Microbial Metabolism Metabolism and Energy Catabolism vs Anabolism; Exergonic vs Endergonic rxns Using ATP to make endergonic rxns run Enzymes as Biological Catalysts Lowering of Activation Energy Specificity, recyclability Factors which affect Enzymatic Rate (pH, temp, inhib.) Metabolic Control Cellular Respiration: Oxidative Catabolism Oxidation-Reduction Reactions(NAD+, FAD+ trucks) C6H12O6 + 6O2 -->6CO2 + 6H2O + Energy (ATP) Glycolysis (6C glucose--> 2 pyruvate + 2NADH +2ATP Krebs Cycle (2 pyruvate-->6CO2 + 8NADH +2FADH2 + 2ATP Electron Transport Chain (Cashing in on e-) FADH2 + NADH + O2 --> lots of ATP + H2O + NAD+ + FAD+ Terminal aerobic electron acceptor O2--->H2O Anaerobic bacteria use nitrate, sulfate, carbon dioxide Fermentation is not anaerobic respiration Performed by facultative anaerobes Restart glycolysis by recycling NADH->NAD+ in side rxns Acid and/or Gas common (pH drop) Alcohol Fermentation (yeast, some bacteria) Ethanol and carbon dioxide produced Lactic Acid Fermentation (bacteria, muscles) Heterolactic Fermentation (several bacteria) Acetoin: a neutral product in VP test Use of Other Food Molecules for Energy Lipid Catabolism to Acetyl CoA Protein Catabolism to Kreb’s Cycle Molecules Deamination, Ammonium, and pH rise

Energy from chemical bonds  Usable cellular energy (ATP) Metabolism: Breakdown of Food Fuels Construction of Biomolecules Food molecules (high energy) Complex biomolecules (high energy) Breakdown (Catabolism) Construction/ Synthesis (Anabolism) Energy from chemical bonds  Usable cellular energy (ATP) Waste molecules (low energy) Simple molecules (low energy)

Cellular Reactions Either Use or Liberate Energy Catabolic/Breakdown Reactions release energy Molecules become more disorganized or less structured X Y + + Z Anabolic/Buildup Reactions absorb energy Molecules become more ordered and complex ATP needed to power endothermic reactions A B + + ATP C

Both Breakdown and Buildup Reactions Have Activation Energies Breakdown Reactions Release Energy: Exergonic/exothermic Activation Energy Z X + Y X Y + + Energy Level Z Time Buildup Reactions Absorb or Require Energy: Endergonic/endothermic C A B + + ATP C Activation Energy Energy Level A+ B Time

Microbial Metabolism Metabolism and Energy Catabolism vs Anabolism; Exergonic vs Endergonic rxns Using ATP to make endergonic rxns run Enzymes as Biological Catalysts Lowering of Activation Energy Specificity, recyclability Factors which affect Enzymatic Rate (pH, temp, inhib.) Metabolic Control Cellular Respiration: Oxidative Catabolism Oxidation-Reduction Reactions(NAD+, FAD+ trucks) C6H12O6 + 6O2 -->6CO2 + 6H2O + Energy (ATP) Glycolysis (6C glucose--> 2 pyruvate + 2NADH +2ATP Krebs Cycle (2 pyruvate-->6CO2 + 8NADH +2FADH2 + 2ATP Electron Transport Chain (Cashing in on e-) FADH2 + NADH + O2 --> lots of ATP + H2O + NAD+ + FAD+ Terminal aerobic electron acceptor O2--->H2O Anaerobic bacteria use nitrate, sulfate, carbon dioxide Fermentation is not anaerobic respiration Performed by facultative anaerobes Restart glycolysis by recycling NADH->NAD+ in side rxns Acid and/or Gas common (pH drop) Alcohol Fermentation (yeast, some bacteria) Ethanol and carbon dioxide produced Lactic Acid Fermentation (bacteria, muscles) Heterolactic Fermentation (several bacteria) Acetoin: a neutral product in VP test Use of Other Food Molecules for Energy Lipid Catabolism to Acetyl CoA Protein Catabolism to Kreb’s Cycle Molecules Deamination, Ammonium, and pH rise

Activation Energy Activation energy Energy needed to allow the reactants to form products Necessary for a chemical reaction to proceed Activation energy is needed even for breakdown reaction to get them going Activation Energy Z X + Y Energy Level Time In the laboratory, we heat the reactants in order to provide activation energy for a chemical reaction Inside the cell, a different mechanism is required as heating up the reactants is not possible Lower the energy required for the reaction

