Lecture 18 Bioenergetics intro and MCQ.pdf

Introduction to Bioenergetics 4BICH001W Biochemistry Dr Sarah K Coleman Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous). ...

Introduction to Bioenergetics 4BICH001W Biochemistry Dr Sarah K Coleman Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous).  What is Bioenergetics? All organisms need to acquire energy, all cells require energy. The form of an organism is influenced by how it acquires that energy. ▪ plants have large leaf surface area for photosynthesis ▪ carnivores tend to be fast moving to catch moving prey. ▪ herbivores have large stomachs to ferment large amounts of grass. ▪ Structure and function relationship!  What is Bioenergetics? Bioenergetics is the flow of energy through living organisms The energy is required to overcome the second law of thermodynamics “In a natural thermodynamic process, the sum of the entropies of the interacting thermodynamic systems increases.” This means – if energy is not used to maintain an ordered state, the system will become more disorganised (increase in entropy). A simple system…  Complex systems… Does life break the 2nd Law of Thermodynamics?  Complex systems… Living systems become more ordered Living systems use energy to overcome local entropy Disorder within the surrounding increases Entropy within the Universe increases Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous).  Bioenergetics is Metabolism For organisms to grow, cells need energy, precursor metabolites and reducing power (electrons). Metabolism is: – use of food to produce energy – use of food to create the building blocks – use of energy to run cellular processes – use of building blocks and energy to create larger, more complex molecules – a series of enzymatic reactions  Bioenergetics is Metabolism What is metabolism? All the chemical reactions going on in an organism. It is split into two basic sets of reactions: Catabolism - reactions that breakdown the foodstuffs that are taken in. These reactions release; energy, simple (3,4,5 or 6 carbon) compounds and reducing power (electrons). Anabolism - biosynthetic reactions used by a cell to make new material and larger molecules. These reactions use; energy, simple compounds and the reducing power released in catabolism.  Metabolism = catabolism + anabolism Catabolism is: Anabolism is: Degradative Synthetic Oxidative Reductive Energy yielding Energy requiring Uses a variety of starting Has well defined starting materials materials Has well defined products Has a variety of products Uses NAD+ or NADP+ Uses NADPH  OILRIG Oxidation is LOSS of electrons Reduction is GAIN of electrons  Thermodynamics = Energy Changes When looking at the energy changes in biological systems we need to measure: Internal Energy (E) Total energy of the system Enthalpy (H) Heat content Entropy (S) Degree of disorder Gibbs Free Energy (G) Energy available to do work Temperature (T) Temperature of the system in Kelvin Actual values of E, H, S, and G are impossible to measure, but we can measure changes in their values  Thermodynamics Refresher… We look at changes in these factors; i.e. initial versus final states. The capital Greek letter delta ‘ Δ ’ always indicates ‘the change in’. So G = Gfinal – Ginitial G is a measure of the amount of energy potentially available to do work G of a reaction is dependent on the internal energy of the system and the change in entropy of the system. G = H - TS Free Energy is related to the total chemical energy of the system and hence to the chemical stability of the system. If Free Energy is high we have a potentially unstable system and the system will tend to go to a lower Free Energy state. This is likely to be a spontaneous change. If change in Free Energy is zero, the system is at equilibrium. To shift a system from equilibrium, energy will need to be put in. Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous).  