1. Biochemistry Sixth Edition Chapter 31 The Control of Gene Expression Part I: Prokaryotes Copyright © 2007 by W. H. Freeman and Company Berg Tymoczko Stryer

2. Thyroid hormone receptor  Transcription factor  Activates specific genes Thyroid hormone

3. constitutive expression vs. regulated expression

4. The control of gene expression * Cell type * Developmental stage * Environmental changes Genome  transcriptome  proteome Gene expression critical step

8. Gene regulation in prokaryotes (simple organism, common mechanism) Carbon source: glucose When glucose is low: lactose (disaccharide)

9.  -galactosidase activity can be monitored by X-Gal Application: TA cloning

10. Growing in a new nutrient: enzyme level induction

11. Lactose is not an inducer

14. Two other proteins are also induced: Galactoside permease and thiogalactoside transacetylase (lactose transport) (detoxification) These proteins are associated with the same environmental change: Expression levels are regulated together! Such coordinated unit of gene expression: “Operon”

15.  -galactosidase : z galactoside permease : y thiogalactoside transacetylase : a Mutant studies: z - y + a +  no z; y and a are ok Mutant: z, y, a are expressed in the absence of lactose  constitutive mutant

16. Mutant studies: Mutant: z, y, a are expressed in the absence of lactose  constitutive mutant  All three genes are regulated by a common element that is different from z, y, a themselves: “ i ” Wildtype inducible: i + z + y + a + Constitutive mutant: i - z + y + a + Is i activator or repressor?

17. Mutant studies: Episome: genetic material (plasmid)  Diploid bacteria (by conjunction) Example: i + z - / (e)i - z + (chromosome/episome) Is this strain inducible or constitutive for  -gal? Does i on the chromosome repress z on episome? How about i - z + / (e)i + z - ? A diffusible repressor is encoded by the i gene  trans-acting factor

18. The operon model p: promoter sites o: operator site (regulatory DNA seq.) i: the repressor, binds to o z;y;a : polygenic or polycistronic RNA transcript

20. Lac repressor-DNA  dimer/tetramer Monomer has helix- turn-helix: for major groove binding Consequence of lac repressor binding to operator?

24. Inducer: allolactose

25. Another example: pur repressor and pur operon pur repressor: * dimeric, 31% identical to lac repressor, similar in 3D structure * represses genes involved in purine biosynthesis * pur repressor binds DNA only when bound to a small molecule  corepressor * Binds specific inverted-repeated sequence

26. pur operator: >20 19 operons, 25 genes

28.  catabolic repression

30. Dimer Inverted-repeated binding site  Upregulate RNA pol. II 50x

31. Dimer of CAP bound to DNA

33. Sequence-specific DNA binding proteins and motif

34. Gene regulation depends on regulatory sites Symmetry in DNA sequence  Protein symmetry

36. Hydrogen bonds

37. Many prokaryotic DNA-binding proteins have HTH motif Recognition helix: amino acids  major groove bases Another helix: backbone interaction (dimeric)

38. Other proteins bind DNA through a pair of  strands Methionine repressor

39. Eukaryotic DNA-binding motif: 1. homeodomain Similar to HTH Heterodimeric proteins  asymmetric seq.

40. Eukaryotic DNA-binding motif: 2. Basic-leucine zipper (bZip) Coiled-coil

41. Eukaryotic DNA-binding motif: 3. Cys 2 His 2 zinc-finger domain 1. Tandem sets of small domains (zinc finger) (ex. >10) 2. A-helix contact bases in the groove