Biology, Math Modeling, Teaching

Modeling demo: enzyme kinetics

When using this demo, students can alter the reaction rate, substrate, or enzyme concentrations. The simulation motivates understanding what a basic mechanistic model of enzyme kinetics would consist of.

Screenshot_20181214-180031_Chrome.jpg

After running a simulation, the predicted dynamics of the product and substrate are plotted.

Screenshot_20181214-180132_Chrome.jpg

The model behind the simulation is:

\frac{dS}{dt} = - r*E*S\\  \frac{dE}{dt} = 0\\  \frac{dP}{dt} = r*ES

First I ask them a series of questions to motivate the model:

  1. How is the amount is substrate changing?
  2. When can substrate become product?
  3. If you had no enzyme could you get a product?
  4. How does the amount of enzyme change over time? I

Then I ask them to write how substrate and products change over time both mathematically and in English. In math language, \frac{dE}{dt} means “enzyme changing over time”. For example,

\frac{dS}{dt} = - r*E*S

means “the change in substrate over time is decreasing with the reaction rate and the amount of substrate and enzyme.”

 

 

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s