Name: Fey Ali

Biology 102 Genome Exercise (6 points)

You will find an interactive genome exercise linked to the course Web site on the page for todays topic. Follow the instructions to learn more about genome resources. Be sure to read carefully and think about what youre doingthe objective is not just to get the answers, but to learn about the genome and how to investigate it. Answer the questions below by using Microsoft Word and typing in the grey boxes. Save the completed worksheet to your F: drive or flash drive for future reference, print out a copy and turn it in. 1. From the GNN Web page, list: a. One bacterium whose genome has been sequenced Anabaena b. One plant whose genome has been sequenced Arabidopsis Thaliana c. One insect whose genome has been sequenced Anopheles Gambiae d. One mammal other than humans whose genome has been sequenced Gallus Gallus 2. a. b. c. d. Basic information about your protein: AAF36695 Which protein did you choose? Ferroportin1 What organism is it found in? Danio Rerio How many amino acids long is your protein? 562 Using the three-letter code, what are the proteins first three amino acids?
Met-Asp-Ser

e. Briefly describe in your own words the function of your protein in the model organism:
Ferroportin 1 is an iron regulted transport memebrane protein, mutatuions of this protein is commonly expressed in zebrafish (malfunction in the regulation of iron cycling).

3. What protein involved in human disease did you find that was similar to the model-organism protein you chose (give its official gene symbol from the Gene database)? SLC40A1 Solute Carrier Family 40, Membrane 1. 4. Using the information in the Gene and CCDS databases, find out a little about the gene itself: a. Which chromosome is your gene located on? Chromosome 2 b. Using the three-letter code, what are the proteins first three amino acids?
Met-Thr-Arg

c. d. e. f.

How long is the gene, in base-pairs (bp) of DNA? How many introns does your gene have? How long is the actual coding sequence of your gene? Briefly describe in your own words the function of the human protein:
SLC40A1 export siron from intestinal cells.

190,425,315

7
1713

6. Tell what human disease this gene is associated with, and in your own words, very briefly summarize what you learned about the disease from OMIM (this means, dont cut and paste from OMIM: look up medical terms that you dont know and summarize very briefly). Dont put information about the gene or what the normal or mutant protein does here; just tell a little about the disease itself. There are 15 identified mutations in SLC40A that result in 4 types of Hemochromatosis. Hemochromatosis is a metoblic disorder resulting from iron overload, or the excess absorption of iron in the intestinal tracks. http://ghr.nlm.nih.gov/gene/SLC40A1 http://depts.noctrl.edu/biology/courses/102/genome/frame3.htm 7. Find a specific allele of your gene that causes disease and tell a little about how that allele produces the disease. For example, is it a missense, nonsense or frameshift mutation? Does it prevent the protein from being produced at all, alter its function, affect splicing or have some other effect? Is it a dominant or recessive allele? Is it sex-linked or autosomal? Ferroprotin 1 is an iron regulating trans-membrane protein responsible for the cycling of iron and most 15 identified mutations result in the 4 identified hemochromatosis in which results in a change in amino acid sequence that restricts the transport and releases iron, causing build up of iron in the intestinal track. Hemochromatosis 4 is autosomal dominant, all others are autosomal recessive. Hemochromatosis type 4 is due to a missence mutation in the 2q32 allele. There are three base pair deletions resulting in the
deletion of a valine. This deletion results in an altered function of SLC40A1 gene, which impairs iron homeostasis in response to hepcidin.

8. Give one specific reference from the scientific literature that would be a possible source of more information on your gene (the journal, year, volume and pages will be enough). Hint: you dont have to go to PubMed for thisthere are references listed in some of the database information you saw during the exercise.
De Domenico, I., Ward, D. M., Nemeth, E., Vaughn, M. B., Musci, G., Ganz, T., Kaplan, J. The molecular basis of ferroportin-linked hemochromatosis. Proc. Nat. Acad. Sci. 102: 8955-8960, 2005. [PubMed: 15956209]

9. Now that you have some tools for looking at genomic information, lets see if you can apply them to a new problem. Below, please give the first 15 nucleotides of the coding sequence of the human RPE65 gene, and the corresponding first 5 amino acids of the RPE65 protein.
Ala-Thr-Ala-Ala-Gly-Ala-Gly-Cys-Thr-Gly-Gly-Gly-Cys-Cys-Cys Met-Phe-Ala-Ile-Gln

10. How many exons does the RPE65 gene have?

14