1. Eukaryotic origins of DNA replication are regulated so that DNA is only replicated once per cell cycles. Explain the major points of regulation of this process in eukaryotes.
2. Name three common ways in which DNA lesions are incurred. What is required for these DNA lesions to result in a mutation?
3. The human disease known as Xeroderma Pigmetosum (XP) arises from mutations in at least seven different genes. The resulting deficiencies are generally in enzymes associated with some part of the pathway for nucleotide excision repair. The various types of XP are denoted A through G (XPA, XPB...XPG), with some additional variants classified together as XP-V. Fibroblast cultures from healthy individuals and those from patients with XPG are irradiated with UV light. The DNA is isolated from these cells, denatures and the resulting single stranded DNA is examined by ultracentrifugation.
a. Samples from the normal fibroblasts show a significant reduction in the average molecular weight of the single-stranded DNA after irradiation but samples from the XPG fibroblasts show no such reduction. Why not?
b. If you assume that an NER system is operative in the fibroblasts, which step might be defective in the cells of patients with XPG? Explain.
4. In eukaryotes most genes are normally turned off and RNA polymerases do not function without activation. In bacteria RNA polymerase can transcribe almost any gene in the absence of bound inhibitors. Suggest two reasons for this different between bacteria and eukaryotes. Explain your reasoning.
5. There are roughly 3000 transcription factors encoded by the human genome and thus control the expression of human genes. However, there are more than 20000 genes. Explain how specific gene activation can be achieved when there are tenfold fewer gene activators than there are genes.
6. Suggest and defend three different cellular mechanisms that could establish a gradient of either a protein or an mRNA during maturation of an oocyte.
7. This question is double weighted.
In class we discussed various types of microarray-type assays. Design a series o experiments aimed that uses two different types of microarrays to:
a. Identify a gene that encodes a specific protein, the expression of which is controlled by a salt-stress activated transcription factor (microarray type 1).
b. Once you have explained how you will identify this gene, design a subsequent experiment that uses the second type of microarray to identify genes whose expression is altered by the presence or absence of the protein described in part a.