PCR, Taq polymerase & gel electrophoresis

The big idea: Often a scientist starts with far too little DNA to study — a single hair, a drop of blood, or a trace of cells.

PCR (the polymerase chain reaction) solves this by making millions of copies of a chosen piece of DNA, automatically, inside a machine called a thermal cycler.

It works by repeating a three-step cycle over and over. The amount of DNA roughly doubles every cycle, so after about 30 cycles a tiny sample becomes enough to analyse.

PCR (polymerase chain reaction)

A laboratory technique that makes many copies of (amplifies) a specific length of DNA.

Amplify

To make many copies of a piece of DNA, so a tiny sample becomes a large, usable amount.

Thermal cycler

The machine that runs PCR by repeatedly heating and cooling the sample through the cycle's temperatures.

Primer

A short single strand of DNA that binds to a matching sequence and marks where copying should begin.

Taq polymerase

The heat-stable enzyme used in PCR; it adds DNA nucleotides to build the new complementary strand.

Why PCR is so powerful: Because the DNA roughly doubles each cycle, the increase is exponential: 1 → 2 → 4 → 8 → 16 …

Just 30 cycles turns one copy into over a billion — which is why PCR can work from a vanishingly small starting sample.

Each PCR cycle has three steps, and the key to the whole technique is that the temperature is changed at each step for a specific reason.

Get the temperatures the wrong way round and PCR fails — so examiners love asking you to explain why each temperature is needed.

One cycle = three temperatures: 1. Denaturation (~95 °C). Very high heat breaks the hydrogen bonds holding the two strands together, so the double helix separates into two single strands.

2. Annealing (~55 °C). Cooling lets short primers bind (anneal) to their matching sequence on each single strand, marking the start point for copying.

3. Extension (~72 °C). At Taq polymerase's optimum temperature, the enzyme adds nucleotides to each primer, building a new complementary strand.

Why Taq polymerase — not an ordinary one: The denaturation step reaches about 95 °C. An ordinary enzyme would be denatured (its shape destroyed) at that temperature and would stop working.

Taq polymerase is heat-stable (thermostable) — it survives the high heat without denaturing, so the same enzyme keeps working every cycle and does not need to be replaced.

Taq comes from Thermus aquaticus, a bacterium that lives in hot springs, so its enzymes naturally tolerate high temperatures.

Once PCR has made plenty of DNA, scientists often want to see and compare the fragments. They do this with gel electrophoresis, which sorts fragments by size.

Gel electrophoresis — sorting by size: DNA samples are loaded into wells at one end of a jelly-like gel, and an electric current is switched on.

DNA carries a negative charge, so it is pulled through the gel towards the positive electrode.

The gel acts like a sieve: smaller fragments move further, while larger fragments are held back near the wells. The result is a pattern of bands sorted by size.

A memory hook: PCR copies; the gel sorts.

Temperatures in order: Hot splits (95 °C denatures), cool sticks (55 °C anneals primers), warm builds (72 °C Taq extends).

On a gel: small = fast = far.

How this skill is assessed: On Paper 3 a data question often shows a PCR gel and asks you to explain why the temperature is changed at each step of a cycle — give a separate reason for the hot, cool and warm steps.

A 1-mark item asks for a reason Taq polymerase is suitable for PCR — the answer is that it is heat-stable and is not denatured at ~95 °C.

Gel data questions also ask you to state the no-DNA control (the lane with no band) or to predict how the gel would change — both reward reading the bands carefully.

✓ Why this scores full marks: Each step is given a distinct reason tied to its temperature — strands separating, primers binding, Taq extending.

A 3-mark 'explain' wants the cause linked to the effect at each step, not just the temperatures listed.