INTRODUCTION

Gel electrophoresis is a common technique used in the laboratory for the purpose of visualizing
and separating large molecules such as DNA and protein. In the process of protein visualization
and separation, two factors, namely: the natural charge and size of the protein, are taken into
account. Protein electrophoresis usually involves Sodium Dodecyl Sulfide (SDS) and
polyacrylamide gel (SDS-Page).

Figure 1. Sodium Dodecyl Sulfide Structure (from Sigma-Aldrich)

The negatively-charged SDS molecules bind to the hydrophobic amino acid residues on the
inside of the protein, disrupting the noncovalent interactions; effectively giving the proteins a
linear structure. This allows for a better movement of the proteins through the gel network.
Then, the denatured proteins are loaded onto the polyacrylamide gel and electrophoresis may
commence. As the SDS-coated protein molecules navigate through the gel matrix, smaller
molecules are able to move faster than bigger molecules. Thus, the proteins are separated by
size or molecular weight. Once proteins have been separated, they may now be visualized for
analysis. Protein visualization is accomplished by staining the samples with a dye called
Coomassie Brilliant Blue that identifies most proteins.
Proteins are classified into three main groups according to solubility, function and shape:
globular, fibrous and membrane. Globular proteins are spherical water-soluble molecules. The
shape of these proteins is critical to their respective functions, and as discussed earlier, the
proteins have a possibility of denaturation. Environmental changes such as in temperature or in
pH levels may disrupt the bonds that give the proteins their three-dimensional shape. These
external factors, such as heat and acid, and their effects on the protein samples, will be
observed.

Figure 2. 3D structure of human serum albumin (from Protein Data Bank)