Microbial Metabolism
Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Microbial Metabolism: The Chemical Crossroads of Life Chapter 8 Copyright © The McGraw-Hill Companies, Inc) Permission required for reproduction or display. Metabolism Nutrients from outside or from internal pathways Pyruvate Acetyl CoA Glyceraldehyde-3-P Amino acids Sugars Nucleotides Fatty acids Proteins Peptidoglycan RNA + DNA Complex lipids Relative complexity of molecules Glycolysis Krebs cycle Respiratory chain Fermentation Macromolecules Building blocks Glucose Precursor molecules + ATP NADH Yields energy Chapter 8, pages 198 to 231 Uses energy Uses energy 1 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach 8.1 The Metabolism of Microbes • Metabolism: All chemical reactions and physical workings of the cell • Functions of metabolism • Assembles smaller molecules into larger macromolecules needed for the cell • Degrades macromolecules and yields energy • Energy is conserved in the form of ATP or heat Metabolism • Anabolism (biosynthesis): process that results in synthesis of cell molecules and structures • Catabolism: breakdown of bonds of larger molecules into smaller molecules • usually requires energy input • often release energy Chapter 8, pages 198 to 231 2 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Enzymes • Enzymes are catalysts • Catalysts - chemicals that increase the rate of a chemical reaction without becoming part of the products or being consumed in the reaction How do Enzymes Work? • Energy of activation: the amount of energy which must be overcome for a reaction to proceed. • Act as a physical site where the reactant molecules (substrates) can be positioned for various interactions Chapter 8, pages 198 to 231 3 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Enzyme Structure • Most are protein • Can be classified as simple or conjugated • Simple enzymes- consist of protein alone • Conjugated enzymes (haloenzyme) - contain protein and nonprotein molecules • Protein (now called the apoenzyme) and one or more cofactors • Cofactors are either organic molecules (coenzymes) or inorganic elements (metal ions) Conjugated Enzyme Structure Chapter 8, pages 198 to 231 4 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Apoenzymes: Specificity and the Active Site • Exhibits levels of molecular complexity called the primary, secondary, tertiary, and quaternary organization • The actual site where the substrate binds is a crevice or groove called the active site or catalytic site Enzyme-Substrate Interactions • For a reaction to take place, a temporary enzymesubstrate union must occur at the active site • “Lock-and-key” fit • The bonds are weak and easily reversible Chapter 8, pages 198 to 231 5 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Cofactors: Supporting the Work of Enzymes • Metallic cofactors • Include Fe, Cu, Mg, Mn, Zn, Co, Se • Activate enzymes, help bring the active site and substrate close together, and participate directly in chemical reactions with the enzyme-substrate complex • Coenzymes • Organic compounds that work in conjunction with an apoenzyme to perform a necessary alteration of a substrate • Removes a chemical group from one substrate molecule and adds it to another substrate • Vitamins: one of the most important components of coenzymes Classification of Enzyme Functions • Site of action • Type of action • Substrate Chapter 8, pages 198 to 231 6 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Location and Regularity of Enzyme Action • Either inside or outside of the cell • Exoenzymes break down molecules outside of the cell • Endoenzymes break down molecules inside of the cell Rate of Enzyme Production • Constitutive enzymes: always present and in relatively constant amounts • Regulated enzymes: production is either induced or repressed in response to a change in concentration of the substrate Chapter 8, pages 198 to 231 7 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Synthesis and Hydrolysis Reactions Transfer Reactions by Enzymes • Oxidation-reduction reactions • A compound loses electrons (oxidized) • A compound receives electrons (reduced) • Other enzymes that play a role in necessary molecular conversions by directing the transfer of functional groups: • Aminotransferases • Phosphotransferases • Methyltranferases • Decarboxylases Chapter 8, pages 198 to 231 8 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach The Role of Microbial Enzymes in Disease • Many pathogens secrete unique exoenzymes • Help them avoid host defenses or promote multiplication in tissues • These exoenzymes are called virulence factors or toxins The Sensitivity of Enzymes to Their Environment • Enzyme activity is highly influenced by the cell’s environment • Enzymes generally operate only under the natural temperature, pH, and osmotic pressure of an organism’s habitat • When enzymes subjected to changes in normal conditions, they become chemically unstable (labile) • Denaturation: the weak bonds that maintain the native shape of the apoenzyme are broken Chapter 8, pages 198 to 231 9 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Direct Controls on the Action of Enzymes • Competitive inhibition: The cell supplies a molecule that resembles the enzyme’s normal substrate, which then occupies and blocks the enzyme’s active site • Noncompetitive inhibition: The enzyme has two binding sites- the active site and the regulatory site; a regulator molecule binds to the regulatory site providing a negative feedback mechanism Control Mechanisms for Enzymes Chapter 8, pages 198 to 231 10 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Controls on Enzyme Synthesis • Enzyme repression: decrease enzyme expression • Enzyme induction: increase enzyme expression 8.2 The Pursuit and Utilization of Energy • Energy in Cells • Exergonic reaction: a reaction that releases energy as it goes forward • Endergonic reaction: a reaction that is driven forward with the addition of energy Chapter 8, pages 198 to 231 11 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Cell Energy Production A Closer Look at Biological Oxidation and Reduction • Biological systems often extract energy through redox reactions • Redox reactions always occur in pairs- an electron donor paired with an electron acceptor • Electron donor (reduced) + electron acceptor (oxidized) Electron donor (oxidized) + electron acceptor (reduced) • The energy in the electron acceptor can be captured to phosphorylate ADP or some other compound, storing the energy in a high-energy molecule like ATP Chapter 8, pages 198 to 231 12 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Oxidation/Reduction • Oxidation is losing electrons • Reduction is gaining electrons • Oxidation is always linked to reduction Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1 Na 281 Reducing agent gives up electrons. Cl 287 Oxidizing agent accepts electrons. Na Oxidized cation 28 2 Cl 288 Reduced anion Electron Carriers • Repeatedly accept and release electrons and hydrogens • Most carriers are coenzymes that transfer both electrons and hydrogens • Some transfer electrons only • Most common carrierNAD (nicotinamide adenine dinucleotide) Chapter 8, pages 198 to 231 13 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Adenosine Triphosphate The Metabolic Role of ATP • When used in a chemical reaction, must be replaced • Ongoing cycle • Adding a phosphate to ADP replenishes ATP but it requires an input of energy • In heterotrophs, this energy comes from certain steps of catabolic pathways Chapter 8, pages 198 to 231 14 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Substrate Level Phosphorylation • ATP can be used to drive reactions Glucose + ATP Glucose-6-phosphate + ADP • Some compounds can be used to make ATP Phosphoenolpyruvate + ADP pyruvate + ATP • This is called substrate level phosphorylation 8.3 The Pathways • Metabolism uses enzymes to catalyze reactions that break down (catabolize) organic molecules to materials that cells can then use to build (anabolize) larger, more complex molecules. • Reducing power and energy are needed in large quantities for the anabolic parts of metabolism; they are produced during the catabolic part of metabolism. • Pathway- a series of biochemical reactions Chapter 8, pages 198 to 231 15 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Catabolism: Getting Materials and Energy • Glucose is often the nutrient catabolized • Three major pathways • Aerobic respiration: series of reactions that convert glucose to CO2 and allows the cell to recover significant amounts of energy; requires oxygen • Fermentation: Use only glycolysis to incompletely oxidize glucose • Anaerobic respiration: Does not use molecular oxygen as the final electron acceptor Glucose Metabolism Chapter 8, pages 198 to 231 16 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Aerobic Respiration • Series of enzyme-catalyzed reactions • Electrons are transferred from fuel molecules to oxygen as a final electron acceptor • Principal energy-yielding scheme for aerobic heterotrophs • Provides both ATP and metabolic intermediates for many other pathways in the cell • Glucose is the starting compound • Glycolysis enzymatically converts glucose through several steps into pyruvic acid Glycolysis Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. AEROBIC RESPIRATION ANAEROBIC RESPIRATION FERMENTATION Glycolysis Glycolysis Glycolysis Glucose Glucose ATP ATP NADH NADH CO2 CO2 CO2 Acetyl CoA C Fermentation