Genome and Proteome
What you need to know (based on the AQA specification)
What you need to know (based on the AQA specification)
The concept of the genome as the complete set of genes in a cell and of the proteome as the full range of proteins that a cell is able to produce.
- Genome — the complete set of genetic material (all DNA) in a cell, including every gene
- Proteome — the full range of proteins that a cell is able to produce
The proteome is larger than the genome, because alternative splicing of pre-mRNA allows one gene to code for more than one protein. You can explore this further in genome projects in Unit 8.
Structure of mRNA and tRNA
What you need to know (based on the AQA specification)
What you need to know (based on the AQA specification)
The structure of molecules of messenger RNA (mRNA) and of transfer RNA (tRNA).
mRNA
mRNA (messenger RNA) is a single-stranded polynucleotide chain produced during transcription. Key features:
- Contains the nitrogenous base uracil (U) instead of thymine — uracil pairs with adenine (A)
- Carries the genetic code from the nucleus to the ribosome
- The code is read in groups of three adjacent bases called codons (e.g. CUG) — each codon codes for a specific amino acid
tRNA
tRNA (transfer RNA) carries amino acids to the ribosome during translation. Key features:
- A single polynucleotide chain folded into a clover-leaf shape — hydrogen bonds form between complementary bases within the molecule, maintaining this structure
- Has an amino acid attachment site at one end, where a specific amino acid binds
- Has an anticodon — a sequence of three bases complementary to a specific mRNA codon, allowing tRNA to recognise and bind to the correct position on the mRNA
Common exam mistakes — mRNA vs tRNA
- Both mRNA and tRNA contain uracil, not thymine — don’t say tRNA has thymine
- tRNA is single-stranded but folds back on itself with internal hydrogen bonds — it is not double-stranded
- Codons are on mRNA; anticodons are on tRNA
- tRNA is shorter than mRNA, not longer
Overview Transcription & Translation
Transcription
What you need to know (based on the AQA specification)
What you need to know (based on the AQA specification)
Transcription as the production of mRNA from DNA. The role of RNA polymerase in joining mRNA nucleotides.
Transcription is the production of mRNA from a DNA template. It takes place in the nucleus:
- DNA helicase unwinds the double helix and breaks the hydrogen bonds between bases, separating the two strands
- One strand acts as the template strand — free RNA nucleotides align alongside it by complementary base pairing
- Uracil (U) is used in RNA instead of thymine — uracil pairs with adenine; cytosine pairs with guanine
- RNA polymerase joins adjacent RNA nucleotides by phosphodiester bonds, building the new mRNA strand
- Formation of phosphodiester bonds is a condensation reaction — requires ATP
Common exam mistake — transcription
When describing transcription, say RNA nucleotides align against the template strand, not DNA nucleotides. RNA polymerase catalyses the formation of phosphodiester bonds between RNA nucleotides; it does not form hydrogen bonds (the hydrogen bonds form between the RNA nucleotides and the DNA template strand).
What does 3' → 5' direction mean?
What does 3' → 5' direction mean?
Each nucleotide has a sugar with numbered carbon atoms. The 3’ carbon carries an –OH group; the 5’ carbon is where the phosphate attaches. In a polynucleotide strand, one end has a free 5’ phosphate (the 5’ end) and the other has a free 3’ –OH (the 3’ end). RNA polymerase moves along the template strand from its 3’ end to its 5’ end, and always builds the new mRNA strand from the 5’ end to the 3’ end.
Pre-mRNA and Splicing
What you need to know (based on the AQA specification)
What you need to know (based on the AQA specification)
In prokaryotes, transcription results directly in the production of mRNA from DNA. In eukaryotes, transcription results in the production of pre-mRNA; this is then spliced to form mRNA.
In prokaryotes, transcription produces mRNA directly. It can be translated immediately.
In eukaryotes, transcription first produces pre-mRNA, which contains:
- Introns — non-coding sequences that do not code for amino acids
- Exons — coding sequences that do code for amino acids
The introns are removed and the exons are joined in a process called splicing, producing the final mRNA molecule. This mRNA then leaves the nucleus through nuclear pores and travels to a ribosome in the cytoplasm for translation.
Translation
What you need to know (based on the AQA specification)
What you need to know (based on the AQA specification)
Translation as the production of polypeptides from the sequence of codons carried by mRNA. The roles of ribosomes, tRNA and ATP.
