Bioenergetics Lecture Notes PDF

Bioenergetics Marc A. Ilies, Ph. D. Lehninger - Chapter 13 [email protected]; lab 517, office 517A (Tu, Fr 3-5) For questions, comments please use the discussion tool in Canvas ©MAI...

Bioenergetics Marc A. Ilies, Ph. D. Lehninger - Chapter 13 [email protected]; lab 517, office 517A (Tu, Fr 3-5) For questions, comments please use the discussion tool in Canvas ©MAIlies2024 1  Bioenergetics and metabolism Metabolism: a highly coordinated cellular activity in which many multi-enzyme systems (metabolic pathways) cooperate to: - obtain chemical energy by capturing solar energy or degrading energy-rich nutrients from the environment; - convert nutrient molecules into the cell’s own characteristic molecules, monomeric precursors, etc; - polymerize monomeric precursors into macromolecules (proteins, polysaccharides, nucleic acids) - synthesize and degrade biomacromolecules required for specialized cellular functions (membrane lipids, intracellular messengers, pigments, etc) Metabolic pathways involve specific chemical transformation that convert precursors (CO2, glucose, etc) into products via various chemical intermediates called metabolites. Life on Earth - carbon based; depending on chemical form of carbon used: - autotrophs - use CO2 from atmosphere as main C source; self-sufficient 2  Cell function: Muscle Contraction Active Transport Thermogenesis Reductive, Oxidative, endergonic exergonic Energy Energy Utilization (Biosynthesis) (Biodegradation) Production Independent control of anabolism and catabolism is very important 3 Types of metabolic pathways 4 Chemical bond formation and breakage 5  Most Common Classes of Reactions in Biochemistry 1. Reactions with C-C bond formation or breakage 2. Internal rearrangements, isomerizations and eliminations 3. Group transfers reactions 4. Oxidation/Reduction reactions 5. Free radical reactions 6 1. Reactions that make or break C-C bonds Carbonyls often involved due to their ability to stabilize α-carbanions 7  2. Isomerisation and elimination reactions - isomerisation: - elimination: 8  3. Group Transfer Reactions - transfer of a group (e.g. acyl, glycosyl, phosphoryl, etc) from one nucleophile to another (nucleophilic substitution): 9  Inorganic phosphate groups are an important leaving groups in many biochemical reactions - (orto)phosphate: tetrahedral structure, similarly with the structure of water: (charge is delocalized on all 4 O atoms !) 10  Inorganic phosphate groups are an important leaving groups in many biochemical reactions - pyrophosphate can also act as leaving group: nucleophile hexokinase leaving group 11  Bioenergetics and thermodynamics - considering the general reaction: kdir aA + bB cC + dD kinv - at equilibrium the rate of the direct reaction equals the rate of the inverse reaction: vdir = kdir [A]a[B]b = vinv = kinv [C]c[D]d kdir [A]a[B]b = kinv [C]c[D]d kdir [C]c[D]d Keq = = kinv [A]a[B]b - the relationship between equilibrium constant, G0 (standard free-energy change), and temperature: G0 = _ RT ln Keq (the force driving the system towards equilibrium) 12  In biochemistry, by convention: (at pH = 7, [H2O] = 55.5 M) [Mg2+] = 1 mM 13 14 13 15  Consecutive reactions - biochemical pathways - G values in a pathway are additive; if the sum is negative, then the pathway can proceed in the forward direction - the free energy change for ATP hydrolysis is large and negative; phosphorylation is done with ATP instead of phosphate: 16  Three reasons why ATP “likes” to lose its terminal phosphate 1 A fourth reason is the products of 2 3 ATP hydrolysis are more easily solvated and are thus more stable. The products are more stable than the ATP in all cases 17 Mg2+ shields negative charges in ATP and ADP 18 Other compounds with large free energy of hydrolysis 19 Other compounds with large free energy of hydrolysis 20 Example: ATP → ADP + P ∆G = - 30.5 kJ/mol Glu + P → Glu-6P ∆G = + 13.8 kJ/mol Glu + ATP → Glu-6P + ADP ∆G = - 16.7 kJ/mol 21 Other compounds with large free energy of hydrolysis 22 Acetyl-CoA 23 ATP provides energy by group transfers, not simple hydrolysis 24 ATP provides energy by group transfers, not simple hydrolysis Highest energy High energy compounds can donate phosphates to lower energy compounds. Kinases are responsible for these types of reactions. 