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Week 2 Lecture Material October 2001

Week 2 Lecture Material October 2001. Metabolism. Metabolism. Chemical processes taking place in the cell Chemicals from which cells are built are called nutrients Metabolism generates the essential elements of the cell and the energy to put them together in an organized fashion.

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Week 2 Lecture Material October 2001

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  1. Week 2 Lecture MaterialOctober 2001 Metabolism

  2. Metabolism • Chemical processes taking place in the cell • Chemicals from which cells are built are called nutrients • Metabolism generates the essential elements of the cell and the energy to put them together in an organized fashion

  3. Why Does Metabolism Take Place? • For metabolism to take place, there has to be a chemical which is willing to give up electrons. • This chemical is called the electron donor • organic: carbohydrates, lipids, aromatics, etc. • inorganic: ammonia, sulfide, ferrous iron, etc. • If there is an electron donor, then there must be an electron acceptor • oxygen, nitrate, sulfate, ferrous iron, pyruvic acid, etc.

  4. What Types of Reactions Occur During Metabolism? • Oxidation/Reduction Reactions with Chemical as Donor • carbon oxidized to CO2 • ammonia oxidized to nitrate • sulfur oxidized to sulfate • Oxidation/Reduction Reactions with Chemical as Acceptor • carbon dioxide reduced to CH4 • nitrate reduced to nitrogen gas

  5. Where is Metabolism Important in Environmental Management • Agriculture waste management • Domestic wastewater treatment • Protection of drinking water from pathogens and taste and odors • Bioremediation of contaminated groundwater, soil, and air • Biological corrosion of structures • Fresh and marine ecosystem productivity

  6. Ecosystem Management

  7. Wastewater Treatment

  8. Treatment of Air Emissions

  9. Airplane Deicing

  10. Sludge Land Application and Spills

  11. Bioremediation of Gas Spills

  12. Composting Explosives

  13. Metabolism Basics • Energetics • Enzyme Function • Oxidation/Reduction Half Reactions • Electron Carriers • Energy Carriers

  14. Energetics • Chemical energy is released when compounds are oxidized • The amount available for useful work is defined as free energy (G) kCal or kJ • Go’ is negative: energy is released and reaction is spontaneous as written (exergonic) • Go’ is positive: the reaction is not spontaneous as written and is referred to as endergonic

  15. Change in Free Energy A + B C + D • Go’ = free energy of reaction at standard conditions, all reactants and products at 1 molar, and pH 7 • Gof = free energy of formation • need to make sure the reaction is balanced Go’ = Gof [C + D] - Gof [A + B]

  16. Free Energy of Reaction Example H2S + 8 Fe3+ 8 Fe2+ + SO42- H2S + 8 Fe3+ 8 Fe2+ + SO42- + 10H+ H2S + 8 Fe3+ + 4 H20 8 Fe2+ + SO42- + 10H+ Go’ = Gof [C + D] - Gof [A + B] Go’ = ?

  17. Enzymes • Free energy does not tell us how fast a spontaneous reaction proceeds • Many spontaneous biological reactions are slow because of the activation energy of reactions • Enzymes reduce the activation energy of a reaction • Activation energy is the energy required to bring all reactants to the reactive state

  18. Activation Energy Free Energy Reaction Progress

  19. Enzyme Catalyzed Reactions • Enzymes are specific to reaction classes or a specific reaction • The reactant is called the substrate (S) • The binding of the enzyme to the substrate is called the enzyme/substrate complex (ES) • The binding site is called the active site • The product is called the product (P) E + S ES E + P

  20. Aldolase

  21. Oxidation/Reductions • catalysis is a series of oxidation/reduction reactions that liberate energy • many substrates can serve as either electron donors or acceptors • in most reactions, electrons are given up to intermediate electron carriers

  22. Electron Carriers • During metabolism electrons are transferred from the primary electron donor (Substrate)to the terminal electron donor via an electron carrier • In catabolism, nicotinamide adenine dinucleotide (NAD) is most often used ½ NAD+ + ½ H+ + e- ½ NADH

  23. NAD+ as an Electron Carrier

  24. NADH as an Electron Carrier

  25. Reduction Potential • the degree to which substrates can serve as e donors or acceptors is related to their reduction potential, Eo’ • Eo’ measured relative to H2 in volts • Eo’ values given for the reduction ¼ O2 + H+ + e- ½ H20 Eo’ = 0.82 v • the lower the Eo’, the greater the ability to donate electrons • thus glucose/CO2 (-0.43v) has a higher ability to donate electrons than oxygen/ H20 (0.82v)

  26. Coupled Half Reactions • as stated earlier, in catabolic reactions, there are a series of oxidation/reduction reactions • thus one substrate is oxidized and another is reduced • these are written as coupled half reactions

  27. Example of Coupled Half ReactionOxygen as Terminal Acceptor ½ NAD+ + ½ H+ + e- ½ NAD Eo’ = - 0.32 v ¼ O2 + H+ + e- ½ H20 Eo’ = 0.82 v ½ NADH ½ NAD+ + ½ H+ + e- Eo’ = 0.32 v ¼ O2 + H+ + e- ½ H20 Eo’ = 0.82 v ¼ O2 + ½ NADH + ½ H+ ½NAD+ + ½ H20 Eo’ = 1.12 v