Acetyl CoA C C C C C Glucose FADH 2 FADH2 Krebs CO2 NADH Krebs CO2 Acetaldeh yd e Lactic acid NADH ATP First phosphorylation Ethanol ATP ATP 1 ADP Or other alcohols, acids, gases Electrons Electrons Electron transport Electron transport O2 is final electron acceptor. ATP produced 38 No oxygen electron acceptors (examples: SO4 2-, NO3-, CO32-) ATP produced 2 to 36 An organic molecule is final electron acceptor (pyruvate, acetaldehyd e, etc.). ATP produced PO4 C C C C C C C C C C C C C C 2 Second phosphorylation Glucose-6-phosphate PO4 2 Fructose-6-phosphate C ATP 3 ADP PO4 PO4 C 4 Dihydroxyacetone phosphate (DHAP) Fructose-1,6-diphosphate (F-1,6-P) C Split of F-1,6-P; subsequent reactions in duplicate PO4 C C C C Glyceraldehyde-3 phosphate C C PO4 C C PO4 C C C 5 6 To electron transport NAD Glyceraldehyde-3-P (G-3-P) PO4 NAD NADH NADH PO4 C C C Diphosphoglyceric acid Substrate-level phosphorylation PO4 ADP ATP C C C PO4 C C PO4 C C C PO4 ADP ATP 3-phosphoglyceric acid PO4 C To electron transport C C 7 PO4 PO4 C C C 2-phosphoglycericacid C C C 8 PO4 C C Phosphoenolyruvicacid C C C C C C Substrate-level phosphorylation 9 ATP C ATP C C Goes to Krebs cycle or fermentation Chapter 8, pages 198 to 231 PO4 Pyruvicacid C Goes to Krebs cycle or fermentation 17 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Pyruvic Acid- A Central Metabolite • Pyruvic acid from glycolysis serves an important position in several pathways • Different organisms handle it in different ways • In strictly aerobic organisms and some anaerobes, pyruvic acid enters the Krebs cycle The Krebs Cycle: A Carbon and Energy Wheel • Pyruvic acid is energy-rich, but its hydrogens need to be transferred to oxygen • Takes place in the cytoplasm of bacteria and in the mitochondrial matrix in eukaryotes • Produces reduced coenzymes NADH and FADH2, 2 ATPs for each glucose molecule Chapter 8, pages 198 to 231 18 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Krebs Cycle The Respiratory Chain: Electron Transport and Oxidative Phosphorylation • The final “processing mill” for electrons and hydrogen ions • The major generator of ATP • A chain of special redox carriers that receives electrons from reduced carriers (NADH and FADH2) and passes them in a sequential and orderly fashion from one redox molecule to the next. Chapter 8, pages 198 to 231 19 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Electron Transport System • NADH oxidized Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Electrons pass through membrane carriers • Carriers are called “cytochromes” Cell wall H H H H H H H H • Protons pumped out H H H Cytochromes H H H H H • Protons pass through ATP synthase to form ATP Cytoplasm ATP synthase Cell membrane with ETS ADP H H H ATP H The Terminal Step • Oxygen accepts the electrons • Catalyzed by cytochrome aa3 (cytochrome oxidase) • 2 H+ + 2 e- + 1/2O2 H2O • Most eukaryotic aerobes have a fully functioning cytochrome system • Bacteria exhibit wide-ranging variations which can be used to differentiate among certain genera of bacteria Chapter 8, pages 198 to 231 20 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach ATP Yield from Aerobic Respiration Anaerobic Respiration • Functions like the aerobic cytochrome system except it utilizes oxygen-containing ions rather than free oxygen as the final electron acceptor • The nitrate and nitrite reduction systems are best known, using the enzyme nitrate reductase • Denitrification: when enzymes can further reduce nitrite to nitric oxide, nitrous oxide, and nitrogen gas- important in recycling nitrogen in the biosphere Chapter 8, pages 198 to 231 21 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Fermentation • The incomplete oxidation of glucose or other carbohydrates in the absence of oxygen • Uses organic compounds as the terminal electron acceptors and yields a small amount of ATP • Many bacteria can grow as fast using fermentation as they would in the presence of oxygen • This is made possible by an increase in the rate of glycolysis • Permits independence from molecular oxygen Products of Fermentation in Microorganisms • Products of Fermentation in Microorganisms • Alcoholic beverages • Organic acids • Dairy products • Vitamins, antibiotics, and even hormones • Two general categories • Alcoholic fermentation • Acidic fermentation Chapter 8, pages 198 to 231 22 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Fermentation Pathways Alcoholic Fermentation Products • Occurs in yeast or bacterial species that have metabolic pathways for converting pyruvic acid to ethanol • Products: ethanol and CO2 Chapter 8, pages 198 to 231 23 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Acidic Fermentation Products • Extremely varied pathways • Lactic acid bacteria