Bioenergetics and High-Energy Compounds

Bioenergetics and high-energy compounds

Department of Medical Chemistry and Clinical Biochemistry 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital

2017 Bioenergetics

how organisms gain, convert, store and utilize energy Gibbs free energy

G = H − TS ⇒ ∆G = ∆H − T∆S = Qp − T∆S

G decrease in a biological process represents its maximum recoverable work.

equilibrium: ∆G = 0 spontaneous (exergonic) process: ∆G < 0 (it can do work) endergonic process: ∆G > 0 Gibbs free energy

one of the thermodynamic potentials no information on the rate – it is given by the mechanism (im-)possibility of a process given only by the initial and final states a catalyst (enzyme) can accelerate equilibrium aainment, not change its state ⇒ possibility of coupling = ∆H depends on temperature: equilibrium: T ∆S

∆H ∆S ∆G = ∆H − T∆S − + Both enthalpically favored (exothermic) and entropically favored. Spontaneous (exergonic) at all temperatures. − − Enthalpically favored but entropically opposed. Sponta- = ∆H neous only at temperatures below T ∆S . + + Enthalpically opposed (endothermic) but entropically fa- = ∆H vored. Spontaneous only at temperatures above T ∆S . + − Both enthalpically and entropically opposed. Unspontaneous (endergonic) at all temperatures. Rewrien from Voet, D., Voet, J. G.: Biochemistry, John Wiley & Sons, Inc., 2011 (4th edition) Chemical equilibria

Reaction a A + b B c C + d D [C]c[D]d ∆G =∆ G0 + RT ln [A]a[B]b

(∆G0 = standard G change of the reaction) constant term — depends only on the reaction variable term — depends on temperature and concentrations of reactants and products

Equilibrium

∆G = 0 c d [C] [D] −∆G0 ⇓ K = = e RT eq [ ]a[ ]b 0 A B ∆G = −RT ln Keq

0 ∆G and Keq directly related 0 −1 10-fold change in Keq changes ∆G by 5.7 kJ mol Free energy changes

0 X 0 X 0 ∆G = ∆Gf (products) − ∆Gf (reactants)

0 0 ∆Gf = ∆G of formation

0 −1 0 −1 Compound ∆Gf (kJ mol ) Compound ∆Gf (kJ mol ) acetaldehyde 139.7 glyceraldehyde-3-phosphate2– 1285.6 acetate 369.2 H+ 0.0 a acetyl-CoA 374.1 H2 (g) 0.0 3– cis-aconitate 920.9 H2O (l) 237.2 3– CO2 (g) 394.4 isocitrate 1160.0 2– CO2 (aq) 386.2 α-ketoglutarate 798.0 – – HCO3 587.1 lactate 516.6 3– citrate 1166.6 l-malate2– 845.1 dihydroxyacetone2– 1293.2 OH– 157.3 ethanol 181.5 oxaloacetate2– 797.2 fructose 915.4 phosphoenolpyruvate3– 1269.5 2– fructose-6-phosphate 1758.3 2-phosphoglycerate3– 1285.6 4– fructose-1,6-bisphosphate 2600.8 3-phosphoglycerate3– 1515.7 2– fumarate 604.2 pyruvate– 474.5 α-d-glucose 917.2 succinate2– 690.2 2– glucose-6-phosphate 1760.3 succinyl-CoA 686.7a a for formation from free elements + free CoA Rewrien aer Voet, D., Voet, J. G.: Biochemistry, John Wiley & Sons, Inc., 2011 (4th edition) Free energy changes

standard state activity 1 mol l−1 25 ◦C 1 bar biochemical standard state water activity = 1 pH = 7 substances undergoing acid-base dissociation: c = total c of all species at pH = 7 Coupled reactions

A + B C + D ∆G1

D + E F + G ∆G2

A + B + E C + F + G ∆G3 = ∆G1 + ∆G2 < 0

Glucose phosphorylation: Glc + ATP Glc-6- P + ADP

endergonic reaction: glucose + P glucose-6- P ∆G00 = 13.8 kJ mol−1 exergonic reaction: 00 −1 ATP + H2O ADP + P ∆G = −30.5 kJ mol coupled reaction: Glc + ATP Glc-6- P + ADP ∆G00 = −16.7 kJ mol−1 Redox potential also oxidation-reduction (reduction) potential expresses the substance’s readiness to accept electrons n – ox + e red (half-cell) Voet, D., Voet, J. G.: Biochemistry, John Wiley & Sons, Inc., 2011 (4th edition) n e– Aox + Bred Ared + Box

