Matthew E. Jurek Week 5: Difference between revisions

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(→‎Saccharomyces Genome Database: answered question about L-glutamate)
(→‎Saccharomyces Genome Database: deleted a space in the GLT1 answer of expression)
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**''GDH2''- Expression is regulated by nitrogen catabolite repression and intracellular ammonia levels. [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GDH2 GDH2]
**''GDH2''- Expression is regulated by nitrogen catabolite repression and intracellular ammonia levels. [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GDH2 GDH2]
**''GLN1''- Expression is regulated by nitrogen source and by amino acid limitation. [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GLN1 GLN1]
**''GLN1''- Expression is regulated by nitrogen source and by amino acid limitation. [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GLN1 GLN1]
**''GLT1'' - Expression is regulated by nitrogen source. [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GLT1 GLT1]
**''GLT1''- Expression is regulated by nitrogen source. [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GLT1 GLT1]
* Using the [http://pathway.yeastgenome.org/cpd-search.shtml compound search tool of SGD], search on "L-glutamate".  How many pathways does it participate in?
* Using the [http://pathway.yeastgenome.org/cpd-search.shtml compound search tool of SGD], search on "L-glutamate".  How many pathways does it participate in?
**"L-glutamate" participates in 26 pathways as a reactant and 30 as a product.  It is also found in a number of reactions that have not yet been assigned a pathway. [http://pathway.yeastgenome.org/YEAST/new-image?type=COMPOUND&object=GLT L-glutamate]
**"L-glutamate" participates in 26 pathways as a reactant and 30 as a product.  It is also found in a number of reactions that have not yet been assigned a pathway. [http://pathway.yeastgenome.org/YEAST/new-image?type=COMPOUND&object=GLT L-glutamate]
* 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.
* 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.''
* What parameters for these reactions can you find using this database?  ''HINT:  the literature portion of the individual gene pages may be helpful.''

Revision as of 12:53, 14 February 2013

Matthew E. Jurek BIOL398-03/S13

Assignment Page

User Page

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 the following homologs in humans: GLUD1 and GLUD2. Deficiencies in these result in hyperinsulinism-hyperammonemia syndrome as well as other neurological disorders. GDH2
  • How is the expression of each of these genes regulated?
    • GDH1- Expression is regulated by carbon and nitrogen sources. GDH1
    • GDH3- Expression is regulated by carbon and nitrogen sources. GDH3
    • GDH2- Expression is regulated by nitrogen catabolite repression and intracellular ammonia levels. GDH2
    • GLN1- Expression is regulated by nitrogen source and by amino acid limitation. GLN1
    • GLT1- Expression is regulated by nitrogen source. GLT1
  • Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?
    • "L-glutamate" participates in 26 pathways as a reactant and 30 as a product. It is also found in a number of reactions that have not yet been assigned a pathway. L-glutamate
  • 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.
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