Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Photosynthesis wikipedia , lookup
Citric acid cycle wikipedia , lookup
Light-dependent reactions wikipedia , lookup
Photosynthetic reaction centre wikipedia , lookup
Electron transport chain wikipedia , lookup
Oxidative phosphorylation wikipedia , lookup
Metalloprotein wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
11/19/2012 LECTURE PRESENTATIONS For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark Chapter 14 Lectures by John Zamora Middle Tennessee State University Catabolism of Organic Compounds © 2012 Pearson Education, Inc. I. Fermentation • 14.1 Energetic and Redox Considerations • 14.2 Lactic and Mixed-Acid Fermentations • 14.3 Clostridial and Propionic Acid Fermentations • 14.4 Fermentations Lacking Substrate-Level Phosphorylation • 14.5 Syntrophy © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 1 11/19/2012 14.1 Energetic and Redox Considerations • Two mechanisms for catabolism of organic compounds: – Respiration • Exogenous electron acceptors are present to accept electrons generated from the oxidation of electron donors – Fermentation • Electron donor and acceptor are the same compound • Relatively little energy yield © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.1 Energetic and Redox Considerations • In the absence of external electron acceptors, organic compounds can be catabolized anaerobically only by fermentation (Figure 14.1) – ATP is usually synthesized by substrate-level phosphorylation • Energy-rich phosphate bonds from phosphorylated organic intermediates transferred to ADP • Redox balance is achieved by production of fermentation products © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 2 11/19/2012 Figure 14.1 The essentials of fermentation © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.2 Lactic and Mixed-Acid Fermentations • Fermentations are classified by either the substrate fermented or the products formed • A wide variety of organic compounds can be fermented – Lactic acid bacteria produce lactic acid – Lactic acid fermentation can occur by • homofermentative and • heterofermentative pathways © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 3 11/19/2012 14.2 Lactic and Mixed-Acid Fermentations © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.2 Lactic and Mixed-Acid Fermentations • Mixed-acid fermentations – Generate acids • Acetic, lactic, and succinic – Sometimes also generate neutral products • Example: butanediol – Characteristic of enteric bacteria © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 4 11/19/2012 14.3 Clostridial and Propionic Acid Fermentations • Clostridium species ferment sugars, producing butyric acid – Butanol and acetone can also be by-products © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.3 Clostridial and Propionic Acid Fermentations • Some Clostridium species ferment amino acids using a complex biochemical pathway known as the Strickland reaction © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 5 11/19/2012 3 Lactate 14.3 Clostridial3 Pyruvate and Propionic Acid Fermentations Acetate CO2 2 Oxalacetate • Secondary fermentation – The fermentation of fermentation products 2 Malate CoA transfer – Fermentation of ethanol plus acetate by Clostridium kluyveri 2 Propionate 2 Fumarate • Propionic acid fermentation Propionyl CoA – Propionibacterium and related 2prokaryotes 2 Succinate produce propionic acid as a major fermentation2 Succinyl productCoA 2 Methylmalonyl CoA Overall: 3 Lactate 2 propionate acetate CO2 H2O G0 171 kJ © 2012 Pearson Education, Inc. (3 ATP) Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.4 Fermentations Lacking SubstrateLevel Phosphorylation • Fermentations of certain compounds do not yield sufficient energy to synthesize ATP – Catabolism of the compound can then be linked to ion pumps that establish a proton or sodium motive force – Propionigenium modestum catabolizes succinate under strictly anoxic conditions • Establishes a sodium motive force • Sodium motive force forms ATP © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 6 11/19/2012 14.4 Fermentations Lacking Substrate-Level Phosphorylation • Oxalobacter formigenes catabolizes oxalate and produces formate – Formate is excreted from the cell • Export of formate from the cell establishes a proton motive force • Proton motive force forms ATP © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.5 