1. Darrell R. Davis Department of Medicinal Chemistry http://www.pharmacy.utah.edu/medchem/faculty/davis/biol3510.html Translation and tRNAs

2. Ribosome

3. Overall Structure of Ribosome

4. RNA structures of Large Subunit

5. tRNAs on the Ribosome

7. Some Tetraloops in 16S RNA http://www.rna.icmb.utexas.edu RNA Secondary Structure

8. tRNA Phe

9. Yeast tRNA Folding Saenger

10. Unusual Pairing in tRNAs

11. Base Stacking and Intercalation

12. U-turns, The Anticodon

13. Circles represent nucleosides that are Always present. Gold are invariant or semivariant The RNA Modification Database http://medlib.med.utah.edu/RNAmods/ tRNA Modifications in Eukarya and Bacteria

14. Grosjean, H., Chantrenne, H. (1980) Mol. Biol. Biochem. Biophys.32, 347-367. RNA (0.1 mM, 1 M NaCl)  G° 37 kcal/mol  H° kcal/mol T m °C GGGCCC CCCGGG -7.9-63.060.2 AAAUUU UUUAAA 1.4-32.1-12.5 AAA UUU 3.2-13.2 -87 Intrinsic properties of 3 base-pair RNA hairpin interactions

15. Human tRNA Lys,3 and E.coli tRNA Lys

16. Saenger (1988) “Principles of Nucleic Acid Structure” pp. 347 ms 2 t 6 A (A9) Adenosine Uridine Pseudouridine (  )(F) mcm 5 s 2 U (U9)mnm 5 s 2 U (U8) Codon-Anticodon Interactions

17. Effects of mnm 5 s 2 U on base-pairing and stacking - s 2 U base pair stabilization

18. Summary The ribosome is a large “molecular machine” for making proteins tRNAs bind 3 sites on the ribosome, Amino-acyl, Peptidyl, Exit RNAs (rRNA, tRNA, and mRNA) are seldom “linear”, but fold into complex structures. tRNAs can all be folded into a “cloverleaf” secondary structure tRNAs all form an “L-shaped” 3D structure tRNAs contain many non-canonical pairs and triples Modifications are clustered in the functionally important areas Modifications are conserved in the 3 kingdoms of life. Modification in the tRNA anticodon help normalize the binding affinity for the mRNA.