Enzyme Kinetics Computer Simulation

When you click Submit (at the bottom of this web page) it will save your work on the server for me.

DO NOT Click submit more than once!

TAB OR USE THE MOUSE Between the fields....

Answer the questions as best you can. The boxes will expand as you type if you need more space. (Don't worry if it is a one word answer. The box size is standard.)

Name:

(Include all the names in your group (last name, first). Maximum group size = 3.

This assignment requires that you install a program (NetLogo) on your computer.
The program is available for almost every kind of computer.  You have to register, but, it is fairly straighforward.
http://ccl.northwestern.edu/netlogo/download.shtml

This model is quite sophisticated and unless you follow the directions, may be above the level of freshmen in college (AP Biology).

Go slowly and FOLLOW the directions. ALL of them (especially the ones that say read!)

Do them in order, since some require your input BEFORE you run the simulation.

Open the model page. http://ccl.northwestern.edu/netlogo/models/EnzymeKinetics

Read the "WHAT IS IT?" section.

Question 1:  If the ratio of Kc/Kd is low what does that imply for the rate of catalysis? What if Kc/Kd is hight?

Start the NetLogo 5.3.1 program (not the 3D version).

Click on File. 

Click on Models Library

Click on Chemistry & Physics

Click on Chemical Reactions

Click on Enzyme Kinetics

Note there are 7 buttons and 5 sliders you can adjust.

The ticks--normal speed slider adjusts the speed of simulation. Slow and you can watch the molecules interact. Fast and you get your data faster.

Setup-restarts the model with a fixed number of enzymes (red) and the indicated number of substrate (slider labeled volume). 

Add substrate and add inhibitor buttons let you adjust the amount of substrate/inhibitor as the simulation is running. Leave them alone!

The "Pause?" button makes the simulation stop after 30 computer cycles. This allows you to measure the velocity of the reaction at the same time in each run. 

The Record V and clear MM buttons are for a simulation you will run later. For now, leave them alone.

Kc, Kd and Kr are the rate constants as indicated in the explanation on the site.

Run 1 Set:
Set the "pause?" to On
Volume Kc Kd Kr
1000 10 100 100
Click Setup and then Go to start the model. Record the Velocity after 30 "ticks." 

Run 2 Set:
Set the "pause?" to On
Volume Kc Kd Kr
1000 100 10 100
Again, click Setup and then Go to start the model. Record the Velocity after 30 "ticks."

Question 2:  Compare the two velocities in runs 1 & 2. How do they compare with what you expected in question 1.

Play for a few minutes with the simulation to familiarize yourself with the graph (green = substrate; red=enzyme substrate complex; blue=product).

Run 3 Set:
Set the "pause?" to Off
Set the ticks---faster slider to about 1/3 of the way from the left edge (so you can see what is happening.)
Volume Kc Kd Kr
500 10 10 10

Question 3: Compare the green and the blue lines. What do their paths represent? What does the red line represent. As you run out of substrate (let the simulation run for a long time) what happens to the red line? What does the red line's plateau represent?

Run 4 Set:
Set the "pause?" to Off

Let's set Kd=0 so as to reduce the number of variables

Set the ticks---faster slider to about close to the left edge (so you can see what is happening.)

Volume Kc Kd Kr
100 10 0 10

Question 4: Compare the green and the blue lines. What do their paths represent? Why does the blue line stay near zero initially? What does the red line represent. As you run out of substrate (let the simulation run for a long time) what happens to the red line? What does the red line's plateau represent?

Run 5 What happens to the velocity (rate) of the reaction as you change the amount of substrate?

Set the "pause?" to Off

Let's set Kd=0 so as to reduce the number of variables

Set the ticks---faster slider to about close to the left edge (so you can see what is happening.)

Volume Kc Kd Kr
1000 100 0 100

Watch the velocity number as the reaction progresses.

Set the "pause?" to On-this will stop the reactions after 30 computer cycles. 

Set the ticks--faster slider to faster so that you can record data quickly.

Run the simulation 10 times as below, recording the velocity after each run in a table like the one below. 

ALSO, click on Record V after each run, which will record the velocity at 30 clicks on the MM Graph.

Volume Kc Kd Kr Velocity
100 100 0 100 -
200 100 0 100 -
300 100 0 100 -
400 100 0 100 -
500 100 0 100 -
600 100 0 100 -
700 100 0 100 -
800 100 0 100 -
900 100 0 100 -
1000 100 0 100 -

Question 5: Describe the curve in the Michaelis-Menten Curve box.

What happens to the velocity of an enzyme catalyzed reaction as you increase the concentration of substrate? Why?

Remember, the boxes will expand as you type if you need more space.

Run 6 (assuming you are still with me,)

Set "pause? to Off.

Set the ticks---faster slider to mid-way (so you can see what is happening, but not sit around forever waiting for data....)

Volume Kc Kd Kr
1000 100 0 100

When the green line drops close to zero, click "go" to stop the simulation, then click the add substrate button, then start the simulation again ("go").

Click "go" to stop things, click "setup" (to restart the simulation from scratch).

Click "go" to start things again, BUT, this time click "add inhibitor" as soon as the simulation starts to run.. What happens now if you"add substrate"?

Go wild. See what you can learn from the simulation.

Question 6: What else can you tell me about how enzymes work based on this simulation?

Question 7: Read "Things to Notice", "Thiings to Try". Notice those things. Try those things. What did you learn?

Question 8: What do you think of the simulation?   There are a lot of model simulations that use this software and that you now have in the model library. Your feedback is v ery important.


       This web page is being hosted at Dr. Gottfried's mdgottfried.net account. Technical questions should be referred to drg.atm@gmail.com