Elizabeth Polidan Week5

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[[BIOL398-03/S13:Week_5|Week 5 Assignment]]
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'''Saccharomyces Genome Database - SGD'''
'''Saccharomyces Genome Database - SGD'''
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#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?  
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*GDH1, GDH2, and GDH3 have homologs in humans.
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*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?  
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**Deficiencies in the human homologs of glutamate dehydrogenase have been linked to hyperinsulinism-hyperammonemia syndrome and neurological disorders.
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**GDH2 has a homolog in humans.
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#How is the expression of each of these genes regulated?  
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***Deficiencies in the human homologs are linked to hyperinsulinism-hyperammonemia syndrome and neurological disorders.
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*GDH1 – expression regulated by Carbon and Nitrogen sources; expression high for both ethanol and glucose
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*How is the expression of each of these genes regulated?  
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*GDH3 – expression regulated by Carbon and Nitrogen sources; induced by ethanol and repressed by glucose
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**GDH1 – expression regulated by Carbon and Nitrogen sources; expression high for both ethanol and glucose
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*GDH2 – expression regulated by ammonia concentration
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**GDH3 – expression regulated by Carbon and Nitrogen sources; induced by ethanol and repressed by glucose
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*GLN1 – expression regulated by nitrogen source and by amino acid limitation
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**GDH2 – expression regulated by ammonia concentration
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*GLT1 – expression regulated by nitrogen source
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**GLN1 – expression regulated by nitrogen source and by amino acid limitation
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#Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?  
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**GLT1 – expression regulated by nitrogen source
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*L-glutamate participation in pathway reactions
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*Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?  
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**As a reactant: 26  
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**L-glutamate participation in pathway reactions
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**As a product: 30
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***As a reactant: 26  
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#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.  
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***As a product: 30
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*[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13 SGD Pathway]
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*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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*[[Image:SGD.jpg]]
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**The extensive references for these genes will provide concentrations, feed rates, limiting rates, and experimental data from which we can extract parameters.
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#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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*Answer
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[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13 SGD Pathway]
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[[Image:SGD.jpg]]
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----
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'''Kyoto Encyclopedia of Genes and Genomes - KEGG'''
'''Kyoto Encyclopedia of Genes and Genomes - KEGG'''
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*[http://www.genome.jp/kegg-bin/show_pathway?sce00250 KEGG Pathway]
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*[[Image:KEGG.jpg]]
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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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#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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**12
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*Answer
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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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#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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**Yes, for example:
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*Answer
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***Reference strings for other databases, not just links.
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***Sequences are right up front, not just links.
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***A lot of it is just presented in different ways.
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[http://www.genome.jp/kegg-bin/show_pathway?sce00250 KEGG Pathway]
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[[Image:KEGG.jpg]]
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----
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'''Reactome'''
'''Reactome'''
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*[http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=68322&FOCUS_PATHWAY_ID=2666288&ID=2666287 Reactome]
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*[[Image:REACTOME.jpg]]
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[http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=68322&FOCUS_PATHWAY_ID=2666288&ID=2666287 Reactome]
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[[Image:REACTOME.jpg]]

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Elizabeth Polidan

BIOL 398.03 / MATH 388

  • Loyola Marymount University
  • Los Angeles, CA, USA

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Week 5 Assignment

Saccharomyces Genome Database - SGD

  • 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 homolog in humans.
      • Deficiencies in the human homologs are linked to hyperinsulinism-hyperammonemia syndrome and neurological disorders.
  • How is the expression of each of these genes regulated?
    • GDH1 – expression regulated by Carbon and Nitrogen sources; expression high for both ethanol and glucose
    • GDH3 – expression regulated by Carbon and Nitrogen sources; induced by ethanol and repressed by glucose
    • GDH2 – expression regulated by ammonia concentration
    • 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?
    • L-glutamate participation in pathway reactions
      • As a reactant: 26
      • As a product: 30
  • What parameters for these reactions can you find using this database? HINT: the literature portion of the individual gene pages may be helpful.
    • The extensive references for these genes will provide concentrations, feed rates, limiting rates, and experimental data from which we can extract parameters.

SGD Pathway

Image:SGD.jpg



Kyoto Encyclopedia of Genes and Genomes - KEGG

  • 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?
    • 12
  • 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?
    • Yes, for example:
      • Reference strings for other databases, not just links.
      • Sequences are right up front, not just links.
      • A lot of it is just presented in different ways.

KEGG Pathway

Image:KEGG.jpg



Reactome

Reactome

Image:REACTOME.jpg

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