DNA Structure and Replication

Deoxyribonucleic acid (DNA) is the molecule of heredity. Understanding its structure is essential to explaining how genetic information is stored, replicated, and expressed. This lesson covers the Watson-Crick model, the chemical composition of nucleotides, Chargaff's rules, and the mechanism of semi-conservative replication — all key topics for AQA A-Level Biology.

The Structure of a Nucleotide

A DNA nucleotide consists of three components:

A phosphate group — provides the structural backbone and forms phosphodiester bonds with adjacent nucleotides.
A deoxyribose sugar — a five-carbon (pentose) sugar. In DNA the sugar lacks a hydroxyl group on carbon 2 (hence "deoxy").
A nitrogenous base — one of four options: adenine (A), thymine (T), cytosine (C), or guanine (G).

Bases are classified into two groups:

Type	Bases	Structure
Purines	Adenine, Guanine	Double-ring structure
Pyrimidines	Thymine, Cytosine	Single-ring structure

Key Definition: A nucleotide is the monomer of nucleic acids, consisting of a phosphate group, a pentose sugar, and a nitrogenous base joined by condensation reactions.

The Watson-Crick Model

In 1953, James Watson and Francis Crick proposed the double helix model of DNA, building on X-ray crystallography data from Rosalind Franklin and Maurice Wilkins, and the chemical data from Erwin Chargaff.

Key features of the model:

DNA is a double helix — two polynucleotide strands wound around each other.
The two strands are antiparallel — one runs 5' to 3' and the other runs 3' to 5'. The 5' end has a free phosphate group; the 3' end has a free hydroxyl group on the deoxyribose.
The sugar-phosphate backbone is on the outside of the helix, providing structural support.
The nitrogenous bases point inwards and are joined by hydrogen bonds between complementary base pairs.
Complementary base pairing: adenine pairs with thymine (A=T, two hydrogen bonds), and guanine pairs with cytosine (G≡C, three hydrogen bonds).
A purine always pairs with a pyrimidine, which keeps the width of the helix constant at approximately 2 nm.
One complete turn of the helix is 3.4 nm and contains 10 base pairs, so each base pair is separated by 0.34 nm.

Exam Tip: Questions often ask why the double helix has a constant diameter. The answer is that a purine (two rings) always pairs with a pyrimidine (one ring), giving a consistent total of three rings across the helix.

Chargaff's Rules

Before the structure of DNA was determined, Erwin Chargaff analysed the base composition of DNA from multiple organisms and established two important rules:

The amount of adenine equals the amount of thymine (A = T), and the amount of guanine equals the amount of cytosine (G = C).
The ratio of A+T to G+C varies between species but is constant within a species.

These rules directly support complementary base pairing and were crucial evidence used by Watson and Crick.

Worked Example 1 — Applying Chargaff's Rules:

A sample of DNA is found to contain 22% cytosine. Calculate the percentage of each other base.

Solution:

If C = 22%, then G = 22% (Chargaff's rule).
A + T = 100% - 44% = 56%.
Therefore A = 28% and T = 28%.

The Sugar-Phosphate Backbone

Nucleotides are joined by phosphodiester bonds formed during condensation reactions. These bonds link the 5' carbon of one nucleotide's sugar to the 3' carbon of the next nucleotide's sugar via the phosphate group.

This creates the sugar-phosphate backbone, which:

Is highly stable, protecting the bases on the interior.
Creates the directionality of each strand (5' → 3').
Is held together by strong covalent bonds, unlike the weaker hydrogen bonds between bases.

The antiparallel arrangement is critical for DNA replication and for the function of enzymes such as DNA polymerase, which can only add nucleotides in the 5' to 3' direction.

Semi-Conservative Replication

DNA replication occurs during the S phase of interphase, before mitosis or meiosis. It is described as semi-conservative because each new DNA molecule consists of one original (parental) strand and one newly synthesised strand.