  28. Eo’ -0.50 + 0.90 Electron Tower Half reactions with lower Eo’ values can reduce half reactions with higher Eo’ values. Accordingly, the higher the half reaction is on the tower, the more likely it is to be an electron donor for cell metabolism. To gain the most energy, the cell will try to maximize the full extent of the tower NAD+/NADH SO4/S2- NO3- /NO2- ½ O2/H20

  29. High Energy Phosphate Bonds • Energy liberated from oxidation/reductions must be converted to usable form • Typically energy transferred to high energy phosphate compounds, the most common of which is ATP • ATP is characterized by the presence of high energy anhydride bonds • Other examples include phosphoenolpyruvate, ADP • High energy bonds designated by ~Pi

  30. Summary of Basics Carbon Electron Donor Energy for Cell Synthesis and Maintenance Energy investment as NADH or ATP Metabolism IntermediateOften these initial reactions are preparatory reactions to get other things going Electrons in NADH are transferred to terminal electron acceptors. This process results in energy captured as ATP which can be used in cell for a variety of purposes Reduced Terminal Acceptors Electrons from oxidation are “carried” by electron carriers primary NADH Oxidized Carbon oxygen water

  31. Aerobic Metabolism of Common Organics • Carbohydrates • Lipids • Saturated Hydrocarbons • Alcohols, Aldehydes, and Ketones • Amino Acids

  32. glucose NAD+ ADP GDP ATP GTP NADH pyruvate Oxidation of Carbohydrates (Glucose) glycolysis CoA-SH Acetyl CoA CoA-SH ½ O2 Citric Acid Cycle e- Electron Transport System H20 Electrons flow in the form of reduced dinucleotides (NADH and FADH) CO2

  33. Steps in Glucose Glycolysis • Stage I: Preparatory reactions • glucose to glyceraldehyde-3-P • Stage II: Oxidation reactions • glyceraldehyde-3-P to pyruvate-

  34. Stage 1: Preparation • glucose is phosphorylated • ATP is used • Fructose-1,6-diphosphate is cleaved to G-3-P and Dihydroxyacetone phosphate

  35. State 2: Oxidation • glyceraldehyde is converted to pyruvic acid • NADH is formed during oxidation of glyceraldehyde-3-P • ATP is formed during conversion of 1,3-DPGA to 3-PGA and PEP to pyruvic acid

  36. Carbon Flow During Respiration:Citric Acid Cycle Citric Acid Cycle

  37. Summary of Glucose Oxidationwater and hydrogen left out of balance glycolysis: C6H12O6 + 2ADP + 2NAD+ 2 pruvate- + 2ATP + 2NADH Preparatory Step: pruvate- + CoA-SH + NAD+ acetyl CoA + CO2 + NADH CAC: Acetyl-CoA + 4NAD+ + FAD+ + GDP 3 CO2 + 4NADH + FADH + GTP Summary of glucose oxidation C6H12O6 + 2ADP + 2GDP + 10NAD+ + 2FAD+ 6 CO2 + 2ATP + 2GTP + 10NADH + 2FADH

  38. Regeneration of Reduced Nucleotides and Energy Production • After oxidation in CAC, a large number of NADH formed and some FADH formed • These must be reoxidized so that they can be recycled • In addition, energy production is necessary • Electron transport accomplishes these tasks.

  39. Electron Transport • NADH is oxidized and donates its electrons and protons to a flavoprotein • This flavoprotein is oxidized and pumps out H+ across membrane • This process continues until electrons are passed to final acceptor, O2 • a gradient established across membrane • this gradient used to drive energy production (ATP)

  40. ATPase Enzyme

  41. Summary of Basics Carbon Electron Donor Energy for Cell Synthesis and Maintenance Energy investment as NADH or ATP Metabolism IntermediateOften these initial reactions are preparatory reactions to get other things going Electrons in NADH are transferred to terminal electron acceptors. This process results in energy captured as ATP which can be used in cell for a variety of purposes Reduced Terminal Acceptors Electrons from oxidation are “carried” by electron carriers primary NADH Oxidized Carbon oxygen water

  42. Acetic Acid, Volatile Acids, Lipids fatty acid CH3 - (CH2)n - COOH Lipids acetyl CoA, NADH, FADH b oxidation glycerol fatty acid oxidized in two carbon increments CO2 acetyl CoA, NADH, FADH pyruvic acid

  43. NAD+ NADH NAD+ NADH NADH NAD Straight Chain Aliphatic Hydrocarbons CH2OH CH3 CHO COOH O2 H2O H2O MMO alcohol acid aldehyde b oxidation

  44. Amino Acids and Proteins proteins peptide bond cleavage amino acids NH3 pyruvic acid, oxalacetic acid ketoglutaric acid CAC CO2 CO2

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