Section: Chemical and Physical Foundations of Biological Systems

31) In an SDS-PAGE procedure, the SDS serves as a detergent. Why are the proteins treated with a detergent before being run through the electrophoresis gel?

1. To coat the proteins with a large positive charge, since amino acid side chains may have positive, negative, or neutral charges, and a large uniform charge is necessary to get good separation in the gel.
2. To allow the electrophoresis to separate the proteins solely on the basis of the length of the primary sequence.
3. To prevent the protein from denaturing so that the electrophoresis can accurately resolve the proteins on the basis of tertiary structure.
4. To break the intramolecular bonds holding the tertiary and primary structure of the protein together, thereby generating linear fragments that may be sorted on size.

SDS is a detergent which denatures the tertiary and secondary structure of a protein. It also coats the protein with a very large negative charge. This electrostatic repulsion pushes the protein in a single long rod shape, allowing the gel to sort various proteins on the basis of primary structure length. Thus (B) is the right answer. A: This answer choice is right except is says positive charge. SDS creates a negative charge. C: Detergents cause denaturing, rather than preventing it. D: SDS will break down tertiary and secondary structure, not primary.