PY4040 PhysChem 2021-22 wk7 Bioenergetics.pptx

PY4040: Introduction to Physical Chemistry for Pharmacy TW7: Introduction to bioenergetics Dr Gemma Shearman 1 Learning Outcomes • To be able to apply classical thermodynamics to living systems • To understand the role of energy transfer molecules in bioenergetics • To understand the role o...

PY4040: Introduction to Physical Chemistry for Pharmacy TW7: Introduction to bioenergetics Dr Gemma Shearman 1 Learning Outcomes • To be able to apply classical thermodynamics to living systems • To understand the role of energy transfer molecules in bioenergetics • To understand the role of coupled reactions in living systems Re-cap: • 2nd Law of Thermodynamics: spontaneous processes increase the entropy of the universe. -ve (exergonic) +ve (endergonic) 0 Predicting spontaneity ALWAYS spontaneous NEVER spontaneous At equilibrium Bioenergetics is the quantitative study of energy transformations in biological systems vs represents the CHANGE in GIBBS FREE ENERGY (of a reaction). represents the CHANGE in GIBBS FREE ENERGY (of a reaction) under STANDARD STATE CONDITIONS. Standard state conditions are: • 1 bar pressure (i.e. 1 x 105 Pa) NB not 1 atm! • For solutions: concentrations of 1 mol dm-3 • Temperature: often reported as 298.15 K, although this is not officially a standard state condition. ’ represents the CHANGE in GIBBS FREE ENERGY (of a reaction) under Thermodynamics vs Kinetics G (reactants) Gibbs free energy Remember: The sign of tells us in which DIRECTION the reaction would have to go to reach equilibrium (the "spontaneous" direction), but gives NO information about RATE at which reaction will go. G (products) ∆𝑟 𝐺 equilibrium Pure reactants Only KINETICS can tell you this! Pure products Equilibrium constant, Keq Q. If K >> 1, which side of the reaction is favoured? The equilibrium constant, Keq, describes the composition of a reaction mixture when at equilibrium: e.g. for a typical chemical reaction The equilibrium constant is given by: And… is related to Keq by: Relating and The change in Gibbs free energy for a reaction (not necessarily under standard conditions!) can be related to by: Where Q (the mass action ratio) is the ratio of products to reactants at a given point in time (here, let’s assume at the starting conditions)… i.e. = NB at equilibrium, Q = Keq hence ! Bioenergetics Bioenergetics: essential for understanding: • • • • how metabolic processes provide energy for the cell the structures of macromolecules how membrane transport processes occur all the fundamental processes that define biochemistry! Bioenergetics  All reactions/processes proceed spontaneously in whatever direction is required to achieve, or at least go toward, equilibrium; "spontaneous" direction is always toward equilibrium. Remember, although we can use bioenergetics to determine whether a process will occur spontaneously, bioenergetics gives us no information as to how fast the process will occur. Energy in the cell Many biochemical reactions are endergonic (not spontaneous, is positive)! These processes are often linked to exergonic processes that provide the ‘energy’ needed. The most common source of cellular energy is supplied by ATP (adenosine triphosphate). STRUCTURE NOT EXAMINABLE FOR PHYS CHEM phosphoester bond ATP phosphoanhydride bond ATP: Adenosine + 3 phosphoryl groups (PO32-) linked sequentially via a phosphoester bond, followed by two phosphoanhydride bonds STRUCTURE NOT EXAMINABLE FOR PHYS CHEM Thermodynamics of ATP hydrolysis ATP has a ‘large’ negative standard free energy change of hydrolysis. (NB: it isn’t actually that big at all, but it’s big enough to make a significant difference in biologically relevant reactions!). Where: Remember: ATP: adenosine triphosphate is as per but ALSO at pH 7! ADP: adenosine diphosphate so… AMP? Pi = orthophosphate, PO43- (also known as ‘inorganic phosphate’) Hydrolysis of ATP The chemical basis of the large, negative free energy change is: 1. The hydrolytic cleavage of the γ-phosphate anhydride bond relieves electrostatic repulsion in ATP. 2. The phosphate formed is stabilized by several resonance forms that are not possible in ATP. Hydrolysis of ATP 3. The ADP product, immediately ionizes, releasing H+ in a medium with low hydrogen ion concentration, pH 7. 