Learning OutcomesDistinguish between the following pairs of terms: catabolic and anabolic pathways; kinetic and potential energy; open and closed systems; exergonic and endergonic reactionsIn your own words, explain the second law of thermodynamics and explain why it is not violated by living organismsExplain in general terms how cells obtain the energy to do cellular workCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Explain how ATP performs cellular work Explain why an investment of activation energy is necessary to initiate a spontaneous reactionDescribe the mechanisms by which enzymes lower activation energyDescribe how allosteric regulators may inhibit or stimulate the activity of an enzymeCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsLearning Outcomes

Overview: The Energy of LifeThe living cell is a miniature chemical factory where thousands of reactions occurThe cell extracts energy and applies energy to perform workSome organisms even convert energy to light, as in bioluminescenceCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Concept 8.1: An organisms metabolism transforms matter and energy, subject to the laws of thermodynamicsMetabolism is the totality of an organisms chemical reactionsMetabolism is an emergent property of life that arises from interactions between molecules within the cellCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Organization of the Chemistry of Life into Metabolic PathwaysA metabolic pathway begins with a specific molecule and ends with a productEach step is catalyzed by a specific enzymeCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Catabolic pathways release energy by breaking down complex molecules into simpler compoundsCellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolismCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsCatabolic Pathways

Anabolic pathways consume energy to build complex molecules from simpler onesThe synthesis of protein from amino acids is an example of anabolismBioenergetics is the study of how organisms manage their energy resources

Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsAnabolic Pathways

Forms of EnergyEnergy is the capacity to cause changeEnergy exists in various forms, some of which can perform workCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The Second Law of ThermodynamicsDuring every energy transfer or transformation, some energy is unusable, and is often lost as heatAccording to the second law of thermodynamics: Every energy transfer or transformation increases the entropy (disorder) of the universeCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Concept 8.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneouslyBiologists want to know which reactions occur spontaneously and which require input of energySpontaneous processes occur without energy input; they can happen quickly or slowlyTo do so, they need to determine energy changes that occur in chemical reactionsCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Free-Energy Change, GA living systems free energy is energy that can do work when temperature and pressure are uniform, as in a living cellCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The 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), and temperature in Kelvin (T): G = H TSOnly processes with a negative G are spontaneousSpontaneous processes can be harnessed to perform workCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Free Energy, Stability, and EquilibriumFree energy is a measure of a systems instability, its tendency to change to a more stable stateDuring a spontaneous change, free energy decreases and the stability of a system increasesEquilibrium is a state of maximum stabilityA process is spontaneous and can perform work only when it is moving toward equilibriumCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-5a Less free energy (lower G) More stable Less work capacity More free energy (higher G) Less stable Greater work capacityIn a spontaneous change The free energy of the system decreases (G < 0) The system becomes more stable The released free energy can be harnessed to do work

Exergonic and Endergonic Reactions in MetabolismAn exergonic reaction proceeds with a net release of free energy and is spontaneousAn endergonic reaction absorbs free energy from its surroundings and is nonspontaneousCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-6aEnergy(a) Exergonic reaction: energy releasedProgress of the reactionFree energyProductsAmount ofenergyreleased(G < 0)Reactants

Fig. 8-6bEnergy(b) Endergonic reaction: energy requiredProgress of the reactionFree energyProductsAmount ofenergyrequired(G > 0)Reactants

Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactionsA 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 oneMost energy coupling in cells is mediated by ATPCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The Structure and Hydrolysis of ATPATP (adenosine triphosphate) is the cells energy shuttleATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groupsCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The bonds between the phosphate groups of ATPs tail can be broken by hydrolysisEnergy is released from ATP when the terminal phosphate bond is brokenThis release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselvesCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-9Inorganic phosphateEnergyAdenosine triphosphate (ATP)Adenosine diphosphate (ADP)PPPPPP++H2Oi

Which can be represented by the graph:

ADP ATP?ADP AMP?

Which can be represented by the graph:

ADP ATP? ADP AMP?

ATP can be broken-down or synthesized Does AMP ADP require or release energy? Is ADP ATP an exergonic or endergonic reaction?Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsSummary

How ATP Performs WorkThe three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATPIn the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reactionOverall, the coupled reactions are exergonic Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactantThe recipient molecule is now phosphorylatedCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-11(b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzedMembrane proteinPiADP+PSoluteSolute transportedPiVesicleCytoskeletal trackMotor proteinProtein moved(a) Transport work: ATP phosphorylates transport proteinsATPATP

The Regeneration of ATPATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)The energy to phosphorylate ADP comes from catabolic reactions in the cellThe chemical potential energy temporarily stored in ATP drives most cellular workCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-12PiADP+Energy fromcatabolism (exergonic,energy-releasingprocesses)Energy for cellularwork (endergonic,energy-consumingprocesses)ATP+H2O

GlycolysisADP ATP: is energy used up or released?

