1. Gene Regulation Chapter 14

2. Learning Objective 1 Why do bacterial and eukaryotic cells have different mechanisms of gene regulation? Why do bacterial and eukaryotic cells have different mechanisms of gene regulation?

3. Prokaryotes Bacterial cells Bacterial cells grow rapidly grow rapidly have a short life span have a short life span Transcriptional-level control Transcriptional-level control usually regulates gene expression usually regulates gene expression

4. Eukaryotic Cells Have long life span Have long life span respond to many different stimuli respond to many different stimuli One gene One gene may be regulated in different ways may be regulated in different ways Transcriptional-level control Transcriptional-level control and control at other levels of gene expression and control at other levels of gene expression

5. KEY CONCEPTS Cells can synthesize thousands of proteins Cells can synthesize thousands of proteins but not all proteins are required in all cells but not all proteins are required in all cells Cells regulate which parts of the genome will be expressed, and when Cells regulate which parts of the genome will be expressed, and when

6. Learning Objective 2 What is an operon? What is an operon? What are the functions of the operator and promoter regions? What are the functions of the operator and promoter regions?

7. Operon A gene complex A gene complex structural genes with related functions structural genes with related functions controlled by closely linked DNA sequences controlled by closely linked DNA sequences Regulated genes in bacteria Regulated genes in bacteria are organized into operons are organized into operons

8. Promoter Region Each operon has a promoter region Each operon has a promoter region upstream from protein-coding regions upstream from protein-coding regions where RNA polymerase binds to DNA before transcription where RNA polymerase binds to DNA before transcription

9. Operator (1) Regulatory switch for transcriptional-level control of operon Regulatory switch for transcriptional-level control of operon Repressor protein Repressor protein binds to operator sequence binds to operator sequence prevents transcription prevents transcription

10. Operator (2) RNA polymerase RNA polymerase bound to promoter bound to promoter is blocked from transcribing structural genes is blocked from transcribing structural genes If repressor is not bound to operator If repressor is not bound to operator transcription proceeds transcription proceeds

11. Learning Objective 3 What is the difference between inducible, repressible, and constitutive genes? What is the difference between inducible, repressible, and constitutive genes?

12. Inducible Genes (1) An inducible operon An inducible operon such as lac operon such as lac operon is normally turned off is normally turned off Repressor protein Repressor protein is synthesized in active form is synthesized in active form binds to operator binds to operator

13. Inducible Genes (2) If lactose is present If lactose is present is converted to allolactose (inducer) is converted to allolactose (inducer) binds to repressor protein binds to repressor protein changes repressor’s shape changes repressor’s shape Altered repressor Altered repressor cannot bind to operator cannot bind to operator operon is transcribed operon is transcribed

14. The lac Operon

15. Fig. 14-2a, p. 307 lac operon Repressor gene PromoterOperatorlac Zlac Ylac A DNA Transcription Repressor protein mRNA Ribosome Translation

16. Fig. 14-2b, p. 307 PromoterOperatorlac Zlac Ylac A RNA polymerase mRNA Transcription mRNA Translation Inducer (allolactose) Transacetylase β-galactosidase Repressor protein (inactive) Enzymes for lactose metabolism Lactose permease lac operon Repressor gene

17. Repressible Genes (1) A repressible operon (trp operon) A repressible operon (trp operon) is normally turned on is normally turned on Repressor protein Repressor protein is synthesized in inactive form is synthesized in inactive form cannot bind to operator cannot bind to operator A metabolite (metabolic end product) A metabolite (metabolic end product) acts as corepressor acts as corepressor

18. Repressible Genes (2) With high intracellular corepressor levels With high intracellular corepressor levels corepressor molecule binds to repressor corepressor molecule binds to repressor changes repressor’s shape changes repressor’s shape Altered repressor Altered repressor binds to operator binds to operator turns off transcription of operon turns off transcription of operon

19. The trp Operon

20. Fig. 14-4a, p. 310 trp operon Repressor gene Promoter Operatortrp Etrp Dtrp Ctrp Btrp A DNA RNA polymerase Transcription mRNA Translation Repressor protein (inactive) Enzymes of the tryptophan biosynthetic pathway Tryptophan (a) Intracellular tryptophan levels low.

