1. CH 3-5: pH, pKa and Acid/Base Structure
The aqueous pH will effect the structure of an acid or base.
This can effect a compounds solubility and even biological activity and mobility.
What is the acid/base structure of the amino acid Lysine at physiological pH? (~pH 7.4)

2. Acid/Base Structure of Lysine at pH 7.4
If the pH > pKa for a specific acidic functional group, this group is said to be in a basic environment, and will exist in its basic form (Conjugate Base).
If the pH < pKa for a specific acidic functional group, this group is said to be in an acidic environment, and will remain in its acid form.
pKa 5.2
pKa ~ 10
pKa ~ 9
Structure of Lysine at pH 7.4:

3. What is the acid/base structure of the amino acid cysteine at pH 11?
pKa ~ 8
pKa 5.2
pKa ~ 9
Structure of Functional Groups depends on pH:
If pH>pKa…functional group is in its base form.
If pH<pka…functional group is in its acid form.