Amino acids — Biomolecules | Organic Chemistry

An α-amino acid carries an amino group and a carboxylic acid on the same carbon. Twenty of them are used to build proteins, they differ only in the side chain, and essentially all of their distinctive behavior comes from having an acid and a base in one small molecule.

They are never neutral molecules

Drawn with a free NH₂ and a free COOH, an amino acid looks like a compound with two untouched groups. It is not. The carboxylic acid (pK_a ≈ 2) is a far stronger acid than the ammonium ion (pK_a ≈ 9–10) is, so the proton moves internally and the molecule exists as a zwitterion: −COO⁻ and −NH₃⁺ at the same time, overall neutral.

This is not a curiosity; it explains the physical properties. Amino acids are high-melting crystalline solids that dissolve in water and not in ether — they behave like salts, because at ordinary pH they are one.

Three species, depending on pH: at low pH everything is protonated and the molecule is a cation (COOH, NH₃⁺). At high pH everything is deprotonated and it is an anion (COO⁻, NH₂). In between sits the zwitterion. Sketching that three-species ladder is how nearly every amino acid question is solved.

The isoelectric point

The isoelectric point, pI, is the pH at which the molecule carries no net charge — the pH where the zwitterion dominates. For an amino acid with no ionizable side chain it is the average of the two pK_a values on either side of the zwitterion:

pI = ½(pK_a1 + pK_a2)

Glycine, with pK_a values near 2.3 and 9.6, has a pI near 6.0 — slightly acidic, not 7, which is worth noticing because the intuition that "neutral means pH 7" is wrong here.

When the side chain ionizes, you average the two pK_a values that flank the neutral form rather than simply the first two. For an acidic side chain such as aspartate that means the two acidic pK_a values, giving a low pI; for a basic side chain such as lysine it means the two basic ones, giving a high pI.

Stereochemistry: one carbon, one answer, two exceptions

Glycine’s net charge against pH. The two pKa values are the only boundaries there are, so the molecule has exactly three states, and the isoelectric point sits at their midpoint because that is where the cation and anion populations are equal.Reading the electrophoresis direction takes two inversions and they do not cancel: first compare the pH with the pI to get the sign, then remember that opposite charges attract. Getting one of the two backwards produces a confident wrong answer.

The α carbon of an amino acid bears four different groups — NH₂, COOH, H and the side chain — so it is a stereocenter, and biology uses essentially only one of the two possibilities: the L amino acids.

Glycine is the exception that is not a stereocenter at all. Its side chain is a hydrogen, so the α carbon has two identical groups and glycine is achiral.
Cysteine is the exception that trips people. It is L like the others, but because sulfur outranks the carboxyl carbon in the CIP priority rules, it is assigned R while the other eighteen chiral ones are S — glycine has no configuration to assign. Nothing about its shape is unusual; the label changed because the priority order did.

L and S are not synonyms, and cysteine is the standing proof. D/L is a relational classification, like the sugars' D/L; R/S is computed from CIP priorities. Two systems, two answers, and they agree only by coincidence.

Grouping the twenty by side chain

Memorizing twenty structures is a poor use of effort compared with grouping them by what the side chain does, which is what determines where each one sits in a folded protein:

Nonpolar — alkyl or aromatic side chains (alanine, valine, leucine, phenylalanine). Hydrophobic, so they end up buried in the protein's interior.
Polar, uncharged — OH, SH or amide side chains (serine, threonine, cysteine, asparagine). Hydrogen bond, often found at the surface or in active sites.
Acidic — a second carboxylic acid (aspartate, glutamate). Negatively charged at physiological pH, low pI.
Basic — an amine or a nitrogen-containing ring (lysine, arginine, histidine). Positively charged at physiological pH, high pI.

Two more are worth singling out. Proline's side chain loops back to its own nitrogen, making a ring and a secondary amine — which stops it adopting the shapes the others can and gives it a special role in protein folding. Cysteine's thiol can be oxidized to form a disulfide bond with another cysteine, the only covalent cross-link in ordinary protein structure.

Worked example — predicting direction of movement in an electric field

Alanine (pI ≈ 6.0) is placed in a buffer at pH 9. Which electrode does it move toward?

Compare pH with pI. The pH is above the pI, so the molecule has lost more protons than it has at its isoelectric point: it carries a net negative charge.

Negative moves toward the positive electrode, the anode.

The general rule is worth holding: pH above pI means negative; pH below pI means positive; pH equal to pI means no movement. That single comparison answers every electrophoresis question in this chapter, and it is also the principle by which proteins are separated in a lab.

What carries forward

The acid–base reasoning here is the same as Module 4's, applied to a molecule with two ionizable groups instead of one. The stereochemistry is Module 6's. What is new is only the biological vocabulary — and the habit of asking, of any amino acid at any pH, which of the three species is present.