Bioenergetics and Thermodynamics PDF

PRINCIPLES OF BIOENERGETICS 1- Bioenergetics and Thermodynamics Definition ▪ The quantitative study of the energy transductions that occur in living cells and of the nature and function of the chemical processes underlying these transductions. Biological Energy Transformations Obey the Laws of Therm...

PRINCIPLES OF BIOENERGETICS 1- Bioenergetics and Thermodynamics Definition ▪ The quantitative study of the energy transductions that occur in living cells and of the nature and function of the chemical processes underlying these transductions. Biological Energy Transformations Obey the Laws of Thermodynamics ▪ The first law (conservation of energy): for any change, the total amount of energy in the universe remains constant; ▪ The second law of thermodynamics: the universe always tends toward increasing disorder (or); in all natural processes, the entropy of the universe increases. ▪ Signs for spontaneous systems… Biochemistry / Dentistry Register your attendance with your university number Make sure that the settings of your phone allow tracking location Go to settings > privacy> location> services> make sure that location services is ON Why Do Chemical Reactions Occur? ▪ The concept of activation energy ▪ ∆G and ∆Go ΔG is a state function?!  ΔG is not affected by the mechanism of the reaction A → B → C ΔGA→B = GB - GA ΔGB→C = GC- GB GC – GA = ΔGA→C ▪ Combustion of glucose in calorimeter Glucose + O2 → CO2 + H2O ΔG = - 680 kcal/mol In the cell Glucose →→→→→→→ CO2 + H2O ΔG = - 680 kcal/mol ΔG is affected by concentration A B ΔG = - - - A B ΔG = - A B ΔG = zero A B ΔG = ++ ΔG measures the tendency of a reaction to proceed towards equilibrium How ΔG and ΔGo relate? ▪ Concentrations of reactants and products = 1 mole/L ▪ ΔG= ΔGo + ▪ ΔG= ΔGo + RT ln RT [Products] [Reactants] 2.3 log [Products] [Reactants] The Standard Free-Energy Change Is Directly Related to the Equilibrium Constant (Keq) ▪ Equilibrium is reached at the end! ▪ At equilibrium: concentration are fixed; rates are exactly equal ▪ The concentrations define the equilibrium constant Glucose 6- phosphate 0.66 mol/L Fructose 6- phosphate 0.33 mol/L ΔG= ΔGo + RT 2.3 log 0.33/ 0.66 ΔGo = + 0.4 kcal/mol Glucose 6- phosphate Fructose 6- phosphate ΔGo = + 0.4 kcal/mol ΔG= ΔGo + RT 2.3 log 0.09/0.9 ΔG= - 0.96 Glucose 6- phosphate 1 mol/L Fructose 6- phosphate 1 mol/L ΔG= ΔGo + RT 2.3 log 1/1 ΔG= ΔGo ΔG & Keq  At equilibrium, DG=0  Can a reaction has a + DGo & still be favorable? G = Gº' + RT ln [C] [D] [A] [B]  [C] [D]  = Gº' + RT ln [A] [B] Gº' = - RTln [C] [D] [A] [B] [C] [D] defining K'eq = [A] [B] Gº' = - RT ln K'eq ΔGº and Keq Keq ΔGº 103 - 4.08 102 - 2.72 101 - 1.36 1 0 10-1 1.36 10-2 2.72 10-3 4.08 How much change in delta G compared to changes in Keq If Keq = 1, then ΔGº = 0 If Keq > 1, then ΔGº < 0 If Keq < 1, then ΔGº > 0 ΔG & Keq ▪ ΔG is additive for multiple subsequent reactions ▪ Keq is multiplicative for subsequent reactions The Effect of Changing Conditions on Equilibria  When a stress is applied to a system at equilibrium, the equilibrium shifts to relieve the stress  Stress: any change that disturbs the original equilibrium  Effect of Changes in Concentration  What happens if a reactant/product is continuously supplied/ removed?  Metabolic reactions sometimes take advantage of this effect  Effect of Changes in Temperature  Endothermic/exothermic are favored by increase/decrease in temperature, respectively.  Effect of a catalyst on equilibrium PRINCIPLES OF BIOENERGETICS 2- Phosphoryl Group Transfers and ATP The energy flow ▪ Ingestion, digestion, & absorption ▪ Metabolism (Acetyl CoA) ▪ TCA ▪ Oxidative phosphorylation  Prokaryotic cells vs. eukaryotic cells  The mitochondria (singular, mitochondrion) (90% of the body’s energy ATP)  The number of mitochondria is greatest in eye, brain, heart, & muscle, where the need for energy is greatest  The ability of mitochondria to reproduce (athletes)  Maternal inheritance ATP  ATP is the energy currency of the cell  What is a high energy molecule?  Why ATP?  Has an intermediate energy value, so can be coupled Is ATP a good long-term energy storage molecule?  