21. Fig. 14-4b, p. 310 trp operon Repressor gene PromoterOperatortrp Etrp Dtrp Ctrp Btrp A DNA Active repressor – corepressor complex mRNA Inactive repressor protein Tryptophan (corepressor) (b) Intracellular tryptophan levels high.

22. Constitutive Genes (1) Are neither inducible nor repressible Are neither inducible nor repressible active at all times active at all times Regulatory proteins Regulatory proteins produced constitutively produced constitutively catabolite activator protein (CAP) catabolite activator protein (CAP) repressor proteins repressor proteins

23. Constitutive Genes (2) Regulatory proteins Regulatory proteins recognize and bind to specific base sequences in DNA recognize and bind to specific base sequences in DNA Activity of constitutive genes Activity of constitutive genes controlled by binding RNA polymerase to promoter regions controlled by binding RNA polymerase to promoter regions

24. Learning Objective 4 What is the difference between positive and negative control? What is the difference between positive and negative control? How do both types of control operate in regulating the lac operon? How do both types of control operate in regulating the lac operon?

25. Negative Control Repressible and inducible operons are under negative control Repressible and inducible operons are under negative control When repressor protein binds to operator When repressor protein binds to operator transcription of operon is turned off transcription of operon is turned off

26. Positive Control (1) Some inducible operons are under positive control Some inducible operons are under positive control Activator protein binds to DNA Activator protein binds to DNA stimulates transcription of gene stimulates transcription of gene

27. Positive Control (2) CAP activates lac operon CAP activates lac operon binds to promoter region binds to promoter region stimulates transcription by tightly binding RNA polymerase stimulates transcription by tightly binding RNA polymerase To bind to lac operon To bind to lac operon CAP requires cyclic AMP (cAMP) CAP requires cyclic AMP (cAMP) cAMP levels increase cAMP levels increase as glucose levels decrease as glucose levels decrease

28. Positive Control

29. Fig. 14-5a, p. 311 Promoter RNA polymerase – binding site CAP- binding site Repressor gene Operatorlac Zlac Ylac A DNA mRNA RNA polymerase binds poorly CAP (inactive) Allolactose Repressor protein (inactive) (a) Lactose high, glucose high, cAMP low.

30. Fig. 14-5b, p. 311 Promoter RNA polymerase – binding site CAP- binding site Repressor gene Operatorlac Zlac Ylac A DNA RNA polymerase binds efficiently Transcription mRNA CAP Translation Galactoside transacetylase cAMP Lactose permease Allolactose Repressor protein (inactive) Enzymes for lactose metabolism β -galactosidase (b) Lactose high, glucose low, cAMP high.

31. Binding CAP

32. Fig. 14-6, p. 312 DNA cAMP CAP dimer

33. Learning Objective 5 What are the types of posttranscriptional control in bacteria? What are the types of posttranscriptional control in bacteria?

34. Posttranscriptional Controls in Bacteria Translational control Translational control regulates translation rate of particular mRNA regulates translation rate of particular mRNA Posttranslational controls Posttranslational controls include feedback inhibition of key enzymes in metabolic pathways include feedback inhibition of key enzymes in metabolic pathways

35. KEY CONCEPTS Prokaryotes regulate gene expression in response to environmental stimuli Prokaryotes regulate gene expression in response to environmental stimuli

36. KEY CONCEPTS Gene regulation in prokaryotes occurs primarily at the transcription level Gene regulation in prokaryotes occurs primarily at the transcription level

37. Learning Objective 6 Discuss the structure of a typical eukaryotic gene and the DNA sequences involved in regulating that gene Discuss the structure of a typical eukaryotic gene and the DNA sequences involved in regulating that gene

38. Eukaryotic Genes Are not normally organized into operons Are not normally organized into operons Regulation occurs at levels of Regulation occurs at levels of Transcription Transcription mRNA processing mRNA processing Translation Translation Modifications of protein product Modifications of protein product

39. Transcription Requires Requires Transcription initiation site Transcription initiation site where transcription begins where transcription begins Promoter Promoter to which RNA polymerase binds to which RNA polymerase binds In multicellular eukaryotes In multicellular eukaryotes RNA polymerase binds to promoter (TATA box) RNA polymerase binds to promoter (TATA box)

