AQA A-level Biology: DNA, Genes, Chromosomes and Protein Synthesis (7402)

This guide follows the AQA specification for AS and A-level Biology (codes 7401 and 7402), first teaching 2015, and covers sections 3.4.1 (DNA, genes and chromosomes) and 3.4.2 (DNA and protein synthesis). Both sections sit in topic 4, which is AS content and is also part of the A-level course. Nothing in them is marked A-level only. You also need the nucleic acid structure in section 3.1.5.

Use the shorter revision notes for recall and the practice questions for testing yourself. The subject hub is at AQA A-level Biology, with a checklist to print and short diagnostic tests if you want to find gaps first. Nucleotide and polymer basics are in Biological Molecules.

Scope of this guide

Section	Skills needed
3.4.1	Compare prokaryotic, eukaryotic nuclear and organelle DNA; define gene, locus and triplet; state the properties of the genetic code; distinguish introns, exons and non-coding repeats
3.4.2	Define genome and proteome; describe mRNA and tRNA; describe transcription (including pre-mRNA splicing) and translation (ribosomes, tRNA, ATP); relate base sequences to amino acid sequences using data supplied; interpret experiments on nucleic acids

The specification says you will not have to recall which codon codes for which amino acid. Any codon table you need will be given in the question. There are no required practicals in these two sections.

3.4.1 DNA, genes and chromosomes

DNA in different places

Feature	Prokaryotic cell	Nucleus of a eukaryotic cell	Mitochondria and chloroplasts
Length	Short	Very long	Short
Shape	Circular	Linear	Circular
Proteins	Not associated with proteins	Associated with proteins called histones	Not associated with proteins

In a eukaryote, one DNA molecule together with its histones forms a chromosome. The histones are why a very long molecule can be packed into a small nucleus: the DNA is wound around them and then coiled further. Organelle DNA resembles prokaryotic DNA, which fits the idea that these organelles are descended from prokaryotes. Prokaryotic DNA has no histones, which is the key contrast with the eukaryotic chromosome.

Genes and the genetic code

A gene is a base sequence of DNA that codes for the amino acid sequence of a polypeptide, or for a functional RNA, including ribosomal RNA and tRNAs. Not every gene makes a protein. A gene occupies a fixed position called a locus on a particular DNA molecule.

A sequence of three DNA bases, a triplet, codes for one amino acid. The code has three properties:

• Universal: a given triplet specifies one particular amino acid whichever organism it is in.
• Non-overlapping: each base is part of one triplet only, so the sequence is read in separate groups of three.
• Degenerate: most amino acids are coded for by more than one triplet.

Degeneracy follows from simple counting. Four bases taken three at a time give 4 x 4 x 4 = 64 possible triplets, but proteins use only 20 amino acids. Three triplets act as stop signals, which leaves 61 for 20 amino acids.

Non-coding DNA in eukaryotes

Much eukaryotic nuclear DNA does not code for polypeptides. There are non-coding multiple repeats of base sequences between genes. Even inside a gene, only some sequences, the exons, code for amino acids. The exons are separated by one or more non-coding sequences, the introns. Prokaryotic genes are not described as having introns in this specification, so link introns to eukaryotes.

Worked example 1: how much of a transcript is coding? A eukaryotic gene is transcribed into a pre-mRNA 3,180 nucleotides long. It contains four introns of 420, 355, 610 and 245 nucleotides. The mature mRNA has 41 non-translated nucleotides before the start codon and 66 after the stop codon. How many amino acids are in the polypeptide?

1. Total intron length = 420 + 355 + 610 + 245 = 1,630 nucleotides.
2. mRNA length = 3,180 - 1,630 = 1,550 nucleotides.
3. Translated region, start codon to stop codon inclusive = 1,550 - 41 - 66 = 1,443 nucleotides.
4. Codons = 1,443 / 3 = 481.
5. One of these is the stop codon, which has no amino acid: 481 - 1 = 480 amino acids.

The shortcut for the other direction: a polypeptide of n amino acids needs at least 3n + 3 nucleotides between and including its start and stop codons.

3.4.2 DNA and protein synthesis

Genome and proteome

The genome is the complete set of genes in a cell. The proteome is the full range of proteins that a cell is able to produce. Two cells from one person have the same genome but can have different proteomes, because different genes are used in different cell types.

