BIOL398-01/S11:Week 4

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.

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 Michaelis-Menten.
 * 3) Chemostat reactor.
 * 4) Exponential growth.

Applying Michaelis-Menten Models
E + S &harr; ES &rarr; E + 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. You may use the matlab code provided at my lionshare folder.
 * Consider a single substrate being converted to product.
 * 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.

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?