The Process of DNA Replication

Helicase binds to the origin of replication and unwinds the double helix by breaking the hydrogen bonds between complementary base pairs, creating a replication fork.
Each separated strand acts as a template for a new complementary strand.
DNA polymerase adds free nucleotides to the exposed bases, following complementary base pairing rules (A with T, G with C). Nucleotides are added in the 5' to 3' direction only.
Because the two strands are antiparallel:
- The leading strand is synthesised continuously in the 5' to 3' direction towards the replication fork.
- The lagging strand is synthesised discontinuously in short fragments called Okazaki fragments (in the 5' to 3' direction away from the replication fork).
DNA ligase joins the Okazaki fragments on the lagging strand by forming phosphodiester bonds, creating a continuous strand.
The result is two identical DNA molecules, each containing one original and one new strand.

Key Enzymes in Replication

Enzyme	Role
Helicase	Unwinds the double helix; breaks hydrogen bonds between base pairs
DNA polymerase	Adds complementary nucleotides in the 5' to 3' direction; proofreads for errors
DNA ligase	Joins Okazaki fragments on the lagging strand
Primase	Synthesises a short RNA primer to provide a 3'-OH group for DNA polymerase to begin

Key Definition: Semi-conservative replication is the mechanism of DNA replication in which each new molecule contains one strand from the original molecule and one newly synthesised strand.

The Meselson-Stahl Experiment (1958)

Matthew Meselson and Franklin Stahl provided experimental evidence for semi-conservative replication.

Method

E. coli were grown for many generations in a medium containing heavy nitrogen (¹⁵N), so all their DNA contained ¹⁵N (heavy DNA).
Bacteria were then transferred to a medium containing normal nitrogen (¹⁴N) and allowed to replicate.
DNA was extracted after each generation and separated by density-gradient centrifugation in caesium chloride (CsCl).

Results

Generation 0 (before transfer): All DNA was heavy (¹⁵N-¹⁵N) — a single band at the bottom.
Generation 1: All DNA was of intermediate density (¹⁵N-¹⁴N) — a single band in the middle. This ruled out conservative replication (which would have produced one heavy and one light band).
Generation 2: DNA showed two bands — one intermediate (¹⁵N-¹⁴N) and one light (¹⁴N-¹⁴N), in equal proportions. This confirmed semi-conservative replication.

Interpretation

Each round of replication produces molecules where one strand is from the parent and one is new. After one round in ¹⁴N, every molecule has one heavy and one light strand. After two rounds, half the molecules have one heavy and one light strand, and half have two light strands.

Exam Tip: Be prepared to predict banding patterns for further generations. After generation 3, you would see 25% intermediate and 75% light DNA. The proportion of intermediate DNA halves with each generation, while the proportion of light DNA increases.

Significance of DNA Structure

The structure of DNA is elegantly suited to its function:

Complementary base pairing allows accurate replication and transcription.
The double helix provides stability and protection for the genetic information.
Hydrogen bonds between bases are individually weak but collectively strong, allowing the strands to be separated for replication and transcription without requiring excessive energy.
The sugar-phosphate backbone provides structural integrity.
The sequence of bases encodes genetic information in the form of codons.
Antiparallel strands are essential for the directional activity of DNA polymerase.

Summary

DNA is a double-stranded helix of nucleotides joined by phosphodiester bonds, with complementary base pairs held by hydrogen bonds.
Chargaff's rules (A=T, G=C) support the base-pairing model.
DNA replication is semi-conservative, involving helicase, DNA polymerase, and DNA ligase.
The leading strand is synthesised continuously; the lagging strand is synthesised in Okazaki fragments.
The Meselson-Stahl experiment confirmed semi-conservative replication using density-gradient centrifugation.

Exam Tip: When describing DNA replication, always state the role of each enzyme, the direction of synthesis (5' to 3'), and the difference between leading and lagging strands. High-mark questions often require you to explain why replication is discontinuous on the lagging strand.