2. AP Biology 2007-2008 Control of Prokaryotic (Bacterial) Genes

3. AP Biology initiation of transcription 1 mRNA splicing 2 mRNA protection 3 initiation of translation 6 mRNA processing 5 1 & 2. transcription - DNA packing - transcription factors 3 & 4. post-transcription - mRNA processing - splicing - 5’ cap & poly-A tail - breakdown by siRNA 5. translation - block start of translation 6 & 7. post-translation - protein processing - protein degradation 7 protein processing & degradation 4 4 Gene Regulation

4. AP Biology Why regulate genes? 1. Maintain homeostasis - gene expression is affected by changes in the external environment 2. Multicellular organisms – have specialized cells  All cells have the full set of genes, but not all genes are needed in each cell (some are turned off)

5. AP Biology Bacteria need to respond quickly to changes in their environment Bacterial metabolism

6. AP Biology Bacterial metabolism if they have enough of a product, need to stop production  why? waste of energy to produce more  how? stop production of enzymes for synthesis STOP

7. AP Biology If they find a new food/energy source…  need to utilize it quickly why? metabolism, growth, reproduction how? start production of enzymes for digestion  Natural selection favors cells that can do this well because it’s COST EFFECTIVE GO

8. AP Biology Enzyme Review

9. AP Biology Allosteric Regulation

10. AP Biology Feedback Inhibition Feedback inhibition  product acts as an allosteric inhibitor of 1 st enzyme in tryptophan pathway  but this is wasteful production of enzymes = inhibition - - Oh, I remember this from our Metabolism Unit!

11. AP Biology Different way to Regulate Metabolism Gene regulation  instead of blocking enzyme function, block transcription of genes for all enzymes in tryptophan pathway = inhibition - Now, that’s a good idea from a lowly bacterium! - -

12. AP Biology so why is this good? saves energy by not wasting it on unnecessary protein synthesis (remember…it’s all about energy!)

13. AP Biology Overview - Gene regulation in bacteria Cells vary amount of specific enzymes produced by regulating gene transcription  turn genes on or turn genes off

14. AP Biology On and Off. Off and On. On and Off. Turn genes OFF example if bacterium has enough tryptophan then it doesn’t need to make enzymes used to build tryptophan Turn genes ON example if bacterium encounters new sugar (energy source), like lactose, then it needs to start making enzymes used to digest lactose STOP GO

15. AP Biology Operon – (What is the structure?) (has all of these)  1. genes grouped together with related functions example: all enzymes in a metabolic pathway  2. promoter = RNA polymerase binding site single promoter controls transcription of all genes in operon transcribed as one unit & a single mRNA is made  3. operator = DNA binding site of repressor protein

16. AP Biology So how can these genes be turned off? Repressor protein  binds to DNA at operator site  blocking RNA polymerase  blocks transcription

17. AP Biology Regulatory gene – codes for a regulatory protein, at different site than the gene it is regulating

18. AP Biology operatorpromoter Operon model DNATATA RNA polymerase repressor = repressor protein operator, promoter & genes they control serve as a model for gene regulation gene1gene2gene3gene4 RNA polymerase Repressor protein turns off gene by blocking RNA polymerase binding site. 1234 mRNA enzyme1enzyme2enzyme3enzyme4

19. AP Biology Two Main Types of Operons Repressible (Synthesis Pathway)  Blocks transcription when there is enough of the product Inducible (Digestive Pathway)  Starts transcription when needs to start making products (like to access a new energy source)

20. AP Biology Synthesis Pathway Model (Repressible) When excess tryptophan is present, it binds to tryp repressor protein & triggers repressor to bind to DNA  blocks (represses) transcription  Usually on

21. AP Biology mRNA enzyme1enzyme2enzyme3enzyme4 operatorpromoter Repressible operon: tryptophan DNATATA RNA polymerase tryptophan repressor repressor protein repressor tryptophan – repressor protein complex (excess tryptophan is present so it binds to tryp repressor protein & triggers repressor to bind to DNA)  blocks (represses) transcription gene1gene2gene3gene4 conformational change in repressor protein! 1234 repressor trp RNA polymerase trp

22. AP Biology Tryptophan operon What happens when tryptophan is present? Don’t need to make tryptophan-building enzymes Tryptophan is allosteric regulator of repressor protein

