Name:

Biology 102

Genome Exercise

due noon Tuesday May 28

(email submissions are fine)

You will find an interactive genome exercise linked to the course Web site on the page for today’s topic. Follow the instructions to learn more about genome resources. Be sure to read carefully and think about what you’re doing—the 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

b.One plant whose genome has been sequenced

c.One insect whose genome has been sequenced

d.One mammal other than humans whose genome has been sequenced

2.Basic information about your protein:

a.Which protein did you choose?

b.What organism is it found in?

c. What is the accession number?

d.How many amino acids long is your protein?

e.Using the three-letter code, what are the protein’s first three amino acids?

f.Briefly describe in your own words the function of your protein in the model organism:

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)?

4.Using the information in the Gene and CCDS databases, find out a little about the gene itself:

a.Which chromosome is the human gene located on?

b.Using the three-letter code, what are the protein’s first three amino acids?

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

d.How many introns does your gene have?

e.How long is theactual coding sequence of your gene?

f.Briefly describe in your own words the function of the human protein:

5.Tell what human disease this gene is associated with, and in your own words, in two or three sentences summarize what you learned about the disease from OMIM (this means, don’t cut and paste from OMIM: look up medical terms that you don’t know and summarize very briefly). Don’t put information about the gene or what the normal or mutant protein does here; just tell a little about the disease itself.

6.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?

7.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 don’t have to go to PubMed for this—there are references listed in some of the database information you saw during the exercise.

8.Now that you have some tools for looking at genomic information, let’s see if you can apply them to a new problem. Below, please give the first 15 nucleotides of the coding sequenceofthe human RPE65 gene, and the corresponding first 5 amino acids of the RPE65 protein.

9.How many exons does the RPE65 gene have?