Chapter 8 Intro to Metabolism Overview: The Energy of Life Thousands of chemical reactions occur inside of a cell; cells = mini factories The cell extracts energy and applies energy to perform work Many examples of energy conversion Chemical kinetic Light chemical Chemical light What other examples of bioluminescence can you think of? What adaptive advantage does bioluminescence provide? Energy Transformation Metabolism - totality of an organisms chemical reactions an emergent property of life that arises from interactions between molecules within the cell Metabolic Pathways Begin with specific molecule (reactant) End with specific product Each step is catalyzed by a specific enzyme LE 8-UN141 Enzyme 1 AB Reaction 1 Enzyme 2 C Reaction 2 Enzyme 3 D Reaction 3 Product Starting molecule Metabolism Bioenergetics - study of how organisms manage their energy resources Catabolic pathways - release energy by breaking down complex molecules into simpler compounds Anabolic pathways - consume energy to build complex molecules from simpler ones Forms of Energy Energy - capacity to cause change (usually to do work) Energy exists in various forms, some of which can perform work Chemical Kinetic Potential Thermal Light LE 8-2 On the platform, the diver has more potential energy. Diving converts potential energy to kinetic energy. Climbing up converts kinetic energy of muscle movement to potential energy. In the water, the diver has less potential energy. The Laws of Energy Transformation Thermodynamics - study of energy transformations Closed system - isolated from its surroundings (liquids inside of a thermos) Open system - energy & matter can be transferred between the system & its surroundings Are organisms open or closed systems? The First Law of Thermodynamics Energy of the universe is constant Energy can be transferred & transformed but not made or destroyed Also called the principle of conservation of energy The Second Law of Thermodynamics During every energy transfer or transformation, some energy is unusable, often lost as heat Every energy transfer leads to an increase in entropy in the universe Entropy (S) a measure of disorder that accounts for randomness Positive entropy spontaneous reactions How do nonspontaneous chemical reactions occur? LE 8-3 Chemical energy Heat CO 2 First law of thermodynamicsSecond law of thermodynamics H2OH2O Biological Entropy Living cells unavoidably convert organized forms of energy to heat Spontaneous processes occur without energy input; they can happen quickly or slowly For a process to occur without energy input, it must increase the entropy of the universe Biological Order and Disorder Cells create ordered structures from less ordered materials Organisms also replace ordered forms of matter & energy with less ordered forms The evolution of more complex organisms does not violate the 2nd law of thermodynamics Entropy (disorder) may in an organism, but the universes total entropy s Free Energy (G) Which metabolic processes are spontaneous? To find out, we must calculate changes in energy for chemical reactions A living systems free energy energy that can do work when temperature & pressure are uniform, as in a living cell Free Energy The change in free energy (G) during a process is related to the change in enthalpy, or change in total energy (H), and change in entropy (TS): G = H - TS Only processes with a negative G are spontaneous Spontaneous processes can be harnessed to perform work G = H - TS G = Change in Gibbs free energy H = Change in enthalpy T = Temperature (K) S = Change in entropy Enthalpy = heat/energy of a system (internal energy + PxV) If G < 0, the reaction is spontaneous If G > 0, the reaction is nonspontaneous Free Energy, Stability, and Equilibrium Free energy - measure of a systems instability; its tendency to change to a more stable state During spontaneous change, free energy decreases & the stability of a system increases Equilibrium - state of maximum stability A process is spontaneous & can perform work only when it is moving toward equilibrium LE 8-5 Gravitational motionDiffusionChemical reaction Brainstorm Why is the concept of free energy so important when we are studying metabolic processes? Video Free energy and metabolism Exergonic reaction - net release of free energy; spontaneous Cellular respiration products store amount of energy less than reactants equal to amount of energy released by reaction Endergonic reaction - absorbs free energy from its surroundings; nonspontaneous Stores free energy (positive G) If a reaction is exergonic, the reverse reaction must be endergonic LE 8-6a Reactants Energy Products Progress of the reaction Amount of energy released ( G < 0) Free energy Exergonic reaction: energy released LE 8-6b Reactants Energy Products Progress of the reaction Amount of energy required ( G > 0) Free energy Endergonic reaction: energy required Equilibrium and Metabolism Reactions in a closed system eventually reach equilibrium & then do no work Cells are not in equilibrium; open systems with constant flow of materials A catabolic pathway in a cell releases free energy in a series of reactions LE 8-7a G = 0 A closed hydroelectric system G < 0 LE 8-7b An open hydroelectric system G < 0 LE 8-7c A multistep open hydroelectric system G < 0 ATP, exergonic, and endergonic reactions Cells do 3 main kinds of work: Mechanical Transport Chemical To do work, cells manage energy resources by energy coupling - using an exergonic process to drive an endergonic one The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) is the cells energy shuttle ATP provides energy for cellular functions Ribose ATP Bonds between the phosphate groups of ATPs tail can be broken by hydrolysis; energy released from ATP Energy is released from ATP when the terminal phosphate bond is broken Release of energy comes from chemical change to a state of lower free energy, not from the phosphate bonds themselves LE 8-9 Adenosine triphosphate (ATP) Energy PP P PP P i Adenosine diphosphate (ADP) Inorganic phosphate H2OH2O + + ATP In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic LE 8-10 Endergonic reaction: G is positive, reaction is not spontaneous Exergonic reaction: G is negative, reaction is spontaneous G = +3.4 kcal/mol G = 7.3 kcal/mol G = 3.9 kcal/mol NH 2 NH 3 Glu Glutamic acid Coupled reactions: Overall G is negative; together, reactions