microbiology ch 05 lecture_presentation

Chapter Title

Chapter 5

2015 Pearson Education, Inc.Basic Chemical Reactions Underlying MetabolismMetabolismCollection of controlled biochemical reactions that take place within a microbeUltimate function of metabolism is to reproduce the organism

2015 Pearson Education, Inc.2

Basic Chemical Reactions Underlying MetabolismMetabolic Processes Guided by Eight StatementsEvery cell acquires nutrientsMetabolism requires energy from light or catabolism of nutrientsEnergy is stored in adenosine triphosphate (ATP)Cells catabolize nutrients to form precursor metabolitesPrecursor metabolites, energy from ATP, and enzymes are used in anabolic reactionsEnzymes plus ATP form macromoleculesCells grow by assembling macromoleculesCells reproduce once they have doubled in size


Metabolism: Overview


Basic Chemical Reactions Underlying MetabolismCatabolism and AnabolismTwo major classes of metabolic reactionsCatabolic pathways Break larger molecules into smaller products Exergonic (release energy)Anabolic pathways Synthesize large molecules from the smaller products of catabolismEndergonic (require more energy than they release)


Figure 5.1 Metabolism is composed of catabolic and anabolic reactions.

2015 Pearson Education, Inc.

Basic Chemical Reactions Underlying MetabolismOxidation and Reduction ReactionsTransfer of electrons from an electron donor to an electron acceptorReactions always occur simultaneouslyCells use electron carriers to carry electrons (often inH atoms)Three important electron carriersNicotinamide adenine dinucleotide (NAD+)Nicotinamide adenine dinucleotide phosphate (NADP+) Flavin adenine dinucleotide (FAD)


Figure 5.2 Oxidation-reduction, or redox, reactions.


Oxidation-Reduction Reactions


Basic Chemical Reactions Underlying MetabolismATP Production and Energy StorageOrganisms release energy from nutrients Can be concentrated and stored in high-energy phosphate bonds (ATP)Phosphorylation inorganic phosphate is added to substrateCells phosphorylate ADP to ATP in three waysSubstrate-level phosphorylationOxidative phosphorylationPhotophosphorylationAnabolic pathways use some energy of ATP by breaking a phosphate bond


Basic Chemical Reactions Underlying MetabolismThe Roles of Enzymes in MetabolismEnzymes are organic catalystsIncrease likelihood of a reaction


Enzymes: Overview


Basic Chemical Reactions Underlying MetabolismThe Roles of Enzymes in MetabolismNaming and classifying enzymesSix categories of enzymes based on mode of actionHydrolasesIsomerasesLigases or polymerasesLyasesOxidoreductasesTransferases



Basic Chemical Reactions Underlying MetabolismThe Roles of Enzymes in MetabolismThe makeup of enzymesMany protein enzymes are complete in themselvesApoenzymes are inactive if not bound to nonprotein cofactors (inorganic ions or coenzymes)Binding of apoenzyme and its cofactor(s) yields holoenzymeSome are RNA molecules called ribozymes


Figure 5.3 Makeup of a holoenzyme.

Inorganic cofactorActive siteCoenzyme(organiccofactor)Apoenzyme (protein)Holoenzyme



Figure 5.4 The effect of enzymes on chemical reactions.

ReactantsActivation energywithout enzymeActivation energywith enzymeProducts


Figure 5.5 Enzymes fitted to substrates.

Active sites similarto substrate'sshapeSubstrateEnzymeEnzyme-substrate complex;active sites become exact shape of substrate


1Enzyme-substratecomplexEnzyme(Fructose-1,6-bisphosphatealdolase)Substrate(Fructose 1,6-bisphosphate)Dihydroxyacetone-PGlyceraldehyde-3PProducts

234Figure 5.6 The process of enzymatic activity.


Enzymes: Steps in a Reaction


Basic Chemical Reactions Underlying MetabolismThe Roles of Enzymes in MetabolismEnzyme activityMany factors influence the rate of enzymatic reactionsTemperaturepHEnzyme and substrate concentrationsPresence of inhibitorsInhibitors block an enzyme's active siteDo not denature enzymesThree types


Figure 5.7 Representative effects of temperature, pH, and substrate concentration on enzyme activity.


Figure 5.8 Denaturation of protein enzymes.