Enzymes Lower Activation Energy and Speed Up Reactions Figure 5.8

Enzymes Are Biological Catalysts Figure 5.2

Enzymes Figure 5.3

Microbial Metabolism Metabolism and Energy Catabolism vs Anabolism; Exergonic vs Endergonic rxns Using ATP to make endergonic rxns run Enzymes as Biological Catalysts Lowering of Activation Energy Specificity, recyclability Factors which affect Enzymatic Rate (pH, temp, inhib.) Metabolic Control Cellular Respiration: Oxidative Catabolism Oxidation-Reduction Reactions(NAD+, FAD+ trucks) C6H12O6 + 6O2 -->6CO2 + 6H2O + Energy (ATP) Glycolysis (6C glucose--> 2 pyruvate + 2NADH +2ATP Krebs Cycle (2 pyruvate-->6CO2 + 8NADH +2FADH2 + 2ATP Electron Transport Chain (Cashing in on e-) FADH2 + NADH + O2 --> lots of ATP + H2O + NAD+ + FAD+ Terminal aerobic electron acceptor O2--->H2O Anaerobic bacteria use nitrate, sulfate, carbon dioxide Fermentation is not anaerobic respiration Performed by facultative anaerobes Restart glycolysis by recycling NADH->NAD+ in side rxns Acid and/or Gas common (pH drop) Alcohol Fermentation (yeast, some bacteria) Ethanol and carbon dioxide produced Lactic Acid Fermentation (bacteria, muscles) Heterolactic Fermentation (several bacteria) Acetoin: a neutral product in VP test Use of Other Food Molecules for Energy Lipid Catabolism to Acetyl CoA Protein Catabolism to Kreb’s Cycle Molecules Deamination, Ammonium, and pH rise

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

Enzymes Become Non-Functional at pH Extremes and High Temperatures Stomach enzyme = folded, functional enzyme Enzyme within a body cell = denatured, non-functional enzyme Enzyme within a body cell Reaction rate is slow at cold temperatures because molecules encounter enzyme less often Enzyme from hot springs bacterium H+ H+ OH- H+ OH- H+ H+ OH- H+ H+ OH- OH- H+ OH- (products formed per second) Enzymatic rate (products formed per second) Enzymatic rate H+ H+ OH- OH- H+ OH- H+ H+ H+ OH- 0 2 4 6 8 10 12 10 20 30 40 50 60 70 pH (in pH units) Temperature (oC)

Factors Influencing Enzyme Activity Competitive inhibition Figure 5.7a, b

Factors Influencing Enzyme Activity Noncompetitive inhibition ATP, pyruvate, end amino acid Figure 5.7a, c

Factors Influencing Enzyme Activity Feedback inhibition Figure 5.8

Microbial Metabolism Metabolism and Energy Catabolism vs Anabolism; Exergonic vs Endergonic rxns Using ATP to make endergonic rxns run Enzymes as Biological Catalysts Lowering of Activation Energy Specificity, recyclability Factors which affect Enzymatic Rate (pH, temp, inhib.) Metabolic Control Cellular Respiration: Oxidative Catabolism Oxidation-Reduction Reactions(NAD+, FAD+ trucks) C6H12O6 + 6O2 -->6CO2 + 6H2O + Energy (ATP) Glycolysis (6C glucose--> 2 pyruvate + 2NADH +2ATP Krebs Cycle (2 pyruvate-->6CO2 + 8NADH +2FADH2 + 2ATP Electron Transport Chain (Cashing in on e-) FADH2 + NADH + O2 --> lots of ATP + H2O + NAD+ + FAD+ Terminal aerobic electron acceptor O2--->H2O Anaerobic bacteria use nitrate, sulfate, carbon dioxide Fermentation is not anaerobic respiration Performed by facultative anaerobes Restart glycolysis by recycling NADH->NAD+ in side rxns Acid and/or Gas common (pH drop) Alcohol Fermentation (yeast, some bacteria) Ethanol and carbon dioxide produced Lactic Acid Fermentation (bacteria, muscles) Heterolactic Fermentation (several bacteria) Acetoin: a neutral product in VP test Use of Other Food Molecules for Energy Lipid Catabolism to Acetyl CoA Protein Catabolism to Kreb’s Cycle Molecules Deamination, Ammonium, and pH rise

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. OIL RIG: Oxidation is loss of e-, reduction is gain of e- Figure 5.9

Oxidation-Reduction In biological systems, the electrons are often associated with hydrogen atoms. Biological oxidations are often dehydrogenations. Or FAD+ FADH2 Sugars, amino acids, fatty acids Figure 5.10

The Energy Stored in ATP Can Be Used to Perform Work in the Cell The energy released by ATP breaking down into ADP and P can power a variety of needs in the cell ADP Energized ATP: P ADP Discharged ATP: P Powering the synthesis of molecule Z: X Y + Z

