amino acid sequence

Meaning: The amino acid sequence is the linear order of residues joined by peptide bonds, read from the free amino end (N-terminus) to the free carboxyl end (C-terminus). Only covalent peptide bonds define it. The R groups then drive folding: hydrophobic residues tend to cluster in the core, and polar or charged ones face water. For many proteins the sequence alone specifies the native fold (Anfinsen's ribonuclease experiment), though chaperones assist some.

Equation: number of possible sequences = 20ⁿ, where n is the number of residues in the chain (dimensionless) and 20 is the number of standard amino acids.

On the MCAT: Expect a mutation passage. Translate mRNA codons (read 5′ → 3′, which gives N → C) and predict the effect of a missense change, such as Glu → Val in sickle cell hemoglobin, on charge, folding or function. Swapping a residue for one with a similar side chain usually matters less than swapping polar for hydrophobic. Other questions cover Edman degradation (sequencing from the N-terminus) and trypsin cutting after Lys and Arg.

Common confusion: Students think denaturing destroys the sequence. Heat or urea disrupts non-covalent interactions (and reducing agents break disulfides), but peptide bonds stay intact, so the primary structure is unchanged. Also, a DNA mutation does not always change the sequence: the genetic code is degenerate, so silent mutations exist.