It has been shown that infectious agents such as viruses often exert a dramatic effect on their host cell's genome architecture. In many cases, viruses induce methylation of host DNA sequences in order to enhance their infectivity. What specific host gene functions would you consider as strong candidates for such methylation by infecting viruses?

A 1-mL sample of the bacterium E. coli is exposed to ultraviolet light. The sample is used to inoculate a 500-mL flask of complete medium that allows growth of all bacterial cells. The 500-mL culture is grown on the benchtop, and two equal-sized samples are removed and plated on identical complete-medium growth plates. Plate 1 is immediately wrapped in a dark cloth, but plate 2 is not covered. Both plates are left at room temperature for 36 hours and then examined. Plate 2 is seen to contain many more growing colonies than plate 1.

Thinking about DNA repair processes, how do you explain this observation?

A strain of E. coli is identified as having a null mutation of the RecA gene. What biological property do you expect to be absent in the mutant strain? What is the molecular basis for the missing property?

You have identified five genes in S. cerevisiae that are induced when the yeast are grown in a high-salt (NaCl) medium. To study the potential roles of these genes in acclimation to growth in high-salt conditions, you wish to examine the phenotypes of loss- and gain-of-function alleles of each. How would your answer differ if you were working with tomato plants instead of yeast?

You have identified five genes in S. cerevisiae that are induced when the yeast are grown in a high-salt (NaCl) medium. To study the potential roles of these genes in acclimation to growth in high-salt conditions, you wish to examine the phenotypes of loss- and gain-of-function alleles of each. How will you do this?

The SOS repair genes in E. coli are negatively regulated by the lexA gene product, called the LexA repressor. When a cell's DNA sustains extensive damage, the LexA repressor is inactivated by the recA gene product (RecA), and transcription of the SOS genes is increased dramatically. One of the SOS genes is the uvrA gene. You are a student studying the function of the uvrA gene product in DNA repair. You isolate a mutant strain that shows constitutive expression of the UvrA protein. Naming this mutant strain uvrA^C, you construct the diagram shown above in the right-hand column showing the lexA and uvrA operons:

Outline a series of genetic experiments that would use partial diploid strains to determine which of the two possible mutations you have isolated.

Describe the 'end-replication problem' in eukaryotes. How is it resolved?