GlycolysisIs energy used up or released when a phosphate group is removed from a molecule?

Summary: What must you know?Is energy released when bonds are broken?Is energy required when bonds are formed?Can the energy released from breaking bonds in reaction A be used to form bonds in reaction B?Is free energy = usable energy or unusable energy?Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Concept 8.4: Enzymes speed up 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 proteinHydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reactionCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-13Sucrose (C12H22O11)Glucose (C6H12O6)Fructose (C6H12O6)Sucrase

The Activation Energy BarrierEvery chemical reaction between molecules involves bond breaking and bond formingThe 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 surroundingsCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-14Progress of the reactionProductsReactantsG < OTransition stateFree energyEADCBADDCCBBAAWhat is happening to the bonds?

Fig. 8-14Progress of the reactionProductsReactantsG < OTransition stateFree energyEADCBADDCCBBAAWhat is happening to the bonds? Weakening; to aid breaking and re-formation

Enzymes Lower the EA BarrierEnzymes catalyze reactions by lowering the EA barrierEnzymes do not affect the change in free energy (G); instead, they hasten reactions that would occur eventuallyAnimation: How Enzymes WorkCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-15Progress of the reactionProductsReactantsG is unaffectedby enzymeCourse ofreactionwithoutenzymeFree energyEAwithoutenzymeEA withenzymeis lowerCourse ofreactionwith enzyme

Substrate Specificity of EnzymesThe reactant that an enzyme acts on is called the enzymes substrate The enzyme binds to its substrate, forming an enzyme-substrate complexThe active site is the region on the enzyme where the substrate bindsInduced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reactionCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-16SubstrateActive siteEnzymeEnzyme-substratecomplex(b)(a)

Substrate bindingOld theory: example of a lock and key for substrate and enzyme bindingNow: Induced fit - interaction also involves conformational changesCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

How does the substrate attach to the active site?The active site must be of a shape that is complementary to the shape of the substrateKeyword: complementary, NOT similarCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Difference between complementary and similarCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsComplementarySimilar

How does the substrate attach to the active site?The active site must bear complementary charge to that of the substrateR groups at active site interact with substrateCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Active sitesOut of the hundreds of amino acids that make up an enzyme, only about 3-12 amino acids make up the active siteThe amino acids may be far apart in the primary sequenceFolding of the polypeptide chain brings them to close proximity to form the active site.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Catalysis in the Enzymes Active SiteIn an enzymatic reaction, the substrate binds to the active site of the enzymeThe active site can lower an EA barrier byOrienting substrates correctlyStraining substrate bondsProviding a favorable microenvironmentCovalently bonding to the substrateCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-17SubstratesEnzymeProducts arereleased.Products Substrates areconverted toproducts. Active site can lower EAand speed up a reaction. Substrates held in active site by weakinteractions, such as hydrogen bonds andionic bonds. Substrates enter active site; enzyme changes shape such that its active siteenfolds the substrates (induced fit).Activesite isavailablefor two newsubstratemolecules.Enzyme-substratecomplex532164

Effects of Local Conditions on Enzyme ActivityAn enzymes activity can be affected byGeneral environmental factors, such as temperature and pHChemicals that specifically influence the enzymeCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Effects of Temperature and pHEach enzyme has an optimal temperature in which it can functionEach enzyme has an optimal pH in which it can functionCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

What Holds the Shape of the Enzymes?Bonds such as hydrogen bonds, ionic bonds, hydrophobic interactions, and disulphide bridges holds the structure of an enzymeThese bonds are easily affected by changes in temperature and pHCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Effects of pHChanges in pH changes the concentration of H+ ions in the mediumAs [H+] changes, charges on the R groups changeThis causes the ionic bonds between charged R groups to break as the charges are no longer complementaryCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Effects of pHThe 3-dimensional structure is then destroyedThe enzyme loses all catalytic activities and is completely denatured.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Effects of temperatureIncreasing temperature causes molecules to vibrate more violentlyWeak bonds break first: H-bonds, hydrophobic interactionsStronger bond break later: ionic bondsCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Effects of temperatureStructure and surface configurations (including active site) are alteredEnzyme losses its catalytic functionsEnzyme is said to be denaturedWhen the structure of the enzyme is fully destroyed, no catalysis takes placeCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-18Rate 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 (C)pH5432106789100 20 40 80 60 100

