. lagging-strand DNA polymerase

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The replication fork in E. coli can pr...

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Question 3

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Indicate true (T) and false (F) statements below regarding the use of homologous recombination in meiosis. Your answer would be a four-letter string composed of letters T and F only, e.g. FFFF. ( ) Meiotic recombination starts with a double-strand break caused by errors in DNA replication. ( ) Meiotic recombination occurs preferentially between DNA from maternal and paternal chromosome pairs. ( ) Holliday junctions can form during meiotic recombination, sometimes in pairs. ( ) During meiotic recombination in human cells, the majority of the invading strands are released, leading to no crossover.

Indicate true (T) and false (F) statements below regarding the initiation of replication in human cells. Your answer would be a four-letter string composed of letters T and F only, e.g. TFFF. ( ) Tens of thousands of replication origins are used each time a cell in our body replicates its DNA. ( ) Different cells in our body use different sets of replication origins. ( ) Both replication forks in a replication bubble are normally active in replication. ( ) Gene expression and chromatin structure can affect the choice of the origins to use as well as the order in which they are activated.

As shown in the following drawing, a researcher has engineered three pairs of LoxP sites (for conservative site-specific recombination) in a region that contains three reporter genes coding for red, yellow, or cyan fluorescent proteins, respectively. Each type of LoxP sequence (shown as a black, gray, or white arrowhead) is specific, meaning it does not recombine with the other types of LoxP sequences. Upon Cre recombinase activation, depending on which recombination event occurs first (which we assume is random), a number of possible combinations of reporters can remain in the final DNA. For each of the following combinations, indicate whether it can (C) or cannot (N) result from this recombination scheme. Do not consider the re-integration of excised DNA, which happens very rarely. Your answer would be a six-letter string composed of letters C and N only, e.g. CCCCNN. ( ) Red and yellow ( ) Red only ( ) Yellow only ( ) Cyan only ( ) Yellow and cyan ( ) Red and cyan

In meiosis, a crossover in one position is thought to inhibit crossing-over in the neighboring regions. This regulatory mechanism …

Which of the following spontaneous lesions in DNA occurs most frequently in a mammalian cell?

In which phases of the eukaryotic cell cycle does homologous recombination often occur to repair DNA damage?

Phase variation helps protect the bacterium Salmonella typhimurium against the immune system of its host by switching the orientation of a certain promoter. This process …

Sort the following steps in the order that they normally happen during the process of repairing double-strand breaks by homologous recombination. Your answer would be a six-letter string composed of letters A to F only, e.g. DEFABC. (A) Ligation (B) DNA synthesis using undamaged DNA as the template (C) DNA synthesis using original DNA as the template (D) Release of the invading strand (E) Strand invasion (F) Nuclease digestion (resection)

Upon heavy damage to the cell's DNA, the normal replicative DNA polymerases may stall when encountering damaged DNA, triggering the use of backup translesion polymerases. These backup polymerases …

Which of the following schematic drawings better depicts the end of mammalian chromosomal DNA?

The sliding clamp and the DNA helicase that function at the replication fork both have three-dimensional structures resembling a ring with a central hole through which DNA is threaded. Which of these proteins, the clamp (C) or the helicase (H), do you think has a wider hole in its structure? Write down C or H as your answer.

What group of mobile genetic elements is largely responsible for the resistance of the modern strains of pathogenic bacteria to common antibiotics?

In the following schematic drawing of a Holliday junction that undergoes branch migration, cutting at which combination of the sites a to d would generate a crossover?

This protein folds into a doughnut shape that can encircle DNA. It can load on the DNA only when the DNA is broken in both strands, so that the DNA can thread through the hole in the protein. Which of the following proteins do you think matches this description?

A replication fork is shown schematically below. The strand labeled A is called the … strand.

Fill in the blank in the following paragraph. Do NOT use abbreviations. "In human cells, the predominant pathway to repair double-strand breaks is …, in which the broken ends are simply rejoined with the concomitant loss of a few nucleotides. This leaves scars at the breakage sites. This pathway can potentially create chromosome translocations."

During DNA replication, the single-strand DNA-binding (SSB) proteins …

In the following schematic drawing, two DNA molecules are shown before and after the action of a protein that is also involved in the process of DNA replication. What is this protein called?