Chapter 6: Bacterial Metabolism
Chapter 6: Bacterial Metabolism MICRBIO 4000 - 0110
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This 21 page Class Notes was uploaded by Victoria Gonzalez on Sunday September 27, 2015. The Class Notes belongs to MICRBIO 4000 - 0110 at Ohio State University taught by Madhura Pradhan,Tammy Bullwinkle in Fall 2015. Since its upload, it has received 20 views. For similar materials see Basic and Practical Microbiology in Microbiology at Ohio State University.
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Date Created: 09/27/15
Chapter 6 Bacterial Metabolism Victoria Gonzalez Terms Metabolism sum total of all the enzymatic chemical reactions in a cell Catabolism processes that harvest energy released during the breakdown of compounds such as glucose using it to synthesize ATP Anabolism processes that synthesize and assemble the subunits of macromolecules using energy of ATP biosynthesis Exergonic describes a chemical reaction that releases energy because the starting compounds have more free energy than the compounds Endergonic chemical reaction that requires a net input of energy because the products have more free energy than the starting compounds Free energy amount of energy that can be gained by breaking the bonds of a compound does not include the energy that is always lost as heat AG change in free energy Enzymes a protein that functions as a catalyst speeding up a biological reaction Active site catalytic site site on an enzyme 0 which the substrate binds ATP the energy currency of cells Hydrolysis of the bonds between its phosphate groups can be used to power endergonic reactions Electron transport chain ETC group of membrane embedded electron carriers that pass electrons from one to another and in the process create a proton motive force Fermentation metabolic process that stops short of oxidizing glucose or other organic compounds completely using an organic intermediate as a terminal electron acceptor Allosteric regulation refers to an enzyme or other protein that contains a site to which a small molecule can bind and change the protein s activity Oxidative phosphorylation synthesis of ATP using the energy of a proton motive force created by harvesting chemical energy Proton motive force form of energy generated as an electron transport chain moves protons across a membrane to create a chemiosmotic gradient Terminal electron acceptor chemical that is ultimately reduced as a consequence of fermentation or respiration Precursor metabolites metabolic intermediates that can be either used to make the subunits of macromolecules or oxidized to generate ATP Chemiosmotic theory the theory that a proton gradient is formed by the electron transport chain and then used to power ATP synthesis Aerobic respiration metabolic process in which electrons are transferred from the electron transport chain to molecular oxygen Anaerobic respiration metabolic process in which electrons are transferred from the electron transport chain to a terminal electron acceptor other than molecular oxygen Fermentation metabolic process that stops short of oxidizing glucose or other organic compounds completely using an organic intermediate such as pyruvate or a derivative as a terminal electron acceptor Photosystem protein complexes within which chlorophyll and other lightgathering pigments are organized located in special photosynthetic membranes Lightdependent reactions processes used by phototrophs to harvest energy from sunlight the energygathering component of photosynthesis Cyclic photophosphorylation type of photophosphorylation in which electrons are returned directly to the chlorophyll used to synthesize ATP without generating reducing power Noncyclic photophosphorylation type of photophosphorylation in which highenergy electrons are drawn off to generate reducing power electrons must still be returned to chlorophyll but they come from a source such as water 61 Metabolism 1 Metabolism all chemical reactions in the cell fueling cell growth a Cells need to i Make