Chapter 8: An Introduction to Metabolism
Chapter 8: An Introduction to Metabolism Biol 5A
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Date Created: 01/27/16
CHAPTER 8: AN INTRODUCTION TO METBOLISM Metabolism: the totality of an organism’s chemical reactions; manages material and energy resources of the cell Metabolic pathway: o Begins with a specific molecule that is altered in steps, resulting in a product (can have multiple starting molecules and products) o Each step is catalyzed by enzymes o Some release energy (exergonic) to break down complex molecules—catabolic pathways (breakdown pathways) ex: cellular respiration—glucose is broken down in the presence of oxygen gas to carbon dioxide gas and water o Some consume energy (endergonic) to build complex molecules—anabolic pathways (biosynthetic pathways) Ex: photosynthesis, synthesis of amino acids and proteins o Energy released from downhill catabolic pathways is stored and used to drive uphill reactions of anabolic pathways Forms of Energy Energy: capacity to cause change o Move matter against opposing forces (gravity and forces) o Rearrange a collection of matter Kinetic energy: relative motion of objects o heat or thermal energy kinetic energy associated with the random movement of atoms or molecules Potential energy: o the energy matter possesses because of its location or structure o arrangement of electrons in bonds between atoms o chemical energy potential energy available for release in chemical reactions complex molecules have high chemical energy The Laws of Energy Transformation Thermodynamics: study of energy transformations that occur in a collection of matter o System: the particular matter under study o Surroundings: everything outside of the system o Isolated system: unable to exchange energy or matter with its surroundings o Open system: energy and matter can be transferred between the system and surroundings o Determines whether a reaction will or will not occur First Law of Thermodynamics o The energy of the universe is constant—energy can be transformed and transferred but not created or destroyed o Principle of conservation of energy Second Law of Thermodynamics o Entropy: measure of disorder or randomness o Every energy transfer or transformation increases the entropy of the universe o Spontaneous process: process that can occur without an input of energy It must increase the entropy of the universe Kinetics The speed or rates of reactions Reaction rates are affected by: o Nature of what is undergoing the reaction—reactions involving acids/salts are faster than those involving the breaking or forming of covalent bonds o Physical state o Concentration (the higher the concentration, the higher the rate of particle collisions) o Temperature o Catalyst: substance that accelerates the forward and the reverse reactions by lowering the activation energy Free Energy ∆G = energy available to do work ∆H = the total energy of the system T = temperature ∆S = change in entropy T∆S represents heat or unusable energy Free energy: the portion of the system’s energy that can perform work when temperature and pressure are uniform throughout the system o The measure of a system’s inability/tendency to change to a more stable state o It will predict if a process will be spontaneous—G and H need to be negative, while T and S will be positive o Every spontaneous process decreases the system’s free energy, and processes with a positive or 0 G-value are non-spontaneous o The higher the G-value, the more unstable the system. The system will tend to change in order to have a lower G-value o As a reaction proceeds to equilibrium, the free energy of the mixture of reactants and products decreases G is at its lowest value Process is spontaneous and can perform work only when it is moving towards equilibrium Exergonic and Endergonic Reactions in Metabolism Exergonic reactions: proceeds with a net release of free energy o Free energy is lost o Occur spontaneously o Negative ∆G and ∆H o Positive ∆S o Increase in entropy and temperature o G = -686J; cellular respiration, hydrolysis Endergonic reactions: one that absorbs free energy from its surroundings o Stores free energy in molecules o Occurs non-spontaneously o Positive ∆G and ∆H o Negative ∆S o Decrease in entropy and temperature o G = +686J; photosynthesis, protein/DNA synthesis Equilibrium and Metabolism Reactions in isolated systems can reach equilibrium Chemical reactions of metabolism are reversible Cells that have reached metabolic equilibrium are dead (living cells are never in equilibrium) Cells are NOT isolated systems To create more order, heat is released and causes disorder in the surroundings Order is maintained by the constant input of energy (loss of order = death) Types of Work Performed by Cells Chemical work o Pushing of endergonic reactions that would not occur spontaneously (synthesis of polymers from monomers) Transport work o Pumping of substances across membranes against direction of spontaneous movement Mechanical work o Beating of cilia, contraction of muscle cells, movement of chromosomes during cellular respiration Energy coupling: the use of exergonic processes to drive energonic ones o Links +∆G with --∆G (spontaneous/exergonic with non-spontaneous/endergonic) o Uses ATP as an immediate source of energy that powers cellular work Structure and Hydrolysis of ATP ATP is used for energy coupling and to make RNA Bonds between the phosphate groups of ATP can be broken by hydrolysis o When the terminal phosphate bond is broken, molecule of inorganic phosphate leaves ATP, becomes adenosine diphosphate (ADP) Exergonic reaction How the Hydrolysis of ATP Performs Work When ATP is hydrolyzed, the release of free energy produces heat Cells are able to use the energy released by ATP to drive endergonic chemical reactions with enzymes Phosphorylated intermediate: recipient with the phosphate group covalently bonded to o The key to coupling exergonic and endergonic reactions, more reactive than an un-phosphorylated molecule Hydrolysis of ATP is also used in transport and mechanical work o Leads to a change in protein’s shape and its ability to bind to another molecule o Sometimes involves phosphorylated intermediate o ATP is bonded non-covalently to motor protein, ATP is hydrolyzed releasing ADP and Pi, then another ATP molecule can bind—at each stage the motor protein changes shape and its ability to bind to the cytoskeleton Regeneration of ATP ATP is renewable, can be regenerated by the addition of P to ADP The energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) o ATP cycle o Formation of ATP is not spontaneous; requires the use of free energy o Catabolic pathways, light energy The Activation Energy Barrier Enzyme: molecule that acts like a catalyst, a chemical agent that speeds up a reaction without becoming consumed by the reaction