Metabolism Enzymes Metabolism and Metabolic Pathways

Enzymes n Proteins which function as biological catalysts n Each biochemical transformation in a cell has a specific enzyme associated with it

Enzymes and Activation Energy

Lock and Key Model n Interaction between enzyme and substrate analogous to a lock and key n Active site n Allosteric sites

Kinetics of an Enzymatically Catalyzed Reaction n Conversion of substrate to product n Concentration of substrate and enzyme constant n All experimental conditions (pH, temp) constant

Effect of [S] on V 0 n Initial linear relationship between increasing [S] and initial reaction velocity n Saturation kinetics n Overall a hyperbolic curve

Michaelis-Menton Kinetics n V max –Maximum reaction rater n K M –Affinity constant –[S] when V 0 = 1/2 V max n Values can be estimated from hyperbolic graph

Lineweaver - Burke Plots n Linearizes Michaelis-Menton plot n Plot 1/V 0 vs 1/[S]

Monod Equation

Metabolism

Definitions n Metabolism: The sum of the biochemical reactions which occur in a cell n Pathway: –A series of connected reactions –A --> B--> C-->D-->E n Catabolism: –Breakdown complex substrates –Generally oxidations

–Energy yielding –Generate reduced electron carriers n Anabolism –Build up complex molecules from precursors –Generally reductions –Energy requiring –Oxidize electron carriers

ATP and Energy Transfer n ATP ADP AMP n High energy (squiggle) phosphate bonds n 7.3 kcal to make or break these bonds n Transfer energy from energy yielding reactions to energy requiring reactions

Mechanisms of Energy Generation n Substrate level phosphorylation n Oxidative phosphorylation n Photophosphorylation

Electron Carriers n Coenzymes –NAD/NADH + H + –FAD/FADH 2 n Transfer electrons from oxidation to reduction reactions n Need for initial electron donor and terminal electron acceptor

NAD/NADH + H +

Understanding Metabolic Pathways n Keep track of: –Elements –Energy (ATP/ADP) –Electrons n Why are there so many steps in the pathways –Energetic constraints –Generation of intermediates

Central Metabolic Pathways n Essential pathways n Found in all organisms n Include: –Glycolysis (EMP) –TCA (Kreb’s) cycle –ETS

Other Pathways n Specific catabolic pathways not found in all organisms n If an organism can convert a compound into an intermediate in Central metabolism, complete mineralization (catabolism to carbon dioxide and water) is possible.

Overview of Pathways

Glycolysis n Conversion of glucose to 2 pyruvate n Most common pathway for initial metabolism of glucose n Anaerobic pathway n Substrate level phosphorylation n Low energy yield/incomplete oxidation n Production of NADH + H +

Fermentation n Reoxidation of NADH + H + to NAD n Organic compound functions as a terminal electron acceptor n Important in –Industrial production of chemicals –Food production: bread, wine, etc.

TCA Cycle n Oxidation of pyruvate to carbon dioxide n Low direct energy yield n Generates large amounts of reduced coenzymes n Produces biosynthetic intermediates

Respiration n Transfer of electrons from electron acceptors to terminal electron acceptors –Aerobic organisms: oxygen –Anaerobic organisms: other inorganic compounds Nitrate Sulfate Iron Carbonate

Electron Transport System n Series of compounds which are alternatively reduced and oxidized n Orientation in the membrane. Net translocation of charge and hydrogen across the membrane

Chemiosmosis n Couples electron transport with ATP generation n Development of transmembrane potential by transfer of electrons and hydrogens n Where H + reenters the cell, ATP synthease is present