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An Introduction to Metabolism chapter 8 1 Energy & Matter Universe is composed of 2 things …… Energy Ability to do work o Force on an object that causes it to move Matter Anything that has mass and occupies space Atoms/elements 2 Metabolism transforming matter and energy Metabolism -- totality of an organism’s chemical reactions Arises from interactions between molecules within the cell 3 Organization of the Chemistry of Life into Metabolic Pathways A metabolic pathway begins with a specific molecule and ends with a product Each step is catalyzed by a specific enzyme Enzyme 1 A B Reaction 1 Starting molecule Enzyme 2 Enzyme 3 D C Reaction 2 Reaction 3 Product 4 Kinds of Pathways Catabolic pathways -- release energy break down complex molecules into simpler compounds Anabolic pathways -- consume energy build complex molecules from simpler ones Bioenergetics -- study of how organisms manage their energy resources 5 6 Chemical Reactions Functionality Catabolic Anabolic Energy Requirements Endergonic Exergonic 7 Chemical Reactions Reactions can be categorized as exergonic or endergonic based on energy gain or loss Chemical reactions require initial energy input (activation energy) Molecules need to be moving with sufficient collision speed The electrons of an atom repel other atoms and inhibit bond formation 8 Energy The ability to do work Work -- force on an object that causes it to move What’s moving? Two kinds of energy Kinetic Potential – can be positional 9 What Is Energy? The two fundamental types Kinetic -- energy of movement o Heat (thermal energy) -- random movement of atoms or molecules Potential -- stored energy (can be because of location!) o Chemical energy -- available for release in a chemical reaction 10 Overview: The Energy of Life Living cell -- miniature chemical factory Energy transformed and stored Energy observed in many forms 11 The Laws of Energy Transformation Thermodynamics -- study of energy transformations Describe availability & usefulness of energy Closed system -- isolated from its surroundings Open system -- energy and matter can be transferred between the system and its surroundings 12 Closed and open hydroelectric systems can serve as analogies G < 0 G = 0 A closed hydroelectric system G < 0 An open hydroelectric system Laws of Thermodynamics First -- In any process, the total energy of the universe remains constant. Principle of conservation of energy Energy can be transferred and transformed Energy cannot be created or destroyed Second -- The entropy of an isolated system not in equilibrium will tend to increase over time, approaching a maximum value at equilibrium. During every energy transfer or transformation, energy is “lost” (the amount of useable energy decreases; 14 disorder increases) Thermodynamics 15 16 Entropy Entropy – randomness Energy conversions increase entropy in the universe Spontaneous processes increase entropy Explosions; car rusting Non-spontaneous process – energy input Rocks rolling uphill 17 Enthalpy Enthalpy (H) – total potential energy of system Total energy = Usable Energy + Unusable Energy Entropy (S) – randomness or disorder (unusable energy) Free Energy (G) – energy available to do work ΔG -- change in free energy ΔG = ΔGfinal – ΔGinitial A negative ΔG – spontaneous Note – as entropy increases, free energy decreases 18 Free Energy & Stability 19 Exergonic Reactions Exergonic reactions release energy Reactants contain more energy than products 20 Exergonic Reactions Exergonic reactions release energy Reactants contain more energy than products 21 Endergonic Reactions Endergonic reactions require an input of energy Products contain more energy than reactants 22 Endergonic Reactions Endergonic reactions require an input of energy Products contain more energy than reactants 23 Coupled Reactions Exergonic reactions drive endergonic reactions The product of an energy-yielding reaction fuels an energy-requiring reaction in a coupled reaction The parts of coupled reactions often occur at different places within the cell Energy-carrier molecules transfer the energy within cells 24 ATP powers cellular work by coupling exergonic reactions to endergonic reactions Cells do work: Mechanical Transport Chemical Cells manage energy resources by energy coupling: the use of an exergonic process to drive an endergonic one 25 The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) -- cell’s energy shuttle ATP provides energy for cellular functions 26 Hydrolysis of ATP High energy phosphate bonds -- broken by hydrolysis Energy release -- chemical change to a state of lower free energy, not from the phosphate bonds themselves 27 Energy from ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic 28 Phosphorylation Pi P Protein moved Motor protein Mechanical work: ATP phosphorylates motor proteins Membrane protein ADP + Pi ATP Pi P Solute Solute transported Transport work: ATP phosphorylates transport proteins P NH3 Glu + NH2 Glu + Pi Reactants: Glutamic acid Product (glutamine) and ammonia made Chemical work: ATP phosphorylates key reactants The Regeneration of ATP ATP -- renewable resource regenerated by addition of a phosphate group to ADP The energy comes from catabolic reactions in the cell The potential energy stored in ATP drives most cellular work 30 LE 8-12 ATP Energy from catabolism (exergonic, energyyielding processes) Energy for cellular work (endergonic, energyconsuming processes) ADP + P i Exergonic Reactions Exergonic reactions release energy Spontaneous? 