describe how the information in DNA is used during transcription and translation to construct polypeptides, including the roles of: RNA polymerase, messenger RNA (mRNA), codons, transfer RNA (tRNA), anticodons, ribosomes

6.2 Protein synthesis – how DNA information is used to build polypeptides

Learning objective

Describe how the information stored in DNA is transferred during transcription and translation to produce a polypeptide chain, and explain the specific roles of RNA polymerase, messenger RNA (mRNA), codons, transfer RNA (tRNA), anticodons, ribosomes and related factors.

6.2.1 Transcription – synthesis of mRNA from a DNA template

6.2.1.1 Where transcription occurs

6.2.1.2 RNA polymerase – promoter recognition & transcription factors

• Core promoter elements

  • Prokaryotes – –35 (TTGACA) and –10 (TATAAT) boxes.
  • Eukaryotes – TATA box (≈ –25 bp) and other upstream elements (CAAT, GC box).

• RNA polymerase

  • Prokaryotes: a single enzyme (core enzyme) recognises the –35/–10 boxes and initiates transcription without additional proteins.
  • Eukaryotes: RNA polymerase II requires a suite of transcription factors (TFIIA, TFIIB, TFIID, etc.) to bind the promoter and unwind DNA.

6.2.1.3 Three stages of transcription

1. Initiation

   • RNA polymerase binds the promoter, unwinds ~10–15 bp of DNA, exposing the template strand (the strand read 3′→5′).
   • RNA synthesis proceeds 5′→3′, adding ribonucleotides to the 3′‑OH of the growing chain.

2. Elongation

   • The enzyme moves along the template strand, incorporating complementary ribonucleotides (A‑U, C‑G).
   • The nascent RNA strand separates from the DNA behind the polymerase, allowing the DNA double helix to re‑form.

3. Termination

   • Prokaryotes – a terminator sequence (ρ‑dependent or intrinsic) causes dissociation of the polymerase.
   • Eukaryotes – transcription ends when RNA polymerase reaches a poly‑adenylation signal (AAUAAA); the primary transcript is released as pre‑mRNA.

6.2.1.4 Pre‑mRNA processing (must be described for the syllabus)

• 5′‑capping: addition of a 7‑methylguanosine cap to the first nucleotide; protects RNA from degradation and promotes ribosome binding.
• Splicing: removal of non‑coding introns by the spliceosome; exons are ligated to give a continuous coding region.
• Poly‑adenylation: ~200 adenine residues are added to the 3′ end, forming the poly‑A tail; enhances stability and is required for export.
• Export: the mature mRNA is transported through nuclear pores into the cytoplasm, where it becomes the template for translation.

6.2.2 Translation – decoding mRNA into a polypeptide

6.2.2.1 Where translation occurs

• Free ribosomes in the cytoplasm – synthesize proteins that function in the cytosol or nucleus.
• Ribosomes attached to the rough endoplasmic reticulum (RER) – synthesize secretory, membrane‑bound or lysosomal proteins.

6.2.2.2 Ribosome structure (syllabus requirement)

6.2.2.3 The genetic code

• Codon: a triplet of nucleotides on mRNA.
• Start codon: AUG (codes for methionine in eukaryotes, formyl‑methionine in prokaryotes).
• Stop codons: UAA, UAG, UGA – do not code for an amino acid.
• 64 possible codons (4³) encode 20 standard amino acids + 3 stop signals.
• Redundancy (degeneracy): most amino acids are specified by more than one codon (e.g., leucine has six codons). This provides a buffer against point mutations.
• Universality: the code is (almost) identical in all organisms, supporting a common ancestry.

6.2.2.4 Steps of translation

1. Initiation

   • The small ribosomal subunit, together with initiation factors, binds the 5′‑cap of the mRNA and scans to the first AUG start codon.
   • The initiator tRNA (charged with methionine) pairs its anticodon UAC with the start codon.
   • The large subunit joins, completing the ribosome (A, P and E sites now present).

2. Elongation

   • A charged aminoacyl‑tRNA enters the A‑site; its anticodon matches the next codon on the mRNA.
   • The peptide bond forms between the peptide attached to the tRNA in the P‑site and the amino acid in the A‑site (catalysed by rRNA peptidyl‑transferase).
   • Translocation moves the ribosome one codon downstream:

     • tRNA in the P‑site shifts to the E‑site and exits.
     • tRNA in the A‑site moves to the P‑site, leaving the A‑site vacant for the next aminoacyl‑tRNA.

3. Termination

   • When a stop codon (UAA, UAG or UGA) enters the A‑site, no tRNA can recognise it.
   • Release factors (eRF1 in eukaryotes; RF1/2 in prokaryotes) bind the A‑site, promoting hydrolysis of the bond between the polypeptide and the tRNA in the P‑site.
   • The completed polypeptide is released; ribosomal subunits dissociate and can be recycled.

6.2.2.5 Supporting molecules

• Amino‑acyl‑tRNA synthetase: each enzyme “charges” a specific tRNA with its correct amino acid, ensuring fidelity of the genetic code.
• tRNA: adaptor molecule with an anticodon region that pairs with the mRNA codon and a 3′‑terminal CCA tail to which the amino acid is attached.
• Release factors: proteins that recognise stop codons and trigger peptide release.

6.2.3 Summary table – key molecular players

6.2.4 From polypeptide to functional protein (A‑Level link)

The linear chain folds into secondary structures (α‑helices, β‑sheets) driven by hydrogen bonding, then into a unique tertiary shape dictated by side‑chain interactions (hydrophobic packing, disulfide bridges, ionic bonds, etc.). Many proteins consist of several polypeptide subunits that assemble into a quaternary structure, giving the final functional molecule.

6.2.5 Flow of information – schematic (text only)

DNA (promoter) ──► RNA polymerase ──► pre‑mRNA
│                     │
│                     ├─► 5′‑capping
│                     ├─► splicing (introns removed)
│                     └─► poly‑A tail
└─► mature mRNA (exported to cytoplasm)
mRNA (5′‑cap) ──► ribosome (small subunit scans) ──► start codon (AUG)
│
└─► Initiator tRNA (Met) pairs at P‑site
└─► Large subunit joins → complete ribosome
A‑site: incoming aa‑tRNA
P‑site: growing peptide chain
E‑site: empty tRNA exits
…elongation cycles…
Stop codon (UAA/UAG/UGA) enters A‑site ──► release factor binds ──► peptide released

6.2.6 Checklist for exam preparation

• State where transcription occurs in eukaryotes and prokaryotes.
• Identify promoter elements (–35/–10 boxes, TATA box) and describe the role of transcription factors.
• Explain the three stages of transcription, including the direction of reading (DNA 3′→5′) and synthesis (RNA 5′→3′) and the distinction between template and non‑template strands.
• Describe the three processing steps of pre‑mRNA and why they are required for export.
• Define codon, start codon (AUG), stop codons (UAA, UAG, UGA) and discuss redundancy and universality of the genetic code.
• Compare ribosome sub‑units in prokaryotes and eukaryotes and name the A, P and E sites.
• Outline initiation, elongation and termination of translation, including the role of initiator tRNA, amino‑acyl‑tRNA synthetase, peptidyl‑transferase and release factors.
• Link the linear polypeptide to secondary, tertiary and (where relevant) quaternary structure.
• Use the summary table to recall the specific function of each molecular component.