are spontaneous AmmoniaGlutamine ATP H2OH2O ADP P i + + + How ATP Performs Work ATP drives endergonic reactions by phosphorylation, transferring a P group to some other molecule (reactant) recipient molecule is now phosphorylated The 3 types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP Review: Explain the process of hydrolysis. LE 8-11 NH 2 Glu P i P i P i P i NH 3 P P P ATP ADP Motor protein Mechanical work: ATP phosphorylates motor proteins Protein moved Membrane protein Solute Transport work: ATP phosphorylates transport proteins Solute transported Chemical work: ATP phosphorylates key reactants Reactants: Glutamic acid and ammonia Product (glutamine) made + + + The Regeneration of ATP ATP - renewable resource regenerated by adding a P group to ADP energy to phosphorylate ADP comes from catabolic reactions in cell chemical potential energy temporarily stored in ATP drives most cell work LE 8-12 P i ADP Energy for cellular work (endergonic, energy- consuming processes) Energy from catabolism (energonic, energy- yielding processes) ATP + Enzymes Catalyst - chemical agent that speeds up a reaction without being consumed Enzyme - catalytic protein Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme- catalyzed reaction LE 8-13 Sucrose C 12 H 22 O 11 Glucose C 6 H 12 O 6 Fructose C 6 H 12 O 6 The Activation Energy Barrier Every chemical reaction involves bond breaking & bond forming Initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA) Activation energy(EA) - energy needed to start a reaction; often supplied in the form of heat from the surroundings LE 8-14 Transition state CD A B EAEA Products CD A B G < O Progress of the reaction Reactants C D A B Free energy How Enzymes Lower the EA Barrier Enzymes catalyze reactions by lowering the EA barrier Enzymes dont affect the change in free- energy (G); instead, they speed up reactions that would occur eventually LE 8-15 Course of reaction without enzyme E A without enzyme G is unaffected by enzyme Progress of the reaction Free energy E A with enzyme is lower Course of reaction with enzyme Reactants Products Substrate Specificity of Enzymes Substrate - reactant an enzyme acts on Enzyme binds to its substrate, forming an enzyme-substrate complex Active site - on enzyme where the substrate binds Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction LE 8-16 Substrate Active site Enzyme Enzyme-substrate complex Catalysis in the Enzymes Active Site In an enzymatic reaction, the substrate binds to the active site Active site lowers EA barrier by Orienting substrates correctly Straining substrate bonds Providing a favorable microenvironment Covalently bonding to the substrate LE 8-17 Enzyme-substrate complex Substrates Enzyme Products 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. Active site (and R groups of its amino acids) can lower E A 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. Substrates are converted into products. Products are released. Active site is available for two new substrate molecules. Effects of Local Conditions on Enzyme Activity Enzyme activity affected by: Temperature and pH Chemicals Substrate concentration Effects of Temperature and pH Each enzyme has an optimal temperature & an optimal pH Most enzymes that affect humans operate best at 35-40C Optimal pH for most enzymes is 6-8 LE 8-18 Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant bacteria) Temperature (C) Optimal temperature for two enzymes Rate of reaction Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) pH Optimal pH for two enzymes 0 Rate of reaction Cofactors Cofactors - nonprotein enzyme helpers; minerals Coenzymes- organic cofactors; vitamins 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 & making the active site less effective LE 8-19 Substrate Active site Enzyme Competitive inhibitor Normal binding Competitive inhibition Noncompetitive inhibitor Noncompetitive inhibition A substrate can bind normally to the active site of an enzyme. 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. Regulation of Enzyme Activity Chemical chaos would result if a cells metabolic pathways were not tightly regulated To regulate metabolic pathways, the cell switches on or off the genes that encode specific enzymes Allosteric Regulation of Enzymes Allosteric regulation - a proteins function at 1 site is affected by binding of a regulatory molecule at another site; can either inhibit or stimulate an enzymes activity Allosteric Activation and Inhibition Most allosterically regulated enzymes are made from polypeptide subunits Each enzyme has active and inactive forms The binding of an activator stabilizes the active form of the enzyme The binding of an inhibitor stabilizes the inactive form of the enzyme LE 8-20a Allosteric enzyme with four subunits Regulatory site (one of four) Active form Activator Stabilized active form Active site (one of four) Allosteric activator stabilizes active form. Non- functional active site Inactive form Inhibitor Stabilized inactive form Allosteric inhibitor stabilizes inactive form. Oscillation Allosteric activators and inhibitors Allosteric Regulation Cooperativity is a form of allosteric regulation that can amplify enzyme activity Cooperativity - binding by a substrate to 1 active site stabilizes favorable conformational changes at all other subunits LE 8-20b Substrate Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. Cooperativity another type of allosteric activation Stabilized active form Inactive form Feedback Inhibition Feedback inhibition - end product of a metabolic pathway shuts down the pathway Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed What kind of feedback loop is this an example of? LE 8-21 Active site available Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Enzyme 2 Intermediate A Isoleucine used up by cell Feedback inhibition Active site of enzyme 1 cant bind theonine pathway off Isoleucine binds to allosteric site Enzyme 3 Intermediate B Enzyme 4 Intermediate C Enzyme 5 Intermediate D End product (isoleucine) Specific Localization of Enzymes Within the Cell Structures within the cell help bring order to metabolic pathways Some enzymes act as structural components of membranes Some enzymes reside in specific organelles, such as enzymes for cellular respiration being located in mitochondria LE 8-22 Mitochondria, sites of cellular respiration 1 m