25  Chemical versatility of ATP (the position of the nucleophilic attack can be determined via 18O labeling) ATP can donate: phosphoryl, pyrophosphoryl or adenylyl groups26  ∆G = - 46 KJ/mol Energy is needed for the condensation and ordered elongation of the monomeric units of DNA, RNA and proteins. This energy can be derived by the breaking of phosphoanhydrides of the ∆G = - 19 KJ/mol component nucleoside triphosphates (NTPs) 27  Transphosphorylation between nucleotides - for DNA elongation we need all four NTPs; their synthesis is achieved by phosphorylation of NDPs with ATP: Nucleoside diphosphate kinase ATP + NDP (or dNDP) ADP + NTP (or dNTP) Adenylate kinase G 'o = 0 2ADP ATP + AMP Creatine kinase ADP + PCr ATP + Cr G 'o = - 12.5 kJ/mol (important in ATP regeneration in muscles) 28  4. Biological oxidation-reduction reactions - various oxidation states for C: - typical redox reaction: 29  Biological oxidation-reduction reactions - Oxidation States of Carbon LEO # of e- owned by C decreases as oxidation increases 30  Biological Oxidations and Reductions (LEO and GER) Oxidation - not only the addition of oxygen but refers to any reaction where electrons are removed. Reduction - addition of electrons - often a molecule will pick up a proton at the same time an electron is added - net effect is the addition of hydrogen: A + e- + H+ AH Thus hydrogenations are reductions and dehydrogenations are oxidations. In biological systems, electrons are transferred most often in the following forms: 1. as hydride ions :H- a proton plus two electrons H+ + 2.e- 2. as hydrogen atoms.H a proton plus an electron H+ +.e- 3. directly.e- 31 Oxidation of biochemical substrates Common scheme: dehydrogenation (oxidation) hydration dehydrogenation (oxidation) Note that protons and electrons are transferred to and from cofactors (NAD+, FAD, NADH, FADH2, etc) 32  Redox Pairs:An oxidation is always accompanied by a reduction. - the tendency to gain electrons can be measured by the standard reduction potential (E'o) in volts The more positive E'o the stronger the oxidizing agent and the > the tendency to accept electrons. The more negative E'o the > the tendency to lose electrons and the stronger the reducing agent. + + NADH + H + FMN NAD + FMNH2 Oxidation- Reduction Oxidation- Reaction Reduction Reaction - Reaction occurs to the right if Go' is < 0 + NADH NADH + +HH+ FMN FMN - Go' the change in free energy is directly related to E'o = Eo for oxidation oxidation reduction semireaction + Eo reduction semireaction Redox Pair E0 (V) + + NAD NAD FMNH FMNH22 2H+/H2 (at pH = 7) - 0.42 + NADH + NADH +HH+ FMN - - 2H + + NAD+/NADH - 0.32 FMN + + 2e 2e ++ 2H FMN/FMNH2 - 0.22 NAD + - + 2e - + 2H + NAD + + 2e + 2H + FMNH FMNH22 Pyruvate/Lactate - 0.19 Redox Pair Redox Pair Redox Pair Redox Pair 1/2O2 + 2H+/H2O + 0.82 Eoo= = -- 0.22 0.22 volt =+ E volt Eo 33 E o= -- 0.32 0.32 volt volt E = Eo+ RT ln electron acceptor  electron donator at 25oC 0.026V electron acceptor E = Eo+ ln electron donator  ΔE must be positive G = -  E for ΔG < 0 i.e. G is directly related to E0 T=298oK =25oC R= 8.315 J/mol.K  = # electrons transferred per molecule  = 96.48 kJ/V.mol (Faraday) 34 3 35 NAD+/NADH redox system Pellagra (it: pelle agra = rough skin) lack of niacin - 3D’s: dermatitis, dementia, diarrhea Precursor (essential) 36 FAD/FADH2 redox system Riboflavin (Vitamin B2) - in cereal, nuts, milk, eggs, green leafy vegetables, lean meat - deficiency: Ariboflavinosis (angular cheilitis itchy eyes, light sensitivity, dermatitis, anemia) 37 38  Goals and Objectives Upon completion of this lecture at minimum you should be able to answer the following: ►What is metabolism, what are metabolic pathways and metabolites? ►Which are the two main metabolic pathways and what are their characteristics? ►Which are the main characteristics of chemical bond formation and breakage? ►Which are the main reaction classes in biochemistry? ►Which are the main reactions that make or break C-C bonds? ►How do isomerisation and elimination reaction proceed? ► What group transfer reactions do you know, and what are their main particularities? What common leaving groups are encountered in these reactions and what are their main particularities? ►How is ΔG influencing bioenergetics and thermodynamics of simple and consecutive reactions, and how is ΔG correlated with Keq and ΔE? ►Which are the main properties of ATP and other compounds with large free energy of hydrolysis? How is the chemical energy stored in these compounds transferred? ►Which are the main characteristics of redox reactions, what type of important redox cofactors do you know, what is their structure and what diseases are associated to their absence in the organism? 39  Drugs and Diseases ►Diseases: pellagra, ariboflavinosis ►Drugs: niacin (vitamin B3), riboflavin (vitamin B2) 40