BL/CH 401 Biochemistry I

Extra Problems

pK of Amino Acid Side Chains and Net Charge

1. For the dipeptide, Glu-Ala, write out the structure and estimate the pK of all ionizable groups.

Using your assigned pK values, determine the net charge at pH 1, 3, 5, 7, 10, 11.

Calculate the pI. (Remember pI = pH where peptide has no net charge.

2. For the tetrapeptide, Glu-Ala-Lys-Tyr, write out structure and estimate pK of all ionizable groups.

With your assigned pK values, determine the net charge at pH 1, 3, 5, 7, 10, 11.

Calculate the pI of this tetrapeptide.

The pK values of the amino acids used in this problem set are:

Ala- 2.4, 9.9

Glu - 2.1, 4.1, 9.5

Lys - 2.2, 9.2, 10.8

Tyr - 2.2, 9.7

Points to Remember:

A. In assigning pK values to ionizable groups in a peptide, assume that the ionizable groups will have the same pK values as they have in the free amino acid.

B. To assign pK values, you must know which groups in the amino acid are associated with which pK value shown after the name of the amino acid in the above list.

C. After you assign pK values, then use them to decide what the charge on the group is at the pH of interest.

D. After you have given a charge to all groups at the pH of interest, then sum them to arrive at the net charge at that pH.

EXAMPLE

For Ala-Lys, there are 3 ionizable groups:

1) alpha-amino group contributed by Ala - assign pK 9.9.

2) alpha-carboxylate group from Lys - assign pK 2.2.

3) side chain amino group from Lys - assign pK 10.8.

Table of Charges at the pH values of interest:

Group	pH 1	pH 3 & 5	pH 7	pH 10	pH 11
Alpha-Amino	+1	+1	+1	0	0
Alpha-Carboxylate	0	-1	-1	-1	-1
Side-Chain Amino	+1	+1	+1	+1	0
Net Charge	+2	+1	+1	0	-1
Peptide Form	"+2 Form"	"+1 Form"	"+1 Form"	"Zero Form"	"-1 Form"

pI = average of pK values for ionizable groups on either side of Peptide Form with Zero Net Charge:
For peptide Ala-Lys example, pI = ((9.9) + (10.8))/2 = 10.35 or about ~10.4.
For peptide to go from +1 Form to Zero Form, Alpha Amino Group must give up its proton which can be stated as the peptide passes through the pK of Alpha-Amino Group being at pH 9.9.
For peptide to go from Zero Form to -1 Form, the Side Chain Amino Group must give up its proton, which means that the peptide passes through the pK of the Side Chain Amino Group being at 10.8.

General Rule:
Average the pK values for transition from +1 form to zero form and zero form to -1 form

It does not matter what types of ionizable groups are present in the peptide since it always has the 3 forms you need to use to find the pK values to average for finding the pI. In other words, all peptides have a +1, a Zero and a -1 form.

Back To: AA Sequence Problems

Back To: Lecture 3