Syntrophy • Syntrophy – A process whereby two or more microbes cooperate to degrade a substance neither can degrade alone • Most syntrophic reactions are secondary fermentations • Most reactions are based on interspecies hydrogen transfer – H2 production by one partner is linked to H2 consumption by the other • Syntrophic reactions are important for the anoxic portion of the carbon cycle © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 7 11/19/2012 Figure 14.9 Syntrophy: Interspecies H2 transfer. Ethanol fermentation: G0 19.4 kJ/reaction Methanogenesis: G0 130.7 kJ/reaction Coupled reaction: G0 111.3 kJ/reaction Reactions Methanogen Ethanol fermenter 2 Ethanol Interspecies hydrogen transfer 2 Acetate Syntrophic transfer of H2 © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.5 Syntrophy • Syntrophy (cont’d) – H2 consumption affects the energetics of the reaction carried out by the H2 producer, allowing the reaction to be exothermic © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 8 11/19/2012 II. Anaerobic Respiration • • • • • • • • 14.6 Anaerobic Respiration: General Principles 14.7 Nitrate Reduction and Denitrification 14.8 Sulfate and Sulfur Reduction 14.9 Acetogenesis 14.10 Methanogenesis 14.11 Proton Reduction 14.12 Other Electron Acceptors 14.13 Anoxic Hydrocarbon Oxidation Linked to Anaerobic Respiration © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.6 Anaerobic Respiration: General Principles • In anaerobic respiration, electron acceptors other than O2 are used • Anaerobic and aerobic respiratory systems are similar – But anaerobic respiration yields less energy than aerobic respiration • Energy released from redox reactions can be determined by comparing reduction potentials Animation: Electron Transport: Aerobic & Anaerobic Conditions © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 9 11/19/2012 14.6 Anaerobic Respiration: General Principles • In the assimilative metabolism of an inorganic compound (e.g., NO3, SO42, CO2) the reduced compounds are used in biosynthesis • During anaerobic respiration, the reduction of inorganic compounds is called dissimilative metabolism because the reduced products are excreted © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.7 Nitrate Reduction and Denitrification • Inorganic nitrogen compounds are the most common electron acceptors in anaerobic respiration • All products of nitrate reduction (denitrification) are gaseous (Figure 14.12) • Denitrification is the main biological source of gaseous N2 © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 10 11/19/2012 Figure 14.12 Steps in the dissimilative reduction of nitrate Nitrate NO3 Nitrate reductase Nitrite Nitrate reduction (Escherichia coli) NO2 Nitrite reductase Denitrification Nitric oxide NO Nitric oxide reductase Gases (Pseudomonas stutzeri) Nitrous oxide N2O Nitrous oxide reductase Dinitrogen N2 © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.7 Nitrate Reduction and Denitrification • The biochemical pathway for dissimilative nitrate reduction has been well studied • Enzymes of the pathway are repressed by oxygen © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 11 11/19/2012 14.8 Sulfate and Sulfur Reduction • Inorganic sulfur compounds can be used as electron acceptors in anaerobic respiration • Reduction of SO42 to H2S proceeds through several intermediates and requires activation of sulfate by ATP. © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.8 Sulfate and Sulfur Reduction © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 12 11/19/2012 14.8 Sulfate and Sulfur Reduction • Many different compounds can serve as electron donors in sulfate reduction – Examples: H2, organic compounds, phosphite 4H2 + SO42- + H+HS- + 4H2O ∆G0’ = -152 kJ CH3COO- + SO42- + 3H+CO2 + H2S + 2H2O ∆G0’ = -57.5 kJ 4HPO3+ SO42- + H+4HPO42- + HS- ∆G0’ = -364 kJ © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.9 Acetogenesis • Acetogens and methanogens use CO2 as an electron acceptor in anaerobic respiration – H2 is the major electron donor for both groups of organisms (Figure 14.16) • Acetogens carry out the reaction 4H2 + H+ + 2HCO3-CH3COO- + 4H2O ∆G0’ = -105 kJ © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 13 11/19/2012 Figure 14.16 The contrasting processes of methanogenesis and acetogenesis Methanogenesis Proton or sodium motive force (plus substrate-level phosphorylation for acetogens) © 2012 