As food in the cells is gradually oxidized, the released energy is used to re-form the ATP so that the cell always maintains a supply of this essential molecule Tissue ATP turnover (mole/day) Brain 20.4 Heart 11.4 Kidney 17.4 Liver 21.6 Muscle 19.8 Total 90.6 90.6 * 551 (g/mole) = 49,920 g ATP Biochemical reactions or pathways!  Are interdependent  Are subjected to thermodynamics laws  Coordinated by sensitive means of communication  Allosteric enzymes are the predominant regulators  Pathways are linear, cyclic or spiral Exergonic reactions and pathways in Biochemistry  Complex structures  simple structures Proteins → amino acids Starch → n glucose glucose + O2 → CO2 + H2O  More specifically  Hydrolysis reactions  Decarboxylation reactions (release pyruvate (C3 ) → acetyl-CoA(C2)  Oxidation with O2 of CO2) +CO2 How do our cells get energy for unfavorable biochemical work?  The coupling concept - phosphoryl transfer reactions How do our cells get energy for unfavorable biochemical work? I. ΔG0 Values are additive i. Through phosphoryl transfer reactions:  Step 2 (+3.3 vs. -4 kcal/mole)  Step 2 + 4 = -2.35 kcal/mole  The net value for synthesis is irrelevant to the presence or absence of enzymes ii. Activated intermediates (step 4 is facilitated by steps 5&6) II. ΔG Depends on Substrate and Product Concentration (step 4 has a ratio of 6/94; +1.65 kcal/mol, if 3/94; -0.4kcal/mol) The Free-Energy Change for ATP Hydrolysis Is Large and Negative ▪ Not fixed and depends on concentrations How do our cells get energy for unfavorable biochemical work? III. Activated Intermediates other than ATP; UTP is used for combining sugars, CTP in lipid synthesis, and GTP in protein synthesis The acetyl CoA as an example of coupling  CoA is a universal carrier (donor) of Acyl groups  Forms a thio-ester bond with carboxyl group THERMOGENESIS  The first law of thermodynamics  Heat production is a natural consequence of “burning fuels”  Thermogenesis refers to energy expended for generating heat  Shivering thermogenesis  Non-shivering thermogenesis PRINCIPLES OF BIOENERGETICS 3- Biological Oxidation-Reduction Reactions (Redox) Oxidation-Reduction reactions (Redox)  Oxidation:  Gain of Oxygen  Loss of Hydrogen  Loss of electrons  Reduction:  Gain of Hydrogen  Gain of electron  Loss of Oxygen  E (redox Potential): it is a POTENTIAL ENERGY that measures the tendency of oxidant/reductant to gain/lose electrons, to become reduced/oxidized  Electrons move from compounds with lower reduction potential (more negative ) to compounds with higher reduction potential ( more positive)  Oxidation and reduction must occur simultaneously D:H AH D A Reduction potential ▪ A- P + B A + B- P Type of reaction What determine the direction of the reaction? ▪ A++ + B++ A+ + B+++ Type of reaction What determine the direction of the reaction? Reduction potential and direction of the reaction A + B- A- + B ΔGº = -ve B oxidized form Redox couple B- reduced form V A B A- B- What is the standard? ▪ Hydrogen electrode ▪ H2 Gas sensor Reduction potential and direction of the reaction H+ + X - H2 X oxidized form X- reduced form + X Redox couple V H2 X X- ΔGº = -ve H+ X- has higher tendency to loose electrons than H2 does  Negative reduction potential Standard reduction potential (Eo) Reduction Potential Oxidized + eSuccinate Acetate NAD+ Acetaldehyde Pyruvate Fumarate Cytochrome+3 oxygen  Reduced α ketoglutarate Acetaldehyde NADH Ethanol Lactate Succinate Cytochrome+2 water ΔEº (V) - 0.67 - 0.60 - 0.32 - 0.20 - 0.19 + 0.03 + 0.22 + 0.82 Calculation of ΔGº from ΔEº ▪ ΔGº = - nƒΔEº – F = Farady constant = 23.06 kcal/ Volt ▪ Calculate ΔGº of the following reaction NAD+ NADH + 1/2O2 + 2e- ΔEº = +0.32 V 2e- O2- ΔEº = +0.82 V ΔGº = - 52.6 kcal/mol NADH O + + H 2O NAD+ Oxidation-Reduction reactions (Redox)  E= EA - ED  ∆Eo = at standard condition  Does ∆E determine the feasibility of a reaction?  ΔGο = -nfΔEο  In other words; energy (work) can be derived from the transfer of electrons Or  Oxidation of food can be used to synthesize ATP Oxidation-Reduction reactions (Redox)  Always involve a pair of chemicals: an electron donor and an electron acceptor (Food vs. NAD+)  NAD+ vs. FAD  NAD+ vs. NADP+ (fatty acid synthesis and reactions) detoxification