Microbial Metabolism Metabolism and Energy Catabolism vs Anabolism; Exergonic vs Endergonic rxns Using ATP to make endergonic rxns run Enzymes as Biological Catalysts Lowering of Activation Energy Specificity, recyclability Factors which affect Enzymatic Rate (pH, temp, inhib.) Metabolic Control Cellular Respiration: Oxidative Catabolism Oxidation-Reduction Reactions(NAD+, FAD+ trucks) C6H12O6 + 6O2 -->6CO2 + 6H2O + Energy (ATP) Glycolysis (6C glucose--> 2 pyruvate + 2NADH + 2ATP Krebs Cycle (2 pyruvate-->6CO2 + 8NADH +2FADH2 + 2ATP Electron Transport Chain and ATP Generation FADH2 + NADH + O2 --> lots of ATP + H2O + NAD+ + FAD+ Terminal aerobic electron acceptor O2--->H2O Anaerobic bacteria use nitrate, sulfate, carbon dioxide Fermentation is not anaerobic respiration Performed by facultative anaerobes Restart glycolysis by recycling NADH->NAD+ in side rxns Acid and/or Gas common (pH drop) Alcohol Fermentation (yeast, some bacteria) Ethanol and carbon dioxide produced Lactic Acid Fermentation (bacteria, muscles) Heterolactic Fermentation (several bacteria) Acetoin: a neutral product in VP test Use of Other Food Molecules for Energy Lipid Catabolism to Acetyl CoA Protein Catabolism to Kreb’s Cycle Molecules Deamination, Ammonium, and pH rise

Aerobic Cellular Respiration: Converting Sugar to ATP C6H12O6 + O2 CO2 + H2O + 36ATP sugar oxygen carbon dioxide oxygen usable energy glucose CO2 NAD+ NADH Glycolysis 2 ATP 2 pyruvates CO2 Cell membrane Krebs Cycle H+ H+ H+ NADH, FADH2 Electron Transport Chain and ATP Synthase (Ox. Phos.) H+ NAD, FAD+ O2 ATP fuels construction/synthesis reactions inside the cell H+ H+ H+ H 2O H+ ~ 30 ATP H+ H+ H+ ATP Synthase H+

Microbial Metabolism Metabolism and Energy Catabolism vs Anabolism; Exergonic vs Endergonic rxns Using ATP to make endergonic rxns run Enzymes as Biological Catalysts Lowering of Activation Energy Specificity, recyclability Factors which affect Enzymatic Rate (pH, temp, inhib.) Metabolic Control Cellular Respiration: Oxidative Catabolism Oxidation-Reduction Reactions(NAD+, FAD+ trucks) C6H12O6 + 6O2 -->6CO2 + 6H2O + Energy (ATP) 1. Glycolysis (6C glucose--> 2 pyruvate + 2NADH +2ATP 2. Krebs Cycle (2 pyruvate-->6CO2 + 8NADH +2FADH2 + 2ATP 3. Electron Transport Chain (Cashing in on e-) FADH2 + NADH + O2 --> lots of ATP + H2O + NAD+ + FAD+ Terminal aerobic electron acceptor O2--->H2O Anaerobic bacteria use nitrate, sulfate, carbon dioxide Fermentation is not anaerobic respiration Performed by facultative anaerobes Restart glycolysis by recycling NADH->NAD+ in side rxns Acid and/or Gas common (pH drop) Alcohol Fermentation (yeast, some bacteria) Ethanol and carbon dioxide produced Lactic Acid Fermentation (bacteria, muscles) Heterolactic Fermentation (several bacteria) Acetoin: a neutral product in VP test Use of Other Food Molecules for Energy Lipid Catabolism to Acetyl CoA Protein Catabolism to Kreb’s Cycle Molecules Deamination, Ammonium, and pH rise

Respiration Aerobic respiration: The final electron acceptor in the electron transport chain is molecular oxygen (O2) in aerobes. 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 anaerobic conditions. Obligate anaerobes perform anaerobic respiration. Fermentation: Glycolysis is restarted as NADH is recycled into NAD+. Pyruvate is reduced when electrons are added to it; acids, ethanol and CO2 are common products. Facultative anaerobes perform fermentation in addition to aerobic respiration.