ferment pyruvate and reduce it to lactic acid • Heterolactic fermentation- when glucose is fermented to a mixture of lactic acid, acetic acid, and carbon dioxide • Mixed acid fermentation- produces a combination of acetic, lactic, succinic, and formic acids and lowers the pH of a medium to about 4.0 8.4 Biosynthesis and the Crossing Pathways of Metabolism • The Frugality of the Cell- Waste Not, Want Not • Most catabolic pathways contain strategic molecular intermediates (metabolites) that can be diverted into anabolic pathways • Amphibolism: the property of a system to integrate catabolic and anabolic pathways to improve cell efficiency • Principal sites of amphibolic interaction occur during glycolysis and the Krebs cycle Chapter 8, pages 198 to 231 24 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Amphibolic Metabolism Amphibolic Sources of Cellular Building Blocks • Pyruvate also provides intermediates for amino acids and can serve as the starting point in glucose synthesis from metabolic intermediates (gluconeogenesis) • The acetyl group that starts the Krebs cycle can be fed into a number of synthetic pathways • Fats can be degraded to acetyl through beta oxidation • Two metabolites of carbohydrate catabolism that the Krebs cycle produces are essential intermediates in the synthesis of amino acids • Oxaloacetic acid • Α-ketoglutaric acid • Occurs through amination • Amino acids and carbohydrates can be interchanged through transamination Chapter 8, pages 198 to 231 25 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Amino Acid Formation Anabolism: Formation of Macromolecules • Monosaccharides, amino acids, fatty acids, nitrogen bases, and vitamins come from two possible sources • Enter the cell from outside as nutrients • Can be synthesized through various cellular pathways • Carbohydrate Biosynthesis • Several alternative pathways • Amino Acids, Protein Synthesis, and Nucleic Acid Synthesis • Some organisms can synthesize all 20 amino acids • Other organisms (especially animals) must acquire the essential ones from their diets Chapter 8, pages 198 to 231 26 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Assembly of the Cell • When anabolism produces enough macromolecules to serve two cells • When DNA replication produces duplicate copies of the cell’s genetic material • Then the cell undergoes binary fission 8.5 It All Starts with Light • Photosynthesis Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Proceeds in two phases • Light-dependent reactions • Lightindependent reactions Glucose H2O ATP 2H + e– NADPH O2 Chloroplast Chapter 8, pages 198 to 231 CO2 27 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Light-Dependent Reactions • Solar energy delivered in discrete energy packets called photons • Light strikes photosynthetic pigments • Some wavelengths are absorbed • Some pass through • Some are reflected • Light is absorbed through photosynthetic pigments • Chlorophylls (green) • Carotenoids (yellow, orange, or red) • Phycobilins (red or blue-green) Light-Dependent Reactions • Bacterial chlorophylls • Contain a photocenter- a magnesium atom held in the center of a complex ringed molecule called a porphyrin • Harvest the energy of photons and converts it to electron energy • Accessory photosynthetic pigments trap light energy and shuttle it to chlorophyll Chapter 8, pages 198 to 231 28 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Photosynthesis Light-Independent Reactions • Occur in the chloroplast stroma or the cytoplasm of cyanobacteria • Use energy produced by the light phase to synthesize glucose by means of the Calvin cycle Chapter 8, pages 198 to 231 29 Microbial Metabolism: The Chemical Crossroads of Life Microbiology: A Systems Approach Calvin Cycle Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CO2 • Fix carbon dioxide • Reverse of glycolysis Splitting 6-carbon intermediate P • Autotrophs P P 3-phosphoglyceric acid P Ribulose-1,5-bisphosphate 5-carbon ADP Calvin Cycle ATP × 2 P P P P ADP ATP • 6 CO2 Glucose P Seriesof7-carbon and5-carbon Intermediates P 1,3-bisphosphoglyceric acid P H P H P NADPH × 2 NADP+ P Glyceraldehyde-3phosphate Glucose Fructoseintermediates Other Mechanisms of Photosynthesis • Oxygenic (oxygen-releasing) photosynthesis that occurs in plants, algae, and cyanobacteria- dominant type on earth • Other photosynthesizers such as green and purple bacteria • Possess bacteriochlorophyll • More versatile in capturing light • Only have a cyclic photosystem I • These bacteria use H2, H2S, or elemental sulfur rather than H2O as a source of electrons and reducing power • They are anoxygenic (non-oxygen-producing); many are strict anaerobes Chapter 8, pages 198 to 231 30
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