CompetitiveinhibitorSubstrateEnzymeReversiblecompetitiveinhibitorSubstrateIncrease insubstrateconcentrationEnzyme

Figure 5.9 Competitive inhibition of enzyme activity.


Enzymes: Competitive Inhibition


Active siteEnzymeAllosteric siteAllosteric (noncompetitive) inhibitionDistorted,nonfunctionalactive siteAllostericinhibitorDistorted active siteSubstrateActive site becomesfunctionalAllosteric activatorAllosteric siteAllosteric activationSubstrate

Figure 5.10 Allosteric control of enzyme activity.


Enzyme-Substrate Interaction: Noncompetitive Inhibition


Figure 5.11 Feedback inhibition.

SubstratePathwayshuts downBoundend-product(allostericinhibitor)Enzyme 1AllostericsitePathwayoperatesFeedbackinhibitionIntermediate AEnzyme 2Intermediate BEnd-productEnzyme 3


Basic Chemical Reactions Underlying MetabolismTell Me WhyHow can oxidation take place in an anaerobic environment, that is, without oxygen?


Carbohydrate CatabolismMany organisms oxidize carbohydrates as primary energy source for anabolic reactionsGlucose is most common carbohydrate usedGlucose is catabolized by two processesCellular respiration Fermentation


Glucose2 Pyruvic acidElectronsELECTRON TRANSPORT CHAINKREBSCYCLEAcetyl-CoAFinal electronacceptorFormation offermentationend-productsPyruvic acid(or derivative)GLYCOLYSISFermentationRespiration

Figure 5.12 Summary of glucose catabolism.


Carbohydrate CatabolismGlycolysisOccurs in cytoplasm of most cellsInvolves splitting of a six-carbon glucose into two three-carbon sugar moleculesSubstrate-level phosphorylation direct transfer of phosphate between two substratesNet gain of two ATP molecules, two molecules of NADH, and precursor metabolite pyruvic acid


Glycolysis: Overview


Carbohydrate CatabolismGlycolysisDivided into three stages involving 10 total stepsEnergy-investment stageLysis stageEnergy-conserving stage


Figure 5.13 Glycolysis.


Glycolysis: Steps


Figure 5.14 Example of substrate-level phosphorylation.

Phosphoenolpyruvate (PEP)HoloenzymePyruvic acidPhosphorylation


Carbohydrate CatabolismCellular RespirationResultant pyruvic acid is completely oxidized to produce ATP by series of redox reactionsThree stages of cellular respiration 1. Synthesis of acetyl-CoA 2. Krebs cycle 3. Final series of redox reaction (electron transport chain)


Figure 5.15 Formation of acetyl-CoA.


Carbohydrate CatabolismCellular RespirationSynthesis of acetyl-CoAResults inTwo molecules of acetyl-CoATwo molecules of CO2 Two molecules of NADH


Carbohydrate CatabolismCellular RespirationThe Krebs cycleGreat amount of energy remains in bonds of acetyl-CoATransfers much of this energy to coenzymes NAD+ and FADOccurs in cytosol of prokaryotes and in matrix of mitochondria in eukaryotes


Carbohydrate CatabolismCellular RespirationThe Krebs cycleSix types of reactions in Krebs cycleAnabolism of citric acidIsomerizationRedox reactionsDecarboxylationsSubstrate-level phosphorylationHydration reaction


Figure 5.16 The Krebs cycle.


Krebs Cycle: Overview


Krebs Cycle: Steps


Carbohydrate CatabolismCellular RespirationThe Krebs cycleResults inTwo molecules of ATPTwo molecules of FADH2Six molecules of NADHFour molecules of CO2


Carbohydrate CatabolismCellular RespirationElectron transportMost significant production of ATP occurs from series of redox reactions known as an electron transport chain (ETC)Series of carrier molecules that pass electrons from one to another to final electron acceptorEnergy from electrons is used to pump protons (H+) across the membrane, establishing a proton gradientLocated in cristae of eukaryotes and in cytoplasmic membrane of prokaryotes


RespirationFermentationPath ofelectronsFinal electronacceptor

Figure 5.17 An electron transport chain.


Electron Transport Chain: Overview


Carbohydrate CatabolismCellular RespirationElectron transportFour categories of carrier moleculesFlavoproteinsUbiquinonesMetal-containing proteinsCytochromesAerobic respiration: oxygen serves as final electron acceptor Anaerobic respiration: molecule other than oxygen serves as final electron acceptor


Figure 5.18 One possible arrangement of an electron transport chain.