new components cell walls membranes ribosomes and nucleic acids 1 These allow the cell to enlarge and divide ii Harvest energy and convert it to a form for powering reactions b Why study metabolism of microbes i New sources of energy biofuels ii Food production iii Identi cation of microbes in the lab iv Models for eukaryotic systems v Targets for antimicrobial drugs c Metabolism the sum of all chemical reactions in a cell i Catabolism breaks things down releasing their energy 1 Fueling reactions 2 Ready source of reducing power ETC for ATP 3 Generates precursors for biosynthesis ii Anabolism biosynthesis assemble units of macromolecules 1 Synthesis of complex organic molecules from simpler ones 2 Requires energy from fueling reactions ATP 3 Requires a source of electrons in the form of reducing power iii ATP made during cataboism is used in anabolism 2 Energetics energy is the capacity to do work a Two types of energy i Potential energy stored ii Kinetic energy energy of motion b Energy cannot be created or destroyed only converted or transferred c Cells obtain their energy from their environment and convert it into a useful form d Most common energy currency ATP also electrons and light e Chemolithoautotrophs microbes that harvest energy from inorganic compounds f Chemoorganotrophs obtain energy by degrading organic compoundsTypes of work a cell needs to do i Chemical work 1 Synthesis of complex molecules anabolic processes ii Transport work 1 Import of nutrients 2 Eliminate waste 3 Maintain ion balance iii Mechanical work 1 Cell motility 2 Movement of structures within cells ex ageHa g Free energy energy available to do work energy released when chemical bonds are broken i AG change in free energy 1 AG exergonic reaction a Reactants have more free energy b Energy is released 2 AG endergonic reaction a Products have more free energy b Reaction requires energy input 3 AG is the same regardless of the number of steps or presence of a catalyst 4 Cells often use multiple steps when degrading or synthesizing compounds a Metabolic pathway series of sequential chemical reactions that converts a starting compound to an end compound b Intermediates can feed into other pathways c Energy released from exergonic reactions is used to power endergonic reactions coupHng 3 Adenosine triphosphate ATP is the energy currency of the cell immediate donor of free energy a Composed of ribose adenine and three phosphate groups b Adenosine diphosphate ADP free energy acceptor i ADP P ATP uses energy ii ATP l ADP P releases energy iii Cells produce ATP during exergonic reactions of catabolism and then use it to power endergonic reactions of anabolism c 3 processes that generate ATP i Substrate level phosphorylation exergonic reactions 1 Free energy is used to phosphorylate ADP to ATP 2 Chemoorganotrophs use this ii Oxidative phosphorylation proton motive force and ATP synthase 1 Proton motive force the form of energy that results from the electrochemical gradient established by the electron transport chain 2 Substance that loses electrons is oxidized 3 Substance that gains electrons is reduced 4 Chemoorganotrophs use this iii Photophosphorylation light energy from the sun and an electron transport chain is used to create a proton motive force 1 Photosynthetic organisms use this iv Cells use enzymes to help orient these reactions and help them go faster v Electron carriers 1 Role of electron carriers harvest energy in stepwise process 2 Electron carriers have reducing power a b c Electrons move from a molecule of low electron af nity tends to give electrons to one with a high electron af nity tends to accept electrons energy is released i This is how cells obtain energy used to make ATP Energy source electron donor Terminal electron acceptor last molecule to accept those electrons i Aerobes use oxygen as the terminal electron acceptor anaerobes do not The greater the difference in electron af nities between the energy source and the terminal electron acceptor the more energy is released 3 ElectronHydrogen carriers