Lecture 2 (2009)

Lecture 2 (2009) - Lecture 2 Topics Finish discussion of...

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Unformatted text preview: Lecture 2 Topics Finish discussion of thermodynamics (G, E) ATP as an universal carrier of chemical energy Role of enzymes and co-factors Summary of Lecture 1 Need for metabolism Provides building blocks for regeneration Energy conversion compatible with C-based life Chemical bonds as stores of energy (H) Rearrangement of bonds release or require H (- H, exothermic; + H, endothermic) Free Gibbs Energy (G) G = H TS G = Go' + RTlnQ G = nFE Review Reduction Potential (E) ... yet another way to express G... Metabolic reactions are often redox reactions, involving transfer of electrons from a donor to an acceptor 1. Direct combination with oxygen (X X + O=O 2. Transfer of the hydride anion (H--H, or H- + H+) 3. Transfer of hydrogen (H, or e- + H+) 4. Direct transfer (e-) 2O X) Lecture 1 Redox reactions can be written as two "half-reactions" (by convention: each is written in the direction of the reduction!) convention reduction Aoxidized + Breduced 1. Aoxidized + e2. Boxidized + e- Areduced + Boxidized Areduced Breduced Electronegativities (Tab. 1) can predict direction of e- transfer See p. 6 Lecture 1 Question: Which "half-reaction" has the higher affinity for electrons at standard conditions ? Reference Electrode: H+ + eH2 "half-reaction" (1M each) (Eo= 0.00 V) Test Electrode: By convention: convention A+ + eA (Eo'= ??? V) "half-reaction" (1M each) If e- flow from reference to test ("test" is stronger e- acceptor): Eo > 0 (+V) If e- flow from test to reference ("test" is weaker e- acceptor): Eo < 0 (- V) See p. 6 Lecture 1 Table 3: Standard Reduction Potentials for Biological "Reduction Half-Reactions" Half- Reactions" "Half-Reaction" 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. 38. (written as reduction) + + + + + + + + + + + + + + + Eo(V) 1.0 0.67 0.58 0.57 0.43 0.42 0.42 0.38 0.35 0.34 0.32 0.32 0.29 0.29 0.24 0.23 0.22 0.22 0.20 0.18 0.17 0.02 0.00 0.03 0.06 0.08 0.22 0.25 0.28 0.29 0.30 0.35 0.37 0.42 0.43 0.77 0.82 1.10 Excited(Chlorophyll)2* Succinate + CO2 + 2H+ + 2e-Ketoglutarate + H2O Acetaldehyde + H2O Acetate + 2H+ + 2eSO32- + H2O SO42- + 2H+ + 2e3+ Ferredoxin (Fe2+) Ferredoxin (Fe ) + e+ H2 (at pH 7.0) 2H + 2e Formate CO2 + H+ + 2e-Ketoglutarate + CO2 + 2H+ + 2eIsocitrate Acetoacetate + 2H+ + 2e-Hydroxybutyrate 2 Cysteine Cystine + 2H+ + 2eNADPH + H+ NADP+ + 2H+ + 2eNAD+ + 2H+ + 2eNADH + H+ + Dihydrolipoic acid Lipoic acid + 2H + 2e3-PGA + Pi 1,3-bisPGA + 2H+ + 2eH2S S + 2H+ + 2e2 Glutathione (reduced) Glutathione + 2H+ + 2eFADH2 (Flavoprotein 0.003-0.091) FAD + 2H+ + 2eFMNH2 FMN + 2H+ + 2eEthanol Acetaldehyde + 2H+ + 2eLactate Pyruvate + 2H+ + 2eMalate Oxaloacetate + 2H+ + 2eButyryl-CoA Crotonyl-CoA + 