Sarah Carratt: Week 4: Difference between revisions

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=== Applying Michealis-Menten Models ===
=== Applying Michealis-Menten Models ===


* Consider a single substrate being converted to product.
# [[Image:Carratt_MMPlot1.jpg|k1 = 2.0, k-1 = 0.0, k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0]]
''E'' + ''S'' ↔ ''ES'' → ''E'' + ''P''
# [[Image:Carratt_MMPlot2.jpg|k1 = 2.0, k-1 = 1.0, k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0]]
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. 
# [[Image:Carratt_MMPlot3.jpg|k1 = 2.0, k-1 = 5.0, k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0]]
# Set k<sub>1</sub> = 2.0, k<sub>-1</sub> = 0.0.  Plot the substrate dynamics for k<sub>2</sub> = 1.0, k<sub>2</sub> = 2.0, k<sub>2</sub> = 5.0, k<sub>2</sub> = 10.0 all on the same graph to see the effect of this parameter.
# Set k<sub>1</sub> = 2.0, k<sub>-1</sub> = 1.0.  Plot the substrate dynamics for k<sub>2</sub> = 1.0, k<sub>2</sub> = 2.0, k<sub>2</sub> = 5.0, k<sub>2</sub> = 10.0 all on the same graph to see the effect of this parameter.
# Set k<sub>1</sub> = 2.0, k<sub>-1</sub> = 5.0.  Plot the substrate dynamics for k<sub>2</sub> = 1.0, k<sub>2</sub> = 2.0, k<sub>2</sub> = 5.0, k<sub>2</sub> = 10.0 all on the same graph to see the effect of this parameter.
You may use the matlab code provided at [https://lionshare.lmu.edu/xythoswfs/webview/fileManager.action?x=y&shareLogin=false&stk=7B20EDA3576916A my lionshare folder].


=== Estimating Michaelis-Menten Parameters ===
=== Estimating Michaelis-Menten Parameters ===

Revision as of 15:15, 6 February 2011

Instructions

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 + S ↔ ES → 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.

  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.

Online Sources

Student Response

Terminology

Exponential Growth Population Example
  1. The Michaelis-Menten equation is used to mathematically illustrate the biological conversion of a substrate and enzyme to a complex and then to a product.
  2. The Lineweaver-Burk experiment is an example of the Michaelis-Menten equation in action. The results were obtained by manipulating the original equation (ie: taking the reciprocal) and converting the MM equation into mx+b format.
  3. A chemostat reaction is a "test" to find the equilibrium point of a system, where the amount of substance consumed equals the amount produced or the amount into the system equals the amount going out.
  4. Exponential growth looks very similar to ex when graphed (pattern: more product=faster growth).

Applying Michealis-Menten Models

  1. k1 = 2.0, k-1 = 0.0, k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0
  2. k1 = 2.0, k-1 = 1.0, k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0
  3. k1 = 2.0, k-1 = 5.0, k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0

Estimating Michaelis-Menten Parameters

Vmax = 0.031551

K = 27.10932



Navigation Guide

Individual Assignments

Sarah Carratt: Week 2 Sarah Carratt: Week 6 Sarah Carratt: Week 11
Sarah Carratt: Week 3 Sarah Carratt: Week 7 Sarah Carratt: Week 12
Sarah Carratt: Week 4 Sarah Carratt: Week 8 Sarah Carratt: Week 13
Sarah Carratt: Week 5 Sarah Carratt: Week 9 Sarah Carratt: Week 14

Class Assignments

Shared Journal: Week 1 Shared Journal: Week 6 Shared Journal: Week 11
Shared Journal: Week 2 Shared Journal: Week 7 Shared Journal: Week 12
Shared Journal: Week 3 Shared Journal: Week 8 Shared Journal: Week 13
Shared Journal: Week 4 Shared Journal: Week 9 Shared Journal: Week 14
Shared Journal: Week 5 Shared Journal: Week 10

Class Notes

Sarah Carratt_1.18.11 Sarah Carratt_2.3.11 Sarah Carratt_2.22.11
Sarah Carratt_1.20.11 Sarah Carratt_2.8.11 Sarah Carratt_2.24.11
Sarah Carratt_1.25.11 Sarah Carratt_2.10.11 Sarah Carratt_3.1.11
Sarah Carratt_1.27.11 Sarah Carratt_2.15.11 Sarah Carratt_3.3.11
Sarah Carratt_2.1.11 Sarah Carratt_2.17.11 Sarah Carratt_3.8.11

Internal Links

BIOL398-01/S11:Assignments BIOL398-01/S11:People BIOL398-01/S11:Sarah Carratt
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