a b C NADNADH 2 es 1 proton i Used to generate a proton motive force that can drive ATP synthesis NADPNADPH 2 es 1 proton i Biosynthesis FADFADHZ 2 es 2 protons i Used to generate a proton motive force that can drive ATP synthesis vi Electrons can be moved through series of redox reactions 1 Oxidation losing electrons a H protons are often lost too dehydrogenation is also an oxidation 2 Reduction gaining electrons a Hydrogenation is a reduction 62 Enzymes 4 Enzymes proteins that function as biological catalysts that speed up the conversion of substrate to product by lowering the activation energy a Very speci c one enzyme at each step of the pathway b Reactions will still occur without enzymes but slower C Enzymes don t affect free energy of reaction AG 0 Enzymes have an active site to which a substrate binds weakly changing the shape of the enzyme slightly induced t e Help orient substrates destabilize existing bonds create microenvironment can play a role in the chemistry of the reaction 2 Enzymes are not used up or permanently changed in a reaction g More than a thousand different enzymes in each cell h Names usually re ect function ase i Factors that affect activity i Temperature proteins denature at high temperatures ii PH iii Salt concentration j Cofactors assist some enzymes i Nonprotein components that help an enzyme s activity magnesium zinc copper other trace elements E f k Coenzymes organic cofactors carbon backbone i Include electron carriers FAD NAD NADP ii One coenzyme can assist different enzymes iii Many are derived from vitamins iv Transfer substances from one compound to another Allosteric regulation i Enzyme activity is controlled by binding to allosteric site ii This distorts the enzyme s shape and prevents or enhances binding of substrate iii Regulatory molecule used is usually the end product of a pathway feedback inhibition iv Feedback regulation could also be by a molecule that increases enzyme activity m Inhibition i Competitive inhibition binds to active site of enzyme 1 Similar chemical structure to substrate 2 Blocks substrate ii Noncompetitive inhibition binds to allosteric site and changes enzyme s shape so a substrate cannot bind to it 1 Regulatory molecules inhibitor changes the shape of the enzyme so that the substrate can no longer bind to the active site This is a reversible action that provides cells with a means to control the activity of allosteric enzymes 2 Enzyme poisons inhibitor permanently changes the shape of the enzyme making the enzyme nonfunctional a Enzyme poisons such as mercury are used in certain antimicrobial compounds 63 Central Metabolic Pathways 5 Central metabolic pathways oxidize glucose to carbon dioxide a Central catabolism iii iv Glycolysis breakdown of glucose 6C to pyruvate 3C TCA Cycle Krebs cycle breaks down carbon to get all electron energy out of glucose possible 1 Only carbon that is left carbon dioxide Respiration uses reducing power Fermentation uses reducing power from glycolysis b Catabolism of glucose vi Step one oxidation of glucose 1 Central metabolism Step two transfer of electrons to terminal electron mm 1 Respiration and fermentation Glucose an energy source that is the starting point for all cellular components proteins lipids carbohydrates nucleic acids Some glucose molecules are completely oxidized for energy other are used in biosynthesis Eukaryote locations 1 Cytoplasm a Glycolysis b Transition c Fermentation 2 Mitochondrial matrix a TCA Krebs 3 Inner mitochondrial membrane a Respiration 4 Chloroplasts a Photosynthesis Prokaryote locations 1 Cytoplasm a Glycolysis b Transition step c TCA Krebs d Fermentation 2 Cytoplasmic membrane a Respiration b Photosynthesis c Some bacteria have specialized inner thyakoidlike membranes 10 c Step one Oxidation of Glucose i Central metabolism ii Includes 4 steps 1 Glycolysis a Occurs with or without oxygen i 6carbon 5 precursor metabolites b Glucose l 2 3carbon pyruvates c Input i Glucose ii 2 ATP d Outputs i 4 ATP 2 net ii 2 NADH iii 2 pyruvate precursor metabolite e