Anthony J. Wavrin Week 5: Difference between revisions

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#Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?  
#Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?  
#* L-glutamate participates in 56 pathways; 30 pathways as a product and 26 pathways as a reactant.
#* L-glutamate participates in 56 pathways; 30 pathways as a product and 26 pathways as a reactant.
#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. [[http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=PWY3O-13&detail-level=2| Link to pathway.]]
#*
[[image:AJW_SGD.gif]]
#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.
#*Throughout the literature, there were some small parameters defined such as salt concentrations.  However, the two large parameters discussed for these reactions were nitrogen, in the form of ammonia, and carbon, primarily in the form of glucose but was also used in the form of ethanol.
#*Throughout the literature, there were some small parameters defined such as salt concentrations.  However, the two large parameters discussed for these reactions were nitrogen, in the form of ammonia, and carbon, primarily in the form of glucose but was also used in the form of ethanol.
==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. [[http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=sce00250&keyword=glutamate| Link to pathway]]
[[image:AJW_kegg.png]]
#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?
#*Below the citric acid cycle, there are 19 genes with 12 of them being present in yeast (highlighted green).
#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?
#*The main difference noted between KEGG and Saccharomyces Genome Database is that KEGG has the whole amino acid and nucleotide sequence listed on the page.
==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.
#*I looked extensively for all of the reactions and subsequent enzymes that were discussed in class however, I was unable to locate GLT1 converting an alpha-ketoglutarate and glutamine to 2 glutamate. [[http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=sce00250&keyword=glutamate| Link to pathway]]
[[image:AJW_reactome.png]]
[[BIOL398-03/S13:Week_5| Week 5 Assignment]]
{{template:Anthony J. Wavrin}}

Latest revision as of 22:39, 14 February 2013

Saccharomyces Genome Database

  • Search for each of the genes encoding the enzymes in our metabolic pathway in the Saccharomyces Genome Database (SGD) and read their gene pages:
    • GDH1
    • GDH3
    • GDH2
    • GLN1
    • GLT1
  1. 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?
    • GDH1 - 1L1F ( Chain: A, B, C, D, E, F) – A deficiency in human glutamate dehydrogenase causes hyperinsulinism-hyperammonemia
    • GDH3 - 1NR1 (Chain: A, B, C, D, E, F) - A deficiency in human glutamate dehydrogenase causes hyperinsulinism-hyperammonemia
    • GDH2 - No human homolog
    • GLN1 - 2OJW – A deficiency in human glutamate synthetase is brain malformation, severe enteropathy, and necrolytic erythema.
    • GLT1 - No human homolog
  2. How is the expression of each of these genes regulated?
    • GDH1- Expression is regulated by carbon and nitrogen.
    • GDH3- Expression is regulated by carbon and nitrogen.
    • GDH2- Expression is regulated by intracellular nitrogen concentration and nitrogen catabolite repression
    • GLN1- Expression is regulated by nitrogen and amino acid limit.
    • GLT1- Expression is regulated by nitrogen.
  3. Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?
    • L-glutamate participates in 56 pathways; 30 pathways as a product and 26 pathways as a reactant.
  4. 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. [Link to pathway.]

  1. What parameters for these reactions can you find using this database? HINT: the literature portion of the individual gene pages may be helpful.
    • Throughout the literature, there were some small parameters defined such as salt concentrations. However, the two large parameters discussed for these reactions were nitrogen, in the form of ammonia, and carbon, primarily in the form of glucose but was also used in the form of ethanol.

KEGG

  1. 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. [Link to pathway]

  1. 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?
    • Below the citric acid cycle, there are 19 genes with 12 of them being present in yeast (highlighted green).
  2. 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?
    • The main difference noted between KEGG and Saccharomyces Genome Database is that KEGG has the whole amino acid and nucleotide sequence listed on the page.

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.
  1. 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.
    • I looked extensively for all of the reactions and subsequent enzymes that were discussed in class however, I was unable to locate GLT1 converting an alpha-ketoglutarate and glutamine to 2 glutamate. [Link to pathway]


Week 5 Assignment

Links

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