BIO520 Final Exam part 2 Spring 2008

Please email this lab to Jim Lund (jiml@uky.edu) or Yeshi (tgyeshi@uky.edu) with a subject line "BIO520 Final Exam" and name the document like so: "LundJ_final" or hand in written answers. Fill in your name on the exam!

You may use any books, notes, web pages, software programs, or related materials to complete this exam. You MAY NOT consult with any person regarding the exams intellectual content.

Exam links

1. This question concerns the human melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor).

a. (2 pts) Give the accession numbers for the RefSeq protein and nucleotide entries for this gene.

b. (1 pt) Give the chromosomal location of this gene (you will be more familiar with the Map Viewer than with the new Sequence Viewer).

c. (1 pt) Is this gene experimentally verified? Fully or partially?

d. (1 pt) Does this gene show alternate splicing?

e. (2 pt) Is this gene and nearby genes part of a segment of conserved synteny with mouse? What is the corresponding region in mouse?

f. (2 pt) What human phenotypes are associated with variants in this gene? Give your source for this information.

g. (2 pt) What group of organisms is this gene found in?

h. (2 pt) Has the structure for this gene been experimentally determined? Is this surprising or to be expected and why?

i. (2 pt) Describe and give the appropriate database ID(s) for known protein domains in the human melanocortin 1 receptor.

2. This question concerns the results of BLAST search using human melanocortin 1 receptor linked at the top of the page.

a. (2 pt) What BLAST program was used and what database was searched?

b. (2 pt) Do these results include every sequence matching the human melanocortin 1 receptor in the database? Support your answer.

c. (2 pt) If you did a multiple sequence alignment of the most distant matches shown in this BLAST result would you be able to identify critical amino acids in this protein? Explain.

3. This question concerns the properties and localization of human melanocortin 1 receptor protein. Relevant analyses (or programs for you to use) are linked at the top of the page.

a. (2 pt) What is the predicted subcellular localization of this protein? Explain your answer.

b. (3 pt) Is this protein predicted to have membrane spanning segments? If so, how many? What is the topology of this protein (Are the N- and C-termini predicted to be cytoplasmic or extracellular)?

5. (4 pt) Use GenMark to find genes in E. coli region 1 genomic sequence linked above. Give a list of the predicted genes with start/end, strand, and a short description of each.

a. (1pt) The ENO2 gene shows a minimum expression level in the 'Cell-cycle Elutriation 0.0hrs' sample and a maximum expression in the 'Sporulation ndt80- Middle'. What is it fold expression change between these two sample points?

b. (2pts) Cluster these genes using hierarchical clustering (do not filter the genes out of the input file). Attach an image of the cluster you generate displayed in TreeView.

c. (2pts) Would k-means clustering by informative on this group of genes? Explain.

d. (2pts) Which experiment(s) do these genes show the greatest expression change in, and are is expression increased or decreased in each experiment (or experiments).

7 a.(2pts) Describe the proteins known to interact with human COMT (Catechol O-methyltransferase).

b. (2pts) With which proteins are both COMT and XRN2 known to interact?

c. (2pts) Were all the protein interactions for COMT found in one study, or do they come from multiple publications? Give citations for each interaction in (First_author, year) short format.

8 a. (3 pts) Are there conserved non-coding sequences near the human melanocortin 1 receptor? Describe each such sequences by its location relative to the human melanocortin 1 receptor (5', intron, 3') and the group of organisms in which each non-coding sequence segment is found.

b. (2 pts) Examine the ZEB2 locus. What is unusual about it?

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