Steps 15 investment steps 610 payoff i Investment ATP is used to add phosphate 2 Pentose phosphate cycle a Primary role is to make essential precursor metabolites for anabolism bnput i 6carbon glucose c Output i NADPH reducing power for anabolics ii Precursor metabolites iii GBP can feed back into glycolysis 3 Transition step a 3carbon pyruvate l 2carbon acetyICoA i Some carbon is lost as carbon dioxide bnput i 2 pyruvate 3carbon c Output i 2 NADH 2 H ii 2 acetyIcoA precursor metabolite iii 2 carbon dioxide carbon loss 4 TCA cycle Krebs cycle a AcetyICoA 2C no organic carbon product b Complete carbon loss Completes the oxidation of glucose Input i 2 acetyIcoA e Output per 2 turns of cycle i 6 NADH 6 H an 11 ii 2 FADHz iii 2 ATP iv 4 carbon dioxide waste carbon lost v Precursor metabolites iii Key outcomes 1 ATP substrate eve phosphorylation 2 Reducing power NADH FADHZ NADPH 3 Precursor metabolites for use in biosynthesis K mum1w V Comparison of the Central i v c 3 in Pamla pr39haaphmh Q I 39E m iiuiietaijunlic Pathways immii mm E V ImpasmnnnmIgl i nmaam mamGas i TIEiwzlwlnlw I39IIIII I i39 gt 7 h ATF F H r p UsmeQbelmmsmn MEIR II ml39MII39t mdlthn PMI In l39 IbI39I i39I39IEdFIii hi39 FIGURE Gum Daniaw of Mmbmilsm WEIpm i 23 me mumm d ll m uilllwilg IEMIII lIiIIIu39LmI nluu illd b l IIIH lIiLIIhuagrEiI idl Lilli Ilia Lydia drum H i uldlllliilg39 1illiim gIIIIIHIIIm1JHIHI39IIlnC i lIIgItilII3939IIIInu MI TJHIEIQ IIDLIH III l 39I IwIilll illg InnEr l dl h 39l ir l39H IIH39I39ilmrlinrlall Erma mrahnli39lm nmnm warnlrlmrl min 1 5 Rle39 llnn Inn Erarmlltlngr wrrm lamMir II Imh39i u mile 11 ihni iHhIrl than 7 hymn516 1n maln I39E39IF hJi Ullrlernhrphnspiwgin iltirt ultinmrh naming thrv rdmmte ATP U cn39 H39iCEIIIIII39 lnlmillil HIIIIIquotIIII I39JHIIII I33 I39ulrnul ulillll I In nharl39nidiz r15 ulIIlC39hIl I13quot ih 39i39l l39i rrlmnn39l39IIIJl Irirl Indmri Ilaquot pyrllml39 lll39 HdH39ru39lhn ua hllrrrlinn HIIrh39nrl Ii39l39lfl39Irlr Wi smm i hn fiul I I39n39a feralnil FHI39I39H39ITII I39HFI I39IFEI39 uwulli r nr nn 12 d Step two Transfer of Electrons to Terminal Electron Acceptor i Respiration 1 Uses reducing power from glycolysis transition step and TCA cycle to synthesize ATP 2 Chemiosmotic theory by Peter Mitchell connects the electron transport chain to ATP synthesis a Electron transport chain generates proton motive force which drives the synthesis of ATP 3 Oxidative Phosphorylation the mechanism for generating ATP which involves a 1 The electron transport chain generates a proton motive force i Membrane embedded electron carriers proton complexes pass electrons to each other releasing energy and move protons using energy generating a proton motive force ii In eukaryotes ETC is in the inner membrane mitochondria 1 Ubiquinone and Cytochrome C move in the lipid membrane to transfer electrons Complex I NADH hydrogenase accepts electrons from NADH Complex II accepts electrons from TCA cycle FADH2 doesn39t pump protons Complex Ill accepts electrons from ubiquinone complexes l and II pumps protons Complex IV accepts electrons from cytochrome C pumps protons transfers electrons to the terminal electron acceptor 02 13 Elbame Transpart Chaln Use 131 From Motlm Farce E i Fromm findingequot lmte 39 T ATP Earnings camplax I complex III CompIx IV E 393 m WM ATP gymnasls I 253 10 w a lnt rmambran 539 ans marl 14 iii In prokaryotes ETC is in the cytoplasmic membrane 1 ICD ETC in prokaryotes varies a single species can have several alternate electron carriers a E coli has versions for high and low 02 concentrations There are different NADH dehydrogenases or alternative enzymes to optimally use different energy electron sources or sources besides organic compound a Chemolithotrophs use H2 or H25 NADH hydrogenase like complex I accepts electrons from NADH Succinate dehydrogenase like complex ll accepts electrons from TCA cycle FADH2 does not pump protons Ubiquinol oxidase like complex IV transfers electrons to terminal oxygen only in aerobic respiration No complex lll equivalent No cytochrome C ubiquinone