9/29/2015 Chapter 8: An Introduction to Metabolism 1. Energy & Chemical Reactions 2. ATP 3. Enzymes & Metabolic Pathways 1. Energy & Chemical Reactions Chapter Reading – pp. 142-148 2 Basic Forms of Energy Kinetic Energy (KE) • energy in motion or “released” energy: • heat (molecular motion) • electric current* (flow of charged particles) • light energy* (radiation of photons) • mechanical energy* (structural movement) • chemical energy* (breaking covalent bonds, flow from high to low concentration) *forms of KE cells use to “do things” 1 9/29/2015 Potential Energy (PE) • stored energy (i.e., not yet released): A diver has more potential Diving converts energy on the platform potential energy to than in the water. kinetic energy. • gravitational potential • chemical bonds* • chemical gradients*, charge gradients* *sources of PE Climbing up converts the kinetic A diver has less potential energy of muscle movement energy in the water cells rely on to potential energy. than on the platform. Illustration of Kinetic & Potential Energy KE highest at b, lowest at a & c PE highest at a & c, lowest at b Laws of Energy Transformation st 1 Law of Thermodynamics “Energy is neither created Principle of Conservation of Energy: nor destroyed, but may be converted to other forms.” Heat CO2 + Chemical energy H2O (a) First law of thermodynamics (b) Second law of thermodynamics nd 2 Law of Thermodynamics “Every energy transfer or • every energy conversion results in transformation increases the a loss of usable energy as HEAT entropy of the universe.” 2 9/29/2015 Chemical Free Energy Gibb’s Free Energy (G) = “chemical PE” DG = Gproducts - Greactants Negative DG: • “loss” of chemical PE (e.g., respiration) • net release of KE (for work or to raise temperature) Positive DG: • “gain” of chemical PE (e.g., photosynthesis) • requires input of KE (e.g., sunlight) DG = 0: • system is at equilibrium Examples of Spontaneous Changes in Free Energy • More free energy (higher G) • Less stable • Greater work capacity In a spontaneous change • The free energy of the system decreases (DG 0) • The system becomes more stable • The released free energy can be harnessed to do work • Less free energy (lower G) • More stable • Less work capacity (a) Gravitational motion (b) Diffusion (c) Chemical reaction • in each case DG is negative and PE decreases Exergonic Reactions Reactants Amount of energy released • net release of energy (∆G < 0) (DG is negative) Energy Products • loss of PE Free energy Progress of the reaction (a) Exergonic reaction: energy released Endergonic Reactions Products Amount of energy • net consumption of required (∆G > 0) energy Energy (DG is positive) Reactants Free energy • gain of PE Progress of the reaction (b) Endergonic reaction: energy required 3 9/29/2015 Activation Energy (EA) Whether endergonic or exergonic, all chemical reactions require some energy input for the reaction to proceed – the A B activation C D energy (EA) Transition state A B EA • all reactions require C D some sort of “spark” Reactants A B ∆G < O C D • this is why sources of chemical PE are Products “stable” Progress of the reaction Mechanical Model of Activation Energy The upright bottle falling over is analogous to an exergonic reaction, yet it still requires some energy input for the bottle to tip over. 2. ATP Chapter Reading – pp. 148-151 4 9/29/2015 ATP – an Ideal Cellular Fuel • useable amount of energy (DG -7.3 kcal/mole) • stable, soluble in water (negatively charged) • terminal phospho- anhydride bond easily broken ATP Hydrolysis • exergonic cleavage of terminal phospho-anhydride bond P P P Adenosine triphosphate (ATP) H2O DG -7.3 kcal/mole) P + P P i + Energy Inorganic phosphate Adenosine diphosphate (ADP) The ATP Cycle ATP + H2O Energy from Energy for cellular catabolism (exergonic, work (endergonic, energy-releasing energy-consuming processes) ADP + P i processes) Exergonic processes (e.g., cellular respiration) provide energy for the endergonic synthesis of ATP, whereas ATP hydrolysis releases energy that can be used for other endergonic activities… 5 9/29/2015 Examples of ATP-powered “Work” Membrane protein P P i Solute Solute transported (a) Transport work: ATP phosphorylates transport proteins ADP ATP + P i Vesicle Cytoskeletal track ATP Motor protein Protein moved (b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzed Coupling of Biochemical Reactions Exergonic reactions fuel (provide energy for) endergonic reactions in cells (i.e, they are “coupled”) • breakdown of exergonic glucose fuels endergonic ATP production exergonic endergonic • ATP hydrolysis fuels most cellular activities Example of Coupling w/ ATP Hydrolysis (a) Glutamic acid NH3 NH2 conversion DGGlu = +3.4 kcal/mol to glutamine Glu Glu Glutamic Ammonia