2H+ + 2e2H+ + 2eH2 (at standard conditions, 1 M = pH 0) Succinate2Fumarate2- + 2H+ + 2e+ UQH2 UQ + 2H + 2e Cytochrome b (Fe2+) Cytochrome b (Fe3+)+ e3+ Cytochrome c1 (Fe2+) Cytochrome c1 (Fe )+ e Cytochrome c (Fe2+) Cytochrome c (Fe3+)+ eRieske Fe-S (Fe2+) Rieske Fe-S (Fe3+)+ e3+ Cytochrome a (Fe2+) Cytochrome a (Fe )+ e + H2O2 O2 + 2H + 2e Cytochrome a3 (Fe2+) Cytochrome a3 (Fe3+)+ e3+ Cytochrome f (Fe )+ e Cytochrome f (Fe2+) + NO2 + H20 NO3 + 2H + 2e Photosystem P700 Fe3+ + eFe2+ + 2H20 O2 + 4H + 4e(Chlorophyll a)2 (Chlorophyll a)2+ + e- Direction of spontaneous electron flow. See p. 3 Reduction Potential E for each "Half-Reaction" (Nernst Equation) 1. Aoxidized + eAreduced E= Eo' RT [e- Acceptor, Aox] + nF ln [e- Donor, Ared] RT [e- Acceptor, Box] + nF ln [e- Donor, Bred] 2. Boxidized + e- Breduced E= Eo' E of Redox Reaction (Aox + Bred Ared + Box) E = EOxidant (A) EReductant (B) Relationship between E and G G = nFE E = G/nF Go' = nFEo' Eo' = Go'/nF See p. 6 Table 3: Standard Reduction Potentials Half-reaction (written as reduction by convention) Excited (Chlorophyll a)2* Acetate + 2H+ + 2eNAD+ + 2H+ + 2ePyruvate + 2H+ + 2e2H+ + 2eAcetaldehyde + H2O NADH + H+ Lactate Eo (V) ~ - 1.00 - 0.58 - 0.32 - 0.18 0.00 + 0.42 + 0.82 (Chlorophyll a)2 + 1.10 e- flow H2 (at standard conditions, 1M each, pH 0) NO2- + H2O 2H2O NO3- + 2H+ +2eO2 + 4H+ + 4e- (Chlorophyll a)2.+ + e- See p. 3 Metabolic "Life Styles" Chemolithotrophs Fully or partially reduced inorganic compounds (e.g., H2, NH3, NO2-, H2S, S2O32-, S, Fe2+) Chemoorganotrophs Organic compounds (e.g., sugars, amino or fatty acids, organic acids, etc.) e- ERed Initial Electron Donor Energy Metabolism Terminal Electron Acceptor (e.g., NO3-, NO2-, SO42-, Fe3+, CO2, partially oxidized organic compounds) Anaerobes O2 E = EOx ERed E = G/nF eAerobes EOx p. 7 Organic Compound Eo ' ( - 0.60 V) (+ 0.42 V) Oxidized Compound G Nitrite (NO2-) Nitrate (NO3-) G H 2O (+ 0.42 V) (+ 0.82 V) 1/2 O2 p. 7 Food CO2 H 2O O2 Reduced Carbon Respiration ENERGY Humans and Animals Heterotrophic Metabolism p. 8 Plants and Photosynthetic Bacteria Autotrophic Metabolism LIGHT Photosynthesis Day Fossil Fuels CO2 H2 O Night O2 Reduced Carbon Respiration ENERGY Food p. 8 Plants and Photosynthetic Bacteria Autotrophic Metabolism LIGHT Photosynthesis Day Fossil Fuels CO2 H2O Night O2 Reduced Carbon Respiration ENERGY Food CO2 H2O O2 Reduced Carbon Respiration ENERGY Humans and Animals Heterotrophic Metabolism p. 8 JACOB VAN RUYSDAEL (1652) 2H2O 2{H2} + O2 2e- + 2H+ (0.7V) ATP O2 (+0.8V) H2O Hydrolysis Reactions of Phosphate Esters and Anhydrides Phosphate esters O R O P OO+ H2O ROH + HO O P OO- p. 9 Phosphate anyhydride O R O P OO O P OO- + H2O R O O P OOH + HO O P OO- p. 9 Acyl phosphate O R C O O P OO- + H2O R O C OH + HO O P OO- p. 9 ATP (Adenosinetriphosphate), ADP, and