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Atlas · "3.4" Genetic information, variation and relationships

3.4.2 DNA and protein synthesis

Protein synthesis turns a DNA base sequence into a chain of amino acids. AQA breaks it into two stages: transcription in the nucleus, then translation at the ribosome. The topic carries an unusually concentrated set of vocabulary-precision rules; every step has at least one phrasing that earns the mark and one that does not.

Transcription copies one DNA strand into a complementary mRNA molecule.

Transcription happens in the nucleus and produces pre-mRNA from a gene. RNA polymerase is the enzyme. Only one of the two DNA strands acts as the template: the antisense strand. The other strand, the sense strand, carries the same base sequence as the resulting RNA (with uracil in place of thymine) and is not read.

  1. RNA polymerase binds to the gene and unwinds the DNA double helix by breaking the hydrogen bonds between the complementary base pairs. The bonds break; they are not hydrolysed.
  2. Free ribonucleotides in the nucleoplasm align opposite the antisense template strand by complementary base pairing. Adenine on the template pairs with uracil in the RNA, because thymine is not a component of RNA. Cytosine and guanine pair as in DNA.
  3. RNA polymerase joins adjacent ribonucleotides by forming phosphodiester bonds via condensation reactions. One water molecule is released per bond formed.
  4. RNA polymerase moves along the template, and the DNA re-anneals behind it. Only about twelve bases are unwound at any one moment, which protects the DNA from damage.
  5. Transcription continues until RNA polymerase reaches a stop signal in the DNA sequence. The new pre-mRNA strand is released.

Pair phosphodiester bond with condensation reaction. Naming one without the other caps the answer below full marks. Hydrolysing hydrogen bonds is rejected at the unwinding step; hydrogen bonds contain no water, and the verb is break. RNA polymerase forms hydrogen bonds and RNA polymerase joins complementary bases are also rejected; polymerase joins nucleotides via phosphodiester bonds, and the hydrogen-bond step is the positioning step.

The product of transcription is pre-mRNA. Its base sequence is complementary to the antisense (template) strand of the DNA, which means it carries the same base sequence as the sense (coding) strand of the gene, except that uracil replaces thymine throughout.

Pre-mRNA is processed: introns are spliced out and exons joined.

In eukaryotic cells, the initial transcription product is pre-mRNA. The gene from which it was transcribed contains coding sequences called exons and non-coding intervening sequences called introns, and the pre-mRNA carries complementary sequence for both. Before the mRNA can leave the nucleus and be translated, the introns must be removed and the exons joined together.

The introns removed mark-scheme shortcut

The phrase introns removed earns two marks in the canonical splicing Describe: one for naming introns as what is addressed, and one for describing the removal. Vaguer phrasing such as pre-mRNA is spliced alone, or introns are taken out, scores nothing. Introns present in mRNA disqualifies the first mark. Introns made of DNA is also wrong throughout; pre-mRNA is RNA, and the introns within it are RNA sequences. After splicing, the mature mRNA exits the nucleus through nuclear pores.

Name introns and describe removed. Vaguer phrasing scores zero. Introns present in mRNA disqualifies mark point 1. Introns made of DNA is wrong throughout; pre-mRNA is RNA, and so are the introns within it.

mRNA and tRNA are RNA messengers with different structures and roles.

Two RNA molecules carry the bulk of the translation work. mRNA carries the codons from the nucleus to the ribosome. tRNA delivers specific amino acids to the ribosome during translation. Both are single-stranded, but their shapes and their roles at the ribosome are very different.

mRNA and tRNA compared.

Feature mRNA tRNA
Length Long; the whole gene's coding sequence Short; approximately 80 nucleotides
Shape Linear, single-stranded Clover-leaf, folded back on itself by internal base pairing
Functional ends Start codon at the 5′ end; stop codon at the 3′ end Amino-acid attachment site at one end; anticodon at the other end
What it carries Codons that code for amino acids One specific amino acid, matched to its anticodon

Every comparison point must name both molecules. mRNA is longer than tRNA scores; tRNA is short does not. A statement about one molecule alone is not a comparison.

Both mRNA and tRNA contain uracil, not thymine. tRNA has thymine is a recurring student error and is rejected.

Anticodon-codon binding

When a tRNA arrives at the ribosome, its anticodon binds complementarily to the next codon on the mRNA. Both complementary and bind are required in the mark scheme; naming one without the other scores zero on this point. The same A-U and G-C pairing rules apply as in transcription. Because the genetic code is degenerate, more than one tRNA species can correspond to the same amino acid: different anticodons, same amino-acid attachment.

Translation assembles the polypeptide codon by codon at the ribosome.

Translation reads the mRNA codon by codon and assembles the corresponding polypeptide chain. The site is the ribosome, a large complex made of ribosomal RNA and proteins, organised into two subunits that assemble around the mRNA strand. The mechanism is a six-event sequence, and each event is its own mark point in the canonical Describe.