Translation is the production of a polypeptide from the sequence of codons on mRNA. It takes place at ribosomes in the cytoplasm.
- mRNA attaches to a ribosome
- tRNA brings a specific amino acid to the ribosome
- The tRNA anticodon binds to the complementary codon on the mRNA by complementary base pairing
- ATP provides energy for the formation of a peptide bond between adjacent amino acids in a condensation reaction
- The tRNA is released (after its amino acid has joined the growing polypeptide chain)
- The ribosome moves along the mRNA to the next codon
- This process repeats, building up a polypeptide chain, until a stop codon is reached — at which point the polypeptide is released
Why is ATP needed for translation?
Why is ATP needed for translation?
ATP provides the energy needed for the formation of peptide bonds between adjacent amino acids. Without ATP, amino acids cannot be joined together and no polypeptide chain can be built.
Common exam mistake — translation
It is the amino acid that joins the growing polypeptide chain, not the tRNA. The tRNA carries the amino acid to the ribosome, but once the peptide bond forms, the tRNA detaches and leaves. Also remember: ATP is used in peptide bond formation. This is regularly missed in exam answers.
What is the role of ribosomes in translation?
What is the role of ribosomes in translation?
Ribosomes provide the site for translation. They have two subunits that hold the mRNA in place and have binding sites for two tRNA molecules simultaneously. The ribosome moves along the mRNA codon by codon, facilitating anticodon–codon base pairing and catalysing peptide bond formation between adjacent amino acids.
Exam Questions
Define genome and proteome.
(2 marks)Hint
Be precise with definitions. Genome relates to genes/DNA. Proteome relates to proteins that CAN be produced.
Mark Scheme
- Genome: Complete set of genes/alleles/genetic material in a cell (1 mark)
- Proteome: Full range of proteins a cell can produce / coded for by DNA/genome (1 mark)
Tips from examiner reports
- Genome = all the DNA (or all the genes) of an organism — don’t say ‘genetic information’, ‘genetic code’, or ‘genetic constitution’
- Proteome = all the proteins produced by the genome/cell — be precise and link it to DNA or the genome
Give three structural differences between an mRNA molecule and a tRNA molecule.
(3 marks)Hint
Think about overall shape, relative length, and the special features each molecule has for its function. Make sure you compare like with like.
Mark Scheme
| mRNA | tRNA | |
|---|---|---|
| 1. | Has codon(s) | Has anticodon (1 mark) |
| 2. | No hydrogen bonds / base pairs | Has hydrogen bonds / base pairs (1 mark) |
| 3. | No amino acid binding site | Has amino acid binding site (1 mark) |
| 4. | Linear / not folded | Clover-leaf shape / folded |
| 5. | Long / many nucleotides | Short / fewer nucleotides |
(Any 3 comparisons for 3 marks)
Comments from mark scheme
- Must be written as comparisons
- Accept “amino acid only bound to tRNA” for binding site point
- Accept “mRNA cannot carry an amino acid, tRNA can”
- Do NOT say tRNA is double-stranded — it is single-stranded with internal base pairing
Tips from examiner reports
- Both mRNA and tRNA contain uracil — don’t say tRNA has thymine
- tRNA has a cloverleaf shape; mRNA is linear — make this the comparison
- mRNA is NOT ‘single-stranded’ vs tRNA ‘double-stranded’ — tRNA is single-stranded with internal base pairing
- Say tRNA has an amino acid binding site, not just ‘has an amino acid’
- Make sure comparisons are on the same row of a table — compare like with like
Describe how one amino acid is added to a polypeptide that is being formed at a ribosome during translation.
(3 marks)Hint
Which molecule brings the amino acid? What specific interaction occurs at the ribosome? What type of bond is formed between amino acids?
Mark Scheme
- tRNA brings specific amino acid (to ribosome) (1 mark)
- Anticodon (on tRNA) binds to codon (on mRNA) by complementary base pairing (1 mark)
- Amino acids join by condensation reaction / peptide bond formed (using ATP) (1 mark)
Comments from mark scheme
- For point 2: accept “anticodon pairs with codon”
- For point 3: accept “condensation reaction” or “peptide bond”
Tips from examiner reports
- In translation, specific tRNA molecules carry specific amino acids — state the specificity clearly
- Don’t just say ‘tRNA carries amino acids’ — emphasise that each tRNA carries a specific amino acid
- State the anticodon (on tRNA) binds to the codon (on mRNA)
Describe how mRNA is formed by transcription in eukaryotes.