BacteriumExteriorCytoplasmicmembraneIntermembranespaceMatrixMitochondrionCytoplasmPhospholipidmembraneNADHfrom glycolysis,Krebs cycle,pentose phosphatepathway, andEntner-DoudoroffpathwayFADH2fromKrebs cycleCytoplasm of prokaryoteor matrix of mitochondrionExterior of prokaryoteor intermembrane spaceof mitochondrionUbiquinoneFMNNADHFADH2NAD+Cyt c1ATP synthaseCyt bH+H+2

1

eeeeH+H+eeeeee

Cyt cCyt aCyt a3H+H+

eeH+H+4H+H+H+H+ADP3H2OATPP+1/2 O2H+H+FAD++

H+


Electron Transport Chain: The Process


Electron Transport Chain: Factors Affecting ATP Yield


Carbohydrate CatabolismCellular RespirationChemiosmosisUse of ion gradients to generate ATPCells use energy released in redox reactions of ETC to create proton gradientProtons flow down electrochemical gradient through ATP synthases that phosphorylate ADP to ATPCalled oxidative phosphorylation because proton gradient is created by oxidation of components of ETCTotal of ~34 ATP molecules formed from one molecule of glucose



Carbohydrate CatabolismAlternatives to GlycolysisYield fewer molecules of ATP than does glycolysisReduce coenzymes and yield different metabolites needed in anabolic pathwaysTwo pathwaysPentose phosphate pathwayEntner-Doudoroff pathway


Figure 5.19 The pentose phosphate pathway.


Figure 5.20 Entner-Doudoroff pathway.

GlucoseGlucose 6-phosphate6-Phosphogluconic acid2-Keto-3-deoxy-6-phosphogluconic acidGlyceraldehyde 3-phosphate (G3P)Pyruvic acidPyruvic acidTo Krebs cycleor fermentationSteps 610of glycolysis


Carbohydrate CatabolismFermentationSometimes cells cannot completely oxidize glucose by cellular respirationCells require constant source of NAD+ Cannot be obtained simply by using glycolysis and Krebs cycleFermentation pathways provide cells with alternative source of NAD+ Partial oxidation of sugar (or other metabolites) to release energy using an organic molecule from within the cell as final electron acceptor


Figure 5.21 Fermentation.


Figure 5.22 Representative fermentation products and the organisms that produce them.


Fermentation



Carbohydrate CatabolismTell Me WhyWhy do electrons carried by NADH allow for production of 50% more ATP molecules than do electrons carried by FADH2?


Other Catabolic PathwaysLipids and proteins contain energy in their chemical bondsCan be converted into precursor metabolitesServe as substrates in glycolysis and the Krebs cycle


Figure 5.23 Catabolism of a fat molecule.

Fatty acid chainsGlycerolLipase3Glycerol+Fatty acidsHydrolysisDHAPTo step 5glycolysisFatty acidTo electrontransport chainAcetyl-CoATo Krebs cycleShorter fatty acidBeta-oxidation


Extracellular fluidProteasesPolypeptideAmino acidsCytoplasmicmembraneCytoplasmDeaminationTo Krebs cycle

Figure 5.24 Protein catabolism.


Other Catabolic PathwaysTell Me WhyWhy does catabolism of amino acids for energy result in ammonia and other nitrogenous wastes?


PhotosynthesisMany organisms synthesize their own organic molecules from inorganic carbon dioxideMost of these organisms capture light energy and use it to synthesize carbohydrates from CO2 and H2O by a process called photosynthesis


Photosynthesis: Overview


Metabolism


PhotosynthesisChemicals and StructuresChlorophylls Type of pigment molecule that photosynthetic organisms use to capture light energyComposed of hydrocarbon tail attached to light-absorbing active site centered on magnesium ionActive sites are structurally similar to cytochrome molecules in ETCStructural differences cause absorption at different wavelengths


PhotosynthesisChemicals and StructuresPhotosystems Arrangement of molecules of chlorophyll and other pigments to form light-harvesting matricesEmbedded in cellular membranes called thylakoidsIn prokaryotes invagination of cytoplasmic membraneIn eukaryotes formed from inner membrane of chloroplastsArranged in stacks called granaStroma is space between outer membrane of granum and thylakoid membrane


Figure 5.25 Photosynthetic structures in a prokaryote.

