Sinh học - Chapter 8: An introduction to metabolism

Chapter 8An Introduction to MetabolismOverview: The Energy of LifeThe 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. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsWhat causes the bioluminescence in these fungi?An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamicsMetabolism is ALL / the totality of an organism’s chemical reactions.Metabolism is an emergent property of life that arises from interactions between molecules within the cell.Metabolism has two basic subdivisions: Anabolism = building / synthesisCatabolism = breaking downCopyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsOrganization of the Chemistry of Life into Metabolic PathwaysA metabolic pathway begins with a specific molecule / substrate and ends with a product.Each step is catalyzed by a specific enzyme in a specific sequence.Metabolic pathways are regulated by various mechanisms.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsMetabolic Pathways are organized into Specific SequencesEnzyme 1Enzyme 2Enzyme 3DCBAReaction 1Reaction 3Reaction 2StartingmoleculeProductCatabolic pathways will 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.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsAnabolic pathways consume / use energy to build complex molecules from simpler ones.The synthesis of protein from amino acids is an example of anabolism.Bioenergetics is the study of how organisms manage their energy resources.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsForms of EnergyEnergy is the capacity to cause change. Energy is the ability to do work.Energy exists in various forms, some of which can perform work.Energy can be converted from one form to another. The Laws of Thermodynamics govern all energy transformations.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsKinetic 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. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsTransformations between potential and kinetic energyClimbing up converts the kineticenergy of muscle movementto potential energy.A diver has less potentialenergy in the waterthan on the platform.Diving convertspotential energy tokinetic energy.A diver has more potentialenergy on the platformthan in the water.The Laws of Energy Transformation: ThermodynamicsA closed system, such as that approximated by liquid in a thermos, is isolated from its surroundings.In an open system, energy and matter can be transferred between the system and its surroundings.Organisms are open systems, and they perform energy transformations to grow and survive.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe First Law of ThermodynamicsThe first law of thermodynamics: the energy of the universe is a constant quantity: – Energy can be transferred and transformed, but it cannot be created or destroyedThe first law is also called the principle of conservation of energy.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe Second Law of ThermodynamicsDuring every energy transfer or transformation, some energy is unusable, and is often lost as heat.The second law of thermodynamics: – Every energy transfer or transformation increases the entropy (disorder) of the universeThe quality of the energy changes - becomes more disordered. (1st law states the quantity is constant)Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe two laws of thermodynamics(a) First law of thermodynamics(b) Second law of thermodynamicsChemicalenergyHeatCO2H2O+Biological Order and DisorderCells create ordered structures from less ordered materials.Organisms also replace ordered forms of matter and energy with less ordered forms.Energy flows into an ecosystem in the form of light and exits in the form of heat.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe evolution of more complex organisms does not violate the second law of thermodynamics.Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe free-energy change of a reaction GBiologists want to know which reactions occur spontaneously and which require the input of energy.For this, they need to determine energy changes that occur in chemical reactions.A living system’s free energy, G, is energy that can do work when temperature and pressure are uniform, as in a living cell.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe change in free energy (∆G) during a process is related to:the change in enthalpy, or change in total energy (∆H)change in entropy (∆S), disorder,and temperature in Kelvin (T): ∆G = ∆H – T∆SOnly processes with a negative ∆G are spontaneous.Spontaneous processes can be harnessed to perform work.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsFree Energy, Stability, and EquilibriumFree energy is a measure of a system’s instability, its tendency to change to a more stable state.During a spontaneous change, free energy decreases, - ∆G ,and the stability of a system increases.Equilibrium is a state of maximum stability.A process is spontaneous and can perform work only when it is moving toward equilibrium.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe relationship of free energy to stability, work capacity, and spontaneous change(a) Gravitational motion(b) Diffusion(c) Chemical reaction More free energy (higher G) Less stable Greater work capacity In a spontaneous change The free energy of the system decreases (∆G 0)(b) Endergonic reaction: energy requiredProgress of the reactionEnergy(a) Exergonic reaction: energy releasedProgress of the reactionFree energyProductsAmount ofenergyreleased(∆G 0)ReactantsEquilibrium and MetabolismReactions in a closed system eventually reach equilibrium and then do no work ∆G = 0Cells are not in equilibrium; they are open systems experiencing a constant flow of materials. A defining feature of life is that metabolism is never at equilibrium.A catabolic pathway in a cell releases free energy in a series of reactions.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsATP powers cellular work by coupling exergonic reactions to endergonic reactions = Energy CouplingA cell does three main kinds of work:ChemicalTransportMechanicalTo 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.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe Structure and Hydrolysis of ATPATP (adenosine triphosphate) is the cell’s energy shuttleATP is composed of: ribose (a pentose sugar) adenine (a nitrogenous base) and three phosphate groupsCopyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe structure of adenosine triphosphate ATP3 Phosphate groupsRiboseAdenineThe bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis.Energy is released from ATP when the terminal phosphate bond is broken.This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Hydrolysis of ATP releases energy to do workInorganic phosphateEnergyAdenosine triphosphate (ATP)Adenosine diphosphate (ADP)PPPPPP++H2OiHow ATP Performs WorkThe three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of 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. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsHow ATP drives chemical work: Energy coupling using ATP hydrolysis(b) Coupled with ATP hydrolysis, an exergonic reactionAmmonia displacesthe phosphate group,forming glutamine.(a) Endergonic reaction(c) Overall free-energy changePPGluNH3NH2GluiGluADP+PATP++GluATP phosphorylatesglutamic acid,making the aminoacid less stable.GluNH3NH2Glu+GlutamicacidGlutamineAmmonia∆G = +3.4 kcal/mol+21ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant.The recipient molecule is now phosphorylated, energy rich and unstable.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsHow ATP drives transport and mechanical work(b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzedMembrane proteinPiADP+PSoluteSolute transportedPiVesicleCytoskeletal trackMotor proteinProtein moved(a) Transport work: ATP phosphorylates transport proteinsATPATPThe Regeneration of ATPATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)ADP + P --> ATPThe energy to phosphorylate ADP comes from catabolic reactions in the cell.The chemical potential energy temporarily stored in ATP drives most cellular work.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe ATP cycle PiADP+Energy fromcatabolism (exergonic,energy-releasingprocesses)Energy for cellularwork (endergonic,energy-consumingprocesses)+ H2OATPEnzymes speed up the rate of metabolic reactions by lowering energy barriersA catalyst is a chemical agent that speeds up a reaction without being consumed by the reactionAn enzyme is a catalytic proteinEnzymes are specific. Enzymes have a shape-match with their substrates.Enzymes are named after their substrate and generally end in -ase.Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsExample of an enzyme-catalyzed reaction: hydrolysis of sucrose by sucraseSucrose (C12H22O11)Glucose (C6H12O6)Fructose (C6H12O6)SucraseThe Activation Energy EA BarrierEvery chemical reaction between molecules involves bond breaking and bond forming.The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA) Activation energy is often supplied in the form of heat from the surroundings.Enzymes lower the amount of EA needed, so the reaction rate is faster.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsExergonic ReactionProgress of the reactionProductsReactants∆G highest rate of reaction.Each enzyme has an optimal pH in which it functions best / forming the maximum enzyme-substrate complexes --> highest rate of reaction.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsEnvironmental factors affecting enzyme activityRate of reactionOptimal temperature forenzyme of thermophilic (heat-tolerant) bacteria Optimal temperature fortypical human enzyme(a) Optimal temperature for two enzymes(b) Optimal pH for two enzymesRate of reactionOptimal pH for pepsin(stomach enzyme) Optimal pHfor trypsin(intestinalenzyme)Temperature (ºC)pH5432106789100 20 40 80 60 100 Cofactors:Cofactors are nonprotein enzyme helpers.Cofactors may be inorganic (such as a metal in ionic form) or organic.Organic cofactors are called coenzymes.Coenzymes include vitamins.Inorganic cofactors include minerals and salts.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsAffect enzyme actionEnzyme InhibitorsCompetitive 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 able to bind with the substrate.Examples of inhibitors include toxins, poisons, pesticides, and antibiotics.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsInhibition of enzyme activity(a) Normal binding(c) Noncompetitive inhibition(b) Competitive inhibitionNoncompetitive inhibitorActive siteCompetitive inhibitorSubstrateEnzymeRegulation of enzyme activity helps control metabolismChemical chaos would result if a cell’s metabolic pathways were not tightly regulated.A cell regulates metabolism by: switching on or off the genes that encode specific enzymes. or by regulating the activity of enzymes.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsAllosteric Regulation of EnzymesAllosteric 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.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsAllosteric Activation and InhibitionMost 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.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsAllosteric Regulation of enzyme activityAllosteric enyzmewith four subunitsActive site(one of four)Regulatorysite (oneof four)Active formActivatorStabilized active formOscillationNon-functionalactivesiteInhibitorInactive formStabilized inactiveform(a) Allosteric activators and inhibitorsSubstrateInactive formStabilized activeform(b) Cooperativity: another type of allosteric activationCooperativity is a form of allosteric regulation that can amplify enzyme activity.In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsIdentification of Allosteric RegulatorsAllosteric regulators are attractive drug candidates for enzyme regulation.Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsFeedback Inhibition: Allosteric Enzyme RegulationIn feedback inhibition, the end product of a metabolic pathway shuts down the pathway. End product builds up and becomes and allosteric inhibitor.Allosteric inhibitor binds to an allosteric enzyme early in the pathway, shutting down the pathway.Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Feedback InhibitionIntermediate CFeedbackinhibitionIsoleucineused up bycellEnzyme 1(threoninedeaminase)End product(isoleucine)Enzyme 5Intermediate DIntermediate BIntermediate AEnzyme 4Enzyme 2Enzyme 3Initial substrate(threonine)Threoninein active siteActive siteavailableActive site ofenzyme 1 nolonger bindsthreonine;pathway isswitched off.Isoleucinebinds toallostericsiteSpecific Localization of Enzymes Within the CellStructures within the cell help bring order to metabolic pathways.Some enzymes act as structural components of membranes.In eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondria.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsOrganelles and structural order in metabolism1 µmMitochondriaEnymes are embedded in the membrane and are organized in a specific sequence for an efficient metabolic pathway.You should now be able to:Distinguish between the following pairs of terms: catabolic and anabolic pathways; kinetic and potential energy; open and closed systems; exergonic and endergonic reactions.In your own words, explain the second law of thermodynamics and explain why it is not violated by living organisms.Explain in general terms how cells obtain the energy to do cellular work.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsExplain how ATP performs cellular work. Explain why an investment of activation energy is necessary to initiate a spontaneous reaction.Describe the mechanisms by which enzymes lower activation energy.Describe how allosteric regulators may inhibit or stimulate the activity of an enzyme.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings