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An amino acid combines carboxylic acid and amine functionality in the same molecule; the name alone does not specify their separation. An alpha-amino acid has its amino nitrogen attached to the carbon immediately adjacent to the carboxyl carbon, the amino acid alpha carbon. For example, ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ is glycine, whereas ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ has an extra intervening carbon and is not an alpha-amino acid. These chemical formulas describe connectivity, not the predominant protonation state in water.

Most common proteinogenic amino acids share the skeleton ${\mathrm{H}}_2\mathrm{N}-\mathrm{CH}(R)-\mathrm{COOH}$, with $R$ the amino acid side chain. In glycine, $R$ is hydrogen; in alanine, $R=\mathrm{C}{\mathrm{H}}_3$. Proline is a useful exception to the displayed primary-amine skeleton: its amino nitrogen is part of a ring and has a second carbon substituent. The shared backbone permits assembly into polypeptides, while different amino acid side chains give the resulting proteins diverse chemistry. ^[ref]

In a chemical solution, protonation changes the electric charges without changing this backbone. Free glycine near neutral pH is predominantly ${\mathrm{H}}_3{\mathrm{N}}^{+}-\mathrm{C}{\mathrm{H}}_2-\mathrm{CO}{\mathrm{O}}^{-}$, a zwitterion. Its positive and negative groups are joined within one molecule; zero net electric charge does not mean absence of local electric charges, nor does it mean the uncharged drawing ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ predominates. Glycine protonation explains how lowering or raising pH changes the balance. ^[ref]

Building a protein joins the carboxyl carbon of one amino acid to the amino nitrogen of another through a peptide bond, an amide linkage. The formal net condensation loses the elements of water; cellular translation uses activated substrates at a ribosome, rather than simply mixing free amino acids in water. Incorporated units are amino acid residues. The interior amide groups no longer have the same acid/base behavior as the two free terminal groups of glycine, so its free-molecule glycine titration cannot be copied independently at every chain position. ^[ref]

Chirality distinguishes most common proteinogenic amino acids from glycine. The other nineteen members of the conventional twenty have a stereocenter at their amino acid alpha carbon; ordinary translation incorporates their L forms. Glycine's two identical hydrogen substituents make it achiral. Thus being an amino acid, or even an alpha-amino acid, does not by itself imply chirality. ^[ref]

The three principal aqueous glycine forms differ by loss of one proton at each step:Call these glycine forms $G^{+}$, $G^0$ and $G^{-}$, respectively: a cation, a zwitterion and an anion, with net electric charges $+e$, $0$ and $-e$, where $e$ is the elementary charge. $G^0$ specifically denotes the zwitterion, not an uncharged amino/carboxyl drawing. The first dissociation removes the carboxyl proton; the second removes a proton from the positively charged nitrogen. The chemical equilibrium changes are reversible, not three permanently separate kinds of glycine. ^[ref]

For all calculations and both diagrams here, explicitly stipulate the pKa values $\mathrm{p}{K}_{a1}=2.35$ and $\mathrm{p}{K}_{a2}=9.78$. These are illustrative model inputs, not measurements from the glycine titration experiment or a claim of universal constants. Actual acid dissociation constants depend on temperature and on the convention used for thermodynamic activity; apparent concentration-based values also depend on ionic strength. For comparison, the inspected textbook tabulates $2.34$ and $9.60$ for glycine, which would give a different isoelectric point. ^[ref]

In an ideal aqueous chemical solution, set $h=[{\mathrm{H}}_3{\mathrm{O}}^{+}]/c^{\circ }=10^{-\mathrm{pH}}$, with $c^{\circ }=1\mathrm{mol}{\mathrm{L}}^{-1}$, and approximate activity coefficients by one. Put $K_1=10^{-2.35}$ and $K_2=10^{-9.78}$ for the stipulated dimensionless acid dissociation constants. The Henderson-Hasselbalch equation gives the adjacent-state ratiosWith analytical concentration $C_T=[G^{+}]+[G^0]+[G^{-}]$, normalization gives the three fractions and mean electric charge in units of the elementary charge:All three fractions are nonnegative and sum to one. At pH $7$, the model gives about $99.832\%$ zwitterion, $0.00224\%$ cation and $0.1657\%$ anion; $\bar{z}\approx -0.00163$. Predominantly zwitterionic therefore need not mean exactly at the isoelectric point.

Setting $\bar{z}=0$ requires $h^2=K_1{K}_2$. Taking the logarithm yieldsAt this model isoelectric point, ${\alpha }_{+}={\alpha }_{-}\approx 0.0001927$ and ${\alpha }_0\approx 0.9996146$: about $0.0193\%$ of each charged form remains. At either pKa, the relevant adjacent fractions are equal, but the third fraction is not mathematically zero. This three-state model neglects the minor uncharged form ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$; macroscopic pKa values alone do not determine its fraction separately from the zwitterion.

A zwitterion has opposite formal electric charges in different regions of a molecule, with zero net electric charge. Phosphatidylcholine provides a membrane-related example. This is stronger than merely having chemical polarity through fractional partial atomic charges. See IUPAC Gold Book: zwitterions.