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Metabolism
Enzymes
Metabolism and Metabolic Pathways
Enzymes
Proteins which function as biological catalysts
Each biochemical transformation in a cell has a specific enzyme associated with it
Enzymes and Activation Energy
Lock and Key Model
Interaction between enzyme and substrate analogous to a lock and key
Active site Allosteric sites
Kinetics of an Enzymatically Catalyzed Reaction
Conversion of substrate to product
Concentration of substrate and enzyme constant
All experimental conditions (pH, temp) constant
Effect of [S] on V0
Initial linear relationship between increasing [S] and initial reaction velocity
Saturation kinetics Overall a hyperbolic
curve
Michaelis-Menton Kinetics
Vmax
– Maximum reaction rater
KM
– Affinity constant
– [S] when V0 = 1/2 Vmax
Values can be estimated from hyperbolic graph
Lineweaver - Burke Plots
Linearizes Michaelis-Menton plot
Plot 1/V0 vs 1/[S]
Monod Equation
Metabolism
Definitions Metabolism: The sum of the
biochemical reactions which occur in a cell
Pathway: – A series of connected reactions– A --> B--> C-->D-->E
Catabolism: – Breakdown complex substrates– Generally oxidations
– Energy yielding– Generate reduced electron carriers
Anabolism– Build up complex molecules from
precursors– Generally reductions– Energy requiring– Oxidize electron carriers
ATP and Energy Transfer ATP <---> ADP <--->
AMP High energy (squiggle)
phosphate bonds 7.3 kcal to make or
break these bonds Transfer energy from
energy yielding reactions to energy requiring reactions
Mechanisms of Energy Generation
Substrate level phosphorylation
Oxidative phosphorylation Photophosphorylation
Electron Carriers
Coenzymes– NAD/NADH + H+
– FAD/FADH2
Transfer electrons from oxidation to reduction reactions
Need for initial electron donor and terminal electron acceptor
NAD/NADH + H+
Understanding Metabolic Pathways
Keep track of:– Elements– Energy (ATP/ADP)– Electrons
Why are there so many steps in the pathways– Energetic constraints– Generation of intermediates
Central Metabolic Pathways
Essential pathways Found in all organisms Include:
– Glycolysis (EMP)– TCA (Kreb’s) cycle– ETS
Other Pathways Specific catabolic pathways not
found in all organisms 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
Conversion of glucose to 2 pyruvate
Most common pathway for initial metabolism of glucose
Anaerobic pathway Substrate level
phosphorylation
Low energy yield/incomplete oxidation
Production of NADH + H+
Fermentation Reoxidation of NADH
+ H+ to NAD Organic compound
functions as a terminal electron acceptor
Important in– Industrial production of
chemicals– Food production: bread,
wine, etc.
TCA Cycle Oxidation of
pyruvate to carbon dioxide
Low direct energy yield
Generates large amounts of reduced coenzymes
Produces biosynthetic intermediates
Respiration
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 Series of compounds
which are alternatively reduced and oxidized
Orientation in the membrane. Net translocation of charge and hydrogen across the membrane
Chemiosmosis
Couples electron transport with ATP generation
Development of transmembrane potential by transfer of electrons and hydrogens
Where H+ reenters the cell, ATP synthease is present