40. Transcription

41. Fig. 14-9a, p. 316 TATA box Transcription initiation site UPE TATA A pre-mRNA A T (a) Eukaryotic promoter elements.

42. Fig. 14-9b, p. 316 TATA box Transcription initiation site UPE pre-mRNA TATA A A T (b) A weak eukaryotic promoter.

43. Fig. 14-9c, p. 316 TATA box Transcription initiation site UPE pre-mRNA TATA A A T (c) A strong eukaryotic promoter.

44. Fig. 14-9d, p. 316 TATA box Transcription initiation site EnhancerUPE pre-mRNA TATA A A T (d) A strong eukaryotic promoter plus an enhancer.

45. Regulated Eukaryotic Gene Promoter Promoter RNA polymerase-binding site RNA polymerase-binding site short DNA sequences (upstream promoter elements (UPEs) or proximal control elements) short DNA sequences (upstream promoter elements (UPEs) or proximal control elements) UPEs UPEs number and types within promoter region determine efficiency of promoter number and types within promoter region determine efficiency of promoter

46. Enhancers (1) Located far away from promoter Located far away from promoter control some eukaryotic genes control some eukaryotic genes Help form active transcription initiation complex Help form active transcription initiation complex

47. Enhancers (2) Specific regulatory proteins Specific regulatory proteins bind to enhancer elements bind to enhancer elements activate transcription by interacting with proteins bound to promoters activate transcription by interacting with proteins bound to promoters

48. Enhancers

49. Fig. 14-11a, p. 317 Enhancer Target proteins RNA polymerase TATA box DNA (a) Little or no transcription.

50. Fig. 14-11b, p. 317 Enhancer DNA TATA box Activator (transcription factor) (b) High rate of transcription.

51. Learning Objective 7 In what ways may eukaryotic DNA-binding proteins bind to DNA? In what ways may eukaryotic DNA-binding proteins bind to DNA?

52. Transcription Factors DNA-binding protein regulators control eukaryotic genes DNA-binding protein regulators control eukaryotic genes some transcriptional activators some transcriptional activators some transcriptional repressors some transcriptional repressors

53. Transcription Factors Each has DNA-binding domain Each has DNA-binding domain 3 types of regulatory proteins 3 types of regulatory proteins Helix-turn-helix Helix-turn-helix Zinc fingers Zinc fingers Leucine zippers Leucine zippers

54. Helix-Turn-Helix Inserts one helix into DNA Inserts one helix into DNA

55. Fig. 14-10a, p. 317 Turn α -helix DNA (a) Helix-turn-helix.

56. Zinc Fingers Loops of amino acids Loops of amino acids held together by zinc ions held together by zinc ions each loop has α-helix that fits into DNA each loop has α-helix that fits into DNA

57. Fig. 14-10b, p. 317 COO – Finger 2 Finger 3 Zinc ion Finger 1 NH 3 + DNA (b) Zinc fingers.

58. Leucine Zipper Proteins Associate as dimers that insert into DNA Associate as dimers that insert into DNA

59. Fig. 14-10c, p. 317 Leucine zipper region DNA (c) Leucine zipper.

60. Learning Objective 8 How may a change in chromosome structure affect the activity of a gene? How may a change in chromosome structure affect the activity of a gene?

61. Gene Activity (1) Changes in chromosome structure Changes in chromosome structure inactivates genes inactivates genes Heterochromatin Heterochromatin densely packed regions of chromosomes densely packed regions of chromosomes contain inactive genes contain inactive genes

62. Gene Activity (2) Active genes Active genes associated with loosely packed chromatin structure (euchromatin) associated with loosely packed chromatin structure (euchromatin) Cells change chromatin structure Cells change chromatin structure from heterochromatin to euchromatin from heterochromatin to euchromatin by chemically modifying histones (proteins associated with DNA to form nucleosomes) by chemically modifying histones (proteins associated with DNA to form nucleosomes)

63. Chromatin Structure

64. Fig. 14-7, p. 314 Heterochromatin: genes silent Chromatin decondensation Nucleosome Histones DNA Transcribed region Euchromatin: genes active

