Week Three – Protein Gel Electrophoresis

A fool's last words: I wonder if these wires are "hot"...

Monday presentation

Because of the MLK holiday, the presentation on protein structure, sample preparation, gel properties, and principles of discontinuous sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) cannot be held. The presentation with notes is available on line and slides with notes are available as a pdf file, formatted for grayscale printing. Make sure that you understand the rationale behind this week's work, and inquire if you need anything clarified.

Recommended resources

Some expectations before starting the work

  • As always, prepare an outline of the planned work
  • You MUST have all of the volume calculations needed to prepare your samples for electrophoresis
  • Prepare to apply any or all of the skills and concepts covered in previous laboratory sessions
  • Be able to describe the overall objectives and specific objectives of this week's work
  • Be prepared to describe the structural organization of proteins and the difference between a protein and a polypeptide
  • Be prepared to describe the basis for separation of macromolecules by SDS-PAGE
  • Be able to explain why your protein samples must be denatured, and the purpose of SDS and other sample buffer components
  • Be prepared to describe molecular mass and define what is meant by a Dalton
  • Be able to describe the purpose of the molecular mass standards and how they are used
  • Be prepared to describe what is meant by %T and %C in reference to polyacrylamide gels
  • Be able to describe the difference between a separating gel and a stacking gel
  • Be prepared to explain why the same protein samples should be run on gels of different density (%T)

Pre-laboratory orientation (by instructor)

  • Safety concerns, including hazards of acrylamide
  • Organization of teams
  • Comments on division of labor and record keeping
  • Suggestions for sample preparation
  • Instructions for finishing gels and mounting a gel in a stand
  • Recommendations for loading and running gels

Follow-up work

  • Turn in initialed notebook pages as you are expected to do each week
  • Download and print off your gel photos when they become available; you need 2 copies of each gel photo per person, and need not print in color
  • Download the annotated writing examples (pdf) to help you with your writing assignments, and obtain a copy of the required writing text if you have not done so already
  • Peruse the section on writing research papers (writing/analytical resources), especially the parts on organization of a research paper and materials/methods; you should refer to this resource fairly often
  • Write up the materials and methods to the first study, to be submitted in the laboratory next week
  • Start on your preparation for the fourth week of the course (Week 4 schedule page)
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Created by David R. Caprette (caprette@rice.edu), Rice University17 Aug 95
Updated 14 Jan 08