side chains

Meaning: The α carbon of an amino acid bonds to an amino group, a carboxyl group, a hydrogen, and the side chain (R group). The backbone is the repeating N–Cα–C unit, and side chains project off it. Side chains sort amino acids into classes: nonpolar (Gly, Ala, Val, Leu, Ile, Met, Pro), aromatic (Phe, Trp, Tyr), polar uncharged (Ser, Thr, Asn, Gln, Cys), acidic (Asp, Glu), and basic (Lys, Arg, His). Glycine's R group is just H, so it is not chiral. Proline's side chain loops back to the backbone nitrogen, which restricts rotation.

On the MCAT: Expect questions on where a residue sits in a folded protein. In water-soluble proteins, hydrophobic side chains usually cluster in the core and polar or charged ones face the solvent. Membrane-spanning regions often show the reverse pattern. Side chains form the interactions of tertiary structure: hydrogen bonds, salt bridges between acidic and basic groups, hydrophobic packing, and disulfide bonds between two Cys. Passages may change pH and ask which side chain gains or loses a proton (compare pH with the side chain pKa), or ask what a mutation does.

Common confusion: Side chains do not form the peptide bond. The α-amino and α-carboxyl groups do. "Acidic" or "basic" amino acid refers to the side chain, because free amino acids have both backbone groups. Side chain charge depends on pH relative to pKa.