(5 marks)Hint
Walk through the steps: what breaks first, which strand is used, how do RNA nucleotides line up, what does RNA polymerase do, and what’s different in eukaryotes vs prokaryotes?
Mark Scheme
- Hydrogen bonds (between DNA bases) break (1 mark)
- (Only) one DNA strand acts as the template (1 mark)
- (Free) RNA nucleotides align by complementary base pairing (1 mark)
- Uracil base pairs with adenine (on DNA) / uracil is used in place of thymine (1 mark)
- RNA polymerase joins (adjacent RNA) nucleotides (1 mark)
- (By) phosphodiester bonds (between adjacent nucleotides) (1 mark)
- Pre-mRNA is spliced (to form mRNA) / introns are removed (to form mRNA) (1 mark)
(Max 5 marks)
Comments from mark scheme
- Ignore DNA helicase
- Reject “hydrolyses hydrogen bonds” for point 1
- For point 3: accept “align to complementary bases” or “align by base pairing”
- Do not credit use of letters alone for bases (write “adenine” not “A”)
- Reject suggestions that RNA polymerase forms hydrogen bonds or joins complementary bases
Tips from examiner reports
- Refer to RNA nucleotides and RNA polymerase — not DNA equivalents
- RNA polymerase does NOT form hydrogen bonds or complementary base pairs — it catalyses addition of RNA nucleotides, forming phosphodiester bonds
- Don’t forget splicing — this is a eukaryote-specific point worth a mark
Describe how a polypeptide is formed by translation of mRNA.
(6 marks)Hint
Cover every stage: where does mRNA go, what brings amino acids, how do they match up, what forms the bond, what happens to the tRNA, and how does the process move along?
Mark Scheme
- (mRNA attaches) to ribosomes / to rough endoplasmic reticulum (1 mark)
- (tRNA) anticodons bind to complementary (mRNA) codons (1 mark)
- tRNA brings a specific amino acid (1 mark)
- Amino acids join by peptide bonds (1 mark)
- (Amino acids join) with the use of ATP (1 mark)
- tRNA released (after amino acid joined to polypeptide) (1 mark)
- The ribosome moves along the mRNA to form the polypeptide (1 mark)
(Max 6 marks)
Comments from mark scheme
- Accept “rough endoplasmic reticulum” for ribosomes
- tRNA release must state it happens after the amino acid has joined
Tips from examiner reports
- It is the amino acid (attached to tRNA) that joins the growing polypeptide chain — not tRNA itself
- ATP is used in peptide bond formation — this was rarely mentioned in student answers
- Both anticodon–codon matching AND specificity of amino acid carried by tRNA are separate mark points — state both
Give the two types of molecule from which a ribosome is made.
(1 marks)Hint
Think about the two major components of a ribosome: one is a type of nucleic acid, the other is a protein.
Mark Scheme
- rRNA (ribosomal RNA / RNA / ribonucleic acid) and protein (polypeptide) (1 mark — must give both)
Comments from mark scheme
- Reject DNA, tRNA, mRNA — only rRNA is accepted for the nucleic acid component
- Ignore: enzymes, bases
Describe the role of a ribosome in the production of a polypeptide. Do not include transcription in your answer.
(3 marks)Hint
Think about what the ribosome physically does: what attaches to it, how many tRNA molecules it holds, what bond it catalyses, and how it moves.
Mark Scheme
- mRNA binds to ribosome (1 mark)
- Has two codons / binding sites (for tRNA) (1 mark)
- (Allows) tRNA with anticodons to bind (1 mark)
- (Catalyses) formation of peptide bond between amino acids (1 mark)
- Moves along mRNA to the next codon (1 mark)
(Any 3 for 3 marks)
Comments from mark scheme
- Accept “it” to refer to the ribosome throughout
In a eukaryotic cell, the base sequence of the mRNA might be different from the sequence of the pre-mRNA. Explain why.
(2 marks)Hint
What does eukaryotic pre-mRNA contain that must be removed before translation can occur?
Mark Scheme
- Introns (in pre-mRNA) (1 mark)
- Removal of introns / splicing (1 mark)
Comments from mark scheme
- “Introns removed” alone scores 2 marks
- Reference to “introns present in mRNA” disqualifies point 1 — allow ECF for point 2
- Accept “mRNA contains only exons” for 1 mark
Comments from mark scheme