---electron_transport.nlogo

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WHAT IS IT?
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This is a model of the electron transport chain that illustrates the behavior of the system when treated with poisons and uncouplers.  The space is divided into two regions: the lower region is the inside of the mitochrondrion and the upper space is the intermembrane region.  In electron transport, protons (yellow circles) are pumped into the intermembrane space in several stages (represented by the blue squares) using active transport and, when there is a strong enough proton gradient, they diffuse back into the inside the mitochrondion through ATP synthase (represented by red squares).  As each proton is pumped across the membrane, NADH is converted to NAD+ (consuming reducing power produced in other reactions in the cell).  As each proton diffuses back into the mitochondrion, ATP synthase captures the energy to phosphorylate ADP to ATP (which provides energy that is consumed in other reactions in the cell).

HOW IT WORKS
------------
Protons that are in the lower space can move into the upper space through the blue squares, but this can only occur when NADH is available to be reduced to NAD.  Furthermore, the propability reduces as the concentration gradient increases. Poisoning ET prevents protons from being pumped into the intermembrane space.  

Protons in the upper spaces can move into the lower space through the red squares, but only when there are more than 10 more protons in the upper than in the lower space and only when ADP is available.  Poisoning ATP synthase prevents protons from diffusing into the inside.

HOW TO USE IT
-------------
Click the "setup" button to reset all of the parameters.

Click "go" to begin the simulation.

Switches are provided that can poison ATP synthase (poison_AS), poison an element in the electron transport chain (poison_ET), or add uncouplers to the system.  

Two sliders allow control of how quickly ATP and NAD are consumed in other reactions in the cell (which control availability of ATP and NADH, which are required for the electron transport chain to function).

Use the Proton Gradient graph to see numbers of protons in the mitochondrial matrix versus the intermembrane space.

Use the ADP-ATP NADH-NAD+ graph to see numbers of available ADP, ATP, NADH, and NAD+ molecules.

Use the ATP and NAD+ Rates graph to see a rolling average of the previous 40 units of time to see rates of production of ATP and NAD+.


THINGS TO NOTICE
----------------
When the electron transport chain begins, which is produced first: NAD or ATP?  When various factors cause the chain to quit functioning, are both NAD and ATP production shut down at the same time?  Which follow the other?  Under what conditions? 


THINGS TO TRY
-------------
Try to figure out how to produce NAD without producing ATP.

Can you produce ATP without producing NAD?  How or why not?


EXTENDING THE MODEL
-------------------
How could you speed up the rates of ATP or NAD production?


CREDITS AND REFERENCES
----------------------
Brewer, S.D. (2004).  Electron Transport: Simulating Proton Gradient,
ADP-ATP, and NADH-NAD+ Interactions.  
http://bcrc.bio.umass.edu/netlogo/models/ElectronTransport/
Biology Computer Resource Center

In other publications, please use:
Copyright 2004 by Steven Brewer.  All rights reserved.  See
http://bcrc.bio.umass.edu/netlogo/models/ElectronTransport/

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