Select any six problems and provide careful, detailed, well-worked out answers. Problem sets should be word processed; I prefer them sent to me electronically, however, dead trees are acceptable.

Some problems are short and relatively easy, others require more extensive work. Provide thorough and complete answers. No question can be answered with just a sentence or two, but no question should require more than one page for a satisfactory answer. I will not complain about additional length if the content is of high quality.

• Be sure to cite any resources other than class notes that you use in preparing your answers. Do NOT simply copy something from a book or paper; use your own words.

• When I suggest a paper as a starting point, read it thoroughly, but do NOT use it as your only resource!

• Some of these problems will seem kind of open-ended; they are intended to be. What I want you to do is pick something you think you'd like to know more about, and check it out.

1. Restriction endonucleases were first discovered in bacteria, where they restrict the growth of viruses by cutting foreign DNA. The restriction endonuclease EcoRI looks for the sequence GAATC. How is it that the bacteria do not cut their own DNA when this sequence is encountered? Some references that may help: (1) Meselson M., Yuan R., "DNA restriction enzyme from E. coli", Nature, 1968, 217, 1110-4; (2) Wilson G.G., Murray N.E., "Restriction and Modification Systems". Annu. Rev. Genet., 1991, 25, 585-627; (3) Kessler C., et. al. "Recognition sequences of restriction endonucleases and methylases", Gene, 1985, 33, 1-102.

2. Gene duplication has been recognized as an important part of evolution since the 1930s. Read these papers: Zhang, Trends Ecology Evol., 2003, 18, 292; Hurles, PLoS Biology, 2004, 2, 0900. Discuss how gene duplication occurs and what can happen to a duplicated gene.

3. Are language groups more closely correlated with variations in human mitochondrial DNA or Y chromosome sequences? Suggest an explanation for the observed result.

4. Locate in GenBank the b-globin gene clusters of humans, chimpanzees, an old-world monkey, and a new-world monkey. Perform a sequence alignment. then use a phylogenetic program such as Phylip to create a tree of these groups. Alternatively, if you use Jalview to do your alignment, you can create your phylogenetic tree within Jalview. Here's a link to a description of the differences between Old World and New World monkeys.

5. Renfrew et al. [Proc. Nat. Acad. Sci., 2007, 104, 8726] present evidence, based on Y chromosome sequencing, regarding the origin of aboriginal Australians. Read this paper (and such cited references as may be necessary). Describe the various hypotheses for answers to this question, the methodology employed, and the authors' conclusions.

6. Although types IA and II topoisomerases exhibit no significant sequence similarity, it has been suggested that they are distantly related based on the similarities in their mechanisms. What are these similarities? Is there any other reason to suggest a common evolutionary mechanism? [One possibly helpful source: "Untangling the Double Helix", James C. Wang, Cold Spring Harbor Press, 2009.]

7. To examine the roles of hydrogen bonds and hydrophobic interactions between transcription factors and DNA, go to FirstGlance: http://firstglance.jmol.org. Enter the PDB id 1tgh in the query box.

This file contains the crystal structure of a human TATA-binding protein and a segment of double stranded DNA.

LI>Once the structure loads, click the "Spin" button to stop the molecule from rotating. Then click the "Contacts" button. Select the radio button for "Chains". Then click on any part of the protein (displayed in blue) to select it as the target.
• Click "Show Atoms Contacting Target" to produce a list of contacts to display. Check only "Show putatively hydrogen-bonded non-water" to display hydrogen bonds between the protein and the TATA box.

• Then click the image viewing option: "Maximum Detail: Target and Contacts Balls and Sticks, Colored by Element"

• Use the zoom and rotatefunctions to answer the following questions:
  • Which of the base pairs in the DNA form hydrogen bonds with the protein? Which contribute to the specific recognition of the TATA box? (Hydrogen bonds should be no longer than 3.3 A.)

  • Which amino acids in the protein interact with the TATA box base pairs?

  • Click "Return to Contacts", and check "Show hydrophobic (apolar van der Waals) interactions". Identify the hydrophobic interactions.

Provide appropriate text and pictures to explain how the molecules interact.

8. Tumpey et al. [Science, 2005, 310, 77; Nature Biotechnol., 2009, 27, 1163] have synthesized the genome of the 1918 flu virus, which killed an estimated 36 million people worldwide. Read the papers cited, and any others you may find helpful, and discuss how the synthesis was carried out, and what was learned about the virus by analysis of its genome.

9. Bases in DNA can undergo a number of accidental chemical transformations. For example, cytosine tends to undergo spontaneous deamination to uracil. U's that occur in DNA are repaired by a three-step process in which the U is excised, producing an abasic site; the remaining sugar phosphate is then removed, and finally a new nucleotide is inserted.

The enzyme that removes the uracil is called uracil DNA glycosylase. How does it distinguish the uracil from thymine, which is the natural base present in DNA? Consult Nature, 1996, 384, 87 and PDB structure 4skn and answer this question thoroughly.