Amino Acids and Peptides: Zwitterions and the Peptide Bond
An amino acid carries an acid and a base in one molecule, so in water it exists as an ion with charges at both ends. How those charges vary with pH sets its behaviour, and joining two of them makes a bond with unusual rigidity.
What a learner can do afterwards
- Draws the dominant form of an amino acid at a stated pH and calculates its isoelectric point from the pKa values
- Explains why the peptide bond is planar using delocalisation and predicts the preferred geometry
- Explains why peptide synthesis needs both activation and protection, and where each is applied
- Predicts the direction an amino acid moves during electrophoresis at a given pH
1 · Read
Every standard amino acid shares one backbone: a central carbon carrying an amino group, a carboxyl group, a hydrogen, and a side chain that sets its habits. In neutral water the carboxyl group hands its proton to the amino group. The result is a zwitterion: one molecule with a positive end and a negative end, and no net charge.
Change the pH and the dominant form changes with it. Strong acid protonates every group, so the molecule becomes a cation. Strong base strips every group, so it becomes an anion. The pH where the charges exactly balance is the isoelectric point, and you find it by averaging the two pKa values that bracket the neutral form. When the side chain itself can gain or lose a proton, those two values may both sit on the acidic side or both on the basic side.
Take glutamic acid, whose side chain is acidic and turns negative near neutral pH. At pH 7 the whole molecule carries a net negative charge, so in an electric field it drifts toward the positive electrode. An amino acid sitting exactly at its isoelectric point stays put, because its net charge is zero. That is the whole logic of electrophoresis: each residue moves toward the electrode opposite to its own net charge.
Joining the carboxyl of one amino acid to the amino of the next releases water and makes a peptide bond. The nitrogen lone pair spreads into the carbonyl, so the link behaves partly double: rotation freezes, the linkage stays planar, and the trans shape wins. In the lab the partners will not simply condense, so each coupling runs as protect, activate, couple, and deprotect. Activation wakes the carboxyl group, and protection keeps every other reactive group out of the reaction.
Charge sets where an amino acid travels, and a stiff planar link chains amino acids into peptides.
2 · Watch
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Where it sits
8 questions wait behind this lesson, each with its answer explained. Every answer feeds the sky: stars light as they are learned, and dim when it is time to come back.