BIOL398-03/S13:Week 5

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BIOL398-03: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Friday, February 15 at midnight PST (Thursday night/Friday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

Contents

Individual Journal Assignment

  • Store this journal entry as "username Week 5" (i.e., this is the text to place between the square brackets when you link to this page).
    • Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
      • Link to your journal entry from your user page.
      • Link back from your journal entry to your user page.
      • Link to this assignment from your journal entry.
      • Don't forget to add the "BIOL398-03/S13" category to the end of your wiki page.

Exploring Pathway Databases

Explore the following pathway databases and answer the questions on your individual journal page. Illustrate your answers with screenshots and/or hyperlinks to database pages.

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
  • 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?
  • How is the expression of each of these genes regulated?
  • Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?
  • 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.

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.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 5 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL398-03/S13" category to the end of the wiki page (if someone has not already done so).

Reflection

  1. What was the purpose of this assignment?
  2. Which of the three databases did you like the most? Why?
  3. Which of the three databases did you like the least? Why?
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