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Introduction to Metabolism

Introduction to Metabolism. Metabolism (The Acquisition and Utilization of Free Energy). Catabolism: exergonic oxidation Anabolism: endergonic processes. Anabolism and Catabolism. ATP. Sources of ATP. Phototrophs: photosynthesis Chemotrophs: oxidation of organic compounds. NADP +.

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Introduction to Metabolism

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  1. Introduction to Metabolism

  2. Metabolism(The Acquisition and Utilization of Free Energy) Catabolism: exergonic oxidation Anabolism: endergonic processes

  3. Anabolism and Catabolism

  4. ATP

  5. Sources of ATP Phototrophs: photosynthesis Chemotrophs: oxidation of organic compounds

  6. NADP+

  7. NADPH

  8. Metabolic Pathways A ——> B ——> C ——> D ——> E

  9. Potential Futile Cycles

  10. Properties of Metabolic Pathways • Irreversible (overall): reversibility of individual steps • Separate Anabolic and Catabolic Pathways • First Committed (Exergonic) Step: others close to equilibrium • Regulation (usually first committed step): often rat-limiting • Compartmentation: transport

  11. Regulation of Metabolic Pathways Specific Controls General Controls

  12. Specific Controls • Control of Enzyme Amount (153B) • Constitutive Enzymes • Inducible Enzymes • Repressible Enzymes • Control of Enzyme Activity (153A) • Regulatory Enzymes • Effectors (Ligands)

  13. General Controls(Integration of Cellular or Organism Functions) • Internal Effectors • Catabolite Repression • Energy Charge • Reduction Potential • External Effectors (e.g. hormones) Significance: Efficiency and Flexibility!

  14. Energy Charge(Daniel Atkinson) Steady-State E.C. = 0.93

  15. Types of Reactions

  16. Group Transfer Reactions

  17. Phosphoryl Group Transfer

  18. Oxidation-Reduction Reactions SH2 + NAD+ + H2O ——> S + NADH + H3O+ SH2: Reduced Substrate S: Oxidized Product NAD+: Electron Acceptor

  19. NAD+

  20. Alcohol Dehydrogenase(Oxidation-Reduction Reaction)

  21. Elimination Reactions

  22. Isomerization Reactions(Intramolecular Hydrogen Shifts)

  23. Racemization and Epimerization Racemization: change stereochemistry of only chiral center Epimerization: change stereochemistry of one chiral center of molecule with more than one chiral centers

  24. Rearrangements(altered carbon skeletons)

  25. Making C-C Bonds

  26. Breaking C-C Bonds

  27. Experimental Approachesto Metabolism

  28. Features of Metabolic Pathways A ——> B ——> C ——> D ——> E Sequences and Energetics Enzymes and Mechanisms Control Mechanisms (Regulation)

  29. Elucidation of Metabolic Pathways A ——> B ——> C ——> D ——> E Metabolic Inhibitors: accumulation of intermediates Biochemical Genetics: mutants Pathway Labeling: isotopes

  30. Metabolic Inhibitors(Accumulation of Intermediates) Iodoacetate: fructose-1,6-bisphosphate Fluoride: 3-phosphoglycerate and 2–phosphoglycerate

  31. Biochemical Genetics(Mutants) Natural Genetic Defects Manipulation of Microorganisms A ——> B ——> C ——> D ——> E Accumulation of Intermediates Growth Requirements (auxotrophic mutants)

  32. Pathway Labeling A* ——> B* ——> C* Stable Isotopes Radioisotopes

  33. Detection of Isotopes • Stable Isotopes • Mass Spectropmetry • NMR • Radioisotopes • Proportional Counting (Geiger Counter) • Liquid Scintillation Counting • Autoradiography

  34. Enzymes and Mechanisms Biochemistry

  35. Control Mechanisms (Regulation) Molecular Biology Biochemistry

  36. Compartmentation(Isolated Organs/Tissues, Cells and Subcellular Organelles) Cell Biology Biochemistry

  37. ATP Phosphoester Bonds: acid and alcohol Phosphoanhydride Bonds: two acids

  38. Kinetic StabilityofPhosphoanhydride Bonds

  39. Coupled Reactions ∆Go’ (kJ/mol) ---------- Fructose-6-P + Pi ——> Fructose-1,6-bisP + H2O +13.3 ATP + H2O ——> ADP + Pi -30.5 ------------------------------------------------------------------------------- Fructose-6-P + ATP ——> Fructose-1,6-bisP + ADP -17.2

  40. Role of ATP • Early stages of nutrient breakdown Glucose + ATP ——> Glucose-6-P + ADP • Interconverson of nucleoside triphosphtes NDP + ATP ——> NTP + ADP Nucleoside Diphosphate Kinase • Physiological processes • Muscle contraction • Active transport

  41. Role of ATP • Additional phosphoanhydride cleavages in highly endergonic reactons (NMP)n + NTP ——> (NMP)n+1 + PPi PPi + H2O ——> 2 Pi Pyrophosphatase

  42. Formation of ATP • Substrate-level phosphorylationX–P + ADP ——> X–H + ATP • Oxidative phosphorylation • Photophosphorylation • Adenylate Kinase reaction2 ADP ——> AMP + ATP

  43. Substrate-level Phosphorylation

  44. Oxidative Phosphorylation

  45. Photophosphorylation

  46. Other “High-Energy” Compounds

  47. Steady State

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