LauraTerada Individual Journal Assignment Week 5: Difference between revisions
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**In reactions not assigned to pathways: 12 | **In reactions not assigned to pathways: 12 | ||
*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. | ||
[[Image:Screen shot 2013-02-12 at 11.59.34 PM.png|thumb|center|Screenshot of the reaction we talked about in class. Source: <i>Saccharomyces</i> Genome Database (SGD), 2013.]] | |||
<center>[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13&detail-level=4&detail-level=3 Link to Pathway on SGD Website]</center> | |||
*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 18:13, 13 February 2013
Exploring Pathway Databases
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?
- The GDH2 gene has a homolog in humans (GLUD1 and GLUD1), and deficiencies of these genes are linked to hyperinsulinism-hyperammonemia syndrome and several other neurological disorders.
- How is the expression of each of these genes regulated?
- GDH1 is levels are high by both ethanol and glucose, two carbon sources. GDH1 is regulated under fermentative growth conditions to undergo glutamate biosynthesis.
- GDH3 is regulated by ethanol and glucose concentrations. Ethanol induces GDH3 expression; however, glucose represses it. GDH3 is is required to balance levels of alpha-ketoglutarate, glutamate, and cell metabolism.
- GDH2 expression is regulated transcriptionally by elements that act as upstream activation sites and as upstream repression sites. GDH2 is also regulated under nitrogen concentrations; when nitrogen (glutamate) is high, transcription of GDH2 is repressed. Moreover, in situations of high ammonia intracellular concentration, GDH2 expression decreases. When extracellular ammonia concentrations increase, GDH2 transcription level decreases.
- GLN1 codes for glutamine synthetase, and it is regulated by ammonia concentration.
- GLT1 gene expression is regulated by glutamate repression and GLN3 activation. This regulation is ultimately dependent on nitrogen and glutamate concentration. With low amounts of amino acid, GLT1 expression is also regulated by GCN4.
- Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?
- As either reactant or product: 56
- In reactions not assigned to pathways: 12
- 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.