Activation energy: initial investment of energy for starting a reaction, energy required to contort the reactant molecules so bonds can break o Amount of energy needed to push reactants uphill so the downhill portion can begin o Supplied as thermal energy that reactants absorb from the surroundings o When enough energy is absorbed, reactants are in the transition state (unstable) o As atoms settle into their new, more stable bonding arrangements, energy is released to the surroundings o Provides a barrier that determines the rate of the reaction How Enzymes Lower the Activation Energy Barrier Heat speeds up a reaction by allowing reactants to attain the transition state more often o Not a good method for biological molecules: High temperature denatures proteins and kills cells Heat would speed up all reactions, not just those that are needed Enzyme lowers activation energy by enabling reactant molecules to absorb enough energy to reach transition state at even moderate temperatures o Cannot change G (make endergonic into exergonic) o Hasten reactions that would eventually occur Allow for dynamic metabolism, determine which chemical processes will be going on in a cell at any particular time because they are so specific o Brings reactants closer to each other, requires less energy Substrate Specificity of Enzymes Substrate: reactant an enzyme acts upon o Enzyme forms an enzymatic substrate complex when it binds to substrate Enzyme’s specificity arises from its shape, which is a consequence of its amino acid sequence Active site: restricted region of the enzyme molecule that binds to the substrate o Formed by only a few of an enzyme’s amino acids Enzymes don’t have stiff structures; change between subtle different shapes in dynamic equilibrium with slight differences in free energy As substrate enters active site, enzyme changes shape slightly due to interactions between substrate’s chemical groups on the side chains of the amino acids that form the active site o Shape change makes active site fit more snuggly around the substrate—induced fit Brings chemical groups of active site into positions that enhance their ability to catalyze chemical reactions Catalysis in the Enzyme’s Active Site Substrate held in active site by weak interactions, H bonds and ionic bonds R groups of a few amino acids of the active site catalyze conversion of substrate to product Lower activation energy and speed up a reaction o In reactions involving two or more reactants, the active site provides a template on which substrates can come together in proper orientation for reaction to occur between them o As the active site clutches its bound substrates, the enzyme may stretch the substrate molecules toward their transition state form, stressing and bending chemical bonds that must be broken o Active site may provide a microenvironment that is more conductive to a particular type of reaction than the solution itself would be without the enzyme o Direct participation of the active site in the chemical reaction Rate at which enzyme converts substrate to product depends on initial concentration of substrate o More substrate molecules, more frequently they access active sites of enzyme molecules o There is a limit as to how fast a reaction can be pushed by adding more substrate o When enzyme population is saturated, the only way to increase its rate of product formation is to add more of the enzyme Effects of Temperature and pH Rate of enzymatic reaction increases with increasing temperatures (optimal temperature) o Too high temperature disrupts hydrogen bonds that stabilize the active shape of an enzyme and it denatures as a result Optimal pH around 6-8 Cofactors Cofactors: non-protein helpers used by enzymes, may be bound tightly to an enzyme as a permanent resident or they may bind loosely and reversibly along with a substrate o Some are inorganic o If it is organic it is called a coenzyme Most vitamins are important because they act as coenzymes or raw materials from which coenzymes are made Enzyme Inhibitors Most enzyme inhibitors bind to the enzyme by weak interactions Competitive inhibitors: reduce productivity of enzymes by blocking substrates from entering active sites o can be overcome by increasing concentration of substrate so active sites become available Noncompetitive inhibitors: impede enzymatic reactions by binding to another part of the enzyme o Cause enzyme molecule to change its shape in a way that the active site becomes less effective at catalyzing conversion of substrate to product Allosteric Activation and Inhibition Allosteric regulation: protein’s function at one site is affected by a regulatory molecule to a separate site, may result in inhibition or stimulation of an enzyme’s activity Most allosterically regulated enzymes are composed from 2 or more subunits, each composed of polypeptide chain with its own active site Two different shapes: o Catalytically active o Inactive Activating or inhibiting regularly molecule binds to regulatory site where subunits join ( allosteric site) Binding of an activator to a regulatory site stabilizes the shape that has active sites Binding of an inhibitor to a regulatory site stabilizes inactive form Allosteric activation methods: o Fluctuating concentrations of regulators can cause a sophisticated pattern of responses in activity of cellular enzymes o Substrate molecule binding to one active site in a multi-subunit enzyme triggers a shape change in all of the subunits, increasing catalytic activity at other active sites Cooperativity: amplifies the response of enzyme to substrates One substrate molecule primers an enzyme to act on additional substrates more readily Allosteric because binding of substrate to one active site affects catalysis in another active site Identification of Allosteric Regulators Hard to categorize allosteric molecules because they bind to enzymes at low affinity, therefore hard to isolate Allosteric regulators exhibit higher specificity for particular enzymes than do inhibitors that bind to the active site Studies designed to find allosteric inhibitors of caspases (protein digesting enzymes) o By targeting caspases, better able to manage inappropriate inflammatory responses Feedback Inhibition Metabolic pathway is switched off by inhibitory binding of its end product to an enzyme that acts early on in the pathway Synthesizing amino acid isoleucine from threonine o As isoleucine accumulates, slows down synthesis by allosterically inhibiting the enzyme from the first step of the pathway Prevents cell from wasting chemical resources Specific Localization of Enzymes within the Cell Some enzymes/enzyme complexes have fixed locations within the cell and act as structural components of membranes Others are in solution within membrane enclosed organelles o Ex: Mitochondria
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