65. Gene Activity (3) Histone tail Histone tail string of amino acids that extends from the DNA-wrapped nucleosome string of amino acids that extends from the DNA-wrapped nucleosome Methyl groups, acetyl groups, sugars, and proteins Methyl groups, acetyl groups, sugars, and proteins may chemically attach to the histone tail may chemically attach to the histone tail may expose or hide genes (turn on or off) may expose or hide genes (turn on or off)

66. Gene Activity (4) Epigenetic inheritance Epigenetic inheritance changes how a gene is expressed changes how a gene is expressed important mechanism of gene regulation important mechanism of gene regulation DNA methylation DNA methylation perpetuates gene inactivation perpetuates gene inactivation patterns repeat in successive cell generations patterns repeat in successive cell generations mechanism for epigenetic inheritance mechanism for epigenetic inheritance

67. Gene Amplification Some genes Some genes products are required in large amounts products are required in large amounts have multiple copies in the chromosome have multiple copies in the chromosome Gene amplification Gene amplification some cells selectively amplify genes by DNA replication some cells selectively amplify genes by DNA replication

68. Gene Amplification

69. Fig. 14-8, p. 315 Drosophila chorion gene Gene amplification by repeated DNA replication of chorion gene region Chorion gene in ovarian cell

70. Learning Objective 9 How may a gene in a multicellular organism produce different products in different types of cells? How may a gene in a multicellular organism produce different products in different types of cells?

71. Differential mRNA Processing Single gene produces different forms of protein in different tissues Single gene produces different forms of protein in different tissues depending on how pre-mRNA is spliced depending on how pre-mRNA is spliced Gene contains a segment that can be either intron or exon Gene contains a segment that can be either intron or exon as intron, sequence is removed as intron, sequence is removed as exon, sequence is retained as exon, sequence is retained

72. Differential mRNA Processing

73. Fig. 14-12, p. 318 Potential splice sites Exon or intron ExonIntron Exon pre-mRNA Differential mRNA processing Exon Functional mRNA in tissue A Functional mRNA in tissue B

74. Learning Objective 10 What types of regulatory controls operate in eukaryotes after mature mRNA is formed? What types of regulatory controls operate in eukaryotes after mature mRNA is formed?

75. mRNA Stability Certain regulatory mechanisms increase RNA stability Certain regulatory mechanisms increase RNA stability allowing more protein synthesis before mRNA degradation allowing more protein synthesis before mRNA degradation Sometimes under hormonal control Sometimes under hormonal control

76. Posttranslational Control (1) In eukaryotic gene expression In eukaryotic gene expression feedback inhibition feedback inhibition modification of protein structure modification of protein structure Protein function change Protein function change by kinases adding phosphate groups by kinases adding phosphate groups by phosphatases removing phosphates by phosphatases removing phosphates

77. Protein Degradation (1) Proteins targeted for destruction Proteins targeted for destruction covalently bonded to ubiquitin covalently bonded to ubiquitin Protein tagged by ubiquitin Protein tagged by ubiquitin degraded in a proteasome degraded in a proteasome

78. Protein Degradation (2) Proteasome Proteasome large macromolecular structure large macromolecular structure recognizes ubiquitin tags recognizes ubiquitin tags Proteases Proteases protein-degrading enzymes protein-degrading enzymes associated with proteasomes associated with proteasomes degrade protein into peptide fragments degrade protein into peptide fragments

79. Protein Degradation

80. Fig. 14-13, p. 318 Target protein Ubiquitin 1 Ubiquitin molecules attach to protein tar- geted for degradation. Ubiquitinylated protein 2 Protein enters proteasome. Proteasome 3 Ubiquitins are released and available for reuse. Protein is degraded into peptide fragments. Peptide fragments

81. Stepped Art Fig. 14-13, p. 318 Target protein Ubiquitin 3 Ubiquitins are released and available for reuse. Protein is degraded into peptide fragments. Peptide fragments 2 Protein enters proteasome. Proteasome 1 Ubiquitin molecules attach to protein tar- geted for degradation. Ubiquitinylated protein

82. KEY CONCEPTS Gene regulation in eukaryotes occurs at the levels of transcription, posttranscription, translation, and posttranslation Gene regulation in eukaryotes occurs at the levels of transcription, posttranscription, translation, and posttranslation

83. Animation: Controls of Eukaryotic Gene Expression CLICK TO PLAY