32 33 The Activation Energy Barrier Chemical reactions -- bond breaking and bond forming The initial energy -- free energy of activation, or activation energy (EA) EA often supplied in the form of heat from the surroundings 34 LE 8-14 A B C D Free energy Transition state A B C D EA Reactants A B G < O C D Products Progress of the reaction How Enzymes Catalyze Reactions Lowering Energy of Activation (EA) Enzymes do not affect the change in free-energy hasten reactions that would occur eventually Biological catalysts Specific for the molecules they catalyze Activity often enhanced or suppressed by their reactants or products 36 LE 8-15 Free energy Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Course of reaction with enzyme G is unaffected by enzyme Products Progress of the reaction Catalysts Catalyst -- chemical agent that speeds up a reaction without being consumed by the reaction Enzyme -- catalytic protein Example: Hydrolysis of sucrose by sucrase Sucrose C12H22O11 Glucose C6H12O6 Fructose C6H12O6 38 Enzymes Enzymes are a type of protein that acts as a catalyst, speeding up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Substrate (sucrose) Glucose Fructose Enzyme (sucrose) 39 LE 8-17 Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit). Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. Substrates Enzyme-substrate complex Active site is available for two new substrate molecules. Enzyme Products are released. Substrates are converted into products. Products Active site (and R groups of its amino acids) can lower EA and speed up a reaction by • acting as a template for substrate orientation, • stressing the substrates and stabilizing the transition state, • providing a favorable microenvironment, • participating directly in the catalytic reaction. Optimal temperature for typical human enzyme An enzyme’s activity can be affected by: General environmental factors o o temperature pH Optimal temperature for enzyme of thermophilic (heat-tolerant bacteria) LE 8-18 0 40 60 Temperature (°C) 20 80 100 Optimal temperature for two enzymes Optimal pH for pepsin (stomach enzyme) Chemicals that specifically influence the enzyme 0 1 2 3 Optimal pH for trypsin (intestinal enzyme) 4 5 pH Optimal pH for two enzymes 6 7 8 9 10 Competitive -- bind to the active site of an enzyme Noncompetitive -- bind to another part of an enzyme A substrate can bind normally to the active site of an LE 8-19 enzyme. Substrate Active site Enzyme Normal binding A competitive inhibitor mimics the substrate, competing for the active site. changes shape makes active site less effective Competitive inhibitor Competitive inhibition A noncompetitive inhibitor binds to the enzyme away from the active site, altering the conformation of the enzyme so that its active site no longer functions. Noncompetitive inhibitor Noncompetitive inhibition Regulation of enzyme activity helps control metabolism Chemical chaos -- if cell’s metabolic pathways were not tightly regulated Cells switch genes on or off that encode specific enzymes 43 Allosteric Regulation of Enzymes Enzymes -- active and inactive forms The binding of activator -- stabilizes the active form The binding of an inhibitor -- stabilizes the inactive form 44 Allosteric activator stabilizes active form. LE 8-20a Allosteric enzyme with four subunits Allosteric regulation function affected by binding of a regulatory molecule at another site Regulatory site (one of four) Active site (one of four) Activator Active form Stabilized active form Oscillation Nonfunctional active site Inactive form Allosteric inhibitor stabilizes inactive form. Inhibitor Allosteric activators and inhibitors Stabilized inactive form 45 Allosteric Regulation Cooperativity -- can amplify enzyme activity Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. Substrate Inactive form Cooperativity another type of allosteric activation Stabilized active form 46 Feedback Inhibition Isoleucine used up by cell End product of a metabolic pathway shuts down the pathway Intermediate A Feedback inhibition Isoleucine binds to allosteric site Active site of enzyme 1 can’t bind Intermediate B theonine pathway off Intermediate C Intermediate D End product (isoleucine) 47