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Part II and Chapter 13

Part II and Chapter 13. Bioenergetics and Metabolism. Bioenergetics and Reactions. Key topics : Learning Goals. Thermodynamics applies to biochemistry Organic chemistry principles at work Some biomolecules are “high energy” with respect to their hydrolysis and group transfers

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Part II and Chapter 13

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  1. Part II and Chapter 13 Bioenergetics and Metabolism

  2. Bioenergetics and Reactions Key topics: Learning Goals • Thermodynamics applies to biochemistry • Organic chemistry principles at work • Some biomolecules are “high energy” with respect to their hydrolysis and group transfers • Energy stored in reduced organic compounds can be used to reduce cofactors such as NAD+ and FAD, which serve as universal electron carriers

  3. Metabolic Pathways Cooperate To: • Obtain Chemical Energy by: • a. Capturing Solar Energy, or • b. Oxidizing Energy Rich Chemicals from the Environment. • Convert Nutrient Molecules to metabolic intermediates, then monomers or waste products. • Polymerize monomers to polymers (proteins, carbohydrates, nucleic acids, lipids). • Synthesize and Degrade (turnover) biomolelcules.

  4. Anabolism and Catabolism

  5. Linear and Circular Pathways

  6. Metabolic Pathways

  7. Auto-Pathways

  8. Pathways Arranged as Multi-Protein Modules Flagella LPS Outer Membrane Peptidoglycan Cytoplasmic Membrane Glycolysis ATPase RNA

  9. 5 Main Classes of Metabolic Reactions • Oxidation-Reduction Reactions • Reactions that Make or Break Carbon-Carbon Bonds • Internal Rearrangements, Isomerizations, Eliminations. • Group Transfer Reactions. • Free Radical Reactions.

  10. Chapter 13 Bionergetics ATP

  11. Showed that Respiration Was Oxidation of Carbon and Hydrogen…thus began Thermodynamics

  12. Laws of Thermodynamics • First Law – for any change, the energy of the universe remains constant; energy may change form or it may be transported, but can not be created or destroyed. • Second Law – The Entropy Law can be stated 3 ways: • 1. Systems tend from ordered to disordered. • 2. Entropy can remain the same for reversible processes but increases from irreversible processes. • 3. All processes tend towards equilibrium. • Everything  Equilibrium = Death. • Third Law – Entropy goes to zero when ordered substances approach absolute zero = 0oK

  13. Thermodynamics Gibbs Free EnergyG and ΔG EnthalpyH and ΔH EntropyS and ΔS ΔG = ΔH - TΔS

  14. Biochemistry Uses ΔGo’ Not ΔGo Standard Conditions (all reactants and products at 1M, gases at 1 atm, Temp = 25C) are Not Biological Conditions So, ΔGo’ takes out water (55.5M), and [H+] is set at pH 7 (not 1M which would be pH=0) and for humans ΔGo’ uses 37oC (310 K), but for bacteria ΔGo’ uses 25oC (298 K)….or the temperature of the environment. ΔGo’ = - RT lnKeq You should be able to do EOC Problems 2 and 3 easily EOC Problem 6: the difference between ΔGo’ and ΔG.

  15. Free energy, or the equilibrium constant, measure the direction of processes

  16. ΔGo’s Are Additive Hexokinase Rxn: Glucose + ATP  Glucose-6-P + ADP Glucose + Pi  Glucose-P + H2O ΔGo’ = 13.8 kJ/mole ATP + H2O  ADP + Pi ΔGo’ = -30.5 kJ/mole Overall = ΔGo’ = -16.7 kJ/mole Exergonic ! So: K’eq = 7.8 x 102 EOC Problems 9 and 12: the ΔGo’ for 2 coupled reactions.

  17. Biochemical Pathways Have Evolved To: • Use reactions that are relevant to metabolic systems: • Makes use of available substrates – with reaction rates that are NOT slow (have too high activation energies even with enzymes!) to produce useful products (which are themselves substrates). And, • Maximize Rates • Evolution’s Toolbox: reactions that work. • : circumvent “impossible” reactions. • : most reactions in organic chemistry occur in biology, except one, the Diels Alder Rxn…but we will see about that.

