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regulation

regulation. course layout. introduction molecular biology biotechnology bioMEMS bioinformatics bio-modeling cells and e-cells transcription and regulation cell communication neural networks dna computing fractals and patterns the birds and the bees ….. and ants. introduction.

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regulation

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  1. regulation

  2. course layout • introduction • molecular biology • biotechnology • bioMEMS • bioinformatics • bio-modeling • cells and e-cells • transcription and regulation • cell communication • neural networks • dna computing • fractals and patterns • the birds and the bees ….. and ants

  3. introduction

  4. electronic pathway

  5. seoul subway

  6. tokyo subway

  7. pyrimidine pathway

  8. protein pathway

  9. from DNA to pathways

  10. biological information Two Types of Biological Information • The genome, digital information • Environmental, analog information

  11. genome information Two types of digital genome information • Genes, the molecular machines of life • Gene regulatory networks, specify the behavior of the genes

  12. what is systems biology? Biological System DNA Biomodules RNA Cells Networks Proteins

  13. a gene network

  14. a gene network in a physical network

  15. what is a genetic circuit? • Jacob & Monod Model of the prokaryotic operon (1961) Repressor RNAP Inducer Gene A Promoter Operator

  16. what is a genetic circuit? • Jacob & Monod Model of the prokaryotic operon (1961) • “It is obvious from analysis of these [bacterial genetic regulatory] mechanisms that their known elements could be connected into a wide variety of ‘circuits’ endowed with any desired degree of stability” A Gene A B Promoter Operator Gene B Promoter Operator

  17. A B C 0 0 0 0 1 0 1 0 0 1 1 1 A B C 0 0 0 0 1 1 1 0 1 1 1 1 A B C 0 0 1 0 1 1 1 0 1 1 1 0 A A And Or Nand 2 Nand 1 Nand C C B B electronic circuits • Basic electrical engineering (digital): • A basic “flip-flop” = memory A C B in1 out1 Stable states (with in1, in2 = 0): out1 out2 0 1 1 0 out2 in2

  18. Gene A examples • A genetic NAND Gate • A genetic flip-flop out1 in1 in2 out2

  19. basic genetic engineering How do you clone a gene? accessexcellence.com/AB/GG/plasmid.html

  20. genetic circuit engineering paradigm 1. Design • Design “genetic circuitry” that demonstrates a rudimentary control behavior, such as oscillations, bistability (like the flip-flop), step activation, a spike, etc. 2. Simulate • Build a simulation (deterministic or stochastic ODEs) encapsulating the design and examine its dynamic behavior (boundary conditions of different stability regimes, parameter sensitivity…). 3. Implement and Test • Use the results of this simulation to pick genetic parts yielding the desired behavior and splice them together in a plasmid. Transform the plasmid into bacteria and observe the behavior of the system. Does it match predictions from the simulation? -- Back to 1

  21. gene expression

  22. gene regulation mechanism Bacteria express only a subset of their genes at anygiven time. • Expression of all genes constitutively in bacteria would be energetically inefficient. • The genes that are expressed are essential for dealing with the current environmentalconditions, such as the type of available food source.

  23. gene regulation mechanism Regulation of gene expression can occur at several levels: • Transcriptional regulation: no mRNA is made. • Translational regulation: control of whether or how fast an mRNA is translated. • Post-translational regulation: a protein is made in aninactive form and later is activated.

  24. gene regulation mechanism Post-translational control Transcriptional control Translational control Lifespan of mRNA Protein activation (by chemical modification) Onset of transcription Protein Translation rate Ribosome DNA mRNA Feedback inhibition (protein inhibits transcription of its own gene) RNA polymerase

  25. Escherichia coli

  26. gene regulation mechanism Operon • A controllable unit of transcription consisting of a number of structural genes transcribed together. Contains at least two distinctregions: the operator and the promoter.

  27. gene regulation mechanism Case study of the regulation of the lactose operon in E. coli • E. coli utilizes glucose if it is available, but can metabolize other sugars if glucose is absent.

