To determine the net charge on a protein you have to know the amino acid sequence and understand the charges on each amino acid residue in the amino acid sequence.  To do this, you have to know the charge on each weak acid on the protein before and after dissociation.  You also have to know the pH of the solution and the pKa of each weak acid on the protein.  You learned all this in previous objectives 1, 10, and 15:

• What is the approximate pKa for all alpha-amino groups and for all alpha-carboxyl groups?
• What are the pKa's for the R-groups of aspartic acid, glutamic acid, histidine, lysine, and arginine?
• Given the pH, predict whether the alpha-amino and alpha-carboxyl groups and the R-groups of the amino acids aspartic acid, glutamic acid, histidine, lysine, and arginine would be neutral or would carry a net negative or net positive charge
• Given the written sequence for a protein, be able to identify the amino-terminus, the carboxyl-terminus, and the R-groups for each residue.
Problem 1: Determine the charge on the following polypeptide at pH = 7.4
NH3+-Ala-Phe-Glu-Lys-Asp-Pro-Asp-COO-

The only available alpha-amino group and alpha-carboxyl group are on the amino-terminus and the carboxy-terminus respectively.  The other alpha-amino and alpha-carboxyl groups were used to make polypeptide bonds and no longer exist.  The amino terminus has a pka of about 9 so it is positively charged.  The carboxy terminus has a pKa of about 2 so it is negatively charged.

The R-Groups of alanine, phenylalanine, and proline are not charged.

The R-group of lysine has a pKa of about 10.5 so it is positively charged.

The R-Groups of both aspartic acid and glutamic acid have a pKa of about 4 so they are both negatively charged.

So, there are a total of two positive charges, one contributed the alpha amino alanine and one contributed by the R-group of lysine.  And, there are a total of four negative charges, one from the alpha-carboxy of aspartate, two from the R-groups of aspartate, and one from the R-group of glutamate.

Adding the charges yields a net charge of a minus 2 on the polypeptide.

Problem 2: Determine the charge on the following polypeptide at pH = 7.4

NH3+-Ala-Phe-Glu-Arg-Arg-Pro-Gly-COO-

The only available alpha-amino group and alpha-carboxyl group are on the amino-terminus and the carboxy-terminus respectively.  The other alpha-amino and alpha-carboxyl groups were used to make polypeptide bonds and no longer exist.  The amino terminus has a pka of about 9 so it is positively charged.  The carboxy terminus has a pKa of about 2 so it is negatively charged.

The R-Groups of alanine, phenylalanine, proline, and glycine are not charged.

The R-group of arginine has a pKa of about 12.5 so it is positively charged.

The R-Groups of glutamate has a pKa of about 4 so it is negatively charged.

So, there are a total of three positive charges, one contributed the alpha amino alanine and two contributed by the R-groups of arginine.  And, there are a total of two negative charges, one from the alpha-carboxy of glycine and one from the R-group of glutamate.

Adding the charges yields a net charge of a plus one charge on the polypeptide.