Peptides and Amino Acids

One backbone, twenty common side chains

Once incorporated into a chain, each amino acid is called a residue. All residues share the same repeating backbone; what distinguishes them is the side chain attached to that backbone. The particular combination and order of side chains determines how the whole molecule behaves.

Side-chain families

Side chains are commonly grouped by chemistry, and the group often predicts behaviour:

• Nonpolar / hydrophobic — alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline. Hydrophobic character increases the tendency to aggregate and to require more careful solubilisation.
• Polar, uncharged — serine, threonine, asparagine, glutamine, tyrosine, cysteine. These contribute hydrogen bonding and, in the case of cysteine, thiol chemistry.
• Acidic, negatively charged at neutral pH — aspartic acid, glutamic acid.
• Basic, positively charged at neutral pH — lysine, arginine, histidine.

Net charge matters

The balance between acidic and basic residues — together with the terminal groups — determines the net charge at a given pH, and therefore strongly influences solubility. A highly charged peptide generally dissolves more readily in aqueous buffer; a predominantly hydrophobic one often does not. This is why the first solvent choice should follow from the sequence rather than from habit.

Residues needing extra attention

Cysteine can form disulfide bridges with another cysteine, either intentionally or unintentionally, so its presence is worth noting before storage and reconstitution. Methionine is susceptible to oxidation. Tryptophan is readily oxidised and contributes absorbance around 280 nm, which affects spectrophotometric quantitation.

Reading a sequence in practice

When reviewing a specification, confirm the exact sequence and any terminal modifications. Seemingly minor differences — one substituted residue, or a blocked terminus — change molecular weight, charge, and measurable behaviour.