B11 Week 7

• Protein structure


  What gives different proteins their specific shapes and properties

  
• Protein


  • Composed of 1 or more polypeptide subunits
  • Must fold into the correct 3-D shape, include the correct cofactors/subunits, and contain any required post-translational modifications
  • Folding is promoted by non-covalent interactions
  • Enzymes involved in the folding process often have weak affinity for the ribosome and stay near the exit tunnel

  
• Polypeptide


  Linear sequence of amino acids linked by peptide bonds, with the carboxyl end of one amino acid joined to the amino end of another

  
• Protein domain


  • The structural units of proteins that usually fold independently and have a particular function
  • Different proteins can contain the same domain
• • Different proteins can vary greatly in size and number of polypeptide subunits
  • 1 polypeptide could contain more than 1 domain
  • 1 protein often contains many domains with different functions
• Translation


  1. Initiation - Ribosome attaches to mRNA and begins translating at the start codon (AUG)

  2. Elongation - Polypeptide chain elongation, series of steps repeated until a stop codon is reached

  3. Termination - Stop codon signals to stop further elongation and release the polypeptide

  
• Ribosome


  Has three sites for association with tRNAs: A (aminoacyl) site, P (peptidyl) site, E (exit) site

  
• Peptide bond formation during elongation

  1. AA-tRNA binds to an empty A site

  2. A new peptide bond is formed between the growing chain and the new amino acid

  3. Large subunit translocates

  4. Small subunit translocates by 3 nucleotides

  
• Translation elongation factors


  Additional proteins that improve the efficiency and accuracy of translation, hydrolyze GTP to drive transitions in the ribosome subunits

  
• Translation initiation


  • AUG is the start codon, ribosome moves 5' to 3' along the mRNA and the polypeptide is built N-terminus to C-terminus
  • Initiation requires proteins called initiator factors (IFs in bacteria, eIFs in eukaryotes)

  
• Translation initiation in prokaryotes

  1. Small ribosomal subunit binds to the first AUG codon guided by the Shine-Dalgarno sequence

  2. Initiation factors (IF1, IF2, IF3) are attached to the small subunit

  
• 1. formylmethionine


  The modified version of methionine that is the initial amino acid in bacterial proteins
• Translation initiation in eukaryotes

  1. Eukaryotes require additional proteins (eIFs) for initiation, which is more complex than in prokaryotes

  2. eIFs bind to the small subunit along with initiator tRNA (Met)

  3. mRNA has its own set of eIFs (eIF4E, eIF4A, eIF4G) that help recruit the small ribosomal subunit and scan for the Kozak sequence

  
• Kozak sequence


  5'-CCACCAUGC-3', a consensus sequence that helps determine the efficiency of translation initiation at a given AUG codon

  
• Translation - Polyribosomes


  Multiple translation initiations typically take place on the same mRNA, with multiple ribosomes associated with an mRNA (Polyribosome or Polysome)

  
• Translation Termination


  Translation continues until the ribosome reaches a stop codon, at which point release factors bind and catalyze the addition of water to free the C-terminus

  
• • Transcription can proceed while translation is occurring in prokaryotes, but not in eukaryotes
  • Ribosomes move in the 5' to 3' direction on the mRNA, while RNA polymerase moves in the opposite direction
  • Each mRNA can be used to produce multiple copies of the encoded protein