Amino Acids and Proteins

The Twenty Amino Acids

Classify side chains: nonpolar (Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, Trp), polar uncharged (Ser, Thr, Cys, Tyr, Asn, Gln), acidic (Asp, Glu), and basic (Lys, Arg, His). Know the special cases — glycine is achiral, proline kinks helices, cysteine forms disulfides, and histidine's $pK_a$ near 6 makes it the physiological proton shuttle. Chiral amino acids appear as L-isomers in proteins.

Ionization and Isoelectric Point

At physiological pH, amino acids are zwitterions: carboxylate negative, ammonium positive. A group is protonated when pH is below its $pK_a$. The isoelectric point averages the two values flanking the neutral species: Acidic residues have low pI, basic residues high; charge at a given pH predicts electrophoretic behavior.