shuttles electrons directly to ubiquinol oxidase Anaerobic respiration harvests less energy because the electron acceptors have a lower electron af nity a Inorganic terminal electron acceptors have lower electron af nity 15 Electron Transport Chain ilees of Proton Motive Fume ATP 5 39nilhase Active trans nril Rotation of lila ella iNADH dehydrogenase Uhlqiulnnli maidase ATP Sgnthesish we mechanim g Hquot 0 M4 Hi 2 or4 H H1 Transporter V V Outside or 39 39 cytoplasmic morner s molecule Cytoplasrn E ucclmate dehydrog enase f b 2 ATP synthases use the energy of the proton motive force to drive the synthesis of ATP i Prokaryotes can use energy of proton motive force to transport substances and power the rotation of agella ii Allows protons to ow down the electrochemical gradient in a controlled manner the energy is used to turn ADP Pi ATP iii Approximately 1 ATP is made from 3 H ii Maximum theoretical energy yield 38 ATP 1 Substrate eve phosphorylation a Glycolysis gained 2 ATP i 2 NADH l 6 ATP b Transition i 2 NADH l 6 ATP c TCA cycle gained 2 ATP i 6 NADH l 18 ATP ii 2 FADH2 I 4 ATP 2 Oxidative phosphorylation a Aerobic respiration gained 34 ATP i Glycolysis 6 ATP of reducing power ii Transition step 6 ATP of reducing power iii TCA cycle 22 ATP of reducing power iii Fermentation redox reactions that regenerate NAD 1 Done by organisms that cannot undergo respiration Because a suitable electron 16 mm 10 acceptor is not available or because they lack an electron transport chain a E coli can use aerobic respiration anaerobic respiration or fermentation facultative anaerobe b Streptococcus pneumonia can only ferment because doesn t have an ETC c Saccharomyces cerevisiae can ferment or use aerobic respiration prefers fermentation in high glucose concentrations regardless of oxygen The only ATP generating reactions are those of glycolysis Excess reducing power is consumed as a way of regenerating NAD a NAD is needed to accept electrons in subsequent rounds of glycolysis without it glycolysis would stop Pyruvate or a derivative acts as the nal electron acceptor 2 ATP are gained per glucose Lactic acid fermentation lactate is the end product with no release of carbon dioxide a Used by some fungi and bacteria to make cheese and yogurt b Human muscle cells use lactic acid fermentation to generate ATP when oxygen is scarce Alcohol fermentation pyruvate converted to ethanol Step one carbon dioxide released Step two ethanol is produced Used by some yeast Used for brewing wine making and baking 006m Homolactic fermentation a One molecule of glucose yields two molecules of lactic acid Heterolactic fermentation a Yields carbon dioxide ethanol and lactic acid Methyl Red test detects low pH from acidic end products 6 Alternative sources of carbon microbes can use a variety of compounds for carbon catabolism beside glucose 17 These compounds are converted to precursor metabolites that can enter appropriate metabolic pathways may be at a different step than with glucose Need a way to get the compound in the cell and the enzymes to break it down by adding water Polysaccharides and disaccharides l Amylases digest starch a polymer of glucose ii Cellulases digest cellulose a polymer of glucose iii Disaccharides are hydrolyzed by speci c disaccharides iv The resulting monosaccharides simple sugars are converted to intermediates in glycolysis Lipids i Fats the most common simple lipids a combination of fatty acids and glycerol 1 Fats are hydrolyzed by lipases 2 Glycerol is converted to the precursor metabolite dihydroxyacetone phosphate which enters glycolysis 3 Fatty acids degraded by Boxidation enter TCA cycle Proteins l Hydrolyzed by proteases break peptide bonds between amino acids ii Carbon skeletons are converted into a precursor metabolite for glycolysis or the TCA cycle 18 7 Chemolithotrophs extract electron energy from inorganic sources rather than organic carbon based molecules and pass the to an electron transport chain and generate a proton motive force a Bacteria are unique in their ability to use reduced