IMAT Biology · Molecular Biology and Gene Expression

DNA Replication: Semi-conservative Copying

Before a cell divides it copies its DNA: the helix is unzipped and each old strand is the template for a new partner, so every copy keeps one old strand.

All Molecular Biology and Gene Expression notes

Why this matters

Replication has been asked as a labelled-strand calculation over several rounds (2015), as a comparison with transcription (2020) and as a plain definition in the 2024 ministry paper. The 2026 paper asked about the history of the double helix.

Concept 1 of 4: Semi-conservative replication and counting labelled strands

Unzip a ladder down the middle and build a new half onto each old half: you get two ladders, each half old and half new. Old strands are never destroyed. After many rounds the two original strands still exist, but they are spread into just two of the many molecules.

Definition

Replication uses each strand of DNA as a template to build a new complementary strand.

It is semi-conservative: each daughter molecule has one parental strand and one new strand.
Starting from one molecule, after n rounds there are $2^n$ molecules and $2^{n+1}$ strands.
The 2 original strands are always in exactly 2 molecules (as long as both are labelled the same way).
Meselson and Stahl (1958) grew bacteria on heavy nitrogen (¹⁵N), moved them to light nitrogen (¹⁴N) and separated the DNA by density: after one round all DNA was of intermediate density; after two rounds, half intermediate and half light.

Molecules after n rounds

\text{molecules} = 2^n, \qquad \text{fraction holding an original strand} = \frac{2}{2^n}

$n$ number of rounds of replication

Worked example

A bacterium whose DNA contains only ¹⁵N is moved to a medium with only ¹⁴N. After two rounds of replication, what fractions of the DNA molecules are heavy (both strands ¹⁵N), intermediate (one of each) and light (both ¹⁴N)?

Practice this conceptself-check · 3 quick reps

Molecules and strands give different fractions

After n rounds there are

2^n

molecules but

2^{n+1}

strands. The 2 original strands are

2/2^n

of the molecules but only

2/2^{n+1}

of the strands. Check which one the question asks for.

Concept 2 of 4: The enzymes of DNA replication and what each one does

Copying DNA is a production line. One enzyme opens the helix, others keep it open and relieve the twisting, one lays a short starter, the polymerase builds the new strand, and a last enzyme seals the gaps. Each step either breaks or makes a particular bond, which is what IMAT options test.

Definition

Replication begins at origins of replication: one on a bacterial circular chromosome, thousands along each eukaryotic chromosome. Each origin opens into a bubble with two replication forks.

DNA polymerase cannot start a strand: it needs a primer with a free 3′ end, made of RNA.
It adds nucleotides only to the 3′ end, so every new strand grows 5′→3′.
The raw materials are deoxyribonucleoside triphosphates; releasing two of their phosphates supplies the energy.
DNA polymerase proofreads. After proofreading and repair only about 1 base in $10^9$ to $10^{10}$ is wrong.
In eukaryotes replication happens in the S phase of interphase. Eukaryotic polymerases have other names (α, δ, ε) but do the same jobs.

Enzyme or protein	Job	Bond made or broken
Helicase	unwinds the helix at the fork and separates the strands	breaks hydrogen bonds between bases
Topoisomerase (DNA gyrase in bacteria)	relieves the over-twisting ahead of the fork	cuts and rejoins phosphodiester bonds
Single-strand binding proteins	keep the separated strands apart	makes or breaks none; they only bind
Primase	lays down a short RNA primer	makes phosphodiester bonds in RNA
DNA polymerase III (bacteria)	extends the primer 5′→3′, pairing each new base with the template, and proofreads	makes phosphodiester bonds
DNA polymerase I (bacteria)	removes the RNA primers and fills the gaps with DNA	breaks and makes phosphodiester bonds
DNA ligase	seals the last gap in the backbone between neighbouring fragments	makes one phosphodiester bond

Practice this conceptself-check · 4 quick reps

DNA polymerase needs a primer; RNA polymerase does not

DNA polymerase can only add to an existing 3′ end, so every new DNA strand starts on a short RNA primer. RNA polymerase in transcription starts a chain on its own. An option saying DNA polymerase begins a new strand from nothing is wrong.

Concept 3 of 4: Leading and lagging strands and Okazaki fragments

The fork opens in one direction, but the two template strands point opposite ways. DNA polymerase can only build 5′→3′. On one template that direction follows the opening fork, so the new strand grows smoothly. On the other it points away from the fork, so the strand has to be built in short pieces, each started again as more template is exposed.

Definition

Replication is semi-discontinuous:

The leading strand is made continuously, towards the fork.
The lagging strand is made in short pieces, the Okazaki fragments (about 1000 to 2000 nucleotides in bacteria, 100 to 200 in eukaryotes), each growing away from the fork.
Each Okazaki fragment needs its own RNA primer; the primers are later replaced with DNA and the fragments joined by DNA ligase.
At the ends of a linear eukaryotic chromosome the last primer cannot be replaced, so chromosomes shorten a little each round. The repeated end sequences, telomeres, protect the genes; telomerase lengthens them in germ cells, stem cells and most cancer cells.