Structure of mRNA and tRNA

Feature	mRNA	tRNA
Shape	Single, linear polynucleotide strand	Single polynucleotide strand folded into a clover-leaf shape
Bonding	No base pairing along its length	Hydrogen bonds between some base pairs hold the fold
Key sites	Groups of three bases called codons	An anticodon of three bases, and a site that binds one specific amino acid
Job	Carries the code from DNA to the ribosome	Brings its amino acid to the codon that matches its anticodon

Both are RNA, so they contain ribose and the base uracil in place of thymine. mRNA is much shorter than the DNA it was copied from, because it copies one gene.

Transcription

Transcription is the production of mRNA from DNA.

1. The enzyme RNA polymerase attaches to the DNA at the start of a gene. The two DNA strands separate and one strand acts as the template.
2. Free RNA nucleotides pair with the exposed bases of the template by complementary base pairing: DNA A pairs with RNA U, T with A, G with C and C with G.
3. RNA polymerase joins adjacent RNA nucleotides by condensation reactions, forming the mRNA strand.
4. At the end of the gene the RNA is released and the DNA strands re-join.

In prokaryotes, transcription results directly in mRNA. In eukaryotes, it makes pre-mRNA, which is then spliced: introns are removed and the exons are joined to form mRNA. This happens in the nucleus, and the mRNA then leaves through a nuclear pore.

Translation

Translation is the production of a polypeptide from the sequence of codons carried by mRNA.

1. mRNA binds to a ribosome. Ribosomes are made of ribosomal RNA and protein.
2. A tRNA with an anticodon complementary to the first codon (the start codon) binds, carrying its amino acid.
3. A second tRNA binds to the next codon. The ribosome holds two tRNAs at once.
4. The two amino acids are linked by a peptide bond in a condensation reaction. ATP supplies the energy needed to join amino acids to tRNA and to form peptide bonds.
5. The ribosome moves along the mRNA one codon at a time. The first tRNA is released to collect another amino acid.
6. At a stop codon no tRNA binds. The polypeptide is released.

Codon problems

Worked example 2. Use this partial codon table (given as data): AUG = Met (start), GGU = Gly, CUU = Leu, ACA = Thr, GCA = Ala, UUA = Leu, UAA = stop.

The template strand of a gene reads TAC CCA GAA TGT CGT AAT ATT. Give the mRNA, the amino acid sequence, and the anticodon of the tRNA that brings the third amino acid.

1. mRNA is complementary to the template: AUG GGU CUU ACA GCA UUA UAA.
2. Read the codons from the start codon: Met - Gly - Leu - Thr - Ala - Leu, then UAA is a stop codon.
3. The third codon is CUU, so its anticodon is complementary: GAA.

Check the answer: seven triplets give six amino acids plus one stop. Writing T in an mRNA is a frequent slip, because RNA has no thymine.

Working backwards. Because the code is degenerate, a protein sequence does not give you one unique DNA sequence. If Leu is coded by six codons, a polypeptide with four leucines could come from 6 x 6 x 6 x 6 = 1,296 different mRNA sequences, if only those residues varied.

Interpreting experiments on nucleic acids

You may be given data and asked what it shows about the role of DNA or RNA.

Worked example 3: where is RNA made? Cultured animal cells were given radioactive uridine for 10 minutes, washed, and grown in unlabelled medium. The table shows the percentage of the cell’s radioactivity found in each region.

Time after wash (min)	Nucleus (%)	Cytoplasm (%)
0	94	6
15	71	29
30	40	60
60	18	82

1. Describe the trend: the nuclear share falls from 94% to 18%, a fall of 76 percentage points, while the cytoplasm rises by the same 76 points.
2. Why uridine? Uracil is found in RNA and not in DNA, so the label ends up in RNA.
3. Conclusion: RNA is made in the nucleus, where it is labelled first, and then moves to the cytoplasm. This fits mRNA carrying a copy of the gene to ribosomes.
4. Limit: the label enters all RNA, including ribosomal RNA and tRNA, so the data alone do not show that the moving RNA is mRNA.

When you evaluate any such experiment, ask what the control was, what the label or inhibitor targets, and whether the evidence is direct or only consistent with the idea.

Common errors

• Writing that prokaryote DNA “has no histones” and stopping: also say it is short and circular.
• Calling an anticodon a part of mRNA, or a codon a part of tRNA.
• Forgetting that introns are removed from pre-mRNA, not from DNA.
• Describing translation without saying that a tRNA carries one specific amino acid.
• Counting the stop codon as an amino acid.
• Saying a gene “codes for a trait” rather than a polypeptide or functional RNA.

Official syllabus

Source document: the AQA specification for AS and A-level Biology (codes 7401 and 7402), first teaching 2015, version 1.5, published by AQA. Sections 3.4.1 and 3.4.2 only.