1. Week 2 Lecture Material October 2001 Metabolism

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

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

5. What Types of Reactions Occur During Metabolism? l Oxidation/Reduction Reactions with Chemical as Donor l carbon oxidized to CO 2 l ammonia oxidized to nitrate l sulfur oxidized to sulfate l Oxidation/Reduction Reactions with Chemical as Acceptor l carbon dioxide reduced to CH 4 l nitrate reduced to nitrogen gas

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

7. Ecosystem Management

8. Wastewater Treatment

9. Treatment of Air Emissions

10. Airplane Deicing

11. Sludge Land Application and Spills

12. Bioremediation of Gas Spills

13. Composting Explosives

14. Metabolism Basics l Energetics l Enzyme Function l Oxidation/Reduction Half Reactions l Electron Carriers l Energy Carriers

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

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

17. Free Energy of Reaction Example H 2 S + 8 Fe 3+ 8 Fe 2+ + SO 4 2 - H 2 S + 8 Fe 3+ 8 Fe 2+ + SO 4 2 - + 10H + H 2 S + 8 Fe 3+ + 4 H 2 0 8 Fe 2+ + SO 4 2 - + 10H +  G o ’ = G o f [C + D] - G o f [A + B]  G o ’ = ?

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

19. Activation Energy Reaction Progress Free Energy

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

21. Aldolase

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

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

24. NAD + as an Electron Carrier

25. NADH as an Electron Carrier

26. Reduction Potential l the degree to which substrates can serve as e donors or acceptors is related to their reduction potential, E o ’ l E o ’ measured relative to H 2 in volts l E o ’ values given for the reduction ¼ O 2 + H + + e - ½ H 2 0  E o ’ = 0.82 v l the lower the E o ’, the greater the ability to donate electrons l thus glucose/CO 2 (-0.43v) has a higher ability to donate electrons than oxygen/ H 2 0 (0.82v)

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

28. Example of Coupled Half Reaction Oxygen as Terminal Acceptor ½ NAD + + ½ H + + e - ½ NAD E o ’ = - 0.32 v ¼ O 2 + H + + e - ½ H 2 0 E o ’ = 0.82 v ½ NADH ½ NAD + + ½ H + + e - E o ’ = 0.32 v ¼ O 2 + H + + e - ½ H 2 0 E o ’ = 0.82 v ¼ O 2 + ½ NADH + ½ H + ½ NAD + + ½ H 2 0  E o ’ = 1.12 v

29. Electron Tower Eo’Eo’ -0.50 + 0.90 Half reactions with lower E o ’ values can reduce half reactions with higher E o ’ 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 SO 4 /S 2- ½ O 2 /H 2 0 NO 3 - /NO 2 -

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

31. Summary of Basics Carbon Electron Donor Metabolism Intermediate Often these initial reactions are preparatory reactions to get other things going Energy investment as NADH or ATP Oxidized Carbon Electrons from oxidation are “carried” by electron carriers primary NADH 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 Energy for Cell Synthesis and Maintenance wateroxygen

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

33. Oxidation of Carbohydrates (Glucose) Citric Acid Cycle Electron Transport System CO 2 e-e- ½ O 2 H20H20 glycolysis Electrons flow in the form of reduced dinucleotides (NADH and FADH) GDP GTP glucose pyruvate ADP ATP NADH NAD + Acetyl CoA CoA-SH

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

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

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

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

38. Summary of Glucose Oxidation water and hydrogen left out of balance C 6 H 12 O 6 + 2ADP + 2NAD + 2 pruvate - + 2ATP + 2NADH Acetyl-CoA + 4NAD + + FAD + + GDP 3 CO 2 + 4NADH + FADH + GTP C 6 H 12 O 6 + 2ADP + 2GDP + 10NAD + + 2FAD + 6 CO 2 + 2ATP + 2GTP + 10NADH + 2FADH glycolysis: CAC: Summary of glucose oxidation Preparatory Step: pruvate - + CoA-SH + NAD + acetyl CoA + CO 2 + NADH

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

40. Electron Transport l NADH is oxidized and donates its electrons and protons to a flavoprotein l This flavoprotein is oxidized and pumps out H + across membrane l This process continues until electrons are passed to final acceptor, O 2 l a gradient established across membrane l this gradient used to drive energy production (ATP)

41. Electron Transport l Each carrier in chain must be capable of reducing the next electron carrier next (i.e. reduction potential must be lower) l The more positive the reduction potential of the final acceptor, the greater the proton gradient l The greater the proton gradient, the greater the energy yield NAD + /NADH 2 Eo’Eo’ -0.50 + 0.90 SO 4 /S 2- ½ O 2 /H 2 0 NO 3 - /NO 2 -

42. ATPase Enzyme

43. Summary of Basics Carbon Electron Donor Metabolism Intermediate Often these initial reactions are preparatory reactions to get other things going Energy investment as NADH or ATP Oxidized Carbon Electrons from oxidation are “carried” by electron carriers primary NADH 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 Energy for Cell Synthesis and Maintenance wateroxygen

44. Acetic Acid, Volatile Acids, Lipids Lipids pyruvic acid glycerol acetyl CoA, NADH, FADH fatty acid CH3 - (CH 2 )n - COOH acetyl CoA, NADH, FADH CO 2  oxidation fatty acid oxidized in two carbon increments

45. Straight Chain Aliphatic Hydrocarbons CHOCOOH aldehyde acid CH 3 NADHNAD O2O2 H2OH2O CH 2 OH alcohol MMO  oxidation NAD + NADHNAD + NADH H2OH2O

46. Amino Acids and Proteins proteins peptide bond cleavage amino acids pyruvic acid, oxalacetic acid ketoglutaric acid CAC CO 2 NH 3 CO 2