CEN 551 Biochemical Engineering

1. CEN 551 Biochemical Engineering Instructor: Dr. Christine Kelly Review chapter 3, 4, 5 Section 4.6 - Regulation

2. Schedule • Today 1/27: chapter 3 and 4 review, chapter 5 • Thursday 1/29: chapter 6 and 7 • Tuesday 2/3: review for exam 1 • Thursday 2/5: exam 1 (chapters 1-7)

3. www.ecs.syr.edu/facutly/kelly/biochemeng

4. Review Chapter 3

5. Michaelis- Menten Kinetics

6. Michaelis-Menten Kinetics • When v= 1/2 Vmax, [S]= Km so Km is sometimes called the half-saturation constant and sometimes the Michaelis constant

7. Damkohler number (Da) maximum reaction rate maximum diffusion V’m kL[Sb] Da>>1 diffusion limiting Da<<1 reaction rate limiting Da = Sb = bulk substrate kL = mass transfer coefficient Da =

8. Effect of Damkohler Number =Km/[Ss]

9. Vocabulary from Chapter 3 Write down vocabulary from chapter 3 that you think I expect you to know without looking in the text or notes.

10. Michaelis-Menten kinetic equation and shape of the plot Factors that can cause denaturation of enzymes Activation energy Rapid equilibrium assumption Quasi-steady state assumption Types of inhibition How does temperature affect enzyme kinetics What are immobilized enzyme Advantage/disadvantage of immobilized enzyme Process in converting reactants to products in immobilized systems

11. What kind of open book problems am I likely to ask? • Here is some data, what are the Michaelis-Menten parameters? • Here is some data, what type of inhibition is exhibited? • Here is some data, are the immobilized enzyme kinetics mass transfer or reaction limited? • Here is some data, what is the activation energy? • Derive one of the inhibition rate expressions – using rapid equilibrium and/or quasi steady state assumption. • Derive batch rate equation using Michaelis-Menten kinetics. • Derive second order differential equation describing substrate concentration within an porous support.

12. Vocabulary (chap 1,2, some of 3)(without notes or texts)

13. Review Chapter 4

14. DNA Movie(A0002902)

16. DNA Replication Movie(A0002701)

21. Transcription Movie(A0001001)

22. RNA Post Processing (Eucaryotes) exon intron exon intron degraded before translation mRNA rejoined

23. Eucaryotic mRNA Processing Movie(A0158701)

24. Code for Protein Synthesis

26. Translation Movie (A0001404)

28. Central Dogma Movie(A0042201)

29. REGULATION

30. Metabolic Regulation: Controlling the rates of reactions in the cell. 1. Genetic level (control of transcription). Controlling the amount of enzymes. Most common in procaryotes. 2. Enzymatic level (control of product formation). Controlling activities of enzymes. Most common in eucaryotes.

32. Genetic Level Control • Feed back repression- end product blocks transcription. • Induction- metabolite (reactant) induces transcription. • Constitutive expression: genes transcribed continuously (always on). • Catabolite Repression: several operons influenced by the presence of glucose. If glucose presence, most operons for other sugar metabolism are regulated off.

33. PROMOTER OPERATOR GENES Genetic Level Control Activator binding site • Repressor: molecule that binds to operator – when bound, transcription off. • Activator: binds to activator binding site, when bound transcription on. • Inducer: binds to repressor or activator – results in transcription on. • Corepressor: binds to repressor – results in transcription off.

34. Transcription Induction

35. Transcription Repression

36. Induction

37. Induction

38. Repression

39. If tryptophan low, the repressor does not bind tryptophan and thus cannot bind to operator. RNA polymerase can bind to the promoter. If tryptophan high, the repressor binds tryptophan, binds to the operator, where it blocks the binding of RNA polymerase to the promoter. Repression

40. lac operon

41. Lac Operon http://www.people.virginia.edu/~rjh9u/lacoperonanim.html

42. Catabolite Repression: Glucose Effect

43. Enzymatic Level Control • Enzymes are transcribed and translated. • Feedback inhibition of allosteric enzymatic reactions.

44. Allosteric Enzymes allosteric inhibitor changes the conformation of the enzyme, distorting the active site and reducing the ability to catalyze the reaction.

45. Feedback Inhibition

46. Types of Feedback Enzyme Inhibition • Isoenzymes: two allosteric enzymes that carry out the same reaction, but are inhibited by different compounds. • Concerted: single enzyme has two allosteric inhibitor sites, each of which cause complete inhibition. • Sequential: more than one allosteric enzyme in sequential reactions. • Cumulative: single enzyme has two or more allosteric inhibitor sites – requires all inhibitors to achieve complete inhibition.

47. Types of Enzymatic Regulation

48. Differences Between Enzyme and Genetic-Level Control • Enzyme level control is fast and relatively quick to reverse, inefficient since unneeded enzymes are produced. • Genetic level control is slow and relatively slow to reverse, efficient for long time control.

49. Transport • Energy-independent transport • simple (passive) diffusion of small and hydrophobic molecules • facilitated diffusion of larger molecules • Energy-dependent transport • occurs against a concentration gradient • uses transmembrane proteins

50. The relative permeability of a synthetic lipid bilayer to different classes of molecules. The smaller the molecule and, more important, the fewer its favorable interactions with water (that is, the less polar it is), the more rapidly the molecule diffuses across the bilayer. Note that many of the molecules that the cell uses as nutrients are too large and polar to pass through a pure lipid bilayer.