Anaerobic respiration by Obligate Anaerobes Terminal electron acceptor Products NO3– (nitrate) NO2–, NH3, N2 (nitrite, ammonia, and nitrogen gas) SO4– (sulfate) H2S (hydrogen sulfide) CO32 – (carbonate) CH4 (methane) Peee-ewe! (stinky) H+ H+ H+ NADH, FADH2 Electron Transport Chain and ATP Synthase (Ox. Phos.) H+ NAD, FAD+ O2 H+ H+ H+ H 2O H+ ~ 30 ATP H+ H+ H+ ATP Synthase H+

Two Net ATP are Made in Glycolysis by Substrate Level Phosphorylation 1 glucose 2 (net) ATP made by substrate-level phosphorylation rather than by oxidative phosphorylation 2 pyruvate

Fermentation by Facultative Anaerobes 1 glucose Fermentation by Facultative Anaerobes NADH is recycled to NAD+ in order to keep glycolysis running Alcohol fermentation Produces ethyl alcohol + CO2 Lactic acid fermentation produces lactic acid. Homolactic fermentation produces lactic acid only. Heterolactic fermentation produces lactic acid and other compounds. Figure 5.19

Fermentation Products Are Mostly Acids with Some Gases Figure 5.18b

Fermentation (Change to Yellow Means Acid is Present; Durham Tubes Collect Gas) Figure 5.23

Microbial Metabolism Metabolism and Energy Catabolism vs Anabolism; Exergonic vs Endergonic rxns Using ATP to make endergonic rxns run Enzymes as Biological Catalysts Lowering of Activation Energy Specificity, recyclability Factors which affect Enzymatic Rate (pH, temp, inhib.) Metabolic Control Cellular Respiration: Oxidative Catabolism Oxidation-Reduction Reactions(NAD+, FAD+ trucks) C6H12O6 + 6O2 -->6CO2 + 6H2O + Energy (ATP) Glycolysis (6C glucose--> 2 pyruvate + 2NADH +2ATP Krebs Cycle (2 pyruvate-->6CO2 + 8NADH +2FADH2 + 2ATP Electron Transport Chain (Cashing in on e-) FADH2 + NADH + O2 --> lots of ATP + H2O + NAD+ + FAD+ Terminal aerobic electron acceptor O2--->H2O Anaerobic bacteria use nitrate, sulfate, carbon dioxide Fermentation is not anaerobic respiration Performed by facultative anaerobes Restart glycolysis by recycling NADH->NAD+ in side rxns Acid and/or Gas common (pH drop) Alcohol Fermentation (yeast, some bacteria) Ethanol and carbon dioxide produced Lactic Acid Fermentation (bacteria, muscles) Heterolactic Fermentation (several bacteria) Acetoin: a neutral product in VP test Use of Other Food Molecules for Energy Lipid Catabolism to Acetyl CoA Protein Catabolism to Kreb’s Cycle Molecules Deamination, Ammonium, and pH rise

Lipid Catabolism Krebs Cycle CO2 glucose CO2 2 ATP 2 pyruvates CO2 H+ NADH, FADH2 H+ NAD, FAD+ O2 H+ H+ H+ H 2O H+ ~ 30 ATP H+ H+ H+ ATP Synthase H+ Figure 5.20

Protein Catabolism Produces Alkaline Ammonium Extracellular proteases Protein Amino acids (Peptone) Deamination, decarboxylation, dehydrogenation Organic acid Krebs cycle NH4+ CO2 H2

Biochemical tests and Dichotomous Keys Are Used to ID Prokaryotes Figure 10.8

Microbial Metabolism Metabolism and Energy Catabolism vs Anabolism; Exergonic vs Endergonic rxns Using ATP to make endergonic rxns run Enzymes as Biological Catalysts Lowering of Activation Energy Specificity, recyclability Factors which affect Enzymatic Rate (pH, temp, inhib.) Metabolic Control Cellular Respiration: Oxidative Catabolism Oxidation-Reduction Reactions(NAD+, FAD+ trucks) C6H12O6 + 6O2 -->6CO2 + 6H2O + Energy (ATP) Glycolysis (6C glucose--> 2 pyruvate + 2NADH +2ATP Krebs Cycle (2 pyruvate-->6CO2 + 8NADH +2FADH2 + 2ATP Electron Transport Chain (Cashing in on e-) FADH2 + NADH + O2 --> lots of ATP + H2O + NAD+ + FAD+ Terminal aerobic electron acceptor O2--->H2O Anaerobic bacteria use nitrate, sulfate, carbon dioxide Fermentation is not anaerobic respiration Performed by facultative anaerobes Restart glycolysis by recycling NADH->NAD+ in side rxns Acid and/or Gas common (pH drop) Alcohol Fermentation (yeast, some bacteria) Ethanol and carbon dioxide produced Homolacticactic Acid Fermentation (bacteria, muscles) Heterolactic Fermentation (several bacteria) Acetoin: a neutral product in VP test Use of Other Food Molecules for Energy Lipid Catabolism to Acetyl CoA Protein Catabolism to Kreb’s Cycle Molecules Deamination, Ammonium, and pH rise