BIOL398-01/S11:Week 4

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BIOL398-01: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Monday, February 07 at midnight PST (Sunday night/Monday 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 4" (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 "BIOL398-01/S11" category to the end of your wiki page.

Terminology

  • Explain the following terms in your own words.
  1. The Michaelis-Menten model of enzyme kinetics.
  2. The experiment required for the Lineweaver-Burk approach to estimating parameters for Michealis-Menten.
  3. Chemostat reactor.
  4. Exponential growth.

Applying Michealis-Menten Models

  • Consider a single substrate being converted to product.

E + SESE + P with an initial substrate concentration of 1.0 and an initial enzyme concentration of 0.05. Use the Michaelis-Menten matlab model to explore the following.

  1. Set k1 = 2.0, k-1 = 0.0. Plot the substrate dynamics for k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0 all on the same graph to see the effect of this parameter.
  2. Set k1 = 2.0, k-1 = 1.0. Plot the substrate dynamics for k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0 all on the same graph to see the effect of this parameter.
  3. Set k1 = 2.0, k-1 = 5.0. Plot the substrate dynamics for k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0 all on the same graph to see the effect of this parameter.

You may use the matlab code provided at my lionshare folder.

Estimating Michaelis-Menten Parameters

  • Consider the following data:

[S] = 11.0, 16.7, 20.0, 25.0, 33.3, 50.0

V = 0.00952, 0.01111, 0.01282, 0.01515, 0.01852, 0.02128

Apply the Lineweaver-Burk technique to determine Vmax and K.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 4 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 "BIOL398-01/S11" 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. What aspect of this assignment came most easily to you?
  3. What aspect of this assignment was the most challenging for you?
  4. What (yet) do you not understand?
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