2-Bioenergy-biochemistry 2 (1) (2).pdf

Dr. Mohannad Jazzar Hebron University  Bioenergetics : The quantitative study of energy transductions in living cells and the physical-chemical nature underlying these processes. It’s a branch of biochemistry concerned with transformation of energy and use of enzymes by living system...

Dr. Mohannad Jazzar Hebron University  Bioenergetics : The quantitative study of energy transductions in living cells and the physical-chemical nature underlying these processes. It’s a branch of biochemistry concerned with transformation of energy and use of enzymes by living system The Flow of Electrons Provides Energy for Organisms Autotrophes Heterotrophes All these reactions involving electron flow are oxidation- reduction reactions  LAWS OF THERMODYNAMICS We need to understand System, Heat, and Work FIRST LAW (Law of conservation of energy) Energy cant be created nor destroyed but changed from one form to other The total E leave the system = Total E enters the system – stored internal E In biological recation inside cell System: We are interested in Enthaply H ΔH = H product – H reactants Exothermic Or Endothermic  LAWS OF THERMODYNAMICS SECOND LAW (The equilibrium constant is a measure of Directionality) ΔG: calculate how far from equilibrium a reaction lies under specific conditions and how much energy will be released to reach equilibrium ΔG under specific standard conditions Keq = 1  LAWS OF THERMODYNAMICS We need to understand System, Heat, and Work SECOND LAW (Law of thermodynamic spontaneity, Possibility) 1-Physical chemical changes give useful energy undergo irreversible degradation into a random form called entropy 2- total amount of energy in this universe declines with time Enthalpy H (The total energy of a system) is equal to: Free energy G (The usable energy) + entropy S (the unusable energy). ∆G = ∆H – T∆S Exergonic OR endergonic When ΔH is highly negative and ΔS is highly positive… This reaction is Favorable  LAWS OF THERMODYNAMICS Keq > 1.... ΔG has negative value.... Reaction goes spontaneoslay to the right (Forward) A+ B --------------------C+D Keq < 1.... ΔG has positive value.... Reaction goes spontaneoslay to the left (Reverse)  ENERGY Useful Useless [Entropy] Free energy can do work at constant P, T Heat Energy do work at constant P, varying T this impossible in livings  Entropy Degree of randomness and disorderness Change within………to explain this follow the following examples Tea kettle Glucose oxidation Glucose + 6O2 6CO2 + 6H2O Information entropy  Aspects of 2nd Law 1. We must know system, surrounding, and universe system 2. Standard state in which pH=7, T=298K, Concentration=1M, Atm.P=1 3. Enthalpy H=E+PV , enthalpy means warm within, or heat content , Surrounding E=internal energy, PV pressure times volume. Universe 4. Change in free energy is given by DG = DH - TDS that is change in free energy ,enthalpy and entropy respectively 5. When chemical reaction proceeds toward equilibrium then: S increased and DS positive DG decreased or negative DH negative ( when system looses heat), and positive when system absorbs heat Nucleophiles: functional groups rich in electrons and capable of donating them Electrophiles: electron-deficient functional groups that seek electrons The relative electronegativities: F>O>N>C=S>P=H Cleavage of a C-C or C-H bond  Equilibrium Constants and Standard Free-Energy Change For the reaction: aA + bB cC + dD DGreaction = DGo’reaction + RT ln([C]c[D]d/[A]a[B]b) At equilibrium: Keq = [C][D]/[A][B] and DGreaction = 0, so that: DGo’reaction = -RT ln Keq The standard free-energy change is directly related to the equilibrium constant Standard free-energy changes are additive Equilibrium constants are multiplicative  Phosphagens: Energy-rich storage molecules in animal muscle Phosphocreatine (PC) and phosphoarginine (PA) are phosphoamides Have higher group-transfer potentials than ATP Produced in muscle during times of ample ATP Used to replenish ATP when needed via creatine kinase reaction Fire flashes: glowing reports of ATP From chemical energy into light energy. An pyrophosphate cleavage of ATP to form luciferyl adenylate. In the presence of O2 and luciferase, the luciferin undergoes a multiple step oxidative decarboxylation to oxyluciferin and accompanied by remission of light.  Equilibrium Constants and Actual Free-Energy Change For real-life situation in cell biology we will use the ΔG’ For the reaction: aA + bB cC + dD DG’ = DGo’ + RT ln ([C]c[D]d/[A]a[B]b) Is a function of reactant and product concentrations and of the tempreture The actual free energy of ATP hydrolysis is very diffrent Phosphorylation potential  Reaction coupling ΔG1 = 13.8 kJ/mol and ΔG2 = -30.5 kJ/mol  Chemical logic and common biochemical Reactions Cells have the capacity to carry out thousands of specific (Enzyme catalyzed reactions) On the enzyme active sites (Breaking and Forming of the new bonds) Reactions in living cells includes: - Oxidation-reduction (Dehydrogenases) - Group transfer reactions (Kinases) - H2O addition/removal (Hydrolases) - Formation double bond (Lyases) - Isomerization (Isomerases) - Make and break C-C bonds (Ligases)  Cells need energy to do all their biological work To generate and maintain its highly ordered structure (biosynthesis of macromolecules). To generate motion (mechanical work). To generate concentration and electrical gradients across cell membranes (active transport). To generate heat and light.  The Free Energy of ATP Energy from oxidation of metabolic fuels is largely recovered in the form of ATP high-energy phosphoanhydride bonds  Charge repulsion  Resonance stabilization  High Entropy  Hydrolysis of phosphoenolpyruvate (PEP) Catalyzed by pyruvate kinase, this reaction is followed by spontaneous tautomerization of the product. Pyruvate, tautomerization is not possible in PEP, and thus the products of hydrolysis are stabilized relative to reactants.  Phosphagens: Energy-rich storage molecules in animal muscle High-energy phosphate compound Phosphocreatine (PC) and phosphoarginine (PA) Have higher group-transfer potentials than ATP Produced in muscle during times of ample ATP Used to replenish ATP when needed via Creatine and arginine kinase reaction  Phosphoryl-Group Transfer Phosphoryl-group-transfer potential - the ability of a compound to transfer its phosphoryl group Energy-rich or high-energy compounds have group transfer potentials equal to or greater than that of ATP Low-energy compounds have group transfer potentials less than that of ATP Phosphoryl-Group Transfer Larg free enrgy change that company ATP hydrolysis High-energy phospahte compound 1 cal = 4.184 J ATP provides energy by group transfers, Not by simple hydrolysis --- in two steps A phosphoryl group is first transferred from ATP to glutamate The phosphoryl group is Glutamine displaced by NH3 and synthase released as Pi ATP can carry energy from high-energy phosphate compounds produced by catabolism to compounds such as glucose, converting them into more active forms Nucleophilic displacement reaction of ATP Thioesters---Hydrolysis of acetyl- coenzyme A Acetyl-CoA is a thioester with a large, negative, standard free energy of hydrolysis. Thioesters contain a sulfur atom in the position occupied by an oxygen atom in oxygen esters. NADH and NADPH act with dehydrogenases as soluble electron carriers From vitamin niacin (source of the nicotinamide) NADH absorb at 340 nm. Most dehydrogenase that use NAD or NADP bind the cofactor in the conserved protein domain Vit-B3 What are the effects of Niacin Deficiency ? Dermatitis Diarrhea Dementia death Structure of oxidized and reduced FAD and FMN Flavin Nucleotides are tightly bound in flavoproteins. Accepts 1 or 2 electrons