In SDS-PAGE the polyacrylamide gel serves as the stationary phase, the buffer (Tris-HCl in this case) as the mobile phase and an electrical source/ cathode and anode terminal. The aim of SDS-PAGE is to separate peptide chains in a protein sample according to molecular weight by sieving them through a gel matrix under the influence of an electric current. The setup for an SDS-PAGE experiment is shown in Figure 1.0
Figure 1.0- An illustration of a simple SDS-PAGE setup
Based on the figure above it can be observed that big proteins (high MW) travel a shorter distance than that of smaller proteins (low MW). This is because bigger proteins have a difficult time in traversing through the gel matrix unlike smaller proteins that have much ease in going about them due to their small size. The complicated gel matrix hinders the free passage of the longer proteins that travel towards the positive electrode (anode) much more than it affects the smaller proteins which also travel in the same direction due to their net negative charge provided by SDS. If the set up was to be let alone for a set time the proteins would have traveled a considerable distance along the gel in the form of separated horizontal bands marking their position. The distance between the bands may account for the difference in size and therefore MW of the protein...