Three families, one thread: amino acids carry both an acid and a base group, so they behave unusually; join them by peptide bonds and you get proteins (including enzymes); and DNA stores information through hydrogen-bonded base pairs. The chemistry you already know — acids and bases, condensation, hydrogen bonding, ligand substitution — explains all of it.
Amino acids — zwitterions & acid/base behaviour
An α-amino acid has an amine group and a carboxylic acid group on the same carbon: H2N–CHR–COOH, where R varies. Because it carries both an acid and a base, an amino acid behaves as both.
- Around neutral pH the acid group donates its H+ to the amine group on the same molecule, giving a zwitterion: +H3N–CHR–COO− (overall neutral, but with both a + and a − charge).
- In acid solution the –COO− is protonated → a cation: +H3N–CHR–COOH.
- In alkaline solution the –NH3+ loses H+ → an anion: H2N–CHR–COO−.
🧪 Exam-style questions
Which is the structure of the zwitterion of the amino acid alanine, CH3CH(NH2)COOH?
Which is the main species present in a solution of the amino acid at pH = 14?
Source: AQA A-Level Chemistry past papers.
Proteins — peptides & structure
Amino acids join by peptide bonds: the –COOH of one reacts with the –NH2 of the next, forming an amide link (–CO–NH–) and releasing water — a condensation reaction. A chain of them is a protein. Heating with hot aqueous acid (or alkali) hydrolyses the peptide bonds back to the constituent amino acids.
- Primary — the sequence of amino acids in the chain.
- Secondary — the chain coils into an α-helix or folds into a β-pleated sheet, held by hydrogen bonds between the C=O and N–H of the backbone.
- Tertiary — the overall 3-D shape, held by interactions between the R groups: hydrogen bonds, S–S disulfide bridges (between two cysteines), and ionic interactions.
A mixture of amino acids from a hydrolysed protein can be separated and identified by thin-layer chromatography: colourless amino acids are located with ninhydrin or UV light and identified by their Rf values (see chromatography).
🧪 Exam-style questions
Which interaction is mainly responsible for holding a protein’s secondary structure in an α-helix?
In a protein, explain why the interaction between two cysteine R groups differs in strength from the interaction between a serine R group (–CH2OH) and an aspartic acid R group (–CH2COOH).
Show answer
Two cysteine R groups (each –CH2SH) form a disulfide (S–S) bridge. 1 mark
The serine and aspartic acid R groups form a hydrogen bond (between –OH and –COOH). 1 mark
The disulfide bridge is stronger than the hydrogen bond… 1 mark
…because a disulfide bridge is a covalent bond, whereas a hydrogen bond is not. 1 mark
Source: AQA A-Level Chemistry past papers.
Enzymes, DNA & cisplatin
Enzymes
Enzymes are proteins that act as catalysts. Each has a stereospecific active site whose shape is complementary to one substrate. Because the active site has a definite 3-D shape, only one enantiomer of a chiral substrate fits — the mirror image cannot bind, just as a left hand won’t fit a right glove. A drug can act as an inhibitor by binding to the active site and blocking it; computers are used to design molecules with the right complementary shape.
DNA
A nucleotide is a phosphate ion bonded to 2-deoxyribose (a pentose sugar), which is bonded to one of four bases (adenine, cytosine, guanine, thymine). Nucleotides link through covalent bonds between the phosphate of one and the sugar of the next, giving a sugar–phosphate backbone with the bases hanging off it. Two strands run alongside each other, held together by hydrogen bonds between complementary base pairs, twisted into a double helix.
Adenine pairs with thymine (two hydrogen bonds); cytosine pairs with guanine (three hydrogen bonds). The pairing is fixed by where the H-bond donors and acceptors sit on each base, which is why the two strands are complementary.
Cisplatin
Cisplatin, [Pt(NH3)2Cl2], is a Pt(II) anticancer drug. It stops a cancer cell dividing by preventing DNA replication: in a ligand replacement reaction, its chloride ligands are replaced as bonds form between the platinum and nitrogen atoms on guanine bases, cross-linking the DNA so the strands cannot separate. Because it also affects healthy dividing cells, it has adverse side effects — so society weighs the benefits against the harms.
🧪 Exam-style questions
When cisplatin bonds to DNA, which ligand replacement occurs?
Which statement about enzymes is not correct?
After cisplatin enters a cell, one chloride ligand is replaced by a water molecule. Give the equation for this reaction.
Show answer
[Pt(NH3)2Cl2] + H2O → [Pt(NH3)2Cl(H2O)]+ + Cl− 2 marks
(One mark for the correct formula and + charge of the complex; one for balancing, with Cl− released.)
Source: AQA A-Level Chemistry past papers.
Pulling it together
The whole topic reuses chemistry you already own: acid–base behaviour explains zwitterions; condensation and hydrolysis build and break proteins; hydrogen bonding shapes proteins and pairs DNA bases; optical isomerism explains why an enzyme picks one enantiomer; and ligand substitution explains cisplatin.
- Drawing a zwitterion without both charges, or giving the wrong ion for the stated pH.
- Naming the wrong bonding for each protein level — secondary is backbone H-bonds; tertiary adds S–S bridges and ionic interactions.
- Swapping the base pairs or their H-bond counts — A–T (2), C–G (3).
- Saying cisplatin “damages” DNA vaguely — it prevents replication by a ligand replacement bonding Pt to N on guanine.
Examiner reports note that structure marks are lost to careless charges and bonds — a zwitterion missing a charge, a peptide link drawn without the N–H, base pairs with the wrong number of hydrogen bonds. Draw them deliberately.
- Amino acids: H2N–CHR–COOH form zwitterions (+H3N–CHR–COO−); cation in acid, anion in alkali.
- Proteins: amino acids joined by peptide bonds (condensation, water lost). Primary = sequence; secondary = α-helix / β-pleated sheet held by hydrogen bonds; tertiary = folded shape held by H-bonds, S–S disulfide bridges and ionic interactions. Hydrolysis (hot HCl) → the amino acids.
- Enzymes are proteins with a stereospecific active site — only one enantiomer of a substrate fits. Drugs can act as inhibitors by blocking the active site.
- DNA: nucleotide = phosphate + 2-deoxyribose + base; a sugar–phosphate backbone; two strands held by hydrogen-bonded base pairs (A–T two H-bonds, C–G three) in a double helix.
- Cisplatin [Pt(NH3)2Cl2] stops DNA replicating by a ligand replacement — the two Cl− are replaced as Pt bonds to N atoms on guanine, cross-linking the strands.