The purpose of this method is to separate proteins according to their size, and no other physical feature. In order to understand how this works, we have to understand the two halves of the name: SDS and PAGE.
SDS
Since we are trying to separate many different protein molecules of a variety of shapes and sizes, we first want to get them to be linear so that the proteins no longer have any secondary, tertiary or quaternary structure (i.e. we want them to have the same linear shape). Consider two proteins that are each 500 amino acids long but one is shaped like a closed umbrella whle the other one looks like an open umbrella. If you tried to run down the street with both of these molecules under your arms, which one would be more likely to slow you down, even though they weigh exactly the same? This analogy helps point out that not only the mass but also the shape of an object will detrmine how well it can move through and environment. So we need a way to convert all proteins to the same shape - we use SDS.
Figure 1. This cartoon depicts what happens to a protein (pink line) when it is incubated with the denaturing detergent SDS. The top portion of the figure shows a protein with negative and positive charges due to the charged R-groups of the particular amino acids in the protein. The large H represents hydrophobic domains where nonpolar R-groups have collected in an attept to get away from the polar water that surrounds the protein. The bottom portion shows that SDS can break up hydrophobic areas and coat proteins with many negative charges which overwhelms any positive charge in the protein due to positively charged R-groups. The resulting protein has been denatured by SDS (reduced to its primary structure) and as a result has been lenearized.
SDS (sodium dodecyl sulfate) is a detergent (soap) that can dissolve hydrophobic molecules but also has a negative charge (sulfATE) attached to it. Therefore, if a cell is incubated with SDS, the membranes will be dissolved and the proteins will be soluablized by the detergent, plus all the proteins will be covered with many negative charges. So a protein that started out like the one shown in the top part of figure 1 will be converted into the one shown in the bottom part of figure 1. The end result has two important features: 1) all proteins contain only primary structure and 2) all proteins have a large negative charge which means they will all migrate towards the positve pole when placed in an electric field. Now we are ready to focus on the second half - PAGE.
