Anthony J. Wavrin Week 5
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:
- 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
- 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.
- 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.
- 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.
- 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.