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1 BIS ffice ours TUE (2-3 pm) Rebecca Shipman WED (9:30-10:30 am) TUE (12-1 pm) Stephen Abreu TUR (12-1 pm) FRI (9-11 am) Steffen Abel

2 Lecture 2 Topics Finish discussion of thermodynamics (ΔG, ΔE) ATP as an universal carrier of chemical energy Role of enzymes and co-factors

3 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 (Δ)( Rearrangement of bonds release or require Δ (- Δ, exothermic; + Δ, endothermic) Free Gibbs Energy (ΔG)( ΔG = Δ TΔS ΔG = ΔG o + RTlnQ ΔG = nfδe Review

4 Reduction Potential (E) Many steps in metabolism are redox reactions (e - transfer) 1. Direct (e - ) 2. ydrogen () 3. ydride ( - ) 4. Combination with A oxidized + B reduced A reduced + B oxidized Two half-reactions 1. A oxidized + e - A reduced 2. B oxidized + e - B reduced Determine E (E o, Nernst Equation) ΔE = E xidant (A) E Reductant (B) ΔG = nfδe Review

5 Chemolithotrophs Fully or partially reduced inorganic compounds (e.g., 2, N 3, N 2-, 2 S, S 2 2-3, S, Fe 2+ ) Initial Electron Donor Chemoorganotrophs rganic compounds (e.g., sugars, amino or fatty acids, organic acids, etc.) e - E Red Energy Metabolism ΔE = E x E Red ΔE = ΔG/nF Terminal Electron Acceptor (e.g., N 3-, N 2-, S 2-4, Fe 3+, C 2, partially oxidized organic compounds) Anaerobes 2 Aerobes e - E x p. 7

6 rganic Compound E o xidized Compound ( V) ( V) ΔG Nitrate (N 3- ) Nitrite (N 2- ) ΔG ( V) ( V) 2 1/2 2 p. 7

7 Food C Reduced Carbon Respiration umans and Animals ENERGY eterotrophic Metabolism p. 8

8 Plants and Photosynthetic Bacteria Autotrophic Metabolism LIGT Photosynthesis Fossil Fuels Day C Reduced Carbon Night Respiration ENERGY Food p. 8

9 Plants and Photosynthetic Bacteria Autotrophic Metabolism LIGT Photosynthesis Fossil Fuels Day C Reduced Carbon Night Respiration ENERGY Food C Reduced Carbon Respiration umans and Animals ENERGY eterotrophic Metabolism p. 8

10 JACB VAN RUYSDAEL (1652) 2 2 2{ 2 } + 2 2e ( 0.7V) 2 (+0.8V) 2

11 ydrolysis Reactions of Phosphate Esters and Anhydrides Phosphate esters R P R + P p. 9

12 Phosphate anyhydride R P P R P + P p. 9

13 Acyl phosphate R C P R C + P p. 9

14 ATP (Adenosinetriphosphate),, ADP, and Their Mg 2+ Complexes Phosphoester bond Phosphoanhydride bonds N N 2 N (Adenine) N N - P - P - P Mg 2+ - (Ribose) MgATP p. 10

15 Phosphoanhydride bond N N 2 N N N - P - P - Mg 2+ MgADP p. 10

16 Electrostatic bond strain Ionization of ADP product Resonance stabilization of Pi (see Table 4) ATP

17 Creatine Phosphate and Arginine Phosphate Creatine-P + ADP ATP + Creatine (K eq = 1) P N + C N N C N 2 + Pi N C 3 N C 3 C C Creatine Phosphate (Mammals) Creatine p. 11

18 Creatine Phosphate and Arginine Phosphate P N C N 2 + N P N C N 2 Arg N C 3 Met C N 3 ATP C Gly C Arginine Phosphate (Crustaceans) Creatine Phosphate p. 11

19 Compound ΔG o (kj/mol) Phosphoenolpyruvate (Pyruvate + Pi) Transfer Potential Type of Compound Enolic phosphate Cause for ΔG o of ydrolysis Tautomerization of product (Pyr); Resonance stability of Pi Table 4: Standard Free Energies of ydrolysis 1,3-Bisphosphoglycerate (3-PGA + Pi) Acyl phosphate Ionization of product (3-PGA); Resonance stability (Pi, 3-PGA) Phosphocreatine (Creatine + Pi) Guanidine phosphate Resonance stability of product (creatine) Pyrophosphate (PPi) (Pi + Pi) Phosphoric acid anhydride Electrostatic bond strain in PPi substrate; Ionization and resonance stability of Pi group Compounds with decreasing ΔG o of hydrolysis ATP (ADP + Pi) Same as PPi Same as PPi ADP (AMP + Pi) Same as PPi Same as PPi Acetyl-CoA (and other thioesters) (Acetate + CoA-S) Thioester No resonance stabilization of Acetyl-CoA; Ionization and resonance stabilization of acetate Glucose-1-P (Glucose + Pi) Phosphate semiacetal Bonds in glucose-1-p not that strained Glucose-6-P (Glucose + Pi) Phosphate ester Bonds in glucose-6-p not strained AMP (Adenosine + Pi) Phosphate ester Bonds in AMP not strained; Adenosine does not ionize Phosphate (Pi) Phosphate p. 4

20 Catabolism ΔG = Δ TΔS Coupling (<100%) ADP ATP ΔG = Δ TΔS Coupling (<100%) Anabolism

21 Enzymes coordinate many reactions into metabolic networks (pathways) via shared intermediates integrate ΔG s and provide specificity do NT change ΔG of a reaction!!! but, they decrease its activation energy inrease rate (10 7 to fold) of attaining equilibrium (ΔG is not a kinetic constant) rate (flux) can be regulated

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24 N 3 C C The 20 Protein Amino Acids (constituents of enzymes) R L-Amino Acid

25 A. Nonpolar,, Aliphatic R-GroupsR 2 N C C 2 N C C 2 N C C C C 3 C 3 C C 3 Glycine Gly, G Valine Val, V C 3 Leucine Leu, L 2 N C C C 2 N C C C C 3 N S C 3 Methionine Met, M Proline Pro, P C 3 Isoleucine Iso, I p. 12

26 B. Aromatic R-GroupsR 2 N C C 2 N C C 2 N C C N Tryptophan Trp, W Tyrosine Tyr, Y Phenylalanine Phe, F p. 12

27 C. Polar, Uncharged R-GroupsR 2 N C C 2 N C C 2 N C C S C C 3 C N 2 Cysteine Cys,C Threonine Thr, T Asparagine Asn, N 2 N C C 2 N C C C N 2 Serine Ser, S Glutamine Gln, Q p. 13

28 D. Positively Charged R-GroupsR 2 N C C 2 N C C 2 N C C N N N istidine is, C N N 2 Arginine Arg R N 2 Lysine Lys, K E. Negatively Charged R-GroupsR 2 N C C 2 N C C C Aspartate Asp, D C Glutamate Glu, E p. 13

29 F. Peptide Bond G. Isopeptide Bond R 1 R 2 R 1 N 3 3 N C C N C C - 3 N C C N ( ) 4 C C - Lysine R 2 3 N C C N C C - C - Glutamate p. 14