Exam 5: DNA Replication, Repair, and Recombination

The RecA/Rad51 protein carries out strand exchange during homologous recombination. Indicate true (T) and false (F) statements about this process below. Your answer would be a four-letter string composed of letters T and F only, e.g. FFFF. ( ) RecA hydrolyzes ATP upon binding to the invading DNA strand. ( ) RecA forces the invading strand into a conformation that fully mimics the geometry of a long DNA double helix. ( ) Sampling of the homologous duplex by the invading strand is likely to occur in triplet nucleotide blocks. ( ) RecA-bound, invading, single-stranded DNA binds and destabilizes the homologous duplex to allow the sampling of its sequence by base-pairing.

Consider three types of mobile genetic elements that are found in our genome: the DNA-only transposons (D), the retroviral-like retrotransposons (R), and the nonretroviral retrotransposons (N). Which type appears to still be active and move in our genome, accounting for a detectable fraction of human mutations? Write down your answer as D, R, or N.

What are the products of deamination of cytosine and 5-methyl cytosine, respectively?

In contrast to vertebrates, there is very little DNA methylation in the genomes of invertebrates such as Drosophila melanogaster and Caenorhabditis elegans. Indicate whether you expect each of the following statements to be true (T) or false (F) regarding 5?-CG-3? dinucleotide sequences in the genome. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTT. ( ) On average, approximately one dinucleotide out of every 16 in the human genome is a CG dinucleotide. ( ) On average, approximately one dinucleotide out of every 256 in the D. melanogaster genome is a CG dinucleotide. ( ) The proportion of CG dinucleotides in the human genome is more than that of C. elegans. ( ) The proportion of CG dinucleotides in the human genome is more than that expected by chance.

If this protein complex does not function normally, the ends of the eukaryotic chromosomes would activate the cell's DNA damage response, causing chromosomal fusions and other genomic anomalies. What is this protein complex called?

What do the enzymes topoisomerase I and topoisomerase II have in common?

The Dam methylase is responsible for methylating the adenine base in GATC sequences in Escherichia coli. Imagine two

The nuclear DNA polymerases in human cells …

You have found a strain of Escherichia coli that has an unusually short doubling time of only 15 minutes, despite the fact that its complete DNA replication should take almost 35 minutes. You also find that there is only one replication origin on its chromosome from which two forks originate, just like the normal process described for E. coli. However, you discover that the origin of replication in this strain has a significantly shorter "refractory period," resulting in the reactivation of the origin before the previous round of replication is over. Based on this model, if you examine the chromosomes of this strain (under conditions of fast growth), how many replication forks would you expect to observe per chromosome on average?

DNA ligases are used in both DNA replication and repair to seal breaks in the DNA. But DNA damage can result in single- or double-strand breaks that are not normal ligase substrates. These need to be processed first before a ligase can act on them. One of the enzymes that is recruited to some of such breaks is called PNK. It has two separate activities on the DNA, both of which can help provide a canonical ligase substrate. Which of the following activities would you expect PNK to have in this context?

DNA glycosylases constitute an enzyme family found in all three domains of life. They can …