DNA structure protein synthesis & mutations (HT only)

SPEC 4.6.1.5 (HT) PAPER 2

Protein Synthesis & Mutations

How the base sequence in a gene builds a working protein — and how a single change can break it. Ribosomes, carrier molecules, folding, and the dominoes of a mutation.

Higher Tier Biology Only

Why This Matters

This lesson is a chain question generator. The classic AQA 5-marker says: "Explain how a mutation could cause this enzyme not to work." Five marks for five linked steps. Miss a link — lose the mark. The chain runs from base change → amino acid change → protein shape change → loss of function.

5

Marks for a typical mutation chain

3

Protein types in spec (enzymes, hormones, structural)

2

Base pairing rules to memorise

The Chain You Must Build

For mutation questions, the mark scheme awards each link: base / triplet change → different amino acid → different protein → different shape → can't do its job. Every link matters — every link earns a mark.

Learning Objectives

By the end of this lesson, you'll be able to:

State the complementary base pairing rules: A pairs with T, C pairs with G.

Give a simple description of protein synthesis (ribosomes, template, carrier molecules, amino acids, folding).

Explain how a change in DNA structure can change the protein made by a gene.

Describe how mutations can affect the protein and how non-coding DNA can switch genes on or off.

Scope Note (Spec)

The spec says: "Students are NOT expected to know or understand the structure of mRNA, tRNA, or the detailed structure of amino acids or proteins." Don't go deeper than the spec asks — ribosomes, "carrier molecules", amino acids, and folding are enough.

Key Terms

Definition

Complementary Base Pairing

In DNA, A always pairs with T, and C always pairs with G. The two strands fit together like puzzle pieces — the bases on one strand match the bases on the other.

Definition

Ribosome

The cell structure where proteins are synthesised. The ribosome reads the gene as a template and assembles amino acids in the correct order.

Definition

Mutation

A change in the DNA — can be a change to a single base, the number of chromosomes, or other genetic material. Mutations occur continuously.

Complementary Base Pairing HT only

The two strands of DNA aren't random — they fit together by base pairing rules:

The Two Rules

A always pairs with T. C always pairs with G. So if one strand reads ACGTA, the matching strand reads TGCAT.

Mark Scheme Trap (Specimen MS Q7.2)

The specimen mark scheme for identifying DNA bases explicitly says: "do not allow U / uracil". Uracil (U) is in RNA, not DNA. In any DNA question — whether identifying bases or stating pairing — always write T for DNA, never U.

Protein Synthesis — Simple Description HT only

The spec uses very specific language for protein synthesis. Learn the exact phrasing:

"Proteins are synthesised on ribosomes, according to a template. Carrier molecules bring specific amino acids to add to the growing protein chain in the correct order." — AQA Spec 4.6.1.5 (HT only)

Three Mark-Scheme Phrases

"Synthesised on ribosomes" — the location

"According to a template" — the gene is the template

"Carrier molecules bring amino acids in the correct order" — the assembly

Carrier Molecules & Amino Acids HT only

The order of bases in the gene controls the order of amino acids in the protein. Carrier molecules deliver each amino acid one at a time, in the right sequence.

The Order Chain

The order of bases in the gene = the template (e.g. 3 bases code for 1 amino acid).

Carrier molecules bring the matching amino acids to the ribosome in the correct order.

Each amino acid is joined to the next, forming a growing chain.

When the chain is complete, it's a protein with a specific sequence of amino acids.

Spec Boundary — What NOT To Say

Don't say "mRNA" or "tRNA" or "transcription/translation" — the spec explicitly says students don't need to know these terms at GCSE. The phrase "carrier molecules" is the spec's wording — use it. (mRNA and tRNA come later at A-Level.)

Protein Folds Into A Unique Shape HT only

Once the protein chain is complete, it doesn't stay as a straight line. It folds up into a specific 3D shape — and that shape is what makes the protein able to do its job.

"When the protein chain is complete it folds up to form a unique shape. This unique shape enables the proteins to do their job as enzymes, hormones, or forming structures in the body such as collagen." — AQA Spec 4.6.1.5 (HT only)

Three Functions Of Proteins (Spec)

Enzymes — biological catalysts (shape gives them an active site to bind a substrate).

Hormones — chemical messengers (e.g. insulin).

Structural proteins — forming structures in the body (e.g. collagen in skin, tendons, bones).

Why The Shape Matters

The protein's shape determines its function. An enzyme works because its active site is shaped to fit a specific substrate. A structural protein like collagen works because its long, strong fibres give tissues mechanical strength. Change the shape — change (or break) the function.

Putting It Together — The Synthesis Chain

The whole chain from DNA to working protein, in 4 steps:

DNA

RIBOSOME

AMINO ACIDS

PROTEIN

The Logic In One Sentence

The order of bases in a gene controls the order of amino acids assembled on the ribosome by carrier molecules. The chain folds into a unique shape, which determines whether the protein can do its job.

Mutations — Continuous Changes HT only

A mutation is a change in the DNA. The key spec point: mutations occur continuously — all the time, in every cell, naturally.

"Mutations occur continuously. Most do not alter the protein, or only alter it slightly so that its appearance or function is not changed." — AQA Spec 4.6.1.5 (HT only)

Two Things To Remember

Mutations happen all the time — they're not rare events. Every cell division can produce errors.