  1. mRNA binds to a ribosome at a start codon.
  2. The ribosome covers two codons of the mRNA at any one time, exposing two tRNA binding positions. This is an explicit mark point.
  3. ATP activates a specific amino acid and attaches it to its corresponding tRNA. This charging step happens before the tRNA arrives at the ribosome.
  4. The tRNA arrives at the ribosome and its anticodon binds complementarily to the next codon on the mRNA.
  5. A peptide bond forms between the amino acid carried by the first tRNA (already at the ribosome) and the amino acid carried by the second (incoming) tRNA. This is a condensation reaction, catalysed by the ribosome's rRNA component, using ATP.
  6. The ribosome translocates by one codon along the mRNA. The first tRNA detaches, and the cycle repeats until a stop codon, where release factor proteins free the completed polypeptide.
ATP has two roles in translation

ATP activates the amino acid onto its tRNA, and ATP is used in peptide bond formation. Both are mark points.

Write codes for. The codon codes for the amino acid. Produces, makes, results in, and forms are all rejected. The unit of the genetic code is the codon (or triplet); bases alone in a degeneracy or codon definition is rejected.

The ribosome translocates along the mRNA. The mRNA does not move along the ribosome. Direction matters; this is the most-flagged drop in extended translation Describes.

Write tertiary structure, rough endoplasmic reticulum, and locus in full. 3-D, 3°, and shape are rejected for tertiary structure. RER is not an AQA abbreviation for rough endoplasmic reticulum and is not credited. Locust is the spelling reject for locus. Quaternary is rejected when the passage describes the product as the polypeptide (singular); quaternary structure requires more than one polypeptide chain.

Pitfall — Events 2 and 3 are the consistently dropped marks

Events 2 and 3 are the consistently dropped marks on the canonical translation Describe.

Event 2 is the ribosome covering two codons of the mRNA at once. Students rarely state this, even though it is its own mark point on the mark scheme. Event 3 is ATP activating the amino acid onto its tRNA before the tRNA arrives at the ribosome. Students often place ATP only at the peptide-bond step and miss the charging step entirely.

Fewer than 15% of students achieved all six marks on the 2025 P1 Q10.1 six-mark translation Describe. Force both events into the answer.

Polysomes amplify protein production; prokaryotes lack the eukaryotic splicing step.

A single mRNA strand can be translated by many ribosomes at once. Once the leading ribosome has cleared the start codon and moved far enough along the strand, a second ribosome can bind at the start and begin its own round of translation. The arrangement is called a polysome.

Polysomes

Up to fifty ribosomes can be engaged on a single mRNA at once, each at a different position along the strand, each producing its own copy of the polypeptide. The biological consequence is amplification: one mRNA template gives many simultaneous polypeptides. The cell can ramp up production of a specific protein without producing more mRNA.

Prokaryote vs eukaryote

Prokaryotes have no nucleus, so transcription and translation are not spatially separated. Ribosomes can begin translating the 5′ end of an mRNA strand while RNA polymerase is still transcribing its 3′ end; the two processes are coupled. Prokaryotic genes also generally lack introns, so prokaryotic mRNA is not spliced. Both features make prokaryotic protein synthesis faster than eukaryotic. The eukaryotic nuclear envelope enforces separation and enables splicing as an additional control step.

The genetic code is universal AND degenerate; the two properties are independent.

The genetic code has two structural properties that are routinely examined together at 3.4.2 and routinely confused. They are independent. Neither causes the other. Naming both, with the right qualifier on each, is the mark structure.

Universal

The genetic code is universal: the same codons specify the same amino acids in (nearly) all organisms. A codon table generated from human cells applies to bacteria, plants, and fungi. The useful consequence is that a gene transferred between species produces the same protein, which is the foundation of genetic engineering. DNA is universal alone is rejected; the answer must name what is universal (codons code for the same amino acids across organisms; or transcription, translation, or ribosomes across species).

Degenerate

The genetic code is degenerate: more than one codon can code for the same amino acid. The mathematical basis is 4³ = 64 possible codons covering only 20 amino acids; the surplus codons are synonymous, typically differing only in the third base of the triplet. The consequence is a buffering effect: a base substitution in the third codon position often produces a synonymous codon, leaving the protein sequence unchanged. The unit is the codon, not bases alone.

Name what is universal. Same codons code for the same amino acids in all organisms. DNA is universal alone is rejected. The genetic code is degenerate in answer to a universality question is also rejected. Restriction enzymes and sticky ends are not part of universality; they belong to gene cloning.

Pitfall — Universal and degenerate are independent

Universal and degenerate are independent properties. Do not link them.

AQA explicitly rejects the code is universal because it is degenerate. The two properties have no causal relationship. Universal means consistency across species. Degenerate means redundancy within a single organism's coding system. The code happens to be both, but neither is the cause of the other.

2022 P3 Q04.2 saw 55% of students score zero on this distinction. Mastery was 13%; the worst-performing 3.4.2 question in the dataset.

Key terms

  • mRNA
  • tRNA
  • codon
  • ribosome
  • splicing
  • introns removed
  • peptide bond
  • condensation
  • codes for
  • tertiary
  • rough endoplasmic reticulum
  • pre-mRNA