Bio Week 6 Notes
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This 9 page Class Notes was uploaded by Mary Notetaker on Thursday September 29, 2016. The Class Notes belongs to BIO 101 at University of South Carolina taught by Mihaly Czako in Fall 2016. Since its upload, it has received 8 views.
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Date Created: 09/29/16
Biology Chapter 8: Introduction to Metabolism Metabolism changes matter and energy according to thermodynamic laws o Metabolism – totality of an organism’s chemical reactions From Greek “metabole” – change Emergent property that occurs from orderly molecule interactions Organization of Chemistry of Life in metabolic pathways o Metabolic pathway – specific molecules that is altered in a series of defined steps which results in a product Each step catalyzed by a specific enzyme – balance supply and demand o Metabolism manages material and energy resources of cell Catabolic pathways – degradative process where some metabolic pathways release energy by breaking down complex molecules to simpler compounds Major pathway = cellular respiration – sugar glucose and other organic fuels broken down in presence of oxygen to carbon dioxide and water o Pathways can have more than one initial molecule or product o Energy stored in organic molecules becomes available to do cell work (ex: ciliary beating/membrane transport) Anabolic pathways (biosynthetic pathways) consume energy to build complicated molecules form simpler ones Ex: synthesis of protein from amino acid Catabolic/anabolic pathways – downhill/uphill Energy released from downhill reactions can be stored and used to power uphill reactions Bioenergetics – study of how energy flows through living organisms Forms of Energy o Energy – capacity to cause change Used to do work – move matter against opposing forces like gravity and friction Ability to rearrange a collection of matter Exists in various forms Kinetic energy – energy associated with relative motion of objects Thermal energy – kinetic energy associated with random movement of atoms or molecules Heat – thermal energy transfer from one object to another Light – type of energy that can be harnessed for work – powering photosynthesis Potential energy – not kinetic, energy possessed because of location or structure Chemical energy – potential energy of a chemical reaction Organisms are energy transformers Laws of Energy Transformation o Thermodynamics – study of energy transformations that occur in a collection of matter System – matter under study Surroundings – everything outside the system Isolated system – cannot exchange energy or matter with surroundings Open system – energy and matter can be transferred between the system and its surroundings Ex: organisms – absorb energy (light energy in the form of organic molecules and release heat and metabolic waste products to surroundings Laws of Thermodynamics – 2 govern energy transformations in organisms and collections of matter o 1 law of thermodynamics energy can be transferred and transformed but cannot be created or destroyed o 2 law of thermodynamics – energy transfer or transformation increases the entropy of the universe every energy transfer results with some energy unavailable to do work most energy transformations – more usable energy is converted to thermal energy and released as heat o chemical reactions that perform work converts energy to heat a system can use this energy only when there is a temperature difference that results in thermal energy flowing as heat from warmer area to cooler one if temperature is uniform (like in living cells) heat generated will only warm a body of matter (typically the organism) o consequence of usable energy lost as heat to surroundings = each energy transfer makes the universe more disordered entropy – measure of disorder more randomly arranged matter is, greater entropy many cases – entropy seen in disintegration of system’s structure o ex: increasing entropy in decay of unmaintained building some forms of entropy is less obvious 0 takes form of increasing amounts of heat and less ordered matter helps us understand why certain processes are energetically favorable o spontaneous process if a process increases energy by itself – doesn’t need energy input energetically favorable process that decreases entropy on its own – nonspontaneous o happens only if energy is supplied Biological order and disorder o Living systems increase entropy of surroundings – according to thermodynamic law Cells create ordered structures from less organized materials Organismal level – ordered structures also result from simpler starting materials But, organism also takes in organized matter and energy and replaces them with less ordered forms o Ex: animal obtains starch, proteins, and macromolecules from food, catabolic pathways break them down and carbon dioxide and water are released o Depletion of chemical ebergy – accounted for by heat created during metabolism o In history – complex organisms evolved from simpler ancestors Increase in organization over time – in accordance with thermodynamic law Entropy of a system or organism can decrease as long as total entropy of universe (system + surroundings) increases Free energy change determines spontaneity o Free energy change G J Willard Gibbs – 1878 defined function called Gibbs free energy of a system Free energy – portion of system’s energy that can perform work when temperature and pressure are uniform (like in a living cell) Calculated by G = HTS