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Chapter 5

Chapter 5. Microbial Metabolism. Microbial Metabolism. Metabolism is the sum of the chemical reactions in an organism. Catabolism is the energy-releasing processes, catabolic, degradative,generally hydrolytic reaction (use water and break chemical bonds).

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Chapter 5

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  1. Chapter 5 Microbial Metabolism

  2. Microbial Metabolism • Metabolism is the sum of the chemical reactions in an organism. • Catabolism is the energy-releasing processes, catabolic, degradative,generally hydrolytic reaction (use water and break chemical bonds). • Exergonic – produce more energy than consume • Anabolism is the energy-using processes, anabolic, biosynthetic, building of complex molecules from simpler ones, involve dehydration synthesis reactions (reactions that release water) • Endergonic – consume more energy that produce.

  3. Microbial Metabolism • Catabolism provides the building blocks and energy for anabolism. Figure 5.1

  4. ATP stores energy from catabolic reactions and releases it later to drive anabolic reactions and perform other cellular work. The coupling or energy requiring and energy releasing reaction is made possible through the molecule adenosine triphosphate (ATP)

  5. ATP • Is made by dehydration synthesis. • Is broken by hydrolysis to liberate useful energy for the cell. When the terminal phosphate group splits from ATP, adenosine diphosphate is formed and energy is released to drive anabolic reactions

  6. A metabolic pathway is a sequence of enzymatically catalyzed chemical reactions in a cell. • Metabolic pathways are determined by enzymes. • Enzymes are proteins encoded by genes. • The collision theory states that chemical reactions can occur when atoms, ions, and molecules collide. • Reaction rate is the frequency of collisions with enough energy to bring about a reaction. • Reaction rate can be increased by enzymes or by increasing temperature or pressure.

  7. Catalyst • Catalyst speeds up a chemical reaction without being permanently altered themselves • Enzymes are biological catalyst, specific for a chemical reaction, acts on a specific substance called a substrate • The enzyme orients the substrate into position that increases the probability of a reaction • Enzyme substrate complex forms by the temporary binding of enzyme and substrate enable the collison to be more effective and lowers the activation energy of the reaction

  8. Enzymes • Apoenzyme: protein portion of an enzyme, can be the whole enzyme • Cofactor: Nonprotein component, help catalyze by forming a bridge between the enzyme and the substrate • Coenzyme: Organic cofactor, NAD+NADP+FAD Coenzyme A, may assist the enzymatic reaction by accepting atoms removed from the substrate or by donating atoms required by the substrate, electron carriers • Holoenzyme: Apoenzyme + cofactor (coenzyme) Figure 5.3

  9. Enzyme Classification6 classes, named for type of chemical reaction they catalyze • Oxidoreductase Oxidation-reduction reactions • Transferase Transfer functional groups • Hydrolase Hydrolysis • Lyase Removal of atoms without hydrolysis • Isomerase Rearrangement of atoms • Ligase Joining of molecules, uses ATP

  10. Factors Influencing Enzyme Activity • Enzymes can be denatured by temperature and pH Figure 5.6

  11. Factors Influencing Enzyme Activity pH • Temperature Figure 5.5a

  12. Factors Influencing Enzyme Activity • Competitive inhibition – inhibitors fill the active site of an enzyme and compete with the normal substrate for the active site Figure 5.7a, b

  13. Factors Influencing Enzyme Activity Ex – PABA is an essential nutrient of many bacteria in the synthesis of folic acid. Sulfanilamide binds to the enzyme that converts PABA to folic acid, bacteria cannot grow

  14. Factors Influencing Enzyme Activity • Noncompetitive inhibition- inhibitor interacts with another part of the enzyme • Allosteric inhibitor –inhibitor binds to a site other than the substrate binding site and cause the active site to change shape making it non-functional Figure 5.7a, c

  15. Factors Influencing Enzyme Activity • Feedback inhibition – a series of enzymes make an end product that inhibits the first enzyme in the series, this shuts down the entire pathway when sufficient end product has been made Figure 5.8

  16. Energy Production • Nutrient molecules have energy associated with electrons that form bonds between their atoms • Reactions in catabolic pathways convert this energy into bonds of ATP, which serves as a convenient energy carrier

  17. Oxidation-Reduction • Oxidation is the removal of electrons. • Reduction is the gain of electrons. • Redox reaction is an oxidation reaction paired with a reduction reaction. Figure 5.9

  18. Oxidation-Reduction • In biological systems, the electrons are often associated with hydrogen atoms. Biological oxidations are often dehydrogenations. Figure 5.10

  19. Energy Production • Cells use redox reactions in catabolism to extract energy from nutrient molecules • Cells take nutrients, degrade them from a highly reduced compound with a lot of hydrogen atoms to a highly oxidized compound which can serve as an energy source • Ex – a cell oxidizes a molecule of glucose C6H12C6 to CO2 and H2O, the energy in glucose is removed in a stepwise manner and ultimately trapped by ATP

  20. To produce energy from glucose microbes use two general processes • Cellular respiration • Fermentation • Both start with glycolysis but follow different subsequent pathways

  21. The Generation of ATP • ATP is generated by the phosphorylation of ADP.

  22. Carbohydrate Catabolism • Most organisms oxidize carbohydrates as their primary source of cellular energy, most common is glucose • The breakdown of carbohydrates to release energy • Glycolysis • Krebs cycle • Electron transport chain

