Part 3: DNA, complementary bases and cisplatin

Build a nucleotide and DNA backbone, explain base pairing and connect platinum ligand substitution to interference with replication.

Three components make one nucleotide

A DNA nucleotide contains a phosphate group, 2-deoxyribose and one base: adenine, thymine, guanine or cytosine. The sugar is a pentose; compared with ribose it lacks the OH group at the 2′ carbon. The base attaches to the sugar’s 1′ carbon through nitrogen: N9 in the purines adenine/guanine and N1 in the pyrimidines cytosine/thymine.

The AQA data booklet supplies the relevant sugar, phosphate and base structures. Use them to locate donor atoms and connections; do not connect the sugar to whichever nitrogen happens to be nearest on the printed page. Phosphate protonation/charge depends on the representation and conditions; a phosphate ester in the backbone is not simply a free PO₄³⁻ ion with three charges copied onto every nucleotide.

Covalent links build each strand

Phosphate forms ester connections to the sugar groups, linking the 3′ oxygen of one sugar and the 5′ oxygen associated with the next to make a repeating sugar–phosphate backbone. The bases project from the sugars. The bonds along a strand are covalent; the two complementary strands are associated through base pairing and other interactions.

The two strands run in opposite directions in the double helix. A useful extension of the notation is 5′-AGTC-3′ paired with 3′-TCAG-5′. If both sequences must be written 5′ to 3′, the partner is 5′-GACT-3′. Pay attention to the direction before copying the complementary letters.

Donor and acceptor positions determine complementarity

Adenine pairs with thymine using two hydrogen bonds; guanine pairs with cytosine using three. Suitable N–H donor groups point towards lone pairs on N or O acceptors. The matching patterns and geometry explain complementarity, rather than a general attraction between any two nitrogen-containing bases.

For A–T, adenine’s amino N–H can donate to thymine carbonyl O, and thymine N–H can donate to adenine ring N. For G–C, guanine carbonyl O accepts from cytosine amino N–H, guanine ring N–H donates to cytosine ring N, and guanine amino N–H donates to cytosine carbonyl O. Base-pair drawings should preserve the supplied base structures.

Constructed count: a DNA segment with 18 G–C pairs and 12 A–T pairs has 18 × 3 + 12 × 2 = 78 base-pair hydrogen bonds in this model. Base percentages in ordinary double-stranded DNA obey A = T and G = C; this relation does not automatically apply to a single isolated strand.

A platinum–nitrogen bond can disrupt DNA replication

Cisplatin is cis-[Pt(NH₃)₂Cl₂], a square-planar Pt(II) complex with the two chlorides adjacent. Its overall charge is zero: Pt²⁺ plus two Cl⁻ and two neutral NH₃ ligands. The trans isomer has different geometry and biological behaviour.

Following ligand replacement, platinum forms coordinate bonds to nitrogen donor atoms on guanine, commonly N7. Formation of links involving nearby DNA sites distorts the DNA and interferes with replication. The nitrogen lone pair supplies the pair for the Pt–N coordinate bond; this is not a hydrogen bond and does not require changing platinum from +2.

Cisplatin can also affect healthy cells and have serious adverse effects. At the syllabus level, evaluate a drug by balancing benefit against harm and considering evidence, rather than assuming activity against cancer makes it harmless. Dose choices and treatment decisions are clinical matters, not predictions from this structural diagram.

Quick checks

Original Finesse questions. Reveal the indicative worked solutions after attempting each question; these are not official AQA mark allocations.

Sources