Exergonic and Endergonic Reactions Exergonic reactions release energy Endergonic reactions require energy G = H - TS 1) If G is negative (< 0) energy is released from the reaction 2) If G is positive (> 0) the reaction is energy requiring and is thermodynamically unfavourable Energy liberated in (1) can be used to drive the energy requiring reactions in (2) The reactions are said to be coupled  The ATP cycle couples exergonic and endergonic reactions: free energy transferred from exergonic to endergonic reaction Catabolic reaction Anabolic Breaking down reaction a molecule to Making a larger smaller parts molecule from smaller bits  Metabolism = catabolism + anabolism Catabolism is Anabolism is Degradative Synthetic Oxidative Reductive Energy yielding Energy requiring Uses a variety of starting Has well defined starting materials materials So the overall ΔG is ? So the overall ΔG is ? SEE EARLIER SLIDE  Standard State Conventions for Biochemists: We calculate the Standard Gibbs Free energy change at pH 7 (Go’ ). The units are kJ/mol. ▪ Pure water in a reaction has a value of 1. ▪ [H+] at pH7 in a reaction has a value of 1. Go’ can be calculated from the equilibrium constant for the reaction. At equilibrium Go’ = -R T LnKeq R = 8.3 J/mol/K (the gas constant); T = temperature in Kelvin; Ln = the natural log of the reaction’s equilibrium constant. Biochemistry, Metabolism and Thermodynamics Living organisms maintain a steady state. This is NOT an equilibrium Enzymes change the rate of a reaction (but not the overall G) Enzymes lower the activation energy of a reaction by providing an energetically favourable pathway for a reaction to happen Many metabolic reactions in cells can flow both ways; they are freely reversible Key ‘checkpoint’ steps in a pathway are not reversible and will tend to have large G values Bioenergetics – energy flow thru living systems Bioenergetics – energy flow thru living systems Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous). Molecules of Interest  Adenosine Triphosphate (ATP) Phosphoester bond Phosphoanhydride bonds The modern day energy molecule  Adenosine Triphosphate (ATP) Acts as an energy carrier When hydrolysed, energy is released G0’ = -30.5 kJ/mol Energy used to drive metabolic reactions, mechanical work, heat  Why is energy released upon hydrolysis of ATP? 1. Electrostatic repulsion ATP has 4 adjacent negative charges which repel each other. Hydrolysis allows negatively charged phosphate groups to separate, so a lower energy state is reached.  Why is energy released upon hydrolysis of ATP? 2. Increase of Entropy Equation is: ATP4− + H2O → ADP3− + Pi2− + H+ Two moles of reactants give three moles of produced particles Thus, entropy is increasing. ΔG=ΔH–TΔS Thus, free energy decreased and product formation favoured.  Why is energy released upon hydrolysis of ATP? 3. Resonance stabilization of products The phosphoanhydride bonds in ATP have less resonance stabilization than the hydrolysis products: ADP and especially Pi Resonance stabilization is the delocalised sharing of electrons Four possible resonance structures for orthophosphate  Hydrolysis of ATP is favourable under STANDARD conditions An energy barrier MUST be overcome for hydrolysis of ATP This occurs in active site of enzymes G0’ = -30.5 kJ/mol Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous).  Acyl Phosphates High energy release when bond hydrolysed. G0’ = -49.6 kJ/mol Higher energy level than ATP Used in substrate level CH3 phosphorylation. Kinase enzymes pass phosphate directly to ADP to Acetyl phosphate make ATP Helps maintain required 1,3-Bisphosphoglycerate amount of ATP in cells  Acyl Phosphates An example from glycolysis: 1,3-Bis-phosphoglycerate regenerating ATP. Enzyme: phosphoglycerate kinase G0’ = -49.6 kJ/mol Enol Phosphates High energy release when bond hydrolysed. G0’ = -62 kJ/mol Used in substrate level phosphorylation An example from glycolysis is conversion of phosphoenolpyruvate to pyruvate. Enzyme is pyruvate kinase  Thioesters Thiol, indicates sulphur is present Thioesters are from reaction of carboxylic acids and a thiol group Also high energy release when bond hydrolysed Thioesters may have been ‘early’ high energy compound (before ATP) Hydrolysis Acetyl-CoA gives: or G0’ = -31.5 kJ/mol acetyl-CoA  CoEnzyme A: common intermediate Coenzyme A (CoA) Acetyl-CoA  Nicotinamide Adenine Dinucleotides These can be oxidised (NAD+ and NADP+) or reduced (NADH and NADPH). (Remember OILRIG) Oxidised form can accept two electrons and a proton on to the nicotinamide ring. Act as electron carriers i.e. carriers of reducing power. In electron transport chain (ETC) of mitochondria NADH is oxidised. This reaction has G0’ = -220 kJ/mol. That energy can be used to make 3 ATP molecules.  NAD+ and NADP+ (oxidised forms) Nicotinamide ring  NADH and NADPH (reduced forms) Electrons bind here NADH and NADPH (reduced forms) Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous).  Flavin Adenine Dinucleotide FAD has similar functions to NAD+; it is an electron carrier. Has a flavin ring, not a nicotinamide ring. FAD can be reduced by binding two electrons and two protons to form FADH2. In the ETC of mitochondria oxidisation of FADH2 to FAD occurs. Reaction has G0’ = -180 kJ/mol and can be used to make two molecules of ATP FAD and FADH2 reduced e- form loss  In summary… Cells need energy, precursor metabolites and reducing power (electrons). Catabolism and Anabolism are linked Gibbs Free Energy tells us how much useful work can be obtained ATP is the energy carrier in the cell Acyl phosphates and Enol phosphates are used to make ATP by substrate level phosphorylation NADH, NADPH and FADH2 are electron carriers  Abbreviations list ATP = adenosine triphosphate Acetyl-CoA = acetyl-coenzyme A ADP = adenosine diphosphate FMN = flavin mononucleotide UTP = uridine triphosphate FAD = flavin adenine dinucleotide (oxidised form) UDP = uridine diphosphate FADH2 = flavin adenine dinucleotide (reduced NAD+ = nicotinamide adenine form) dinucleotide (oxidised form) Pi = phosphate (inorganic) NADH = nicotinamide adenine dinucleotide (reduced form) G6P = glucose-6-phosphate NADP+ = nicotinamide adenine E = enzyme dinucleotide phosphate (oxidised form) S = substrate NADPH = nicotinamide adenine P = product dinucleotide phosphate (reduced form) ES = enzyme: substrate complex [ ] = concentration of Any questions: You can type in the chat function box during this live session (synchronous)? Or onto the Question Board in the Biochemistry Blackboard module and I will look at them later (asynchronous). MCQ quiz for Lecture 18: Introduction to Bioenergetics Answers will be given in your Seminar sessions – with further discussion. You must attempt before your seminar session. These quizzes are part of your learning for the Biochemistry module They will aid your on-going studies at the University of Westminster Q1) Bio-energetics ……? Select all the correct options. a) Is unimportant in the study of living systems. b) Allows an ordered state to exist. c) Allows life to break the Laws of Thermodynamics. d) Is the breakdown of nutrients. e) Is the synthesis of complex molecules. Q2) Metabolism has both anabolic and catabolic reactions. Select the correct statement. a) Anabolic synthesis reactions allow the endergonic catabolic reaction to occur. b) The defined starting molecules of catabolism allow the production of ADP. c) Anabolic reactions are endergonic and coupled to catabolic reactions via use of ATP. d) Catabolic reactions have a high positive change in Gibbs free energy. e) Catabolic reactions are reductive and required NAD+. Q4) OILRIG means? a) A way to extract fossil fuels and to contribute to climate change. b) Only In Last Resort will I Graduate. c) Oi, Londoner’s are Rocking in Greenwich. d) Oxidation is Loss and Reduction is Gain of Electrons. e) Open It and Let Revision Insight Grow Q4) Some of the key molecules (and their roles) mentioned in the lecture are? a) ATP; metabolism; Acyl phosphates (All for phosphorylation). b) NAPDH; Enol phosphates; FADH2 (Electron transporters). c) NADH; Acyl phosphates; CTP (Electron transport and energy) d) NADH; FAD; ATP (Electron transport and energy) e) NADH; FAD; Gibbs Free Energy (Electron transport and energy) Q6) A large number of biochemical structures were shown in the lecture slides. Do you need to memorise them to pass this module? Yes – memorisation of content is the only way to pass at University! No – memorisation of structures is not required. However, understanding of how the structure allows the molecule to fulfil its function is important!