Matthew E. Jurek Week 5

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(Saccharomyces Genome Database: put a space between the image and the link)
(Posted KEGG and Reactome questions)
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via [http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13 Superpathway of glutamate biosynthesis]
via [http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13 Superpathway of glutamate biosynthesis]
* 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.''
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==KEGG==
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* Find the pathway we have been discussing in the [http://www.genome.jp/kegg/pathway.html 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.
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* 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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** 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.
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** 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?
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** 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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==Reactome==
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* [http://www.reactome.org/ReactomeGWT/entrypoint.html Reactome] is a third pathway database.  Find our pathway for yeast in this 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.

Revision as of 20:23, 14 February 2013

Matthew E. Jurek BIOL398-03/S13

Contents

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.

Image: pathway.jpg

via Superpathway of glutamate biosynthesis

  • What parameters for these reactions can you find using this database? HINT: the literature portion of the individual gene pages may be helpful.

KEGG

  • 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?

Reactome

  • Reactome is a third pathway database. Find our pathway for yeast in this 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.
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