Discussion Questions on tRNA’s

1. All the tRNA’s have a common cloverleaf structure. Discuss the interactions that favor the tRNA’s all having a very similar structure. Discuss the interactions that favor the tRNA’s having different structures.

2. In what sense is it true that tRNA’s are synthesized with the four standard RNA nucleotides (GAUC). In what sense is this not true?

3. How has it been demonstrated that modified nucleotides are essential to tRNA function?

4. What structure in a polysome determines that the codons of a mRNA are read in units of three nucleotides. What evidence supports this?

5. How does eIF2 distinguish initiator methionine tRNA from the elongation methionine tRNA?

6. Wobble describes alternative base-pairing in the anticodon-codon interaction. What is the explanation for why Wobble is limited to the 3^rd position of the codon.

7. What are the constraints on the evolution of the genetic code?

8. How would Lipman’s results have differed if the ribosome played a role in discriminating between aminoacids inserted into polypeptides.

9. Explain why the synthetases are often refered to as the second genetic code?

10. Explain how analysis of tRNA sequences provides clues to how synthetases distinguish cognate from non cognate tRNA’s

11. Suppose that hypothetically an adenosine residue at position 50 of the lysine tRNA’s is important to recognition of these tRNA’s by the lysine synthetase. How could you investigate this hypothesis using mutagenesis? What results would support the hypothesis? What results would refute the hypothesis? What are the limits to this experimental approach?

12. For most tRNA’s, the synthetase recognizes nucleotides in the anticodon to help distinguish between cognate and non-cognate tRNA’s. What are the exceptions to this rule? Why might these exceptional tRNA’s not use anticodons for synthetase recognition?

13. Describe the two part reaction catalyzed by synthetases to charge a tRNA.

14. What chemical reaction is catalyzed by the editing site of a synthetase. Is this an exergonic or endergonic reaction?

15. At significant frequencies, synthetases will charge non-cognate aminoacids. Explain the steps the synthetase can used to prevent these amino acids from being used to charged the tRNA’s.

16. Explain how a mutation in a non-anticodon nucleotide could result in a non-sense suppressor tRNA?

17. Explain how a mis-sense suppressor masks the effects of a mis-sense mutation?

18. What best explains why cells containing mis-sense suppressor tRNA’s are often sickly?

19. Some mis-sense suppressor tRNA involve altered synthetase interactions for there mechanism. Contrast this mechanism from one that involves the anticodon-codon interaction.

20. Explain why suppressor tRNAs with altered synthetase interactions never function as non-sense suppressors.

21. Explain how frameshift suppressors work?

22. Non-sense suppressors complete with release factors at the ribosome? Explain the consequence of this interaction at the gene with the non-sense mutation and other genes in the cell?