Specifically, discontinuous electrophoresis was performed, which involves two gels of different pH, a sepatating gel and a stacking gel. Glycine and chloride ions are included in the reservoir buffer to create an electrical field gradient. The proteins are concentrated into a focused band travelling through the stacking gel. However, in the more basic separating gel, the gradient collapses and the migration is dependent upon molecular weight. Sodium dodecylsulfate is used to obtain a constant charge-to-mass ratio for all proteins analyzed. Therefore, separation of proteins is based on the frictional coefficient of the particles, which is determined by the size and shape of the particles. A low range protein standard will be used to determine a range of molecular weights for the proteins present in each ribosome. .

             A 2-dimensional SDS-PAGE allows for greater distinction between the bands on a gel. In addition to separation based on size and shape, molecules are also separated based on their isoelectric points, the pH at which there is no net charge on a molecule. A pH gradient is created in a second dimension of the gel to provide improved separation of bands. The results form the one and two-dimensional gels will compared, along with results from literature. .

             The RNA was extracted from the ribosomes using a phenol/chloroform:isoamyl alcohol method, and further analyzed by agarose gel electrophoresis. When cooled, agarose forms hydrogen bonds. The pore size is dependent upon the concentration of agarose used. These pores act as a sieve to slow down the migration of large molecules, and thereby enable separation based on molecular weight. Treatment with SDS is not necessary for nucleic acids, as they already have a constant charge to mass ratio. However, due to the variable 3-dimensional structure of RNA, denaturing conditions must be used to obtain a relationship between molecular weight and migration distance.