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Midterm Policies

Midterm Policies. Covers: Enzymes through Glycolysis Location: If taking midterm in other lecture go directly to the overflow room. Scientific Calculators Only, No Graphing Calculators Bring IDs Come up to TA to ask a question Restroom Policy:

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Midterm Policies

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  1. Midterm Policies • Covers: Enzymes through Glycolysis • Location: • If taking midterm in other lecture go directly to the overflow room. • Scientific Calculators Only, No Graphing Calculators • Bring IDs • Come up to TA to ask a question • Restroom Policy: • Bring exam up to TA, 1 person gone at a time

  2. Office Hour Changes: • This week ONLY • Tuesday 12-2p (Young 4077A) • Canceled: Fri 10-11am • Additional: Thurs 4-6pm • Room: Boelter 5440

  3. Properties of Enzymes • Biological Catalysts • Thermodynamically favorable reactions • Kinetically unfavorable reactions • Higher reaction rates (catalytic power) • Milder reaction conditions • Greater reaction specificity • Capacity for regulation

  4. Properties of Enzymes • Active sites • Stabilize transition states • Geometric and Chemical Complementarity • Probe using good substrates, or good inhibitors; and direct modification or mutation • Cofactors • Metal Ions • Cosubstrates • Prosthetic groups

  5. Catalytic mechanisms • Proximity and orientation effects • Acid-base catalysis • His, Ser, Cys, Tyr, Lys, Arg, Glu, Asp • Covalent catalysis • His, Asp, Cys, Ser, Lys • Metal ion catalysis • Preferential binding (stabilization) of the transition state

  6. Serine proteases • Substrate binding pocket • Catalytic triad: • Serine • Histidine • Aspartate • Preferential binding of the transition state

  7. Enzyme kinetics • Michaelis-menton Kinetics • Saturation kinetics • Assumption/Set up • Initial velocity; Catalysis is rate limiting • Steady state • [S]>>>>>>[E]  [S]>>>>>>>[ES] • [Etotal] = [Efree] + [ES] • Vmax; KM; KCAT; Efficiency

  8. Enzyme inhibitors

  9. Enzyme inhibitors

  10. Enzyme regulation • Amount • Inducible vs Repressible • Transcriptional Repressors vs Activators • Activity • Covalent (phosphorylation) • Non-covalent (allosteric regulators) • Rationale • Biological Efficiency, and flexibility • Competing reactions

  11. Metabolic pathways • Thermodynamics • Standard: Go’ = -RTln[Keq] • In Cell : G= Go’ + RTln[Products/Reactants] • Opposing Pathways • Both thermodynamically favorable • Potential Futile cycle • Most steps reversible • Rate limiting step(s) irreversible and regulated

  12. Metabolic pathways • Elucidation • Accumulation of intermediates • Labeling of intermediates • Enzyme regulation, amount vs activity

  13. Glycolysis • Stage I : Preperatory phase (energy input) • Stage II: Payoff Phase (energy production) Glucose + 2 NAD+ + 2 ADP + 2 Pi 2 Pyruvate + 2 NADH + 2 H+ + 2 ATP

  14. Glycolysis • Most reactions • Near Equilibrium, readily reversible • Glycolysis and gluconeogenesis • Driven by coupling to favorable reaction or removal of products • Other reactions • Far from equilibrium (highly favorable) • Irreversible • Only glycolysis • Regulated

  15. Glycolysis: Each step • Rationale • Thermodynamics • Regulation?

  16. Anaerobic fates of NADH • Regeneration of NAD+ for glycolysis • Homolactic fermentation • In muscle cells undergoing vigorous exercise • Lactate dehydrogenase • Alcoholic fermentation • In yeast (making beer) • Pyruvate decarboxylase and alcohol dehydrogenase

  17. Gluconeogenesis • Pyruvate  Glucose • When there is no other source of glucose • Potential futile cycle with glycolysis • Regulated by same effector as glycolysis but in opposite manner. • Fructose-2,6-bisphosphate

  18. Fructose-2,6-bisphosphate Glycolysis (PFK) Gluconeogenesis (FbPase)

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