Their Mg2+ Complexes Phosphoester bond Phosphoanhydride bonds N N O - NH2 N (Adenine) N O -O P OO O P O - O O P O O (Ribose) H OH H OH Mg2+ MgATP p. 10 NH2 Phosphoanhydride bond N N O N N O -O P O - O O P OH O H OH OH Mg2+ MgADP p. 10 The ATP "Gun" "Spring-loaded" phosphate "bullets" The gun is safe ("kinetically stable"), ... until you pull the trigger (to overcome "activation energy") Compound (hydrolyzed to) G ' (kJ/mol) o Transfer Potential Type of Compound Cause for G ' of Hydrolysis o Table 4: Standard Free Energies of Hydrolysis Phosphoenolpyruvate (Pyruvate + Pi) - 62.2 62.2 Enolic phosphate Tautomerization of product (Pyr); Resonance stability of Pi 1,3-Bisphosphoglycerate (3-PGA + Pi) - 49.6 49.6 Acyl phosphate Ionization of product (3-PGA); Resonance stability (Pi, 3-PGA) Phosphocreatine (Creatine + Pi) - 43.3 43.3 Guanidine phosphate Resonance stability of product (creatine) Pyrophosphate (PPi) (Pi + Pi) - 33.6 33.6 Phosphoric acid anhydride Electrostatic bond strain in PPi substrate; Ionization and resonance stability of Pi group Compounds with decreasing Go' of hydrolysis ATP (ADP + Pi) - 30.5 30.5 Same as PPi Same as PPi ADP (AMP + Pi) - 30.5 30.5 Same as PPi Same as PPi Acetyl-CoA (and other thioesters) (Acetate + CoA-SH) - 31.5 31.5 Thioester No resonance stabilization of Acetyl-CoA; Ionization and resonance stabilization of acetate Glucose-1-P (Glucose + Pi) - 20.7 20.7 Phosphate semiacetal Bonds in glucose-1-P not that strained Glucose-6-P (Glucose + Pi) - 13.9 13.9 Phosphate ester Bonds in glucose-6-P not strained AMP (Adenosine + Pi) - 9.2 9.2 Phosphate ester Bonds in AMP not strained; Adenosine does not ionize Phosphate (Pi) 0.0 0.0 Phosphate p. 4 Compound (hydrolyzed to) G ' (kJ/mol) o Transfer Potential Type of Compound Cause for G ' of Hydrolysis o Phosphoenolpyruvate (Pyruvate + Pi) - 62.2 62.2 Enolic phosphate Tautomerization of product (Pyr); Resonance stability of Pi "Phosphoryl"-group transfer potentials 1,3-Bisphosphoglycerate (3-PGA + Pi) - 49.6 49.6 Acyl phosphate Ionization of product (3-PGA); Resonance stability (Pi, 3-PGA) Phosphocreatine (Creatine + Pi) - 43.3 43.3 Guanidine phosphate Resonance stability of product (creatine) Pyrophosphate (PPi) (Pi + Pi) - 33.6 33.6 Phosphoric acid anhydride Electrostatic bond strain in PPi substrate; Ionization and resonance stability of Pi group Receive P~group ATP (ADP + Pi) - 30.5 30.5 Same as PPi Same as PPi ADP (AMP + Pi) - 30.5 30.5 Same as PPi Same as PPi Acetyl-CoA (and other thioesters) (Acetate + CoA-SH) - 31.5 31.5 Thioester No resonance stabilization of Acetyl-CoA; Ionization and resonance stabilization of acetate Donate P~group Glucose-1-P (Glucose + Pi) - 20.7 20.7 Phosphate semiacetal Bonds in glucose-1-P not that strained Glucose-6-P (Glucose + Pi) - 13.9 13.9 Phosphate ester Bonds in