Scroll down on this page to see all of the steps of the protein electrophoresis tutorial.

Note: In the Case It simulation, protein electrophoresis happens automatically and behind the scenes when the Western blot is run. The tutorial below shows you how to run protein electrophoresis both on the Data Screen and also the Lab Bench. In this example we will load the same protein sample (HIV) into 5 wells, since this was what is done prior to running the Western blot in a previous tutorial.

1. Use the Protein menu (or the Protein button) to open the file "protein HIV.txt" from the Auxilia.txt HIV case, as shown below.

 

2. You can select more than one well by dragging, so drag wells over wells 1-4 to highlight them, then click the 'Load' button.

 

3. Click the white button for well 5, and click the load button again, so that a total of 5 wells are loaded with the HIV protein.

 

4. There are two ways to run the protein gel - using the Run button (left graphic below) or the Run menu (right graphic below)...

...and the gel appears in a window above the main screen, as shown below. Note that the default values are 60 minutes and 10% polyacrylamide. In reality, the individual proteins in the HIV file would not be visible at this point, but in the simulation they are faintly visible so you can see that something is on the gel. To make them visible in an actual laboratory, the individual proteins could be stained either blue or red.

5. Click the blue button below the gel to stain the fragments blue, then click the red button to stain the fragments red, as shown below.

 

6. Click the 'Reload' button to reload the proteins back into the wells.

 

7. Drag the '60' to highlight it, type in '30', and click the 'Set' button as shown below left. Then click the 'Timed run' button to run the gel for 30 minutes.

 

8. Click the 'Hour run' button to restore the default run of 60 minutes.

 

9. Protein gels can also be run at different polyacrylamide settings. Use th 'Protein' menu to change the setting, as shown below.

 

10. Click either the 'Timed run' or the 'Hour run' button to run the gel at this new polyacrylamide setting.

 

11. You can see the size or sequence for any fragment by clicking on it, as shown below (note that clicking on a fragment automatically stains all fragments blue, then designates the clicked fragment in red. The distance traveled is 45.3 units (right side of graphic below), the size is 216 amino acids, and the weight is 26.89 daltons (bottom of graphic below).

Note: clicking a fragment automatically turns the 'smear' effect off, so that the fragments are easier to see (particularly for DNA fragments). To turn the 'smear' effect back on after clicking a fragment, use the 'Options' menu.

 

12. Clicking the 'Sequence' box shows the sequence of amino acids for this particular protein. (Note: The extraneous characters at the end of this particular sequence are not part of the actual sequence, but rather have other functions in the operation of the program.)

 

13. Click the 'Lab Bench' button on the navigation bar at the bottom of the screen, then click the 'Hide gel' button to see the protein electrophoresis setup on the Lab Bench

 

14. Click the 'run gel' toggle-switch on the power source to run the gel, as shown below. The gel should stop when it reaches the timer setting, but if it doesn't you can stop it manually by clicking the left side of the toggle-switch. The rightmost fragments represent the loading dye. See important additional notes in the box underneath the graphic below.

Note: Protein gels are run vertically rather than horizontally, as is the case with DNA gels. In this simulation the loading dye in the gel box moves downwards (see below) to represent it. Note that the words 'THIS SIDE UP' appear to the left of the large gel image, indicating that you are looking sideways at the gel (a necessary consequence of the way this simulation was programmed).

Note: The 'smear slider' appears on the gel box, enabling you to vary the transparency of the faint smear on the protein gel. This feature is more useful when running DNA gels that represent 'geneomic smears'.

Note: Although not shown here, the 'Volts' button above enable you to vary the voltage of the power source, just as when running DNA gels from the Lab Bench.