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Spec Mapping — OCR A-Level Chemistry A (H432) Module 6.2.4 (a) — Amino acids and Module 4.2.5 (c) — Optical isomerism, covering: the general structure of an α-amino acid as H2N–CHR–COOH; amphoteric behaviour and zwitterion formation in aqueous solution; the cation/zwitterion/anion equilibrium as a function of pH and the concept of the isoelectric point (pI); the chirality of α-amino acids (other than glycine) arising from four different groups on the α-carbon; enantiomers, racemic mixtures, and their behaviour with plane-polarised light measured in a polarimeter; and the importance of chirality in drug design (with thalidomide as the canonical example) — refer to the official OCR H432 specification document for exact wording.
Amino acids occupy a central place in biology — they are the building blocks of every protein in every living cell, from haemoglobin to keratin to the enzymes that catalyse essentially every metabolic reaction. From a chemical point of view they are also fascinating because they contain two functional groups in one molecule: an amine (–NH₂) and a carboxylic acid (–COOH). This combination makes them act as both acids and bases at the same time — they are amphoteric — and gives rise to the unique zwitterion form they adopt in water. Amino acids are also (almost always) chiral, which makes them an ideal vehicle for introducing optical isomerism: the α-carbon carries four different groups and so cannot be superimposed on its mirror image. This single piece of stereochemistry has profound consequences — for the structure of every protein, for the action of every enzyme, and for the discrimination between life-saving and life-destroying enantiomers in pharmaceutical drug design.
This lesson covers the OCR A-Level Chemistry A (H432) specification points 6.2.4 (a) (amino acids) and 4.2.5 (c) (optical isomerism / stereochemistry applied to amino acids). It sits at the meeting point of Lesson 6 (amines, providing the basicity argument that protonates the amino group) and Lesson 8 (peptides, where two amino acid residues join via an amide bond to start building a protein). Get the structures, the zwitterion equilibria and the chirality straight here, and Lessons 8-10 follow almost mechanically.
An α-amino acid is one in which the amino group (–NH₂) is attached to the carbon immediately adjacent to the carboxylic acid group. The general structure is:
| Amino acid | R group | Simple? |
|---|---|---|
| Glycine | –H | Simplest, achiral |
| Alanine | –CH₃ | Simplest chiral |
| Valine | –CH(CH₃)₂ | Branched |
| Serine | –CH₂OH | Contains OH |
| Cysteine | –CH₂SH | Contains S |
| Glutamic acid | –CH₂CH₂COOH | Acidic side chain |
OCR does not expect you to memorise all 20 amino acids by name, but you should be able to recognise the α-amino acid structure and draw glycine, alanine and similar simple examples.
Because an amino acid has both an acidic –COOH and a basic –NH₂ group, it can react as both an acid and a base. Compounds that do this are called amphoteric.
The basic –NH₂ is protonated to give an ammonium salt:
H2N−CHR−COOH+HCl⟶+H3N−CHR−COOH+Cl−
The acidic –COOH is deprotonated to give a carboxylate salt:
H2N−CHR−COOH+NaOH⟶H2N−CHR−COO−Na++H2O
In solid and in neutral aqueous solution, an amino acid exists as a zwitterion — a molecule with a positively charged N and a negatively charged carboxylate at the same time:
Key Definition — Zwitterion: A neutral molecule that carries both a positive and a negative charge on different atoms, with the net charge zero.
The zwitterion form explains some odd properties of amino acids:
The isoelectric point (pI) is the pH at which the amino acid is net neutral — exactly balanced between the cation, the zwitterion and the anion.
graph LR
A[Low pH: cation +H3N-CHR-COOH] --> B[pH = pI: zwitterion +H3N-CHR-COO-]
B --> C[High pH: anion H2N-CHR-COO-]
For a "simple" amino acid (one whose side chain is not acidic or basic — alanine, valine, glycine), the pI is the average of the two ionisation pKa values, pI=21(pKa,COOH+pKa,NH3+). For alanine, pKa,COOH=2.35 and pKa,NH3+=9.69, giving pI=6.02. So pure alanine in water sits at pH 6 — slightly acidic of neutral but very close to it — and it is overwhelmingly in the zwitterion form. For amino acids with a charged side chain (lysine has a second amino group, glutamic acid a second carboxylic acid), the pI calculation requires a third pKa and gives pI values far from 6: lysine pI ≈ 9.7 (basic), glutamic acid pI ≈ 3.2 (acidic). This is the chemistry behind why blood at pH 7.4 carries a tiny net negative charge on most proteins — the side chains overall have more carboxylate (deprotonated COOH) than ammonium (protonated NH₃⁺) groups.
Worked Example 1 — alanine at pH 1 (strong acid). At pH = 1, well below both pKa values, every COOH stays protonated and every NH₂ becomes NH₃⁺. The dominant form is the cation:
+H3N–CH(CH3)–COOH
Net charge: +1. In a polyacrylamide gel electrophoresis (PAGE) experiment at pH 1, alanine would migrate toward the negative electrode (cathode).
Worked Example 2 — alanine at pH 6 (≈ pI). At pH = pI = 6.02, [cation] = [anion] and the dominant species is the zwitterion:
+H3N–CH(CH3)–COO−
Net charge: 0. In an electrophoresis experiment at pH 6, alanine would not migrate to either electrode — it sits still at the loading line, which is one of the experimental methods used to determine pI in the lab.
Worked Example 3 — alanine at pH 12 (strong base). At pH = 12, well above both pKa values, COOH is fully deprotonated to COO⁻ and the ammonium loses its proton to give NH₂. The dominant form is the anion:
H2N–CH(CH3)–COO−
Net charge: -1. In electrophoresis at pH 12, alanine would migrate toward the positive electrode (anode).
These three pH regimes — strongly acidic, ≈ pI, strongly basic — are the canonical OCR question pattern. Be ready to draw all three and identify the net charge.
Except for glycine (R = H), every α-amino acid has four different groups attached to the α-carbon: –H, –NH₂, –COOH and –R. Four different groups means the α-carbon is a chiral centre (or stereocentre).
Key Definition — Chiral centre: A carbon atom (or other atom) bonded to four different groups.
Two molecules that are non-superimposable mirror images of each other are called enantiomers. Enantiomers have:
A racemate (or racemic mixture) is a 50:50 mix of the two enantiomers. Because the optical rotations of the two enantiomers cancel out, a racemate has no net optical rotation. This matters because:
A sample of pure single enantiomer rotates the plane of plane-polarised light by a characteristic angle when passed through a polarimeter. The angle depends on:
At the same concentration, the two enantiomers rotate the plane by the same amount but in opposite directions.
Scan the structure for any sp³ carbon. Count the unique groups attached. If all four are different, it is a chiral centre. If two are the same, it is not.
Example: In butan-2-ol, CH₃–CH(OH)–CH₂–CH₃, the C2 carbon has four groups: –CH₃, –OH, –H, –CH₂CH₃. All different → chiral. Butan-2-ol exists as two enantiomers.
Example: In propan-2-ol, (CH₃)₂CH–OH, the C2 carbon has –CH₃, –CH₃, –OH, –H. Two –CH₃ groups are the same → not chiral.
The most famous example is thalidomide — a drug sold in the 1950s as a treatment for morning sickness. One enantiomer was effective as a sedative; the other caused devastating birth defects. The drug was sold as a racemate, so patients received both.
Since then, pharmaceutical regulators have required extensive testing of individual enantiomers before any new chiral drug is approved. Modern drug synthesis uses asymmetric catalysts or chiral pools (like naturally occurring amino acids) to build one enantiomer cleanly.
Other everyday examples:
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