1. Chapter 6 Translation

2. The genetic code

3. Translational reading frames

5. tRNAs are adapter molecules

6. The genetic code

7. Wobble base pairing

8. tRNA splicing

9. tRNA base modification

10. Amino acid activation

11. Aminoacyl tRNA linkage

12. Two adapters are required for translation

13. Editing by tRNA synthetases

14. Recognition of tRNA by synthetases

15. Polypeptide chain growth:N- terminal to C-terminal

16. Ribosomes

18. tRNA binding sites in the ribosome

22. Detailed view of translation

23. The structure of rRNA in the bacterial ribosome

24. The secondary structure of rRNA in the bacterial ribosome

25. The position of protein in the bacterial large subunit

26. The structure of L15 protein in the large subunit

27. Possible mechanism for peptidyl transferase

28. Initiation of translation in eukaryotic cells

29. Initiation of translation in prokaryotic cells

30. Translation termination

31. The structure of eRF1 and tRNA

32. EF-Tu-tRNAEF-G

33. Peptide tunnel

35. Polyribosomes (polysomes)

36. The rescue of a stalled ribosome on an incomplete mRNA

38. Incorporation of selenocysteine into a polypeptide

39. Translational frameshifting

40. INHIBITOR SPECIFIC EFFECT Acting only on bacteria Tetracycline blocks binding of aminoacyl-tRNA to A-site of ribosome Streptomycin prevents the transition from initiation complex to chain-elongating ribosome and also causes miscoding Chloramphenicol blocks the peptidyl transferase reaction on ribosomes Erythromycin blocks the translocation reaction on ribosomes Rifamycin blocks initiation of RNA chains by binding to RNA polymerase Acting on bacteria and eucaryotes Puromycin causes the premature release of nascent polypeptide chains by its addition to growing chain end Actinomycin D binds to DNA and blocks the movement of RNA polymerase Acting on eucaryotes but not bacteria Cycloheximide blocks the translocation reaction on ribosomes Anisomycin blocks the peptidyl transferase reaction on ribosomes α-Amanitin blocks mRNA synthesis by binding preferentially to RNA pol II Table 6-3. Inhibitors of Protein or RNA Synthesis

41. Making a functional protein

42. Molten globule

43. Cotranslational folding

44. Steps of protein folding

45. Hsp70 family of chaperones

46. Hsp60 family of chaperones

48. Protein monitoring

49. The proteosome degrades cellular proteins

50. Formation of protein aggregates can cause human disease

52. The RNA World 1) The RNA World and the Origins of Life 2) Life Requires Autocatalysis 3) Polynucleotides Can Both Store Information and Catalyze Chemical Reactions** 4) A Pre-RNA World Probably Predates the RNA World** 5) Single-stranded RNA Molecules Can Fold into Highly Elaborate Structures** 6) Self-Replicating Molecules Undergo Natural Selection** 7) How Did Protein Synthesis Evolve?** 8) All Present-day Cells Use DNA as Their Hereditary Material

54. The structure of potential preRNA molecules

55. RNAs can fold into complex structures

57. An RNA ribozyme

58. SELEX: Systematic Evolution of Ligands by EXponential enrichment

59. Table 6-4 Biochemical reactions catalyzed by ribozymes. ACTIVITYRIBOZYME Peptide bond formationrRNA RNA cleavage, ligationself-splicing introns DNA cleavageself-splicing introns RNA splicingself splicing introns, snRNAs? RNA polymerization in vitro selected RNA RNA and DNA phosphorylationin vitro selected RNA RNA aminoacylatonin vitro selected RNA RNA alkylationin vitro selected RNA Amide bond formationin vitro selected RNA Amide bond cleavagein vitro selected RNA Gycosidic bond formationin vitro selected RNA Porphyrin metalationin vitro selected RNA

60. RNAs can undergo allosteric changes

61. Hypothesis of the development of modern cells

62. Describe the structure of a tRNA molecule. Explain how a tRNA is made. What is meant by amino acid activation. What are the two catalytic sites of an tRNA synthetase. What are the components of a bacterial ribosome? What is the rate of amino acid addition during translation? What are the two functions of EF-Tu? What is the function of EF-G? Explain the steps of peptide chain elongation catalyzed by a ribosome? Where is energy used in the process of translation? Describe the structure of a bacterial ribosome. Describe translational initiation in eukaryotes. What is different between prokaryotic and eukaryotic translational initiation?

63. How is translation terminated? What is a polysome? A uORF? An IRES? A tmRNA? Briefly explain nonsense mediate mRNA decay. (Nostop mediated mRNA decay?) What are the differences between hardwired changes to the genetic code and translational recoding? Name three antibiotic inhibitors of proteins synthesis. What are the differences between hsp60 and hsp70 mediated protein folding? Explain the process of ubiquitin mediated protein degradation. True or False. According to the RNA World hypothesis, RNA was the first molecule of heredity and catalysis? Explain how you would use selex to identify RNAs that bind to a specific DNA sequence.

64. Chapter 7: Gene Control DNA Binding Motifs Genetics Switches