23. AP Biology Digestive Pathway Model When lactose is present, binds to lac repressor protein & triggers repressor to release DNA  induces transcription  Usually off

24. AP Biology mRNA enzyme1enzyme2enzyme3enzyme4 operatorpromoter Inducible operon: lactose DNATATA RNA polymerase repressor repressor protein repressor lactose – repressor protein complex lactose lac repressor gene1gene2gene3gene4 (lactose is present so it binds to lac repressor protein & triggers repressor to release DNA)  induces transcription RNA polymerase 1234 lac conformational change in repressor protein! lac

25. AP Biology Lactose operon What happens when lactose is present? Need to make lactose-digesting enzymes Lactose is allosteric regulator of repressor protein

26. AP Biology Operon summary Repressible operon  Usually on  usually functions in anabolic pathways synthesizing end products  when end product is present in excess, gene is turned off and cell allocates resources to other uses

27. AP Biology Inducible operon  Usually off  usually functions in catabolic pathways, digesting nutrients to simpler molecules  produce enzymes only when nutrient is available cell avoids making proteins that have nothing to do, cell allocates resources to other uses

28. AP Biology Lac operon http://vcell.ndsu.edu/animations/lacOpe ron/index.htm http://vcell.ndsu.edu/animations/lacOpe ron/index.htm

29. AP Biology There’s more to the story… we have talked about negative regulation  repressor protein binds to the operator, turns off transcription There is also positive regulation  activator binds to the promoter, turns transcription up (amplifies expression)

30. AP Biology Negative Regulation – a repressor protein binds to the promoter and turns transcription off  Lac – inducer (repressor unbinds)  Trp – corepressor (repressor binds) Positive Regulation – an activator binds to the promoter and turns transcription on  Lac – CAP is an activator The lac operon is regulated in 2 ways Overall themes – homeostasis and energy/nutrient conservation

31. AP Biology Prokaryotic vs Eukaryotic Transcriptional Control Bacteria have operons regulated by 1 promoter Eukaryotes have related genes on different chromosomes with different promoters Eukaryotes have control elements for each gene  Control elements – specific nucleotide sequences, unique combination for each gene

32. AP Biology Rest of Today Complete the operon worksheet

33. AP Biology Prokaryotic vs eukaryotic Genomes Protein synthesis Cell respiration ETC.

34. AP Biology

35. RNA DNA is transcribed into  Coding RNA mRNA  Non-coding RNA tRNA rRNA siRNA miRNA

36. AP Biology RNA interference (involves siRNA and miRNA) Small interfering RNAs (siRNA)  short segments of RNA (21-28 bases) bind to mRNA create sections of double-stranded mRNA “death” tag for mRNA  triggers degradation of mRNA  cause gene “silencing” post-transcriptional control turns off gene = no protein produced siRNA

37. AP Biology microRNA small non-coding RNAs (ncRNAs) with approximately 20 nucleotides (nt) length regulate gene expression post-transcriptionally by binding to mRNAs lead to inhibition of translation or mRNA degradation It is predicted that miRNAs regulate approximately 30% of the human protein-coding genome

38. AP Biology RNAi videos Chef video - siRNA https://www.youtube.com/watch?v=H5udFj WDM3E https://www.youtube.com/watch?v=H5udFj WDM3E microRNA https://www.youtube.com/watch?v=dupzE 66J8u4 (5:45 mark) https://www.youtube.com/watch?v=dupzE 66J8u4 https://www.youtube.com/watch?v=4G9W GE1sqgA&list=PL3EE712E4399A54A1 https://www.youtube.com/watch?v=4G9W GE1sqgA&list=PL3EE712E4399A54A1

39. AP Biology miRNA’s

40. AP Biology Action of siRNA siRNA double-stranded miRNA + siRNA mRNA degraded functionally turns gene off Hot…Hot topic in biology mRNA for translation breakdown enzyme (RISC) dicer enzyme

41. AP Biology Applications of microRNA Cancer detection/profiling  Each type of cancer has its own microRNA profile

42. AP Biology Applications cont’d Regulators of gene expression Biomarkers Cardiovascular disease Therapeutics

43. AP Biology 2007-2008 Turn your Question Genes on!

44. AP Biology Rest of Class Create a model of the regulation of the lac operon When you are done, show me