Photosystem embeddedin membrane (sectioned)ChlorophyllThylakoidmembraneActivesiteTail(carbonchain)Thylakoid


PhotosynthesisChemicals and StructuresTwo types of photosystemsPhotosystem I (PS I)Photosystem II (PS II)Photosystems absorb light energy and use redox reactions to store energy in the form of ATP and NADPHLight-dependent reactions depend on light energyLight-independent reactions synthesize glucose from carbon dioxide and water


PhotosynthesisLight-Dependent ReactionsAs electrons move down the chain, their energy is used to pump protons across the membranePhotophosphorylation uses proton motive force to generate ATPPhotophosphorylation can be cyclic or noncyclic


AcceptorLightReactioncenter chlorophyllPossible path ofenergy transferPhotosystem:reaction center

Figure 5.26 Reaction center of a photosystem.


Exterior of prokaryoteor thylakoid space of chloroplast Cyclic photophosphorylationCytochromesCuPhotosystem I FeReaction centerLightCytoplasm ofprokaryoteor stroma ofchloroplastATP synthaseMembrane ofprokaryote orof thylakoid inchloroplast

Membrane ofprokaryote orof thylakoid inchloroplastATP synthasePhotosystem I CytochromesFeLightCytoplasm ofprokaryoteor stroma ofchloroplastLightQuinoneReactioncenterReactioncenterCuNoncyclic photophosphorylationExterior of prokaryoteor thylakoid spaceof chloroplastToCalvin-BensoncycleNADPase

Photosystem II

Figure 5.27 The light-dependent reactions of photosynthesis: Cyclic and noncyclic photophosphorylation.


Photosynthesis: Light Reaction: Cyclic Photophosphorylation


Photosynthesis: Light Reaction: Noncyclic Photophosphorylation



PhotosynthesisLight-Independent ReactionsDo not require light directlyUse ATP and NADPH generated by light-dependent reactionsKey reaction is carbon fixation by Calvin-Benson cycleThree stepsFixation of CO2ReductionRegeneration of RuBP


Figure 5.28 Simplified diagram of the Calvin-Benson cycle.


Photosynthesis: Light-Independent Reaction


PhotosynthesisTell Me WhyAn uninformed student describes the Calvin-Benson cycle as "cellular respiration in reverse." Why is this student incorrect?


Other Anabolic PathwaysAnabolic reactions are synthesis reactions requiring energy and a source of precursor metabolitesEnergy derived from ATP from catabolic reactionsMany anabolic pathways are the reverse of catabolic pathwaysReactions that can proceed in either direction are amphibolic



Figure 5.29 The role of gluconeogenesis in the biosynthesis of complex carbohydrates.


Figure 5.30 Biosynthesis of fat, a lipid.


Figure 5.31 Examples of the synthesis of amino acids via amination and transamination.


Figure 5.32 The biosynthesis of nucleotides.


Other Anabolic PathwaysTell Me WhyWhy is nitrogen required for the production of amino acids by amination?


Integration and Regulation of Metabolic FunctionCells synthesize or degrade channel and transport proteinsCells often synthesize enzymes only when substrate is availableCells catabolize the more energy-efficient choice if two energy sources are availableCells synthesize metabolites they need, cease synthesis if metabolite is available


Integration and Regulation of Metabolic FunctionEukaryotic cells isolate enzymes of different metabolic pathways within membrane-bounded organellesCells use allosteric sites on enzymes to control activity of enzymesFeedback inhibition slows/stops anabolic pathways when product is in abundanceCells regulate amphibolic pathways by requiring different coenzymes for each pathway


Integration and Regulation of Metabolic FunctionTwo types of regulatory mechanismsControl of gene expressionCells control amount and timing of protein (enzyme) productionControl of metabolic expressionCells control activity of proteins (enzymes) once produced


Integration and Regulation of Metabolic FunctionTell Me WhyWhy is feedback inhibition necessary for controlling anabolic pathways?


Figure 5.33 Integration of cellular metabolism (shown in an aerobic organism).


Metabolism: The Big Picture


Important topics ChloroplastStructureFunction Photosynthesis vs. Calvin-Benson cycleGluconeogenesisETC (Electron Transport Chain)