Nernst equation

[A ][B ] ∆G = ∆G0 + RT ln red ox [Aox][Bred] ∆G = −nF ∆E

RT [red] RT [A ][B ] E = E0 − ·ln ⇒ ∆E = ∆E0 − ·ln red ox nF [ox] nF [Aox][Bred] Redox potential

E as an energy scale

Reduced form Oxidized form E0´(V) ΔG0´ acetaldehyde acetate -0,60 – values higher + H2 2H -0,42 (reductant)

isocitrate 2-oxoglutarate + CO2 -0,38 glutathione-SH glutathione-SS -0,34 + + n

NADH + H NAD -0,32 n o o i i t t c

glyceraldehyde-3-phosphate + H3PO4 1,3-bisphosphoglycerate -0,28 c a a e e r r

FADH2 FAD -0,20 c c i i n n

lactate pyruvate -0,19 o

– – o g

+ne –ne g r r e

malate oxalacetate -0,17 e d x n e cytochrome b (Fe2+) cytochrome b (Fe3+) 0,00 e succinate fumarate +0,03 dihydroubiquinone ubiquinone +0,10 cytochrome c (Fe2+) cytochrome c (Fe3+) +0,26

H2O2 O2 +0,29 + values

H2O ½ O2 +0,82 (oxidant) lower Voet, D., Voet, J. G.: Biochemistry, John Wiley & Sons, Inc., 2011 (4th edition)

The actual direction of the reaction depends also on the [red]/[ox] ratio (and/or other factors) Redox potential

E0 = 0 V for standard hydrogen half-reaction (electrode) H+ at pH0, 25 ◦C, 1 bar in equilibrium with Pt-black electrode saturated with H2 pH = 7 ⇒ E00 = −0.421 V High-energy compounds

contain “high-energy bond” hydrolyzed to drive endergonic reactions ATP a central role (universal “energy currency” of the cell) 3 phosphoryl groups bound by one phosphoester and

two phosphoanhydride bonds NH2 phosphoanhydride phosphoester N bonds bond N O O O – O Pγ O Pβ O Pα O O N N O– O– O– H H H H OH OH adenosine AMP ADP

ATP Redrawn according to Voet, D., Voet, J. G.: Biochemistry, John Wiley & Sons, Inc., 2011 (4th edition) ATP

R1 O P + R2 OH R1 OH + R2 O P phosphoryl transfer reaction – enormous metabolic significance

0 −1 ATP + H2O ADP + P ∆G = −30.5 kJ mol 0 −1 ATP + H2O AMP + P P ∆G = −45.6 kJ mol 0 −1 P P + H2O 2 P ∆G = −19.2 kJ mol

kinetic stability, thermodynamic instability (high |−∆G0|) cell energy charge (usually 0.8–0.95) [ ] + 1 [ ] ATP 2 ADP [ATP] + [ADP] + [AMP]

adenylate kinase: ATP + AMP 2 ADP ATP is formed using more exergonic reactions Coupled reactions

A B ∆G00 = 16.7 kJ mol−1

0 [B] −∆G −3 = Keq = e RT = 1.15 · 10 [A]

+ A + ATP + H2O B + ADP + P + H ∆G00 = −13.8 kJ mol−1

[B] [ADP][ P ] 2 Keq = · = 2.67 · 10 [A] [ATP] at equilibrium:

[B] [ATP] 2 5 = Keq = 2.67 · 10 · 500 = 1.34 · 10 [A] [ADP][ P ] the equilibrium B/A ratio is 108times higher! n ATP molecules hydrolyzed ⇒ the ratio is 108ntimes higher! ATP consumption

“low-energy” phosphorylated compounds

NTP interconversions formation of CTP, GTP, UTP, dATP, dCTP, dGTP, dTTP nucleoside diphosphate kinase ATP + NDP ADP + NTP

processes based on protein conformational changes protein folding active transport movements ATP

