Sarah Carratt: Week 4: Difference between revisions

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==Instructions==
==Instructions==


=== Terminology ===
TERMINOLOGY: Define the four terms.


* Explain the following terms in your own words.
MM MODELS: Plot the three examples.
# The Michaelis-Menten model of enzyme kinetics.
# The experiment required for the Lineweaver-Burk approach to estimating parameters for Michealis-Menten.
# Chemostat reactor.
# Exponential growth.


=== Applying Michealis-Menten Models ===
MM PARAMETERS: Apply the Lineweaver-Burk technique to determine Vmax and K.


* Consider a single substrate being converted to product.
==Student Response==
''E'' + ''S'' ↔ ''ES'' → ''E'' + ''P''
[[User:Sarah Carratt|Sarah Carratt]] 21:00, 6 February 2011 (EST)
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. 
# 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 ===
=== Terminology ===
* Consider the following data:
[[Image:Exponential.jpg|thumb|Exponential Growth Population Example]]


[S] = 11.0,    16.7,    20.0,   25.0,    33.3,    50.0
# 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.  
# 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.  
#  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.    
# '''Exponential growth''' looks very similar to e<sup>x</sup> when graphed (pattern: more product=faster growth).


V  = 0.00952, 0.01111, 0.01282, 0.01515, 0.01852, 0.02128
=== Applying Michealis-Menten Models ===


Apply the Lineweaver-Burk technique to determine Vmax and K.
[[Image:Carratt_MMPlot1.jpg|k1 = 2.0, k-1 = 0.0, k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0]]
[[Image:Carratt_MMPlot2.jpg|k1 = 2.0, k-1 = 1.0, k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0]]
[[Image:Carratt_MMPlot3.jpg|k1 = 2.0, k-1 = 5.0, k2 = 1.0, k2 = 2.0, k2 = 5.0, k2 = 10.0]]


== Online Sources ==
=== Estimating Michaelis-Menten Parameters ===
 
* [http://www.biology-online.org/dictionary/Main_Page/ Biology Dictionary]


==Student Response==
V<sub>max</sub> = 0.031551


K = 27.10932


{{Template:SarahCarratt}}
{{Template:SarahCarratt}}

Latest revision as of 19:00, 6 February 2011

Instructions

TERMINOLOGY: Define the four terms.

MM MODELS: Plot the three examples.

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

Student Response

Sarah Carratt 21:00, 6 February 2011 (EST)

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

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


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Class Notes

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