Paul Magnano: Week 5 Individual Journal

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User: Paul Magnano BIOL398-03/S13:Week 5

Saccharomyces Genome Database

  • Which of these genes has a homolog (similar gene related by descent) in humans? What disease does a deficiency of this gene cause in humans?
  • How is the expression of each of these genes regulated?
  • Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?
  • Find the SGD representation of the pathway we are working on in class and attach a screenshot and hyperlink to your journal page. Choose the one that shows all of the reactions we talked about in class and make sure you can relate it to your notes, matching the genes, enzyme names, and reactants/products.
  • What parameters for these reactions can you find using this database? HINT: the literature portion of the individual gene pages may be helpful.

KEGG

  • Take a screenshot of the pathway and then edit it in a graphics program (PowerPoint would work for this) to circle and label the enzymes we are talking about in class. KEGG uses enzyme commission numbers instead of gene or enzyme names to label the reactions. These numbers are a classification system for the type of enzymatic reaction carried out by the enzyme.
  • KEGG also uses a system where a "master" summary pathway compiled from many different organisms is then highlighted with the organism-specific enzymes/genes. How many genes in this pathway exist in yeast?
  • Click on each of the five enzymes of our pathway and read the individual enzyme pages. Is there any new information here that was not represented by SGD?


=Reactome

  • Take a screenshot of the pathway and then edit it in a graphics program (PowerPoint would work for this) to circle and label the enzymes we are talking about in class.
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