Translation

• The genetic code is nearly universal
• A set of three nucleotides, called a codon, encodes an amino acid
• Codons are non-overlapping
• The genetic code does not have punctuation
• The genetic code has directionality
• Degeneracy minimises the effects of genetic mutations by providing another chance for the mutation not to effect the protein
• Translation has more errors as protein is turned over frequently, so it isn't required to be as accurate
• tRNA binds to a specific codon and brings an amino acid with it
• There is at least one tRNA for each amino acid
• tRNAs are single stranded that undergo base pairing to form an L-shaped structure
• Many tRNAs are modified
• The amino acid is added to the 3' (CCA) terminus of the tRNA
• Simple base pairing suggests that each anticodon binds to only one codon, but this is not always the case
• Recognition of the third base by tRNA is less discriminating than the first two
• There is steric freedom, or wobble, in the third base pairing between the mRNA codon and tRNA anticodon
• Binding of an amino acid to tRNA activates the amino acid
• Activation of the amino acid is required because the formation of the peptide bond between free amino acids is thermodynamically unfavourable
• Activation of amino acids forms an amino acid ester on the tRNA
• Activation is done by a specific aminoacyl-tRNA synthetase, consuming 2 ATP and producing an aminoacyl-tRNA
• Aminoacyl-tRNA synthetase must put the correct amino acid onto the tRNA
• Each aminoacyl-tRNA synthetase is highly specific for a given amino acid
• Aminoacyl-tRNA synthetase uses the specific properties of its amino acid substrate to ensure that it is adding the correct amino acid
• Aminoacyl-tRNA synthetase also has proof-reading function to ensure that it is adding the correct amino acid
• Aminoacyl-tRNA synthetase must choose the correct tRNA partner which is recognised by its anticodon, unusual/modified bases, and its structure
• Ribosomes are composed of RNA and proteins that coordinate the interplay of mRNA, tRNA and proteins for protein synthesis
• Key catalytic sites of ribosomes are mainly composed of RNA, with minor contributions from proteins
• In bacteria, the 70S ribosome is composed of large (50S) and small (30S) subunits
• Ribosomes have 3 tRNA binding sites that span the 50S and 30S subunits: Aminoacyl, peptidyl and exit sites
• mRNA is bound within the 30S subunits
• tRNA in the A and P sites are bound to mRNA by anticodon-codon base pairing
• Coupling of transcription and translation in bacteria is possible because both transcription and translation occur in the 5' to 3' direction
• Translation does not begin at the start of the mRNA
• The first translated codon is upstream from the 5' end
•  Initiation

  1. IFs bind to the small subunit and keeps it apart from the large 50S subunit
  2. IFs, initiator tRNA, mRNA and the small subunit form the 30S initiation complex
  3. The large subunit binds to the small subunit initiation complex to form the 70S initiation complex
• 30S initiation complex

  • mRNA binds to rRNA in the small subunit
  • tRNA binds to the AUG codon in mRNA and to the P site in the small subunit
• What is the rate limiting step of translation?

  when the two subunits bind
• Initiator codon: usually AUG (codes for methionine)
• Shine-Dalgarno sequence: purine-rich sequence upstream of the initiator codon
• Translation start signals on prokaryotic mRNA:

  1. Initiator codon
  2. Shine-Dalgarno sequence
• Shine-Dalgarno sequence binds to 16S rRNA in the ribosomal small subunit