ATP formation substrate-level phosphorylation oxidative phosphorylation (photophosphorylation) adenylate kinase reaction phosphagens

ATP turnover average adult resting person about 3 mol h−1 (1.5 kg h−1), i.e. about 40 kg d−1 strenuous activity – up to 0.5 kg min−1 “High-energy bonds”

phosphoanhydrides resonance stabilization higher solvation energy of the hydrolysis products electrostatic repulsion

– – – O O O O O– O– + P – P – P + P – P + P HO O HO O HO O HO O RO – – – – O O O O O O O– O– Redrawn from Berg, J. M.,Gao, G. Tymoczko, J. Jr., J.Biochemistry, L., W. H. Stryer, Freeman L.: and Company, 2012 (8th edition) other anhydrides phosphosulphates, acylphosphates carbamoylphosphate phosphoguanidines (phosphagens) – phosphocreatine, phosphoarginine enol phosphates thioesters there are no high-energy compounds as well!

High-energy compounds

NH2

N N O O O CH3 O O O O H – – H2C C O P O O P N C N CH2 C –O P O P O P O N O N – – + – O O NH2 O O– O– O– H H H H acetylphosphate (acylphosphates)phosphocreatine (phosphamides) OH OH adenosine triphosphate (ATP) O −O P O− NH2 O O N N O O H2C C C CoA S COCH3 – – O O P O P O O N N O– O– H H phosphoenolpyruvate (enolphosphates)acetylcoenzyme A (thioesters) H H OH OH adenosine diphosphate (ADP) Energy metabolism scheme

alternative amino acids fatty acids sugars pathways lactate NADH NAD+ ethanol propionate butyrate butanol fermentative formate NADH + glycolysis NAD H + 2 β-oxidation NAD regeneration CO2 acetate 2,3-butandiol pyruvate succinate

oxidative decarboxylation

citric acid Calvin cycle cycle Ac~S–CoA

CO2

NADH NAD+ NADPH NADP+

hν photosynthetic ADP respiratory chain O electron transport ADP 2 chain oxidative phosphorylation H O photophosphorylation ATP 2 ATP The End

konec – the end Thank you for your aention! one of the thermodynamic potentials no information on the rate – it is given by the mechanism (im-)possibility of a process given only by the initial and final states a catalyst (enzyme) can accelerate equilibrium aainment, not change its state ⇒ possibility of coupling Gibbs free energy = ∆H depends on temperature: equilibrium: T ∆S

0 0 ∆Gf = ∆G of formation Free energy changes

ATP Redrawn according to Voet, D., Voet, J. G.: Biochemistry, John Wiley & Sons, Inc., 2011 (4th edition) phosphoanhydrides resonance stabilization higher solvation energy of the hydrolysis products “High-energyelectrostatic bonds” repulsion

Reduced form Oxidized form E0´(V) ΔG0´ acetaldehyde acetate -0,60 – values higher + H2 2H -0,42 (reductant) isocitrate 2-oxoglutarate + CO2 -0,38 glutathione-SH glutathione-SS -0,34 + + n

NADH + H NAD -0,32 n o o i i t t c glyceraldehyde-3-phosphate + H3PO4 1,3-bisphosphoglycerate -0,28 c a a e e r r

FADH2 FAD -0,20 c c i i n n lactate pyruvate -0,19 o

– – o g

+ne –ne g r r e malate oxalacetate -0,17 e d x n e cytochrome b (Fe2+) cytochrome b (Fe3+) 0,00 e succinate fumarate +0,03 dihydroubiquinone ubiquinone +0,10 cytochrome c (Fe2+) cytochrome c (Fe3+) +0,26

H2O2 O2 +0,29 + values

H2O ½ O2 +0,82 (oxidant) lower alternative amino acids fatty acids sugars pathways lactate NADH NAD+ ethanol propionate butyrate butanol fermentative formate NADH + glycolysis NAD H + 2 β-oxidation NAD regeneration CO2 acetate 2,3-butandiol pyruvate succinate

oxidative decarboxylation

citric acid Calvin cycle cycle Ac~S–CoA

CO2

NADH NAD+ NADPH NADP+

hν photosynthetic ADP respiratory chain O electron transport ADP 2 chain oxidative phosphorylation H O photophosphorylation ATP 2 ATP