Electron Transport Chain

1 collaborator

WHAT IS IT?

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 (poisonAS), poison an element in the electron transport chain (poisonET), 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

Comments and Questions

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Click to Run Model

; add model procedures here
globals [rat atp total_atp nad total_nad time]

to setup
;; (for this model to work with NetLogo's new plotting features,
  ;; __clear-all-and-reset-ticks should be replaced with clear-all at
  ;; the beginning of your setup procedure and reset-ticks at the end
  ;; of the procedure.)
  __clear-all-and-reset-ticks
set total_atp [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
set total_nad [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
ask patches with [(pxcor = (-1 * max-pxcor))] [set pcolor white] 
ask patches with [(pxcor = max-pxcor)] [set pcolor white]
ask patches with [(pycor = (-1 * max-pycor))] [set pcolor white]
ask patches with [(pycor = max-pycor)] [set pcolor white]
ask patches with [pycor = 0] [set pcolor white]

ask patches with [(pycor = 0) and (pxcor = -16)] [set pcolor blue] ;FeS1
ask patches with [(pycor = 0) and (pxcor = -14)] [set pcolor red] ;CytA
ask patches with [(pycor = 0) and (pxcor = -12)] [set pcolor blue] ;FeS2
ask patches with [(pycor = 0) and (pxcor = -10)] [set pcolor red] ;CytA
ask patches with [(pycor = 0) and (pxcor = -8)] [set pcolor blue] ;CytA
ask patches with [(pycor = 0) and (pxcor = -6)] [set pcolor red] ;CytA
ask patches with [(pycor = 0) and (pxcor = -4)] [set pcolor blue] ;CytA
ask patches with [(pycor = 0) and (pxcor = -2)] [set pcolor red] ;CytA

ask patches with [(pycor = 0) and (pxcor = 16)] [set pcolor blue] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 14)] [set pcolor red] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 12)] [set pcolor blue] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 10)] [set pcolor red] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 8)] [set pcolor blue] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 6)] [set pcolor red] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 4)] [set pcolor blue] ;ATP Synthase
ask patches with [(pycor = 0) and (pxcor = 2)] [set pcolor red] ;ATP Synthase

crt 100 [set shape "circle" set size 1 set color yellow set heading random 360 fd random 10]
end 

to go 
let nad_cnt 0
  let atp_cnt 0
  
set nad_cnt 0
set atp_cnt 0
set rat count turtles with [ycor > 0]
ask turtles [

  fd 1
  rt random 60 
  lt random 60 
  if ([pcolor] of patch-at dx dy = white) and (NOT uncouplers) [set heading heading - 180]
  if ([pcolor] of patch-at dx dy = blue) [if (heading >= 270 or heading < 90 ) [ifelse (NOT poison_et) and (random 90 > rat) and (50 - nad > 0) [fd 2 set nad nad + 1 set nad_cnt nad_cnt + 1] [set heading heading - 180] ] ]
  if ([pcolor] of patch-at dx dy = blue) [if (heading  >= 90 and heading < 270 ) [set heading heading - 180]]
  if ([pcolor] of patch-at dx dy = red)  [if (heading  >= 90 and heading < 270 )  [ifelse (NOT poison_as) and (rat > 60 ) and (50 - atp > 0)[ fd 2  if (atp < 50) [set atp atp + 1 set atp_cnt atp_cnt + 1]] [set heading heading - 180] ] ]
  if ([pcolor] of patch-at dx dy = red)  [if (heading >= 270 or heading < 90) [set heading heading - 180]]
  ]
  if (random 200 < atp_consumption) and (atp > 1) [set atp atp - 1]
  if (random 200 < nad_consumption) and (nad > 1) [set nad nad - 1]
  no-display
  plot-levels
  plot-atp
  set total_nad replace-item time total_nad nad_cnt
  set total_atp replace-item time total_atp atp_cnt
    set time time + 1
  if(time >= 40) [set time 0]
  plot-rates 
  display
end 

to plot-levels ;; this creates creates the bar graph 
    set-current-plot "Proton Gradient"
    clear-plot
    plot-pen-down
    set-current-plot-pen "matrix"
    plotxy 1 count turtles with [ycor < 0] 
    set-current-plot-pen "intermembrane"
  plotxy 2 rat 
end 

to plot-atp ;; this creates creates the bar graph 
    set-current-plot "ADP-ATP NADH-NAD+"
    clear-plot
    plot-pen-down
    set-current-plot-pen "adp"
    plotxy 1 (50 - atp) 
    set-current-plot-pen "atp"
    plotxy 2 atp 
    set-current-plot-pen "nadh"
    plotxy 4 (50 - nad) 
    set-current-plot-pen "nad+"
    plotxy 5 nad
end 

to plot-rates ;; this creates creates a line graph 
    set-current-plot "ATP and NAD Rates"
    plot-pen-down
    set-current-plot-pen "atp"
    plot ((sum total_atp) / 40) 
    set-current-plot-pen "nad"
    plot ((sum total_nad) / 40) 
end 

; Copyright 2004 by Steven Brewer.  All rights reserved.
;
; Permission to use, modify or redistribute this model is hereby granted,
; provided that both of the following requirements are followed:
; a) this copyright notice is included.
; b) this model will not be redistributed for profit without permission
;    from the authors.
; Contact the authors for appropriate licenses for redistribution for
; profit.
;
; To refer to this model in academic publications, please use:
; 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/

There is only one version of this model, created almost 10 years ago by Steven Brewer.

Attached files

File	Type	Description	Last updated
Electron Transport Chain.png	preview	Preview for 'Electron Transport Chain'	almost 10 years ago, by Steven Brewer	Download

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