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CATALYSIS OF BIOCHEMICAL REACTIONS Proteins control the metabolism of a cell by catalyzing specific chemical reactions (Start your clickers) Energetics of a typical chemical reaction Model reaction: A and B can be transformed into C and D by rearranging electrons, thus covalent bonds, upon collision. A+B ------> (reactants, substrates) C+D (products) 1. A and B together have some potential energy (in chemical bonds) and kinetic energy (in motion). 2. A and B collide; collision distorts or stresses bonds to the point where they can rearrange electrons; generally, this requires more potential energy (since without stress, one expects electrons to find low energy, stable state): extra energy is “activation energy”. 3.Complex decays to give different (or same) products. What is wrong with this figure (Fig. 6.8)? Rates of uncatalyzed reactions: Rate depends on probabilities of: ! Collision ! Correct orientation ! Activation energy ! Rearrangement Rate will be slow for most uncatalyzed reactions, because: ! Concentrations are low ! Temperature is low Enzyme-catalyzed reaction Enzyme: protein molecule with a three-dimensional shape that specifically promotes the chemical reaction of interest 1. A,B, and E (enzyme catalyst) have some potential energy and kinetic energy. 2. A,B, and E all collide, substrates A and B fitting into the active site of E: kinetic energy of collision (or of later collisions by solvent molecules) provides potential energy to stress bonds sufficiently for rearranging. 3. Complex decays to products C and D and unchanged (or regenerated) E. Rates of enzyme-catalyzed reactions: Rate still depends on probabilities of: (a) Collision (b) Correct orientation (c) Activation energy (d) Rearrangement Enzyme promotes (a), (b), and/or (c). (a) “cage effect”: enzyme forms “cage” around both substrates, increasing collision time. (b) enzyme correctly orients positions of substrates as part of the binding process. (c) enzyme lowers activation energy needed for reaction by distorting bonds of substrates ! active site sterically strains the substrate, and/or ! electric charges in active site relocate electrons of substrates, and/or ! amino acid side chains in active site react covalently with substrate. Examples: Orientation Strain Charge effects An example of an enzyme that sterically strains the substrate: Lysozyme distorts the bonds of one of the sugars in the polysaccharide of a bacterial cell wall It also places a partial charge on the substrate, making it react more easily with water (hydrolysis). Hydrolysis breaks the polysaccharide chain and weakens the wall so that the cell lyses. The enzyme hexokinase changes shape when it binds to the substrate, glucose, increasing the "cage effect" and bringing other effects into play. For some enzymes, a material in the solution different from the substrate can interact with an enzyme’s active site (or other site) and inhibit the enzyme’s activity. Some forms of inhibition are irreversible: e.g., the covalent attachment of the compound DIPF to an essential amino acid in the active site of the enzyme trypsin. Summary Enzyme proteins catalyze reactions in cells. Because of the variety of possible proteins, it is possible for different proteins with different active sites to catalyze all the various metabolic reactions in the cell and thus control the chemical activity in the cell. If enzymes lower the activation energy of most reactions in the cell, will they not reduce the stability of the cell? (a) yes, and it is a good thing (if cytoplasm is too stable, it is as good as frozen) (b) no, because enzyme activity can be turned on and off as the cell requires (c) yes and no: both (a) and (b) have germs of truth