o H – change in system’s enthalpy o S – change in system’s entropy o T – absolute temperature (K) G helps predict spontaneity of process o G = spontaneous H must be negative or TS must be positive decreases system’s free energy o +G or 0G = nonspontaneous o Free Energy, Stability, and Equilibrium G represents difference between free energy of the final state and free energy of the initial state G = G final Ginitial o G can only be negative when process entails a loss of free energy o since there is less free energy, system in final state is less likely to change and more stable free energy = measure of system instability o unstable systems tend to change so they become more stable (higher G to lower G) term for maximum stability – equilibrium o as rxn moves toward equilibrium, free energy of reactants and products lessens systems never spontaneously move away from equilibrium – a process is spontaneous and can do work only when it is moving towards equilibrium Free Energy and Metabolism o Exergonic and endergonic reactions in metabolism Exergonic reaction (outward) – proceeds with a net release of energy Chemical mixture loses free energy, G is negative so spontaneous Magnitude represents the max amount of work the reaction can perform o Greater decrease in free energy, greater potential for work Breaking of bonds requires energy o Energy stored in bonds refers to potential energy that can be released when new bonds form and original bonds break (products must be lower G than reactants) o Endergonic reaction (uphill – absorbs free energy from its surroundings Reaction stores free energy in molecules, G is positive and non spontaneous Magnitude of G is quantity of energy required to drive reaction Equilibrium and Metabolism o Reactions in isolated systems stop work when they reach equilibrium o Cell that reaches metabolic equilibrium (lowest G) is dead – metabolism is never at equilibrium Constant flow of materials in and out of cell stops metabolic pathways from reaching equilibrium Product does not accumulate, becomes reactant in the next step ans waste products are expelled from cell Sequence of reactions is powered by large freeenergy difference between glucose and oxygen at top of energy hill and carbon dioxide and water at downhill end Supply of glucose, other fuels, and oxygen and ability to expel waste = life continues ATP powers cell work by combining exergonic and endergonic reactions Cell does 3 kinds of work Chemical – pushing endergonic reactions that don’t occur spontaneously (synthesis of polymers from monomers) Transport – pumping of substances across membranes against spontaneous movement Mechanical – contraction of muscle cells and movement of chromosomes during cellular reproduction Key feature of cell energy management – energy coupling: use of exergonic process to drive endergonic process ATP mediates most energy coupling in cells and usually acts as immediate source of energy for cellular work o Structure and Hydrolysis of ATP ATP (adenosine triphosphate) – contains sugar ribose, nitrogenous base, and 3 phosphate group chain Nucleoside triphosphate used to make RNA Phosphate bonds broken by hydrolysis – inorganic phosphate leaves ATP which becomes ADP (exergonic) High energy phosphate bonds because hydrolysis releases energy o Reactants have higher energy relative to energy of products ATP useful because energy released during phosphate group loss is greater than most mother molecules High energy because phosphate groups have negative charge which contributes to region of instability – creates equivalent of a compressed spring o How ATP hydrolysis performs work ATP hydrolyzed in tube – free energy release heats surrounding water Useful in body – shivering uses ATP hydrolysis during muscle contraction to warm body In cell – heat generation alone would be inefficient and dangerous o Cell proteins harness energy released to perform chemical, transport, and mechanical cell work o Ex: specific enzymes in cell use energy released by ATP hydrolysis to drive endergonic chemical reactions. IF G of endergonic reaction < energy released by ATP hydrolysis, 2 reactions combined to form exergonic Usually involves phosphorylation – transfer o f phosphate group from ATP to another molecule, recipient molecule covalently bonded to phosphate group to form a phosphorylated intermediate – more reactive and less stable Transport and mechanical work in cell almost always powered by ATP hydrolysis o Changes protein’s shape and ability to bind to another molecule Sometimes occurs through phosphorylated intermediate o Regeneration of ATP Organism constantly uses ATP – renewable resource that can be regenerated through addition of phosphate to ADP Free energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in cell ATP cycle – shuttling of inorganic phosphate and energy – couples cell’s energyyielding process to the energy consuming one ATP formation from ADP – not spontaneous, so free energy used Catabolic pathways (especially cellular respiration) provide energy for endergonic process of ATP production o Plants use light energy to make ATP Enzymes speed up metabolic reactions by lowering energy barriers Enzyme – macromolecule that acts as a catalyst Catalyst – chemical agent that speeds up a chemical reaction without being consumed Without enzyme regulation, chemical traffic through metabolic pathways would take a long time o Activation energy barrier Every chemical reaction involves making and breaking of bonds Usually done by making starting