glucose-6-P not strained AMP (Adenosine + Pi) - 9.2 9.2 Phosphate ester Bonds in AMP not strained; Adenosine does not ionize Phosphate (Pi) 0.0 0.0 Phosphate p. 4 "High Energy" Substrates Cellular Macromolecules ATP + H2O G +G ADP + Pi Intermediates of Metabolism "Low Energy" Products G +G Enzymes (biological catalysts) ... do NOT change G of chemical reactions !!! but decrease their activation energies inrease the rate (107 to 1019-fold) of attaining equilibrium (G is not a kinetic constant!) reaction rates (flux) can be regulated provide specificity and couple reactions coordinate many reactions into metabolic networks (pathways) via shared intermediates A Large -G B F Small -G E OOC NH3 The 20 Protein Amino Acids H C R (constituents of enzymes) L-Amino Acid A. Nonpolar, Aliphatic R-Groups O H2N CH C H OH H2N O CH C CH CH3 CH3 OH H2N O CH C CH2 CH CH3 OH Glycine Gly, G O H2N CH C CH2 CH2 S CH3 HN OH O C Valine Val, V CH3 Leucine Leu, L O OH H2N CH CH CH2 C CH3 OH Methionine Met, M Proline Pro, P CH3 Isoleucine Iso, I p. 12 B. Aromatic R-Groups O H2N CH C CH2 OH H2N O CH C CH2 OH H2N O CH C CH2 OH HN Tryptophan Trp, W OH Tyrosine Tyr, Y Phenylalanine Phe, F p. 12 C. Polar, Uncharged R-Groups O H 2N CH C CH 2 SH OH H2 N O CH C CH OH CH 3 OH H 2N O CH C CH2 C O OH NH2 Cysteine Cys,C O H 2N CH C OH CH 2 OH H 2N O CH C CH2 CH2 C O NH2 Threonine Thr, T Asparagine Asn, N OH Serine Ser, S Glutamine Gln, Q p. 13 D. Positively Charged R-Groups O H2N CH CH2 C OH H2N O CH C CH2 CH2 CH2 N NH NH OH H2N O CH C CH2 CH2 CH2 NH OH Histidine His, H C NH2 Arginine Arg R CH2 NH2 Lysine Lys, K E. Negatively Charged R-Groups O H2N CH C CH2 C OH O OH O H2N CH C OH CH2 CH2 C O Aspartate Asp, D OH Glutamate Glu, E p. 13 F. Peptide Bond G. Isopeptide Bond R1 H 3N C H C O H N R2 C H COO- R1 H3N C H C O H N (CH 2)4 NH 3 C H COO- Lysine H H3N C COOCH 2 CH 2 O C N H R2 C H COO- Glutamate p. 14 Polar and charged side-chain terminal groups and carboxylate-arginine and carboxylate-carboxylate dyads Gutteridge and Thornton (2005) Understanding nature's catalytic toolkit. Trends Biochem Sci 30:622-629 pKa values of polar and charged amino acids Gutteridge and Thornton (2005) Understanding nature's catalytic toolkit. Trends Biochem Sci 30:622-629 Gutteridge and Thornton (2005) Understanding nature's catalytic toolkit. Trends Biochem Sci 30:622-629 CO-FACTORS (Non-protein moieties required for catalytic activity) 1. Metals Structural role (e.g., Mg2+) Catalytic role (e.g., Fe2+) 2. Co-enzymes Co-substrates Organic molecules (catalytic) - If transiently bound (e.g., ATP) Prosthetic group - If covalently bound (e.g., FAD) Must be regenerated if altered in reaction (by same or different enzyme) Most water-soluble vitamins are precursors of co-enzymes see p. 14/15 ...
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