Taxonomy of Finfish (1+2)

6.2.6 Poly Acrylamide Gel Electrophoresis (PAGE)

Native polyacrylamide gel electrophoresis

Acrylamide monomer (CH 2 = CH CO NH 2 ) is co-polymerised with a cross linking agent, usually N.N’- methylene bisacrylamide {CH 2 (NH CO CH = CH 2 ) 2 }, in the presence of a catalyst accelerator chain initiator mixture. This mixture consists of freshly prepared ammonium per sulfate as (0.1 to 0.3% w/v) initiator together with about the same concentration of a suitable base, for example, dimethyl aminopropionitrile (DMAP) or N, N, N’, N’ - tetra methylenediamine (TEMED) as catalyst. Out of the two, the most used is TEMED and proportional increase in its concentration speeds up the rate of gel polymerization. Gelation occurs due to vinyl polymerization. Prior degassing of solution is required since molecular oxygen inhibits chemical polymerization. The relative proportion of acrylamide monomer to cross-linking agent determines the porosity of a gel. Gels may be defined in terms of the total percentage of acrylamide present. Gels may be prepared containing from 3% to 30% acrylamide, corresponding to pore sizes of 0.5nm and 0.2nm, diameter respectively. Polyacrylamide gels may be prepared with a high degree of reproducibility and the precise porosity. This feature makes the method particularly suitable for resolving mixtures of proteins. This feature makes the method particularly suitable for resolving mixtures of proteins. Other features of polyacrylamide

gels include their minimal absorption capacity, their lack of electro-endosmosis and their general suitability for in situ quantitative analysis (as they do not absorb UV) and for various types of histo-chemical analysis. For running of the polyacrylamide gels, the gel slab (earlier gel rods made in glass tubes of uniform diameter were used) is loaded with the sample and attached to the lower submarine unit, filled with the buffer and connected to the power pack for the DC supply.

Denaturing Polyacrylamide gel electrophoresis

In the electrophoretic technique previously discussed, the mobility of biological molecules is influenced by both charge and size. But, if protein samples are treated with certain chemicals so that they have a uniform charge, the electrophoretic mobility then depends primarily on size. The molecular weights of proteins may be estimated if they are subjected to electrophoresis in presence of detergent, SDS and disulfide reducing agent mercaptoethanol. When protein molecules are treated with SDS, the detergent disrupts the secondary, tertiary and quaternary structure, leaving the molecule to produce polypeptide chain in a random coil, imparting an overall negative charge and masking the individual variation in charge. The presence of mercaptoethanol assists in protein denature by reducing all disulfide bonds. In essence, polypeptide chains of constant charge/mass ratio and uniform shape are produced. The electrophoretic mobility of the SDS-protein complexes will be influenced primarily by molecular size; the larger molecules will be retarded by the molecular sieving effect of the gel, while the smaller molecules will have greater mobility.

In practice, a protein of unknown molecule weight and structure is treated with 1% SDS and 0.1 mercaptoethanol in electrophoresis buffer. A standard mixture of proteins with known molecular weights must also be subjected to electrophoresis under the same conditions. After electrophoresis followed by staining, the molecular weight may be determined.