  28. gene regulation mechanism Food source: Glucose : Lactose Glucose : Lactose Glucose : Lactose 1:3 1:1 3:1 Second period of rapid growth with lactose as food source 70 60 29.5 50 14.0 40 43.5 Relative density of cells 30 20 26.5 Initial period of rapid growth with glucose as food source 39.0 13.5 10 0 0 2 3 4 5 0 1 3 4 5 6 0 1 2 1 2 3 4 5 6 7 Time (hours)

  29. gene regulation mechanism Case study of the regulation of the lactose operon in E. coli • Genes that encode enzymes needed to break other sugars down are negatively regulated. • Example: enzymes required to metabolize lactose are only synthesized if glucose is depleted and lactose is available. • In the absence of lactose, transcription of the genes that encode these enzymes is repressed. How does this occur?

  30. gene regulation mechanism Case study of the regulation of the lactose operon in E. coli • All the loci required for lactose metabolism are grouped together into an operon. • The lacZ locus encodes -galactosidase enzyme, which breaks down lactose. • The lacY locus encodes galactosidase permease, a transport protein for lactose. • The function of the lacA locus is unknown. • The lacI locus encodes a repressor that blocks transcription of the lac operon.

  31. gene regulation mechanism Regulatory function Cleaves lactoseto glucose and galactose Membrane transport protein-imports lactose Regulatoryprotein Galactosidase permease ß-galactosidase Lacl LacY LacZ Section of E. coli chromosome lacl lacZ lacY Observations about regulation of lacZ and lacY: Glucose (1) Lacl protein and glucose shut down transcription of lacZ and lacY Lactose E. coli Galactose Galactosidase permease (2) Lactose induces transcription of lacZ andlacY Chromosome ß-galactosidase

  32. gene regulation mechanism Lac operon lacl promoter lacl Operator lacZ lacY lacA Promoter lac operon

  33. gene regulation mechanism Repression and induction of the lactose operon. • The lac operon is under negative regulation, i.e. , normally, transcription is repressed. • Glucose represses transcription of the lac operon. • Glucose inhibits cAMP synthesis in the cells. • At low cAMP levels, no cAMP is available to bind CAP. • Unless CAP is bound to the CAP site in the promoter, no transcription occurs.

  34. gene regulation mechanism When no lactose is present, the repressor binds to DNA and blocks transcription. NO TRANSCRIPTION Functional repressor lacl lacZ lacY RNA polymerase blocked Operator (binding site for repressor)

  35. gene regulation mechanism Repressor plus lactose (an inducer) present. Transcription proceeds. Lactose TRANSCRIPTION BEGINS mRNA -galactosidase Permease repressor lacl+ lacZ lacY

  36. gene regulation mechanism Operons produce mRNAs that code for functionally related proteins. "Polycistronic" mRNA lacZ message lacY message RNA polymerase binds to promoter lacA message lacl promoter lacl Promoter Operator lacZ lacY lacA

  37. cell programming

  38. Diffusing signal E. coli proteins programming cell communities

  39. programming cell communities Program cells to perform various tasks using • Intra-cellular circuits Digital & analog components • Inter-cellular communication Control outgoing signals, process incoming signals

  40. programmed cell applications • Biomedical combinatorial gene regulation with few inputs; tissue engineering • Environmental sensing and effecting recognize and respond to complex environmental conditions • Engineered crops toggle switches control expression of growth hormones, pesticides • Cellular-scale fabrication cellular robots that manufacture complex scaffolds

  41. programmed cell applications pattern formation

  42. programmed cell applications analyte source reporter rings analyte source detection

  43. biological cell programming

  44. biological cell programming

  45. cellular logic

  46. protein expression basics • RNA polymerase binds to promoter • RNAP transcribes gene into messenger RNA • Ribosome translates messenger RNA into protein RNA Polymerase DNA Z Promoter Z Gene

  47. protein expression basics • RNA polymerase binds to promoter • RNAP transcribes gene into messenger RNA • Ribosome translates messenger RNA into protein RNA Polymerase DNA Z Promoter Z Gene

  48. protein expression basics • RNA polymerase (RNAP) binds to promoter • RNAP transcribes gene into messenger RNA • Ribosome translates messenger RNA into protein Transcription RNA Polymerase Messenger RNA DNA Z Promoter Z Gene

  49. protein expression basics • RNA polymerase binds to promoter • RNAP transcribes gene into messenger RNA • Ribosome translates messenger RNA into protein Translation RNA Polymerase Z Protein Transcription Messenger RNA DNA Z Promoter Z Gene

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