1. Chapter 11 Regulation of Gene Expression

2. Regulation of Gene Expression u Important for cellular control and differentiation. u Understanding “expression” is a “hot” area in Biology.

3. Differentiation u Specialization of structure and function of cells u Results from activation/ deactivation of genes

4. General Mechanisms 1. Regulate Gene Expression 2. Regulate Protein Activity

5. Operon Model u Jacob and Monod (1961) - Prokaryotic model of gene control. u Always on the national AP Biology exam !

6. Operon Structure 1. Regulatory Gene 2. Operon Area a. Promoter b. Operator c. Structural Genes

7. Gene Structures

8. Regulatory Gene u Makes Repressor Protein which may bind to the operator. u Repressor protein blocks transcription.

9. Promoter u Attachment sequence on the DNA for RNA polymerase to start transcription.

10. Operator u The "Switch”, binding site for Repressor Protein. u If blocked, will not permit RNA polymerase to pass, prevents transcription.

11. Gene Structures

12. Structural Genes u Make the enzymes for the metabolic pathway.

13. Lac Operon u For digesting Lactose. u Inducible Operon - only works (on) when the substrate (lactose) is present.

14. If no Lactose u Repressor binds to operator. u Operon is "off”, -no transcription, -no enzymes made

15. If Lactose is absent

16. If Lactose is present u Repressor binds to Lactose instead of operator. u Operon is "on”, -transcription occurs, -enzymes are made.

17. If Lactose is present

18. Enzymes u Digest Lactose. u When enough Lactose is digested, the Repressor can bind to the operator and switch the Operon "off”.

19. Net Result u The cell only makes the Lactose digestive enzymes when the substrate is present, saving time and energy.

20. trp Operon u Makes Tryptophan. u Repressible Operon.

21. If no Tryptophan u Repressor protein is inactive, Operon "on” Tryptophan made. u “Normal” state for the cell.

22. Tryptophan absent

23. If Tryptophan present u Repressor protein is active, Operon "off”, no transcription, no enzymes u Result - no Tryptophan made

24. If Tryptophan present

25. Repressible Operons u Are examples of Feedback Inhibition. u Result - keeps the substrate at a constant level.

26. Eukaryotic Gene Regulation u Can occur at any stage between DNA and Protein.

27. DNA packing u DNA is coiled around histones which are then coiled to form supercoil u Less tightly coiled= easier expression

28. DNA packing Histones

29. Chromatin Structure and Expression u Histone Modifications u DNA Methylation u Epigenetic Inheritance

30. Histone Acetylation u Attachment of acetyl groups (-COCH 3 ) to AAs in histones. u Result - DNA held less tightly to the nucleosomes, more accessible for transcription.

32. DNA Methylation u Addition of methyl groups (-CH 3 ) to DNA bases. u Result - long-term shut-down of DNA transcription. u Ex: Barr bodies genomic imprinting

33. Epigenetics u Another example of DNA methylation affecting the control of gene expression. u Long term control from generation to generation.

34. u End of Part 1

35. Transcriptional Control u Enhancers and Repressors u Specific Transcription Factors u Result – affect the transcription of DNA into mRNA

36. Enhancers u Areas of DNA that increase transcription. u May be widely separated from the gene (usually upstream).

38. Post-transcriptional Control u Alternative RNA Splicing Ex - introns and exons u Can have choices on which exons to keep and which to discard. u Result – different mRNA and different proteins.

40. DSCAM Gene u Found in fruit flies u Has 100 potential splicing sites. u Could produce 38,000 different polypeptides u Many of these polypeptides have been found

41. Commentary u Alternative Splicing is a BIG topic in Biology. u About 60% of genes are estimated to have alternative splicing sites. u One “gene” does not equal one polypeptide.

42. Translation Control u Regulated by the availability of tRNAs, AAs and other protein synthesis factors.

43. Protein Processing and Degradation u Changes to the protein structure after translation. u Ex: Cleavage u Modifications u Activation u Transport u Degradation

44. Noncoding RNA u Small RNA molecules that are not translated into protein. u Whole new area in gene regulation.

45. Types of RNA u MicroRNAs or miRNAs. u RNA Interference or RNAi using small interfering RNAs or siRNAs.

46. RNAi u siRNAs or miRNAs can interact with mRNA and destroy the mRNA or block transcription. u A high percentage of our DNA produces regulatory RNA.

47. Morphogenesis u The generation of body form u How do cells differentiate from a single celled zygote into a multi-cellular organism?

48. Induction u Cell to cell signaling of neighboring cells gives position and clues to development of the embryo.

50. Homeotic Genes u Any of the “master” regulatory genes that control placement of the body parts. u Usually contain “homeobox” sequences of DNA (180 bases) that are highly conserved between organisms.

53. When things go wrong

54. Gene Expression and Cancer u Cancer - loss of the genetic control of cell division. u Balance between growth- stimulating pathway (accelerator) and growth- inhibiting pathway (brakes).

55. Proto-oncogenes u Normal genes for cell growth and cell division factors. u Genetic changes may turn them into oncogenes (cancer genes). u Ex: Gene Amplification, Translocations, Transpositions, Point Mutations

56. Proto-oncogenes

57. Tumor-Suppressor Genes u Genes that inhibit cell division. u Ex - p53, p21

58. Cancer Examples u p53 - involved with several DNA repair genes and “checking” genes. u When damaged (e.g. cigarette smoke), can’t inhibit cell division or cause damaged cells to apoptose.

60. Carcinogens u Agents that cause cancer. u Ex: radiation, chemicals u Most work by altering the DNA, or interfering with control or repair mechanisms.

61. Multistep Hypothesis u Cancer is the result of several control mechanisms breaking down. u Ex: Colorectal Cancer requires 4 to 5 mutations before cancer starts.

62. Can Cancer be Inherited? u Cancer is caused by genetic changes but is not inherited. u However, oncogenes can be inherited. u Multistep model suggests that this puts a person “closer” to developing cancer.

63. End of Part 2

64. Transcriptional Control u Enhancers and Repressors u Specific Transcription Factors u Result – affect the transcription of DNA into mRNA

65. Enhancers u Areas of DNA that increase transcription. u May be widely separated from the gene (usually upstream).

67. Post-transcriptional Control u Alternative RNA Splicing Ex - introns and exons u Can have choices on which exons to keep and which to discard. u Result – different mRNA and different proteins.

69. DSCAM Gene u Found in fruit flies u Has 100 potential splicing sites. u Could produce 38,000 different polypeptides u Many of these polypeptides have been found

70. Commentary u Alternative Splicing is a BIG topic in Biology. u About 60% of genes are estimated to have alternative splicing sites. u One “gene” does not equal one polypeptide.

71. Translation Control u Regulated by the availability of tRNAs, AAs and other protein synthesis factors.

72. Protein Processing and Degradation u Changes to the protein structure after translation. u Ex: Cleavage u Modifications u Activation u Transport u Degradation

73. Noncoding RNA u Small RNA molecules that are not translated into protein. u Whole new area in gene regulation.

74. Types of RNA u MicroRNAs or miRNAs. u RNA Interference or RNAi using small interfering RNAs or siRNAs.

75. RNAi u siRNAs or miRNAs can interact with mRNA and destroy the mRNA or block transcription. u A high percentage of our DNA produces regulatory RNA.

76. Morphogenesis u The generation of body form u How do cells differentiate from a single celled zygote into a multi-cellular organism?

77. Homeotic Genes u Any of the “master” regulatory genes that control placement of the body parts. u Usually contain “homeobox” sequences of DNA (180 bases) that are highly conserved between organisms.

80. When things go wrong