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Environmental & Pollution Microbiology Spring 2010

Environmental & Pollution Microbiology Spring 2010 Environmental Regulation of Microbial Metabolism Organized as follows:

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Environmental & Pollution Microbiology Spring 2010

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  1. Environmental & Pollution MicrobiologySpring 2010 • Environmental Regulation of Microbial Metabolism • Organized as follows: • (I.) Metabolism and Energy Transduction: How bacteria gain fuel (catabolism), and how they make more cells (biosynthesis) and the link between fueling reactions (catabolism) and the generation of cellular energy to keep the bacterial “machine” working • (II.) Enzymes: the catalysts that do all of the work • (III.) Transcriptional organization and control: How the metabolic machine is regulated • (IV.) Catabolic pathways: Diverse strategies bacteria use to occupy almost every conceivable niche

  2. I. Metabolism • (1.) Anabolism (= biosynthesis) • (A.) metabolism = anabolism + catabolism • (B.) anabolism = biosynthetic pathways that lead from the 12 precursor intermediates to cellular building blocks • (C.) catabolism = fueling reactions that lead from ingredients of the external medium to the metabolic needs (precursor metabolites, reducedpyridine nucleotides, energy, nitrogen, sulfur) of the biosynthetic pathways

  3. (2.) How do we make sense out of biochemical complexity? • (A.) Employ a unit process approach • (B.) All of the 75-100 known building blocks, coenzymes, and prosthetic groups are synthesized from only 12 precursor metabolites by reactions that employ energy (high energy phosphate bonds from ATP), reducingpower, and sources of nitrogen, sulfur, and single carbon units. • (C.) 12 precursor metabolites • (D.)Role of the 12 precursors as a “pool” linking catabolism and anabolism. ATP, reduced pyridine nucleotide, and C1 units are also provided from catabolism to build the precursor pool

  4. (3.) intermediates formed during catabolism are used for biosynthesis during anabolism by heterotrophs as well as autotrophs • (A.) Consider the resources needed to produce the building blocks to make 1 gram of cells. Treat each pathway as a unit function. Make a list of components (number of enzymes) and metabolic costs (consumption of energy [as high energy phosphate bonds from ATP], reducing power, nitrogen sulfur, and one-carbon units) • (B.) Detailed material balance sheet approach to biosynthesis.

  5. (4.) Nitrogen assimilation • (A.) Precursor metabolites do not contain nitrogen. What is its source? • (i.) Entry into cell • (ii.) organic forms in soil and sediment habitats are often complexed with polyphenols and tannins • (iii.) Always enters biosynthetic pathways in inorganic form, as ammonium ion [NH4+] • (B.) Common inorganic sources • (C.) Assimilative uptake of nitrate -- Importance of ammonia repression. • (D.) Ammonia ultimately is taken into biosynthetic pathways via 2 key enzymatic reactions: glutamine synthetase and glutamate synthase

  6. (5.) Nitrogen fixation • (A.) only found in bacteria and archaea • (B.) mediated by nitrogenase • (C.) sequential electron transfer • (D.) 6 electron needed to convert nitrogen to ammonia, but 8 electrons are actually transferred

  7. (6.) Precursor metabolites do not contain sulfur. What is its source? • (A.) Major assimilative route is via O-acetylserine sulfohydrolase H2S + O-acetyl-L-serine ---> L-cysteine + acetate + H2O • (B.) exogenous sulfur sources • (C.) sulfur source in oxic environments? • (D.) sulfate can be assimilated via ATP sulfurylase to make APS which is phosphorylated further to PAPS

  8. Other components that must be obtained by the cell from its environment • (A.) K – via symport and antiport • (B.) Ca – via symport and antiport • (C.) Fe – via chelation • (D.) Mg – via symport and antiport • (E.) Trace elements (e.g., Mo, Cu, Zn, etc.) – various mechanisms

  9. END – 2/17

  10. RECAPITULATE ----> The important constituents are the 12 precursor metabolites, energy (high energy phosphate bonds from ATP), reducingpower, and sources of nitrogen, sulfur, and single carbon units.

  11. (7.) Catabolism (= fueling reactions) • (A.) Biosynthetic reactions, as discussed above, are remarkably similar among all microbes. In fueling reactions (= catabolism) microbes demonstrate incredible diversity. • (B.) Goal is to produce reducing power in the form of NAD(P)H + H+ (or FADH + H+) and ATP (or Coenzyme A compounds such as acetyl-CoA) • (C.) Two catabolic strategies: fermentation and respiration

  12. (8.) Fermentation • (A.) internally balanced oxidation-reduction reactions with energy conservation • C6H12O6 ---> 2 C3H4O3- + 2 H+ • glucose ---> lactate • (B.) energy is conserved via substrate level phosphorylation • (C.) not all of the potential energy is gained • (D.) importance of excretion of fermentation products • (E.) Diversity of fermentations • (F.) importance of hydrogenases

  13. (9.) Respiration • (A.) oxidation of organic compounds coupled to transfer of electron to an external electron acceptor; starting compounds are completely oxidized; potential difference between reactants and electron acceptor is very large. • (B.) glycolysis • (C.) overview of TCA = citric acid = Krebs cycle • (i.) pyruvate decarboxylated to acetyl moiety which combines with coA; this is added to oxaloacetate to yield citrate; series of dehydrations, decarboxylations, and oxidations regenerates oxaloacetate with CO2 released • (ii.) generation of 4 NADH + FADH + GTP • (D.) link between catabolism and anabolism

  14. 10. Oxidation-Reduction • (A.) fermentations -- redox cycle at substrate level • (B.) respiration -- NADH+H+ ---> membrane-bound carriers (i.) carriers embedded in membrane • (ii.) separate movement of protons and electrons • (iii.) NADH dehydrogenase • (iv.) flavoproteins • (v.) iron-sulfur proteins • (vi.) quinone pool (coenzyme Q) • (vii.) cytochromes • (viii.) terminal cytochrome and electron acceptor • (ix.) the quinone cycle (proton translocation)

  15. (C.) protonmotive force • (i.) charge difference used by cells for: • (a.) ion transport • (b.) motility; rotation of flagellum • (c.) generation of ATP • (ii.) F0F1 ATPase • (iii.) ATP formation • (iv.) 3-4 protons per 1 ATP • (v.) proton translocation can be used for multiple cellular events • (vi.) inhibitors and uncouplers • (a.) inhibitors -- bind to and inactivate cytochromes • (b.) uncouplers -- leakage of protons across membrane

  16. (D.) various electron acceptors can be used in respiration • (i.) denitrification: nitrate reductase, nitrite reductase, nitric oxide reductase, nitrous oxide reductase • (ii.) iron and manganese respiration • (iii.) sulfate reduction • (iv.) methanogenesis • (v.) halogenated organic compounds

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