  18. You be a radical ! You be inonic !

  19. Rich in electrons  donate electrons Electron poor  suck up electrons from donors

  20. The Importance of Carbonyls Nucleophile Electrophile Imines are like carbonyls Here the carbonyl is an electrophile

  21. Making and Breaking Single Bonds

  22. Isomerations are Internally Complex

  23. The Classic Redox Reaction

  24. ATP Hydrolysis

  25. Energy Charge [ATP] + ½ [ADP] [ATP] + [ADP] + [AMP] Energy Charge =

  26. Energy Charge Why the ½ [ADP] ??? It is because of Adenyl Kinase: ADP + ADP ATP + AMP

  27. NucleotideConc, μMNucleotideConc, μM ATP 3,000 GTP 923 ADP 250 GDP 128 AMP 105 GMP 20 dATP 175 dGTP 122 dTTP 77 dCTP 65 UTP 894 CTP 515 cAMP 6 cGMP nd ppGpp 31 NAD+ 790 NADP 54 NADH 16 NADPH 146 FAD 51 FMN 88 AcCoA 231 SuccCoA 15 Nucleotide Intracellular Concentrations* in Salmonella enterica subsp Typhimurium from Bochner and Ames, 1982, J. Biol. Chem 257:9759-9769

  28. Magnesium Stabilizes Tri- and Di-phosphates EOC Problem 19: How much ATP is used in a human/day. EOC Problem 20: About turn over of the α and β phosphates (can you located them above?).

  29. Pyruvate Kinase

  30. 1,3-Bisphosphoglycerate has More Energy Than ATP

  31. Phosphocreatine Is Store of Energy in Muscle

  32. What About Actual ΔG ? ΔG = ΔG’o + RT ln([products]/[substrates]) This is the real, biological ΔG in a cell !! At 25oC RT = 2.48 kJ/mole (2.5 kJ/mole) At 37oC RT = 2.58 kJ/mole (2.6 kJ/mole) We will be doing this a lot later on !

  33. Doing Worked Example 13-2 Using E. coli ΔG = ΔGo’ + RT ln [ADP][Pi]/[ATP] ΔG = -30.5 kJ/mole + [ (8.315 J/mole.K)(310K) ln(1.04mM)(7.9mM)/7.9 mM] ΔG = -30.5 kJ/mole + 2.58 kJ/mole (-6.8) ΔG = -30.5 kJ/mole + (-17.6) ΔG = -48.1 kJ/mole Note: Calculate mM such as 1.04mM = 1.04 x 10-3M In the text for the Human Erythrocyte it works out to ΔG = -52 kJ/mole

  34. Acetyl-CoA (Thiol-ester) Has the Energy of ATP! EOC Problem 21: Cleavage of ATP to AMP + PPi…..why is this different (see Table 13-6 above). (What DNA enzyme did the same? It’s in Chapter 8)

  35. Enzyme Reaction Phosphorylation Intermediates Used to form C-N Bonds

  36. Phosphates: Ranking by the Standard Free Energy of Hydrolysis Phosphate can be transferred from compounds with higherΔG’ to those with lowerΔG’. Reactions such as PEP + ADP => Pyruvate + ATP are favorable, and can be used to synthesize ATP.

  37. Nucleoside Diphosphate Kinase makes NTP’s from ATP and NDP’s

  38. Carbon Redox – Watch the Red Dots (Electrons)

  39. Emf or Eh or Eo

  40. EOC Problem 24: Respiratory chain thermodynamics (we will do this in Chapter 19)…learn it well now!

  41. Calculations Differences between half cells…Example of electron transfer from NADH to cytochrome-b: NADH Eo’ = -.32 v Cyt-b Eo’ = 0.077 v ΔEo’ =Eo’oxidized – Eo’ reduced = 0.077v – (-0.32v) ΔEo’ = 0.397v

  42. Further Calculations What is the ΔG’o for oxidation of NADH by cytochrome-b ΔG’o = - nℱΔEo’ Faraday Constant = 96,480 J/v.mole ℱ = 96.5 kJ/v.mole ΔG’o = - (2) 96.5 kJ/v.mole (0.397v) = - 77 kJ/mole What about the real ΔE ?...and then ΔG ! ΔE = ΔE’o + (RT/nℱ) ln ([products]/[substrates]) EOC Problem 25 and 26 are all about this.

  43. NAD+ + 2e- + 2H+ NADH + H+

  44. Lactic Acid Dehydrogenase = LDH Rossmann fold, a structural motif in Dehydrogenases

  45. Vitamin Niacin is Made from W and Needs to be Amidated for NAD+

  46. FMN and FAD

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