4. ATP has a small solvation energy compared to the solvation energies of ADP, Pi and H+. Thus the products of hydrolysis are stabilized more by solvation than then reactant ATP. 1-2 3 Phosphoryl-transfer reactions Some coupled reactions: examples First step in metabolism of glucose: 1 2 glucose + Pi glucose-6-phosphate + H20 = +13.8 kJ / mol Overall reaction: ATP + H2O ADP + Pi Exergonic therefore ATP hydrolysis WILL = -30.5 kJ / mol drive the phosphorylation of glucose. ATP ADP glucose glucose-6-phosphate Some coupled reactions: examples Fatty acyl-Coenzyme A synthesis: 1 2 ATP AMP + 2Pi = -65.7 kJ / mol Overall reaction: Co-A-SH + Palmitate Palmitoyl-CoA = +31.4 kJ / mol Exergonic therefore ATP (double) hydrolysis WILL drive acyl-CoA synthesis. ATP AMP Co-A-SH + Palmitate Palmitoyl-CoA Biological redox reactions The transfer of electrons is equally as important as the transfer of phosphoryl groups. Oxidation is the loss of electrons, reduction is the gain of electrons… OILRIG! It is easy to tell of an organic compound has been oxidized or reduced. If an organic molecule gains oxygen or loses hydrogen is has been oxidized. If an organic molecule loses oxygen or gains hydrogen, then is has been reduced. Biological redox reactions Oxidation-reduction reactions (Redox reactions) must occur together. Electrons are transferred from the reducing agent to the oxidizing agent such that the reducing agent is oxidized and the oxidizing agent is reduced. Overall, Ecell needs to be positive (since DG = -nFE, where F = 96485 C mol-1) We also know that… Ecell = Ered - Eox Biological redox reactions e.g. Fe3+ + Cu+ Fe2+ + Cu2+ Can be described by the two half reactions (always given as reduction potentials): (1) Fe3+ + e- Fe2+ Eo = +0.77 V (2) Cu2+ + e- Cu+ Eo = +0.16 V For Ecell to be positive, Ecell = Ered - Eox = +0.77 - +0.16 = +0.61 V i.e. the half-cell where reduction occurs is (1) and oxidation occurs in (2). So… again, you can couple together two reactions (one in which oxidation occurs and one reduction) to drive a reaction forwards! Coenzymes as electron carriers NADH and NADPH: NAD+ and NADP+ undergo reversible reduction of the nictotinamide ring… (NAD = nicotinamide adenine dinucleotide) STRUCTURES NOT EXAMINABLE FOR PHYS CHEM Coenzymes as electron carriers NADH and NADPH: The vitamin niacin is the source of the nicotinamide moiety. The half reactions for the reduction potentials are: NAD+ + H+ + 2e- NADH NADP+ + H+ + 2e- NADPH Eo’ = −0.315 V Eo’ = −0.320V Both NAD and NADP are water soluble cofactors that move readily from enzyme to another. Coenzymes as electron carriers NADH and NADPH: • NAD generally functions in oxidations, usually in a catabolic pathway. • NADP generally functions in reductions, typically in an anabolic pathway. A few enzymes can use either NAD or NADP, but most are specific for one or the other. This functional specialization allows cells to maintain two pools of electron carriers with each pool having its own specific function. Coenzymes as electron carriers NADH and NADPH: The general reactions of these cofactors are: AH2 + NAD+ A + NADH + H+ A + NADPH + H+ AH2 + NADP+ The enzymes that catalyse these reactions are oxidoreductases, commonly called dehydrogenases. Coenzymes as electron carriers e.g. (part of) the mitochondrial electron transport chain NAD+ + H+ + 2e- NADH Eo’ = −0.315 V CoQ + 2H+ + 2e- CoQH2 Eo’ = +0.045 V In order for Eo’tot to be positive, the overall reaction must be: CoQ + H+ + NADH + 2e- CoQH2 + NAD+ + 2ei.e. CoQ + H+ + NADH CoQH2 + NAD+ Where Eo’tot = +0.045 - -0.315 = +0.37 V o o Your turn Q. Calculate for the reaction shown in Eqn 1. Q. The reaction: Glutamate + NH4+ glutamine (Eqn 1) is energetically unfavourable. What can you say about for this reaction? Glutamine however can be synthesized in cells by coupling this reaction with an energetically favourable reaction, such as the hydrolysis of ATP, in order to “drive” the process: ATP ADP + Pi (Eqn 2) (= -30.5 kJmol-1 ) For the overall reaction below, = -15.3 kJmol-1 : glutamate + NH4+ + ATP glutamine + ADP + Pi (Eqn 3) Reading list • ‘Physicochemical Principles of Pharmacy’ by A.T. Florence and D. Attwood, 6th Ed. p71-75 (very, very introductory) Accessible online through iCat AND • ‘Thermodynamics of Pharmaceutical Systems : An Introduction for Students of Pharmacy’ by K.A. Connors and S. Mecozzi, 2nd Ed. pp 63-96 & 105-122 (very good and has good end of Chapter questions BUT please be aware that this defines work with the opposite sign to the way that it is taught here (in the UK… ) Accessible online through iCat 2