Pearson Education, Inc. Acetogenesis ( G0 105 kJ) ( G0 136 kJ) Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.10 Methanogenesis • Methanogenesis – Biological production of methane – Carried out by a group of strictly anaerobic Archaea called the methanogens – Involves a complex series of biochemical reactions that use novel coenzymes © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14 11/19/2012 14.10 Methanogenesis • The autofluorescence of coenzyme F420 can be used to identify methanogens microscopically (Figure 14.19) Methanosarcina barkeri Methanobacterium formicicum Figure 14.19 Fluorescence due to the methanogenic coenzyme F420 . The organisms were made visible by excitation with blue light in a fluorescence microscope © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.10 Methanogenesis • H2 is the major electron donor for methanogenesis (Figure 14.20) • Additional electron donors exist – Examples: formate, CO, organic compounds © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 15 11/19/2012 14.11 Proton Reduction • Pyrococcus furiosus – Member of the Archaea – Grows optimally at 100C on sugars and small peptides as electron donors – May have the simplest anaerobic respiration mechanism (Figure 14.23) – Organism uses modified glycolysis and protons in anaerobic respiration linked to ATPase activity © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.12 Other Electron Acceptors • Fe3+, Mn4+, ClO3, and various organic compounds can serve as electron acceptors for bacteria (Figure 14.24) • Fe3+ is abundant in nature and its reduction is a major form of anaerobic respiration © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 16 11/19/2012 Figure 14.24 Some alternative electron acceptors for anaerobic respirations Couple Reaction E0 Fumarate/ Succinate 0.03 Trimethylamine-N-oxide (TMAO)/ Trimethylamine (TMA) 0.13 Arsenate/ Arsenite 0.14 Dimethyl sulfoxide (DMSO)/ Dimethyl sulfide (DMS) 0.16 Ferric ion/ Ferrous ion 0.20 Selenate/ Selenite 0.48 Manganic ion/ Manganous ion 0.80 Chlorate/ Chloride 1.00 © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.12 Other Electron Acceptors • The reduction of arsenate has been employed for cleanup of toxic wastes and groundwater (Figure 14.25) • Halogenated compounds can also serve as electron acceptors via a process called reductive dechlorination (dehalorespiration) © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 17 11/19/2012 Figure 14.25 Biomineralization during arsenate reduction by the sulfate-reducing bacterium Desulfotomaculum auripigmentum Desulfotomaculum can reduce AsO43- to AsO33-, along with sulfate (SO42-) to sulfide (HS-) Appearance of culture bottle after inoculation © 2012 Pearson Education, Inc. Synthetic sample of As2S3 Following growth for 2 weeks and biomineralization of arsenic trisulfide, As2S3 Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.13 Anoxic Hydrocarbon Oxidation • Aliphatic and aromatic hydrocarbons and organic compounds containing only carbon and hydrogen can be oxidized anaerobically • The first step in degradation is the addition of oxygen to the molecule through the incorporation of fumarate • Hydrocarbons are oxidized to intermediates that can be catabolized via the citric acid cycle © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 18 11/19/2012 14.13 Anoxic Hydrocarbon Oxidation • Aliphatic hydrocarbons are straight-chain saturated or unsaturated compounds • Many of them are substrates for denitrifying and sulfate-reducing bacteria • Aromatic hydrocarbons are catabolized by ring reduction and cleavage • Can be degraded by some denitrifying, ferric iron-reducing, and sulfate-reducing bacteria © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.13 Anoxic Hydrocarbon Oxidation • Methane – The simplest hydrocarbon – Can be oxidized under anoxic conditions by a consortia containing sulfate-reducing bacteria and methanotrophic archaea CH4 + SO42- + H+ CO2 + HS- + 2H2O ∆G0’ = -18 kJ © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 19 11/19/2012 Figure 14.28 Anoxic methane oxidation Methanotrophic Archaea (ANME-types) Sulfate-reducing Bacteria Organic compounds © 2012 Pearson Education, Inc. Mechanism for cooperative degradation of CH4. An organic compound or some other carrier of reducing power transfers electrons from methanotroph to SRB. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI III. Aerobic Chemoorganotrophic Processes • 14.14 Molecular Oxygen as a Reactant and Aerobic Hydrocarbon Oxidation • 14.15 Methylotrophy and Methanotrophy • 14.16 Sugar and Polysaccharide Metabolism • 14.17 Organic Acid Metabolism • 14.18 Lipid Metabolism © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 20 11/19/2012 14.14 Oxygen as a Reactant and Hydrocarbon Oxidation • Oxygen used as a direct reactant in certain biochemical reactions • Oxygenases – Enzymes that catalyze the incorporation of atoms of oxygen from O2 into organic compounds – Two classes: • Monooxygenases: incorporate one oxygen atom • Dioxygenases: incorporate both oxygen atoms © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.14 Oxygen as a Reactant and Hydrocarbon Oxidation • Many microbes can use aliphatic and aromatic hydrocarbons as electron donors when growing aerobically • Oxygenases are central enzymes in these biochemical reactions • Aerobic degradation of aromatic compounds involves ring oxidation © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 21 11/19/2012 14.15 Methylotrophy and Methanotrophy • Methylotrophs use compounds that lack C–C bonds as electron donors and carbon sources • Methanotrophs are methylotrophs that use CH4 – The initial step in methanotrophy requires methane monooxygenase (MMO) – In the MMO reaction, CH4 is converted to CH3OH and H2O – Other oxidation steps convert CH3OH to CO2 – The steps in CH4 oxidation to CO2 CH4CH3OH CH2O HCOO-CO2 © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.16 Sugar and Polysaccharide Metabolism • Sugars and polysaccharides are common substrates for chemoorganotrophs • Polysaccharides such as cellulose and starch are common in nature – Their breakdown yields hexoses and pentoses • Starch is fairly soluble and readily degraded by many fungi and bacteria employing amylases © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 22 11/19/2012 14.16 Sugar and Polysaccharide Metabolism • Cellulose is fairly insoluble and its degradation typically involves attachment of microbes to cellulose fibrils and production of cellulases (Figure 14.34) • Cellulose degradation is restricted to relatively few bacteria groups, including the gliding bacteria Sporocytophaga and Cytophaga (Figure 14.35) Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI © 2012 Pearson Education, Inc. Figure 14.34 Cellulose digestion. Cellulose fiber Bacteria Transmission electron micrograph showing attachment of the cellulosedigesting bacterium Sporocytophaga myxococcoides to cellulose fibers. © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 23 11/19/2012 Figure 14.35 Cytophaga hutchinsonii colonies on a cellulose–agar plate Cellulose digestion Areas where cellulose has been hydrolyzed are more translucent © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.17 Sugar and Polysaccharide Metabolism • Pentoses are required for the synthesis of nucleic acids • If pentoses are not readily available from the environment, organisms must synthesize them • The major pathway for pentose production is the pentose phosphate pathway © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 24 11/19/2012 14.17 Organic Acid Metabolism • Organic acids can be metabolized as electron donors and carbon sources by many microbes • C4–C6 citric acid cycle intermediates (e.g., citrate, malate, fumarate, and succinate) are common natural plant and fermentation products and can be readily catabolized through the citric acid cycle alone • Catabolism of C2 and C3 organic acids typically involves production of oxalacetate through the glyoxylate cycle © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 14.18 Lipid Metabolism • Lipids are abundant in nature and readily degraded by many microbes • Catabolism of fats is initiated by hydrolysis of the ester bond, yielding fatty acids and glycerol, by extracellular lipases (Figure 14.41) – Phospholipases are a class of lipases that attack phospholipids • Fatty acids are oxidized by beta-oxidation to acetyl-CoA, which is then oxidized to CO2 by citric acid cycle © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 25 11/19/2012 Figure 14.41 Lipases Glycerol Fatty acid Fatty acid Activity of lipases on a fat Fatty acid Lipase Phospholipase B Fatty acid Fatty acid Phospholipase A Phospholipase C Phospholipase activity on phospholipid Phospholipase D © 2012 Pearson Education, Inc. Marmara University – Enve303 Env. Eng. Microbiology – Prof. BARIŞ ÇALLI 26