1. Regulation of Gene Expression In Prokaryotes

2. Regulation of Gene Expression Constituitive Gene Expression (promoters) Regulating Metabolism (promoters and operators) Regulating Development (sigma switches)

3. Constituitive Gene Expression (promoters) promoter coding sequence

4. Regulating Metabolism (promoters and operators) promoter coding sequence operator

5. Major and minor grooves - protein binding

7. Recognition involves the major groove

8. Regulatory Proteins Bind DNA

9. Many regulatory proteins are dimers and bind to palindromes negative controlpositive control

10. repressor activated genes OFF repressor deactivated genes ON repressor activated genes OFF repressor deactivated genes ON precursor moleculesmacromolecule energy substrate product Synthetic Pathway Degredative Pathway Repressors & metabolic pathways

11. Metabolic signals and repressor activity metabolic signal molecule DNA binding site repressor protein gene off gene ongene off gene on

12. the lac operon

13. Lactose Metabolism

14. the metabolic signal for repression

15. Negative Control When activated by binding of the metabolic signal molecule, the lac repressor binds to the operator, blocking RNA polymerase

16. Negative control in the lac operon

17. the lac operon

18. Conventional interpretation of dominance - focusing on enzyme function

19. Conventional interpretation of codominance - focusing on enzyme function

20. But alternatively, control regions can be involved - a recessive operator mutation

21. But alternatively, control regions can be involved - a dominant operator mutation

22. But alternatively, control regions can be involved - one inducer mutation

23. But alternatively, control regions can be involved - another inducer mutation

24. the Lac control region

25. Cyclic AMP

26. Positive Control cAMP is present when glucose is unavailable cAMP binds to CAP protein, which then binds to the promoter binding of the CAP-cAMP complex to the promoter, activates it

27. CAP-cAMP positioning of CTD

28. CAP-cAMP acts in formation of closed promoter

29. The Lactose Operon: Control of a degredative pathway

30. Practice

31. Answers

33. Trp operon, control of a a biosynthetic pathway

34. The Tryptophan Operon: Control of a synthetic pathway

35. Tryptophan Synthesis allosteric protein

36. Attenuation of trp

37. The leader sequence: two trp codons and a stop codon

38. The mechanism of attenuation - termination

39. Region 2 can bind with 1 or 3, but affinity for 1 is higher

40. Over riding attentuation if shortage of trp causes ribosome to stall, 2 binds with 3 …no terminator hairpin forms

41. Control of development: Sigma switching

42. Different sigmas and their regions of homology

43. RNA polymerase in bacteria core enzyme sigma Sigma factors recognize promoters and disassociate when the RNA polymerase binds to the promoter, leaving the core enzyme to make the transcript RNA polymerase

44. Phage SPOI (in B. subtilis) 3 phases of gene expression –Early phase –Mid phase –Late phase Each phase uses a different sigma, each recognizing a different promoter The genes of each phase all have the same kind of promoter, recognized by one of the sigma factors

45. Early phase. Early genes have promoters recognized by the host’s RNA polymerase. gp28 is an early protein that acts as a sigma factor for the middle phase genes. gp28 has a higher affinity for the CORE’s binding site than it’s own sigma, thus displacing the host’s sigma and turning off the early genes and turning on the mid genes. Middle phase. Middle phase genes have promoters recognized by gp28. Gp33 and gp34 are middle proteins that act as a sigma factor for the late genes. Late phase early transcripts early proteins, including gp28 host sigma late transcripts late proteins gp33-34 sigma middle transcripts middle proteins, including gp33, gp34 gp28 sigma Sigma Switching

46. Lambda

47. Lysogenic Life Cycles - Temperate Viruses

48. Genetic map of Lambda

49. 3 phases again

50. N antitermination

51. Q antitermination

52. cI and cro duke it out

53. Establishing Lysogeny

54. Maintaining Lysogeny

55. Induction SOS

56. Prokaryote versus Eukaryote Comparison Step 1 promoter Step 2 Prokaryotes Step 1 promoter Step 2 Eukaryotes promoter sigma Transcription Factor (eukaryotic sigma)

57. Positive control in eukaryotes - gene enhancers

58. Gene activation in Eukaryotes: A different complicated initiation complex for each different context in which a gene is expressed