prelim 2 outline

prelim 2 outline - Enzymes and Catalysis Definition of an...

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Enzymes and Catalysis Definition of an enzyme: proteins that accelerate the rate or velocity of a chemical reaction by lowering the energy of activation associated with the reaction. An enzyme is a catalyst, it accelerates a chemical reaction, but is not changed by the reaction . Enzymes cannot invent new chemical reactions, nor do they alter equilibrium constants (a thermodynamic constant). Requirements for a reaction to occur: if two molecules collide with both the proper orientation (p=probability factor) and sufficient energy (f). Therefore, the rate of a chemical reaction can be described as: Rate of reaction= p * f * Z [Z= collision frequency] Apoenzyme : the inactive, protein component of an enzyme. Lacks essential cofactor or prosthetic group(metal) Cofactor: Small organic or inorganic molecule required to activate an apoenzyme, if it is tightly bound, it is a prosthetic group Holoenzyme: apoenzyme with bound cofactor. The active form of the enzyme Substrate binding site: part of the protein that binds the substrate Active site: contains the essential amino acids residues that perform catalysis Isozymes: variant forms of the same enzyme. For example, some enzymes are found in both the cytoplasm and mitochondrion. They are similar but encoded on distinct genes Allosteric Site: Regulatory site that can bind a small molecule that modulates the properties of the enzyme (activity or affinity of substrates). Enzyme specificity: the active site: The enzymes tertiary structure creates a precise pocket for an individual substrate, using amino acid residues to provide the necessary charge and hydrophobic characteristics to accommodate any type of molecule as substrate Lock and key model : the substrates fits into a precise structure on the enzyme in a static interaction Induced fit model : the confirmation of the enzymes and substrate are not fully performed until contact. Contact induces a conformation change in the enzyme and substrate that results in a precise conformation suitable for catalysis (can induce substrate strain). Induces strain can aid in enzyme catalysis Asymmetry of the binding site: The enzyme can only bind one orientation of the symmetrical molecule. L-configuration and D-configuration (can differentiate between optical isomers) and also between alpha and beta linkages Amino acid residues away from the active site matter! Mechanism for catalysis: 1
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-have to overcome potential energy barrier (can be reached with increased heat or pressure) -enzymes serve to lower the potential energy barrier associated with many reactions -transition state is not an intermediate and cannot be isolated, rather it is an energetic state. -enzymes do no change the thermodynamics of a reaction, the delta G of the reaction is unchanged, only the pathway leading to a lower energy of activation is changed between the catalyzed and uncatalyzed reaction Transition state analogs- inhibitors that resemble transition or reaction intermediates and can bind very tightly to the enzyme
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prelim 2 outline - Enzymes and Catalysis Definition of an...

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