  23. Glycolysis 6-carbon sugar is split into 2 3-carbon sugars, the sugar is oxidized, releasing energy and their atoms rearrange to form 2 molecules of pyruvic acid • The oxidation of glucose to pyruvic acid, produces ATP and NADH. 1 - 6 carbon sugar 2 - 3 carbon sugars

  24. Preparatory Stage Preparatory Stage Glucose 1 • 2 ATPs are used • Glucose is split to form 2 Glucose-3-phosphate Glucose 6-phosphate 2 Fructose 6-phosphate 3 Fructose 1,6-diphosphate 4 5 Glyceraldehyde 3-phosphate (GP) Dihydroxyacetone phosphate (DHAP) Figure 5.12.1

  25. Energy-Conserving Stage 6 1,3-diphosphoglyceric acid 7 • 2 Glucose-3-phosphate oxidized to 2 Pyruvic acid • 4 ATP produced • 2 NADH produced • Net 2 ATP 3-phosphoglyceric acid 8 2-phosphoglyceric acid 9 Phosphoenolpyruvic acid (PEP) 10 Pyruvic acid Figure 5.12.2

  26. Pyruvic Acid • Pyruvic acid can be channeled into the next step of either fermentation of cellular respiration

  27. Alternatives to Glycolysis • Pentose phosphate pathway: • Uses pentoses and NADPH • Operates with glycolysis • Entner-Doudoroff pathway: • Produces NADPH and ATP • Does not involve glycolysis • Pseudomonas, Rhizobium, Agrobacterium

  28. Cellular Respiration • ATP generating process in which molecules are oxidized and the final electron acceptor is almost always an inorganic molecule

  29. Intermediate Step • Pyruvic acid (from glycolysis) cannot enter the Krebs cycle directly • In a preparatory step it most lose one molecule of CO2 and becomes a two carbon compound (decarboyxlated) • The 2c-carbon complex – acetyl group attaches to coenzyme A through a high energy bond • Result is acetyl-coenzyme A, 2 acetyl-CoA per glucose

  30. Krebs Cycle – TCA cycle – Citric Acid Cycle • Series of redox reactions that transfer potential energy in the form of electrons to electron carriers, chiefly NAD • For every Acetyl-CoA – 2 ATP, 4 CO2, 6 NADH, 2 FADH

  31. The Electron Transport Chain • A series of carrier molecules that are, in turn, oxidized and reduced as electrons are passed down the chain. • Series of reductions that indirectly transfer the energy stored in the coenzymes formed in the Krebs cycle to ATP

  32. Respiration • Aerobic respiration: The final electron acceptor in the electron transport chain is molecular oxygen (O2). • In prokaryotes – results in 38 ATP • In eukaryotes – results in 36 ATP, lose energy shuttling electrons across mitochondria membrane • Anaerobic respiration: The final electron acceptor in the electron transport chain is not O2. Yields less energy than aerobic respiration because only part of the Krebs cycles operations under anaerobicconditions. • ATP levels vary with the organism and the pathway, not all carrier in the electron transport chain are used

  33. Fermentation • Glucose can be converted to another organic product in fermentation • Releases energy from oxidation of organic molecules • Does not require oxygen • Does not use the Krebs cycle or ETC • Uses an organic molecule as the final electron acceptor • Produces only a small amount of ATP

  34. Fermentation Figure 5.18b

  35. Other Energy Sources • Microbes can oxidize lipids and proteins for energy • Lipids are broken down by lipases which break fats down into fatty acids and glycerol components. Each component is then metabolized separately • Beneficial for oil spills

  36. Lipid Catabolism Figure 5.20

  37. Proteins are broken down by proteases and peptidases which break down proteins to amino acids and then convert them by deamination,(removal of the amino group, to enter the Krebs cycle. The amino group is converted to an ammonia ion which can be excreted from the cell.

  38. Protein Catabolism Extracellular proteases Protein Amino acids Deamination, decarboxylation, dehydrogenation Krebs cycle Organic acid

  39. Biochemical tests • Used to identify bacteria.

  40. Photosynthesis • Photo: Conversion of light energy into chemical energy (ATP) • Synthesis: Fixing carbon into organic molecules • Photosynthesis – synthesis of complex organic compounds from single inorganic substances

  41. Photosynthesis • Conversion of light energy from the sun into chemical energy • Chemical energy is used to convert CO2 from atmosphere to more reduced carbon compounds, primarily sugars • Synthesis of sugar by using carbon atoms from CO2 gas is call carbon fixation • In photosynthesis electrons are taken from hydrogen atoms of water, an energy poor molecule, and incorporated into sugar, an energy rich molecule

  42. Species that use light energy are phototrophs. • Species that obtain energy from chemicals in their environment are chemotrophs. • Organisms that need only CO2 as a carbon source are autotrophs. • Organisms that require at least one organic nutrient as a carbon source are heterotrophs. • These categories of energy source and carbon source can be combined to group prokaryotes according to four major modes of nutrition.

  43. Photoautotrophs are photosynthetic organisms that harness light energy to drive the synthesis of organic compounds from carbon dioxide. • Chemoautotrophs need only CO2 as a carbon source, but they obtain energy by oxidizing inorganic substances, rather than light. • These substances include hydrogen sulfide (H2S), ammonia (NH3), and ferrous ions (Fe2+) among others. • This nutritional mode is unique to prokaryotes.

  44. Photoheterotrophs use light to generate ATP but obtain their carbon in organic form. • This mode is restricted to prokaryotes. • Chemoheterotrophs must consume organic molecules for both energy and carbon. • This nutritional mode is found widely in prokaryotes, protists, fungi, animals, and even some parasitic plants.

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