Effect of Concentration on Rate of ReactionCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings(a) Assuming sufficient substrate concentration(b) Assuming fixed enzyme concentration

CofactorsCofactors are nonprotein enzyme helpersCofactors may be inorganic (such as a metal in ionic form) or organicExample of inorganic cofactors : heme in hemaglobinAn organic cofactor is called a coenzymeCoenzymes include vitamins, e.g. NADCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

CofactorsCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsHeme in hemoglobim NAD

Enzyme InhibitorsCompetitive inhibitors bind to the active site of an enzyme, competing with the substrateNoncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effectiveExamples of inhibitors include toxins, poisons, pesticides, and antibioticsCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-19(a) Normal binding(c) Noncompetitive inhibition(b) Competitive inhibitionNoncompetitive inhibitorActive siteCompetitive inhibitorSubstrateEnzyme

Competitive InhibitionHow can the inhibition be overcome? Increase the substrate concentrationCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Non-competitive InhibitionHow to increase rate of reaction? Increase enzyme concentrationCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Concept 8.5: Regulation of enzyme activity helps control metabolismChemical chaos would result if a cells metabolic pathways were not tightly regulatedA cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymesCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Allosteric Regulation of EnzymesAllosteric regulation may either inhibit or stimulate an enzymes activityAllosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the proteins function at another siteCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Allosteric Activation and InhibitionMost allosterically regulated enzymes are made from polypeptide subunitsEach enzyme has active and inactive formsThe binding of an activator stabilizes the active form of the enzymeThe binding of an inhibitor stabilizes the inactive form of the enzymeCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-20a(a) Allosteric activators and inhibitors InhibitorNon-functionalactivesiteStabilized inactiveform Inactive formOscillationActivatorActive formStabilized active formRegulatorysite (oneof four)Allosteric enzymewith four subunitsActive site(one of four)

Cooperativity is a form of allosteric regulation that can amplify enzyme activityIn 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 Cummings

Fig. 8-20b(b) Cooperativity: another type of allosteric activation Stabilized activeformSubstrateInactive form

Feedback InhibitionIn feedback inhibition, the end product of a metabolic pathway shuts down the pathwayFeedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is neededCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Identification of Allosteric RegulatorsAllosteric regulators are attractive drug candidates for enzyme regulationInhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responsesCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-21aSHSubstrateHypothesis: allostericinhibitor locks enzymein inactive formActive form canbind substrateSSSHSHActivesiteCaspase 1Known active formKnown inactive formAllostericbinding siteAllostericinhibitorEXPERIMENT

Fig. 8-21bCaspase 1RESULTSActive formInhibitorAllostericallyinhibited formInactive form

Specific Localization of Enzymes Within the CellStructures within the cell help bring order to metabolic pathwaysSome enzymes act as structural components of membranesIn eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondriaCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

*Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change*Figure 8.6a Free energy changes (G) in exergonic and endergonic reactions*Figure 8.6b Free energy changes (G) in exergonic and endergonic reactions*For the Cell Biology Video Space Filling Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.*For the Cell Biology Video Stick Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.

*Figure 8.9 The hydrolysis of ATP*For the Cell Biology Video Stick Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.

*Figure 8.11 How ATP drives transport and mechanical work*Figure 8.12 The ATP cycle*Figure 8.13 Example of an enzyme-catalyzed reaction: hydrolysis of sucrose by sucrase*Figure 8.14 Energy profile of an exergonic reaction*Figure 8.14 Energy profile of an exergonic reaction*Figure 8.15 The effect of an enzyme on activation energy*For the Cell Biology Video Closure of Hexokinase via Induced Fit, go to Animation and Video Files.

*Figure 8.16 Induced fit between an enzyme and its substrate*For the Cell Biology Video Closure of Hexokinase via Induced Fit, go to Animation and Video Files.

*For the Cell Biology Video Closure of Hexokinase via Induced Fit, go to Animation and Video Files.

*For the Cell Biology Video Closure of Hexokinase via Induced Fit, go to Animation and Video Files.

*Figure 8.17 The active site and catalytic cycle of an enzyme*Figure 8.18 Environmental factors affecting enzyme activity*Figure 8.19 Inhibition of enzyme activity*Figure 8.20a Allosteric regulation of enzyme activity*Figure 8.20b Allosteric regulation of enzyme activity*Figure 8.21 Are there allosteric inhibitors of caspase enzymes?*Figure 8.21 Are there allosteric inhibitors of caspase enzymes?