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Name: Fey Ali

Biology 102Genome 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 toread carefully and think about what youre doingthe objective is not just to get theanswers, 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. Basic information about your protein: AAF36695

a. Which protein did you choose? Ferroportin1

b. What organism is it found in? Danio Rerio

c. How many amino acids long is your protein? 562

d. 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-organismprotein 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 2b. Using the three-letter code, what are the proteins first three amino acids?

Met-Thr-Arg

c. How long is the gene, in base-pairs (bp) of DNA? 190,425,315

d. How many introns does your gene have? 7

e. How long is the actual coding sequence of your gene? 1713

f. Briefly describe in your own words the function of the human protein:SLC40A1 export siron from intestinal cells.

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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 pastefrom 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 alleleproduces 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 ofiron 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 autosomaldominant, 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 thedeletion of a valine. This deletion results in an altered function of SLC40A1 gene, which impairsiron 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 databaseinformation you saw during the exercise.

De Domenico, I., Ward, D. M., Nemeth, E., Vaughn, M. B., Musci, G., Ganz, T., Kaplan, J. The molecularbasis 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 ofthe 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

http://ghr.nlm.nih.gov/gene/SLC40A1http://depts.noctrl.edu/biology/courses/102/genome/frame3.htmhttp://ghr.nlm.nih.gov/gene/SLC40A1http://depts.noctrl.edu/biology/courses/102/genome/frame3.htm