This exercise is intended to give you practice with two things: learning amino acids and working with pH.
Important: drawing only the side chains will not provide practice in working with pH.

The pK_a values for the different amino acids are in Table 3-5 in the text.

Draw the complete structure of each amino acid named at the specified pH's. In each case, draw the form that would be the most common in solution.

Example: Draw the structure of alanine at pH 2.0, 7.0, and 10.0
The pK_a's of alanine are 2.34 (α-COOH) and 9.69 (α-NH₃⁺).

Note: Since I've had problems including the diagrams with this file, I'm inserting both diagrams in a different version at the end of the exercise, so please check there.

Explanation: At pH 2.0 most molecules in solution have protonated carboxyl and amine groups.
At pH 2.34 half of the molecules have protonated carboxyl groups, and half have charged carboxyl groups (the conjugate base form).
At pH 7.0, however, all of the amino acids have protonated amine groups and charged carboxyl groups.
At pH 9.69, half of the molecules in solution have protonated amine groups, and half have amine groups that have donated H⁺ (have become the conjugate base form, which has no charge).
At pH 10.0 the majority of molecules in solution have the conjugate base form of the amine.
I find it helpful to write the pK_a above each arrow as a visual reminder.

1. Leucine at pH 2.0, pH 7.0, and pH 10.0

2. Tyrosine at pH 2.0, pH 7.0, pH 9.4, and pH 11.0

3. Glutamine at pH 1.9, pH 6.5, and pH 9.5

4. Histidine at pH 1.5, pH 4.0, pH 7.0, and pH 9.5

5. Arginine at pH 1.8, pH 7.0, pH 10.0, and pH 12.6

6. Glutamate at pH 2.0, pH 3.5, pH 6.5, and pH 10.0

Peptides and pH

When amino acids are joined by a peptide bond, the only α-amine and α-carboxyl groups that accept or donate H⁺ are the terminal ones. Side chains, though, can still donate or accept H⁺.
The side chain pK_a's are almost certainly modified by adjacent groups, but for this exercise continue to use the values given in Table 3-5.

Example: Draw the dipeptide P-I at pH 2.0, pH 7.0, and pH 10.0

First draw the two amino acids connected by a peptide bond. Prolyl-isoleucine has only two ionizable groups: the two terminals of the backbone. This form is shown below at neutral pH, so changing it for pH 2.0 simply requires adding H⁺ to the terminal COO^-. Changing it for pH 10.0 requires removing H⁺ from the terminal NH₃⁺. Since proline and isoleucine are nonpolar amino acids, their side chains don't change.

1. Draw the dipeptide L-W at pH 1.5, pH 7.0, and pH 10.0

2. Draw the dipeptide A-N at pH 1.5, pH 7.0, and pH 10.0

3. Draw the dipeptide K-T at pH 1.5, pH 7.0, pH 9.0, and pH 11.0

4. Draw the dipeptide C-D at pH 3.0, pH 7.0, pH 9.0, and pH 11.0

The pI of a molecule is the pH at which it has a net charge = 0. This is the middle of the range in which molecules have a net charge of 0, or the average of the two pK_a 's on each end of the range.

5. Look at the dipeptides you drew and find the form of each that has a net charge of 0. What is the pI for each dipeptide? You may find it helpful to fill in the table.

Diagrams of titration examples are below. The top line is the alanine titration, followed by making the dipeptide prolyl-isoleucine, and, finally, the titration of prolyl-isoleucine.

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