inorganic chemicals as energy sources The amount of energy gained depends on the source of electrons as well as the terminal electron acceptor which may not be oxygen Usually found in very speci c environments where reduced inorganic compounds are found Autotrophs need to X carbon dioxide to ful ll the cell s carbon needs The amount of energy gained in metabolism depends on the energy source and the terminal electron acceptor f Chemolithotrophs incorporate carbon dioxide into an organic form carbon xation b g The rst enzyme of the electron transport chain will vary depending on the electron source h Terminal electron acceptor may not be 02 anaerobic respiration i Hydrogen bacteria energy from hydrogen gas i Can also use simple organic compounds for energy j Sulfur bacteria energy from hydrogen sul de H25 i Some members can live at a pH of less than 1 Iron bacteria energy from reduced iron Fe2 i ron oxide is present in the sheaths of these bacteria l Nitrifying bacteria energy from ammonia NH3 or nitrite HNOz i Important in the nitrogen cycle 19 9 Photosynthesis conversion of radiant light energy into chemical energy a 6 C02 H2X I C6H1206 X 6 H20 i X oxygen or sulfur b Light reactions lightdependent reactions capture energy and convert it to ATP i Reactioncenter pigments donate excited electrons to electron transport chain 1 Chlorophyll a plants algae cyanobacteria 2 Bacteriochlorophylls anoxygenic bacteria ii Oxygenic photosynthesis 1 Two photosystems I and II a Cyclic photophosphorylation i Photosystem donates electrons for proton gradient to produce ATP ii Reactioncenter chlorophyll is the terminal electron acceptor b Noncyclic photophosphorylation linear i Used when cells need both ATP and reducing power ii Electrons from photosystem II drive photophosphorylation then are donated to photosystem I iii Photosystem replenishes electrons by splitting water and generates oxygen iv Electrons from photosystem I reduce NADP to NADPH 2 Plants and algae photosystems in the membranes of the thyakoids Within the stroma of chloroplasts a Endosymbiont theory theory that ancestors of mitochondria and chloroplasts were bacteria that had been residing within other cells in a mutually bene cial partnership 3 Cyanobacteria photosystems in the membranes of the thyakoids located within the cell 20 iii Anoxygenic photosynthesis 1 Have a single photosystem 2 Cannot use water as an electron donor so they use electron donors such as hydrogen gas hydrogen sul de or organic compounds 3 Purple bacteria photosystems are in cytoplasmic membrane folds a Photosystem is similar to photosystem II b Electron energy is insuf cient to reduce NAD to NADH so they expend ATP and use reversed electron transport ETC uphill to generate reducing power 4 Green bacteria photosystems are in specialized chlorosomes attached to the cytoplasmic membrane a Photosystem is similar to photosystem I b Electrons can be used to either generate proton motive force or reduce NAD 21 c Lightindependent reactions use ATP to synthesize organic compounds carbon xation i Carbon xation 1 Chemolitoautotrophs inorganic enerQY and photoautotrophs light energy use carbon dioxide to synthesize organic compounds 2 Consumes a lot of ATP and reducing power to make organic molecules a The reverse process of oxidizing compounds to carbon dioxide liberates a lot of energy catabolism 3 Calvin cycle most commonly used a 6 turns of the cycle for a net gain i G3P 1 Can be converted intol fructose6phosphate b Consumes i 18 ATP ii 12 NADPH iii 6 carbon dioxide 4 Some bacteria and archaea use reverse steps in the TCA cycle instead of the Calvin cycle diversity 10 Anabolic pathways building cell components a Not all carbon from every glucose molecule is completely oxidized for max energy some is used to make macromolecules for the cell b Prokaryotes have remarkably similar biosynthesis pathways Use central metabolic pathways for precursors If enzymes are lacking the end product must be supplied by the environment an
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