Feature	Leading strand	Lagging strand
Direction of growth	5′→3′, towards the fork	5′→3′, away from the fork
How it is made	continuously, in one piece	in short Okazaki fragments
RNA primers needed	one, at the origin	one for every fragment
Work for DNA ligase	very little	joins every pair of neighbouring fragments

Practice this conceptself-check · 3 quick reps

The lagging strand is not built 3′→5′

No strand is ever built 3′→5′. The lagging strand is built 5′→3′ like the leading strand, but in pieces, each pointing away from the fork. An option saying one strand grows 3′→5′ is wrong.

Concept 4 of 4: Key experiments: DNA as the genetic material and its structure

Each famous experiment answered one question: is the gene DNA or protein, what shape is DNA, and how is it copied? Learn each name with its method and its answer, because IMAT asks for the pairing, not the details.

Definition

The classic evidence, in order:

Transformation showed a chemical passes genes between bacteria; Avery's group showed that chemical is DNA.
Hershey and Chase confirmed that viruses inject DNA, not protein.
Chargaff, Franklin and Watson and Crick solved the structure.
Meselson and Stahl showed how it is copied.

Using DNA as a tool (cloning, PCR, gel electrophoresis) belongs to the biotechnology chapter.

Who and when	What they did	What it showed
Griffith (1928)	mixed heat-killed virulent pneumococci with live harmless ones; the mice died	a 'transforming principle' can pass between bacteria
Avery, MacLeod and McCarty (1944)	destroyed each type of molecule in the extract in turn	the transforming principle is DNA
Chargaff (about 1950)	measured the bases in DNA from many species	A = T and G = C
Hershey and Chase (1952)	labelled phage protein with ³⁵S and phage DNA with ³²P	only DNA enters the bacterium: genes are DNA
Franklin and Wilkins (1951 to 1953)	X-ray crystallography of DNA fibres	a regular helix with the backbone on the outside
Watson and Crick (1953)	built the double-helix model	base pairing suggests how DNA is copied
Meselson and Stahl (1958)	grew bacteria in ¹⁵N then ¹⁴N and separated DNA by density	replication is semi-conservative

Practice this conceptself-check · 3 quick reps

X-ray crystallography, not electron microscopy, revealed the helix

Franklin's evidence came from the pattern X-rays make after passing through DNA fibres. Electron microscopes, chromatography and electrophoresis played no part in finding the double helix.

Summary — formulas & gotchas at a glance

A revision cheat-sheet for the formulas and gotchas above. Click any concept name to jump back to its full explanation.

Formulas (1)

Semi-conservative replication and counting labelled strands
Molecules after n rounds
$\text{molecules} = 2^n, \qquad \text{fraction holding an original strand} = \frac{2}{2^n}$

Reference tables (3)

The enzymes of DNA replication and what each one does7 rows

Enzyme or protein	Job	Bond made or broken
Helicase	unwinds the helix at the fork and separates the strands	breaks hydrogen bonds between bases
Topoisomerase (DNA gyrase in bacteria)	relieves the over-twisting ahead of the fork	cuts and rejoins phosphodiester bonds
Single-strand binding proteins	keep the separated strands apart	makes or breaks none; they only bind
Primase	lays down a short RNA primer	makes phosphodiester bonds in RNA
DNA polymerase III (bacteria)	extends the primer 5′→3′, pairing each new base with the template, and proofreads	makes phosphodiester bonds
DNA polymerase I (bacteria)	removes the RNA primers and fills the gaps with DNA	breaks and makes phosphodiester bonds
DNA ligase	seals the last gap in the backbone between neighbouring fragments	makes one phosphodiester bond

Leading and lagging strands and Okazaki fragments4 rows

Feature	Leading strand	Lagging strand
Direction of growth	5′→3′, towards the fork	5′→3′, away from the fork
How it is made	continuously, in one piece	in short Okazaki fragments
RNA primers needed	one, at the origin	one for every fragment
Work for DNA ligase	very little	joins every pair of neighbouring fragments

Key experiments: DNA as the genetic material and its structure7 rows

Who and when	What they did	What it showed
Griffith (1928)	mixed heat-killed virulent pneumococci with live harmless ones; the mice died	a 'transforming principle' can pass between bacteria
Avery, MacLeod and McCarty (1944)	destroyed each type of molecule in the extract in turn	the transforming principle is DNA
Chargaff (about 1950)	measured the bases in DNA from many species	A = T and G = C
Hershey and Chase (1952)	labelled phage protein with ³⁵S and phage DNA with ³²P	only DNA enters the bacterium: genes are DNA
Franklin and Wilkins (1951 to 1953)	X-ray crystallography of DNA fibres	a regular helix with the backbone on the outside
Watson and Crick (1953)	built the double-helix model	base pairing suggests how DNA is copied
Meselson and Stahl (1958)	grew bacteria in ¹⁵N then ¹⁴N and separated DNA by density	replication is semi-conservative

Watch out for (4)

Molecules and strands give different fractions
→ Semi-conservative replication and counting labelled strands
DNA polymerase needs a primer; RNA polymerase does not
→ The enzymes of DNA replication and what each one does
The lagging strand is not built 3′→5′
→ Leading and lagging strands and Okazaki fragments
X-ray crystallography, not electron microscopy, revealed the helix
→ Key experiments: DNA as the genetic material and its structure

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