Individual Journal Week 5

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Revision as of 02:04, 15 February 2013 by Helena M. Olivieri (Talk | contribs)
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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?
    • GDH2 has a homologue in humans and can result in hyperinsulinism-hyperammonemia syndrome and various neurological disorders as a result of deficiencies.
  • How is the expression of each of these genes regulated?
    • GDH1: expression regulated by nitrogen and carbon sources
    • GDH3: expression regulated by nitrogen and carbon sources
    • GDH2: expression sensitive to nitrogen catabolite repression and intracellular ammonia levels
    • GLN1: expression regulated by nitrogen source and by amino acid limitation
    • GLT1: expression regulated by nitrogen source
  • Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?
    • As a product L-glutamate participates in 30 pathways. As a reactant it participates in 26 pathways.
  • 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.

Image:Screen Shot 2013-02-14 at 10.04.34 PM.png

  • What parameters for these reactions can you find using this database?
    • Carbon, Nitrogen, and Ammonia feed concentrations tend to be the parameters sited on the database.

KEGG

Image:Screen Shot 2013-02-14 at 11.03.54 PM.png

  • Find the pathway we have been discussing in the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Note that this is a general metabolic database, so you will need to first filter based on organism, Saccharomyces cerevisiae. Make sure you can relate it to your notes, matching the genes, enzyme names, and reactants/products.
  • 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?
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