Field Mapping

This writeup is to give you some guidance about writing up the gel-electrophoresis lab. Here are a few helpful points.

1. The writeup should be about 6, double spaced. You can exclude the figures from your page count, particularly since the LP figures have really small type and so have to be made large.
   
   When writing this lab up, think about what you are doing is testing a model of the relationship between the drag force and a driving force, which may come from the elelctric field or the current flow. How are these related mathematically? In a free body diagram?
2. Be sure that you include relevant images in your writeup, and that those images have clear captions that describe the experiment being run (e.g., what dye, solution, time)
3. As usual, your writeup should have 4 parts:
   • Background: What model are you testing here? What experiments would you do to test this model? Discuss applications of the model. Be sure to reference your sources.
   • Experimental description: materials, protocol - enough detail for someone to repeat your experiment.
   • Results: Describe your observations, include data either in tabular, graphical, or image form, in a way that clearly displays what you have measured. Important: Include scanned copies of your original data notes -- get these from whoever took them down in the lab, and be sure to credit that person!
   • Discussion. What aspects of the model were tested in each section? What were the results, agreement or disagreement? Expand on this, make the logical argument that the model is supported. If the model is not supported, then why? Be specifc. What experimental factors led to an apparent falsification of the model. Be quantitative here, as much as is possible.

   Below are some questions to guide your thinking and discussions.

   1. What are the charged ions in the solution?
      1. At Ph = 8, what is the charge state of each of the components? How do they contribute to the current? How far are they apart?
      2. For pure DI water, is there a current? What causes the dye molecules to move?
      3. For the NaCl, why was the current lower than predicted? How much is the gel heated by the current (each box contained 500 ml of water)
   2. What is the effect of the agarose gel? (look up electroosmotic flow). Does it inhibit the current? Enhance the flow of dye?
   3. What are the driving forces on the molecules?
   4. For each dye, what is the size, molecular weight and charge state of each molecule? What about fastblast .. What can we learn about it from the experiment? The concentration of Bpb is 20 mg/L. How many dye molecules are there? How far are they apart? Which dye moves faster and why?
   5. For each solution, what is the drift velocity of the dye molecules? What is the force on each molecule? What is the drag force? What is the electric force? How do they compare? Are there any discrepancies.
   6. Originally the water had a pH of 9. Bpb will turn from blue to yellow at low pH. What does this tell you about the experiment in the salt solution? What is the role of the buffer?
   7. http://en.wikipedia.org/wiki/Buffer_solution
   8. http://en.wikipedia.org/wiki/Tris
   9. http://en.wikipedia.org/wiki/Acetic_acid
   10. http://en.wikipedia.org/wiki/Ethylenediaminetetraacetic_acid