Glutamine acid (b) Conversion NH3 reaction coupled 1 P 2 with ATP ADP NH2 ADP ATP P i hydrolysis Glu Glu Glu Glutamic Phosphorylated Glutamine acid intermediate DGGlu = +3.4 kcal/mol (c) Free-energy NH3 NH2 change for ATP ADP P i coupled Glu Glu reaction DGGlu = +3.4 kcal/mol DGATP = 7.3 kcal/mol + DGATP = 7.3 kcal/mol Net DG = 3.9 kcal/mol 6 9/29/2015 3. Enzymes & Metabolic Pathways Chapter Reading – pp. 142, 151-159 Enzymes are Biological Catalysts Biochemical reactions such as the one below will not occur spontaneously without a catalyst: Sucrase Sucrose Glucose Fructose (C12H22O11) (C6H12O6) (C6H12O6) Enzymes are biological catalysts made of protein or RNA that determine when reactions occur. • the production and regulation of enzymes give a cell complete control over all of the biochemical reactions that occur within the cell Enzymes Lower Activation Energy Course of reaction EA without without enzyme enzyme EA with enzyme is lower Reactants Course of DG is unaffected reaction by enzyme with enzyme Free energy Products Progress of the reaction 7 9/29/2015 Enzymes physically bind Substrates Substrate The “fit” of substrate into active site is Active sites highly specific and due to molecular complementarity Enzyme Enzyme-substrate complex • complementary in Substrate physical shape (“hand in glove”) Active site • complementary in chemical properties (attraction between opposite charges, Enzyme Enzyme-substrate complex hydrophobic regions) The Catalytic Cycle of Enzymes 1 Enzyme available with empty active • every enzyme has a site unique substrate & Active site Substrate thus catalyzes a (sucrose) specific reaction 2 Substrate binds to enzyme with induced fit Enzyme Glucose (sucrase) Fructose • cells produce 1000s of different H2O enzymes, all of 4 Products are released which are proteins 3 Substrate is encoded by a converted to particular gene products Factors effecting Enzyme Activity Optimal temperature for Optimal temperature for typical human enzyme enzyme of thermophilic (heat-tolerant) Optimal temperature bacteria and pH for a given enzyme depend on the environment in which Rate of reaction of Rate it normally functions 0 20 40 60 80 100 Temperature (ºC) (a) Optimal temperature for two enzymes Optimal pH for pepsin Optimal pH (stomach enzyme) for trypsin Deviation from the (intestinal enzyme) optimal conditions can result in denaturation and loss of enzyme activity Rate of reaction of Rate 0 1 2 3 4 5 6 7 8 9 10 pH (b) Optimal pH for two enzymes 8 9/29/2015 Enzyme Regulation Substrate Active site Competitive inhibitor Enzyme Noncompetitive inhibitor (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition Enzymes can be regulated by inhibitors in two general ways: 1) Competition between inhibitor & substrate for active site 2) Remotely inducing the active site to change shape Competitive Enzyme Inhibition Substrate Competitive Competitive inhibitor inhibition involves binding of an inhibitor to Enzyme the active site • inhibitor must be reversible to be able Reversible Substrate competitive to regulate in inhibitor response to concentration Increase in substrate irreversible inhibitors concentration Enzyme essentially poison the enzyme Allosteric Enzyme Regulation Substrate Allosteric Distorted regulation Active site Enzyme active site involves the binding of a substance to Allosteric site an enzyme Allosteric Allosteric inhibition inhibitor outside the (non-competitive) active site Substrate Distorted Active site • induces change active site in shape of active site Allosteric site • must be Allosteric activator reversible Allosteric activation 9 9/29/2015 Cooperativity With many multimeric enzymes, the binding of substrate to one active site can stabilize the “active conformation” of other active sites, thus increasing the frequency with which they bind substrate. Substrate • this is a type of allosteric regulation since active sites are regulated in a Inactive form Stabilized active non-competitive form manner (b) Cooperativity: another type of allosteric activation Metabolic Pathways Most biological processes, whether anabolic (building) or catabolic (breaking down), require a series of chemical reactions (i.e., a pathway) Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1 Reaction 2 Reaction 3 Starting Product molecule • each step in a metabolic pathway is catalyzed by a specific enzyme • a missing or inactive enzyme can prematurely shut down a metabolic pathway, leading to the accumulation of potentially dangerous intermediates Initial substrate (threonine) Feedback Active site available Threonine in active site Inhibition Enzyme 1 (threonine The end-products of Isoleucine deaminase) used up by metabolic pathways can cell be important reversible Intermediate A Feedback enzyme