Discussion Questions Elongation and Termination

 

  1. What is meant by the term “Molecular Mimicry”? Give three examples of molecular mimicry in translational elongation.  If a molecule exhibits molecular mimicry, what does that suggest about the way the molecule interacts in the cell?

 

  1. Describe the position of the tRNA’s in the hybrid sites of the ribosome at the following points in translation.
    1. Immediately after initiation
    2. Prior to interactions with eEF-1a
    3. Immediately after disassociation of eEF-1a
    4. Immediately after transpeptidase activity
    5. After hydrolysis of the GTP by eEF-2

 

  1. Why is it useful to distinguish decoding from delivery of tRNA’s during elongation?

 

  1. The ribosome uses proof reading during decoding?  What makes some proof-reading steps more “energy expensive” than others.

 

  1. What is the role of the ribosome and the A-site in the ribosome during proof reading?

 

  1. What is meant by misincorporation during translation? What causes misincorporation? It is reported than on average only 1 in 400 misincorporation events results in loss of protein activity?  What is going on with the other 399 misincorporation events?

 

  1. Streptomycin interferes with proofreading.  Why would this make Streptomycin an “antibiotic”?

 

  1. What is unusual about eEF-2 GTP/GDP activity that distinguishes from most G-proteins.

 

  1. eEF1a and eEF2 are both phosphoproteins.  Insulin triggers the phosphorylation of eEF1a but triggers the dephosphorylation of eEF2.  Based the the effects of insulin on initiation, what would you predict would be the effects of phosphorylation on eEF1a and eEF2

 

  1. Contrast the structure of the ternary complex with eIF2 with the ternary complex associated with eEF1a.

 

  1. What are the roles of the E site of the ribosomes?

 

  1. Regarding the role of the E site, why is it predicted that ribosomes might have a higher misincorporation rate immediately after initiation than at other times of decoding by eEF1a

 

  1. How can a mutant tRNA act as a nonsense suppressor?  Why can’t a nonsense suppressor for one of the three stop codons, suppress nonsense mutations that results from the other two stop codons?

 

  1. Would an E. coli cell containing an amber suppressor (UAG) be able to use UAG as a stop codon for any of its 6000 genes.

 

  1. Cells can use UGA as either a stop codon or as a codon for selenocysteine.  How does the cell distinguish which UGA are used as stop codons from those used for selenocysteine.

 

  1. Why cann’t mRNA encoding selenoproteins use UGA as a stop codon?

 

  1. How does RF-1 participate in decoding?

 

  1. What is the role of RRF in prokaryotes.  Eukaryotes have genes for RRF homologues, but these proteins are only found in mitochondria or plastids. What is the significance of this limited subcellular distribution?

 

  1. The polyA Binding Protein 1 (PABP1) interacts with eRF3?  What is believed to be the significance of this interaction?

 

  1. In what sense is the complex of eRF1 and eRF3 like the ternary complex of initiation?  What components of the initiation complex are analogous to eRF1 and eRF3?