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Chapter 8: An Introduction to Metabolism Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Marie Maynard Daly – American biochemist who did extensive research into the metabolism of the arterial wall in the 1960s. Her worked helped to uncover several processes related to aging. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: The Energy of Life • The living cell is a miniature chemical factory where thousands of reactions occur • The cell extracts energy and applies energy to perform work • Some organisms even convert energy to light, as in bioluminescence © 2011 Pearson Education, Inc. Bioluminescence by a fungus Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 8.1: An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics • Metabolism is the totality of an organism’s chemical reactions © 2011 Pearson Education, Inc. 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 © 2011 Pearson Education, Inc. Figure 8.UN01 Enzyme 2 Enzyme 1 A Reaction 1 Starting molecule Enzyme 3 D C B Reaction 2 Reaction 3 Product • Catabolic pathways release energy by breaking down complex molecules into simpler compounds • Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism © 2011 Pearson Education, Inc. • Anabolic pathways consume energy to build complex molecules from simpler ones • The synthesis of protein from amino acids is an example of anabolism © 2011 Pearson Education, Inc. Forms of Energy • Energy is the capacity to cause change • Energy exists in various forms, some of which can perform work • Kinetic energy is energy associated with motion • Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules • Potential energy is energy that matter possesses because of its location or structure • Chemical energy is potential energy available for release in a chemical reaction • Energy can be converted from one form to another © 2011 Pearson Education, Inc. Figure 8.2 Transformations between kinetic and potential energy On the platform, a diver has more potential energy. Climbing up converts kinetic energy of muscle movement to potential energy. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Diving converts potential energy to kinetic energy. In the water, a diver has less potential energy. Figure 8.3 The two laws of thermodynamics Heat Chemical energy (a) First law of thermodynamics (b) Second law of thermodynamics The First Law of Thermodynamics • According to the first law of thermodynamics, the energy of the universe is constant – Energy can be transferred and transformed, but it cannot be created or destroyed • The first law is also called the principle of conservation of energy © 2011 Pearson Education, Inc. The Second Law of Thermodynamics • During every energy transfer or transformation, some energy is unusable, and is often lost as heat • According to the second law of thermodynamics – Every energy transfer or transformation increases the entropy (disorder) of the universe © 2011 Pearson Education, Inc. Exergonic and Endergonic Reactions in Metabolism • An exergonic reaction proceeds with a net release of free energy and is spontaneous • An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous © 2011 Pearson Education, Inc. Figure 8.6 Free energy changes (G) in exergonic and endergonic reactions Reactants Free energy Amount of energy released (∆G<0) Energy Products Progress of the reaction (a) Exergonic reaction: energy released Free energy Products Amount of energy released (∆G>0) Energy Reactants Progress of the reaction (b) Endergonic reaction: energy required Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions • A cell does three main kinds of work – Chemical – Transport – Mechanical • To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one • Most energy coupling in cells is mediated by ATP © 2011 Pearson Education, Inc. Figure 8.8 The structure of adenosine triphosphate (ATP) Adenine N O –O P O– O P O– O P C C N C CH HC O O O N CH2 O O– H Phosphate groups H H Ribose H OH Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings NH2 OH N Figure 8.9 The hydrolysis of ATP P P P Adenosine triphosphate (ATP) H2O Pi + Inorganic phosphate P P Adenosine diphosphate (ADP) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Energy Figure 8.11 How ATP drives cellular work P i P Motor protein Protein moved (a) Mechanical work: ATP phosphorylates motor proteins Membrane protein ADP + ATP P Pi P Solute Solute transported (b) Transport work: ATP phosphorylates transport proteins P Glu + NH3 Reactants: Glutamic acid and ammonia NH2 + P i Glu Product (glutamine) made (c) Chemical work: ATP phosphorylates key reactants Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings i Figure 8.12 The ATP cycle ATP hydrolysis to ADP + P i yields energy ATP synthesis from ADP + P i requires energy ATP Energy from catabolism (exergonic, energy yielding processes) ADP + P Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings i Energy for cellular work (endergonic, energyconsuming processes) Concept 8.4: Enzymes speed up metabolic reactions by lowering energy barriers • A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction • An enzyme is a catalytic protein • Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction © 2011 Pearson Education, Inc. Figure 8.13 The effect of enzymes on reaction rate. Course of reaction without enzyme EA without enzyme Free energy EA with enzyme is lower Reactants ∆G is unaffected by enzyme Course of reaction with enzyme Products Progress of the reaction Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 8.14 Induced fit between an enzyme and its substrate Substrate Active site Enzyme- substrate complex Enzyme (a) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings (b) Figure 8.15 The active site and catalytic cycle of an enzyme 1 Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit). Substrates Enzyme-substrate complex 6 Active site is available for two new substrate molecules. Enzyme 5 Products are Released. Products Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 2 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. 3 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. 4 Substrates are Converted into Products. Figure 8.16 Environmental factors affecting enzyme activity Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria Rate of reaction Optimal temperature for typical human enzyme 0 60 40 20 80 100 Temperature (Cº) (a) Optimal temperature for two enzymes Rate of reaction Optimal pH for pepsin (stomach enzyme) 0 1 2 3 4 5 pH Optimal pH for trypsin (intestinal enzyme) 6 OptimalpH for two two enzymes enzymes (b) Optimal pH for Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 7 8 9 10 Cofactors & Coenzymes • Cofactors are nonprotein enzyme helpers • Cofactors may be inorganic (such as a mineral in ionic form) or organic • An organic cofactor is called a coenzyme • Coenzymes include vitamins © 2011 Pearson Education, Inc. Enzyme Inhibitors • Competitive inhibitors bind to the active site of an enzyme, competing with the substrate • Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective • Examples of inhibitors include toxins, poisons, pesticides, and antibiotics © 2011 Pearson Education, Inc. Figure 8.17 Inhibition of enzyme activity A substrate can bind normally to the active site of an enzyme. Substrate Active site Enzyme (a) Normal binding A competitive inhibitor mimics the substrate, competing for the active site. 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. Competitive inhibitor (b) Competitive inhibition Noncompetitive inhibitor (c) Noncompetitive inhibition Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Allosteric Regulation of Enzymes • Allosteric regulation may either inhibit or stimulate an enzyme’s activity • Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site © 2011 Pearson Education, Inc. Figure 8.19 Allosteric regulation of enzyme activity Allosteric enyzme with four subunits Regulatory site (one of four) Active site (one of four) Allosteric activater stabilizes active from Activator Active form Stabilized active form Oscillation Allosteric activater stabilizes active form NonInactive form Inhibitor functional active site Stabilized inactive form (a) Allosteric activators and inhibitors. In the cell, activators and inhibitors dissociate when at low concentrations. The enzyme can then oscillate again. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. Substrate Inactive form Stabilized active form (b) Cooperativity: another type of allosteric activation. Note that the inactive form shown on the left oscillates back and forth with the active form when the active form is not stabilized by substrate. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings