Final answer:
Electrophoretic mobility in proteins is determined by molecular weight, isoelectric point, and the net charge of the protein. The amino acid composition affects the net charge and, together with the other factors, influences the protein's migration in an electric field and its water solubility.
Step-by-step explanation:
The three features of proteins most important in determining their electrophoretic mobility are molecular weight (MW), isoelectric point (pl), and the net charge of the protein at the given pH of the electrophoresis buffer.
Molecular weight affects the rate of protein migration due to size and resistance through the gel matrix. Isoelectric point (pl) is critical because it is the pH at which the protein carries no net electrical charge and will not move in an electric field.
The net charge, determined by the amino acid composition and the pH of the buffer, influences the direction and rate of movement because proteins will migrate towards the electrode with the opposite charge.
Proteins are composed of varying amino acids that lend different physical properties to the proteins. These properties include whether the protein is polar or apolar, and acidic or basic. These factors, in turn, determine solubility, with polar or charged (acidic or basic) proteins being typically more water soluble.
The common amino acids in a protein can influence its charge; for example, more acidic or basic amino acids can give the protein a higher net charge at a given pH. The separation during electrophoresis will be influenced by how these amino acids affect the protein’s charge under the assay's conditions.