molecule highly unstable by absorbing energy from surroundings o When new bond forms, energy released as heat and molecule becomes stable Energy required to change molecules for the bonds to break – free energy of activation, activation energy Amount of energy needed to get reactions to top of energy barrier Often supplied by heat in form of thermal energy that is absorbed from surroundings o Accelerates reactant molecules so they collide more frequently and with more force o Molecules have absorbed enough energy to break bonds – reactants are in unstable conditions known as transition state Provides barrier that determines reaction rate o Reactants must absorb enough energy to reach top of activation barrier in order for a reaction to occur o How enzymes speed up reactions Proteins, DNA, and other complex cellular molecules have high free energy and have potential to decompose spontaneously – thermodynamically favored Heat can increase reaction rate by allowing reactants to reach the transition state more often, but bad for biological systems High temp denatures proteins and kills cells Heat speeds up all reactions, not just those needed Reason for use of catalysts Enzyme catalyzes reaction by lower the activation energy allowing the molecule to reach the transition rate with less energy Does not change G Allows cell to have dynamic metabolism – routes chemicals smoothly through metabolic pathways Enzymes specific for reactions o Substrate specificity of enzymes Substrate – reactant an enzyme acts on Enzyme binds to substrate and forms enzymesubstrate complex While enzyme/substrate join, catalytic action of enzyme converts substrate to product o Ex: enzyme sucrose catalyzes hydrolysis of disaccharide sucrose into 2 monosaccharides Enzyme reaction = specific (results from shape of enzyme and substrate) Enzyme recognizes specific substrate among related compounds o Occurs because enzymes are proteins with unique 3D configurations – consequence of amino acid sequence Active site Only restricted region of enzyme molecule binds to substrate o Usually pocket or groove on surface of enzyme where catalysis occurs o Usually active site is formed by few enzyme’s amino acids – rest of protein = framework that determines active site shape Enzyme is not a rigid structure Change subtly between different shapes in dynamic equilibrium Shape that best fits substrate isn’t always one with lowest energy Even as substrate enters enzyme, shape changes due to interactions and fits to substrate o Called induced fit, brings chemical groups of active site into positions that enhance ability to catalyze reaction o Catalysis in Enzyme’s active site Most enzymatic reactions, substrate held in active site by weak interactions – hydrogen/ionic bonds R groups of some amino acids making up active site catalyze conversion of substrate to product which departs form active site Enzyme can then take other substrate molecule into active site Fast reaction – single enzyme acts on 1000 substrate molecules/second (some are faster) Most metabolic reactions – reversible Enzyme can catalyze forward or reverse reaction, depending on G Depends mainly on concentrations of reactants and products, net effect is always in direction of equilibrium Enzyme use variety of mechanisms to lower activation energy and speed up reaction 2 or more reactants: active site makes template for substrates to join together in correct orientation for reaction to occur as active site grabs bound substrates, enzyme may stretch molecules toward transitionstate form, stressing/bending chemical bonds that must be broken during reaction. Activation energy is proportional to difficulty of breaking bonds, distorting substrate helps approach transition state and reduces amount of G needed active site may provide microenvironment more helpful to a particular type of reaction than the solution would be without the enzyme amino acids in active site directly participate in reaction, could involve covalent bonding between substrate and side chain of enzyme’s amino acid, next steps would restore side chains to original states rate at which amount of enzyme converts substrate to product is partial function of initial substrate concentration –more substrate molecules available, more frequently they access active sites of the enzyme molecules limit to how fast the reaction can be pushed by adding more substrate to enzyme’s fixed concentration o at some point – concentration of substrate will be high enough that all enzyme molecules have engaged active sites o when product exits active site, another substrate enters at this substrate concentration, enzyme is saturated and reaction rate is determined by speed at which active site coverts product to substrate o when enzyme population is saturated, only way to increase formation rate is to add more enzyme o cells often increase reaction rate by producing more enzyme o Effects of Local conditions on enzyme activity – page 155 Temperature and pH Optimal conditions favor most active shape for enzyme Rate of enzymatic reaction increases w/ increasing temperature (to certain point) o Because substrates collide with active sites more frequently with increased movement o Above a certain temperature, enzyme speed drops dramatically Thermal agitation – disrupts hydrogen, ionic, and weak bonds that secure active enzyme shape, protein molecule denatures Enzyme has optimal temperature for greatest rate – allows greatest number of collisions and fastest conversion of reactants to product molecules