Biochemistry (intro)
The idea
Biochemistry applies organic and physical chemistry to the molecules of life, which fall into four families: proteins (polymers of amino acids), carbohydrates, lipids, and nucleic acids. The unifying chemistry is mostly familiar — condensation reactions join monomers with loss of water, hydrolysis reverses them, and the resulting macromolecules fold into shapes dictated by the intermolecular forces you already know: hydrogen bonds, ionic attractions, and the hydrophobic effect. Your background in functional groups and acid–base equilibria is exactly the toolkit these molecules demand.
Amino acids deserve special attention because they are amphoteric: each carries a basic amino group and an acidic carboxyl group, so its net charge depends on pH. At low pH both groups are protonated (net +1); at high pH both are deprotonated (net −1); in between lies the zwitterion, where the molecule is internally charged but net neutral. The pH at which the average net charge is zero is the isoelectric point, pI, and for a simple amino acid with no ionizable side chain it is the average of the two relevant pKa values. This single idea underlies how proteins are separated by electrophoresis and how enzymes respond to their surroundings.
A common misconception is picturing an amino acid in solution as a neutral molecule with intact COOH and NH₂ groups. Near physiological pH it is overwhelmingly the zwitterion, with the proton already transferred from the carboxyl to the amino group — which is why amino acids behave like salts, melting high and dissolving readily in water.
Worked example
Glycine has two ionizable groups: the carboxyl with pKa1 = 2.34 and the protonated amino group with pKa2 = 9.60. Determine glycine's isoelectric point, and state its dominant form and net charge at pH 7.0.
- Recall what pI means: it is the pH at which glycine carries zero average net charge, sitting between the carboxyl losing its proton and the amino group losing its proton.
- For an amino acid whose only ionizable groups are the carboxyl and amino, the zwitterion is the neutral species, so pI is the average of the two pKa values that bracket it.
- Compute: pI = (pKa1 + pKa2)/2 = (2.34 + 9.60)/2 = 11.94/2 = 5.97.
- Evaluate the form at pH 7.0: since 7.0 is above pKa1 (carboxyl deprotonated, −1) but below pKa2 (amino still protonated, +1), the dominant species is the zwitterion ⁺H₃N–CH₂–COO⁻.
- Determine the net charge and sanity-check: the +1 and −1 cancel, so the net charge is essentially zero, but because pH 7.0 sits slightly above pI 5.97 the molecule is on average a touch negative — consistent with glycine migrating slowly toward the positive electrode in electrophoresis at neutral pH.
Answer. Glycine's isoelectric point is pI = 5.97; at pH 7.0 it exists mainly as the zwitterion with a net charge near zero (very slightly negative).
Check your understanding
- Why is the isoelectric point of a simple amino acid the average of its two pKa values, and how would a charged side chain change that calculation?
- Why does an amino acid in water behave more like an ionic salt than like a typical neutral organic molecule?
- How does the condensation that forms a peptide bond relate to the hydrolysis that digestion uses to break it, and what is conserved between them?
- How would you predict the direction an amino acid migrates in an electric field if you knew only its pI and the solution pH?
Build the foundations first
Biochemistry (intro) builds on these concepts. If any feel shaky, start there.