Most mutations have no effect — or only a very slight one. The protein still works.

Common Error

Students often write "mutations always change the protein". This is wrong. The spec says most do not alter the protein. Only a few mutations cause a significant change.

When A Mutation DOES Change The Protein HT only

The "few" mutations that matter: a change in the DNA leads to a change in the protein — via a chain of effects.

"A few mutations code for an altered protein with a different shape. An enzyme may no longer fit the substrate binding site, or a structural protein may lose its strength." — AQA Spec 4.6.1.5 (HT only)

If the protein is an ENZYME

The mutation changes the protein's shape, which changes the shape of the active site. The substrate no longer fits. The reaction doesn't happen.

If the protein is STRUCTURAL

The mutation changes the protein's shape, which means the structure (e.g. collagen) loses its strength. Tissues may become weaker.

The Mutation Chain HT only

This is the chain that the 5-mark question is testing. Each box = one mark in the mark scheme.

Non-Coding DNA HT only

Not every part of DNA codes for a protein. The bits that don't are called non-coding DNA — but they're not useless. They control which genes get switched on.

"Not all parts of DNA code for proteins. Non-coding parts of DNA can switch genes on and off, so variations in these areas of DNA may affect how genes are expressed." — AQA Spec 4.6.1.5 (HT only)

Two Types Of Mutation Effects

Mutation in...What it doesCoding DNA

(a gene)Changes the amino acid sequence → changes the protein's activity (e.g. enzyme stops working)Non-coding DNA

(between genes)May change how genes are switched on or off → changes which proteins are made or how much

Mark Scheme Phrase (MS Nov 2020 P2 Q4.4)

The 1-mark question asks how non-coding parts affect gene expression. The mark scheme answer: "(non-coding parts) can switch genes on / off". Memorise that exact wording.

Examiner Alerts

Three traps that cost marks on every HT paper.

Alert 1 — "Most mutations" vs "all mutations"

The spec says most mutations do NOT alter the protein (or only slightly). Writing "mutations always change the protein" is wrong. Use the word "most" or "some" — not "all".

Alert 2 — U vs T (Specimen MS Q7.2)

DNA bases are A, C, G, T. The Specimen mark scheme for identifying DNA bases explicitly says "do not allow U". Uracil (U) is in RNA, not DNA. Always write T for DNA — in identification, pairing, or sequence questions.

Alert 3 — Use the spec's exact phrases

Mark schemes reward exact wording: "synthesised on ribosomes", "carrier molecules", "correct order", "unique shape", "active site", "substrate no longer fits". Don't paraphrase — the spec uses these phrases for a reason.

PEE Worked Example

Question: A mutation occurs in a gene that codes for an enzyme. Explain how this mutation could cause the enzyme to stop working. 5 marks

P

Point 1: The mutation changes the sequence of bases (or the triplet code) in the gene.

E

Evidence: Because a sequence of three bases codes for one amino acid, the change in bases means a different amino acid is brought to the ribosome by the carrier molecule.

P

Point 2: The protein chain therefore has a different sequence of amino acids.

E

Evidence: When the protein folds, it folds into a different shape.

P

Conclusion: The enzyme's active site shape has changed, so the substrate no longer fits — the enzyme cannot catalyse the reaction.

Why This Scores 5/5 (matches Specimen MS Q7.3)

Five distinct mark-scheme points: (1) change in bases / triplet; (2) change in amino acid; (3) change in protein; (4) change in shape / active site; (5) substrate no longer fits. Every link in the chain earns one mark. Miss a link — lose a mark.

Practice Question

Collagen is a structural protein that gives strength to tendons and skin. A scientist observes that a person with a particular mutation in a collagen gene has very weak tendons.

(a) Suggest how the mutation could lead to weak tendons. 4 marks

(b) Most mutations have no effect on the protein. Explain why. 2 marks

(a)

Mark scheme chain (any 4 marks):

The mutation changes the sequence of bases in the gene (1)

This changes the sequence of amino acids in the collagen protein (1)

The protein folds into a different shape (1)

The collagen loses its strength — so the tendons are weaker (1)

(b)

Many mutations do not change the amino acid coded for (1) — OR — only cause a slight change in the protein

So the protein's shape and function are not changed (1)

Note: Part (a) tests the structural protein side of the spec ("structural protein may lose its strength"). Part (b) tests the "most mutations do not alter the protein" point. Total 6 marks.

Recap — 3 Takeaways

Base Pairing & Synthesis

A pairs with T, C pairs with G. Proteins are synthesised on ribosomes, using DNA as a template. Carrier molecules bring amino acids in the correct order; the chain folds into a unique shape.

The Mutation Chain

5-mark chain: base change → amino acid change → protein shape change → active site no longer fits substrate (enzyme) OR structural protein loses strength (e.g. collagen). Each link = one mark.

Most Mutations Don't Matter

Most mutations have no effect on the protein, or only a slight effect. Non-coding DNA can switch genes on or off — so variations there affect gene expression.

The One-Sentence Synthesis

The order of bases in a gene controls the order of amino acids in a protein, which determines the protein's shape, which determines its function. Change any link in the chain — you can change the protein.

NEXT: Lesson 6.04 — Genetic Inheritance (alleles, Punnett squares, dominant & recessive)