Mitochondrial Electron Transport Chain

This model simulates the processes of proton transport and ATP formation in a mitochondrion. Students may observe the processes and explore the impacts of ETC inhibitors, ATP synthase inhibitors, uncoupling proteins, or absence of oxygen on these processes. This model is modified from a NetLogo simulation developed by Steven Brewer (2004). Detailed membrane structures, rules of proton movement and regulation, and oxygen impacts are constructed in this model to provide a powerful dynamic visualization to support NGSS-aligned active learning.

Grades: 6-12:
NGSS Standards: HS-LS1-7

HOW IT WORKS

Components

ETCs: purple patch areas
ATP synthases: green patch areas
uncoupling proteins: pink patch area
lipid bilayer:yellow patch area with lipids
NADH: orange flat hexagons
NAD: gray flat hollow hexagons
Protons: orange circles containing a plus
Oxygens: white double circles
Water: white and red molecules
ATP: invisible in the model but can be tracked in the plot of "ATP Yields".

Rules

NADH molecules in the matrix pass a proton (H+) to an electron transport chain (ETC).
A functional ETCs transports H+ into the inter membrane space. An ETCs will not function if 1) it is poisoned (e.g., by an inhibitor), 2) oxygen is blocked, or 3) H+ gradient is too high (arbitrarily set as 200 times higher in this simulation).
A functional ATP synthase allows H+ to move into matrix. If oxygens are present, water and ATP will be produced. An ATP synthase will not function if 1) it is inhabited, or 2) H+ gradient is too low (there must be ten more protons in intermembrane space than in the matrix).
An uncoupling protein allows H+ to move into matrix if activated. If oxygens are present, water will be produced, but no ATP will be produced.

HOW TO USE IT

1. Click on the "setup/reset" button to initiate or reset the model.

2. Put down the time you want to model to run. For a preliminary investigation, put down a big number (e.g., 1000000) to get a sufficient observation time.

3. Click on the "Run/pause" button to run or pause the model. Click on the "Run a tick" button to run the model for just one tick.

4. Use switches to explore/test the impacts of ETC inhibitors, ATP synthase inhibitors, uncoupling proteins, or absence of oxygen on the production of ATP.

5. Use sliders to adjust the formation rate of NADH and the consumption rate of ATP.

**Run the model at a lower speed to get a better visual effect.**

THINGS TO NOTICE AND TRY

When using the model, pay attention to how protons move. Can you infer which side of the model represents the matrix and which side represents the intermembrane space? What is the evidence in the model?
What happens when oxygen is blocked? The absence of oxygen first affect the ETCs or ATP synthases? What is the evidence in the model?
What happens when ETCs are poisoned? How does it affect the proton gradient and formation of ATP? Will it also affect ATP synthases? How and what is your evidence?
What happens when ATP synthases are poisoned? How does it affect the proton gradient and formation of ATP? Will it also affect ETCs? How and what is your evidence?
What happens when uncoupling proteins are activated? How does it affect the proton gradient and formation of ATP? Will it also affect ETCs and/or ATP synthases? How and what is your evidence?
How do NADH affect the proton gradient and formation of ATP? What is your evidence?
What are the real-life examples of the simulated scenarios above?

CREDITS AND REFERENCES

This model is made by Dr. Lin Xiang at the University of Kentucky .If you mention this model in a publication, we ask that you include the citations below.

Xiang, L. (2019). Cellular Respiration: Mitochondrial Electron Transport Chain. Department of STEM Education, University of Kentucky, Lexington, KY.

This model is modified based on the ElectronTransport model initially developed by Steven Brewer.

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.

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