Chapter 6 Enzymes 6 1 An Introduction to Enzymes Most Enzymes Are Proteins the exception is a small group of catalytic RNA if an enzyme is broken down into its amino acids its catalytic activity is always destroyed cofactor enzymes coenzyme either one or more inorganic ions Fe2 Mg2 Mn2 or Zn2 that aid a complex organic or metalloorganic molecule that aids enzymes o act as transient carriers of specific functional groups a coenzyme or metallic ion that is bound very tightly or prosthetic group even covalently to the enzyme protein holoenzyme coenzyme and or metal ions a complete catalytically active enzyme with its bound o apoenzyme or apoprotein the protein part of a holoenzyme some enzyme proteins are modified covalently by phosphorylation glycosylation and other processes involved in the regulation of enzyme activity Enzymes Are Classified by the Reactions They Catalyze each enzyme has a four part classification number and a systematic name which identifies the reaction it catalyzes 6 2 How Enzymes Work active site more rapidly a pocket on the enzyme the specific environment in which a given reaction can occur o substrate upon by the enzyme the molecule that is bound in the active site and acted Enzymes Affect Reaction Rates Not Equilibria the starting point for either the forward or the reverse a catalyst increases the rate of reaction ground state reaction in an equilibria or the contribution to the free energy of the system by an average molecule just because an equilibrium is favored does not mean the rate will be fast o rate depends on the activation energy the difference between the energy levels of the ground the state at the top o the energy hill where the formation transition state of reactants or products is equally likely activation energy state and the transition state reaction rates can be increased by raising the temperature and or pressure increasing the number of molecules with enough energy to overcome the barrier catalysts lower the activation energy reaction intermediates finite chemical lifetimes rate limiting step determine the rate transient chemical species in a reaction that have the step or steps with the highest activation energy that Reaction Rates and Equilibria Have Precise Thermodynamic Definitions equilibrium constant K eq describes an equilibrium o directly related to the overall standard free energy change for the reaction rate of a reaction is determined by the concentration of reactants and a rate constant k o rate equation k is a proportionality constant that reflects the probability of reaction under a given set of conditions A Few Principles Explain the Catalytic Power and Specificity of Enzymes The rate enhancements and source of energy for enzymes can be explained in two parts reaction o The rearrangement of covalent bonds during an enzyme catalyzed o Non0covalent interactions between enzyme and substrate Binding energy the energy derived from enzyme substrate interaction o Major source of free energy used by enzymes to lower the activation energies of reactions How enzymes use non covalent binding energy o Free energy is released when many weak bonds are formed as well as a result of interactions between an enzyme and its substrate This binding energy contributes to specificity as well as to catalysis o Weak interactions are optimized in the reaction transition stat Weak Interactions between Enzyme and Substrate Are Optimized in the Transition State enzymes are structurally complementary to their substrates o they are not perfect matches however because that would impede o in order to catalyze reactions an enzyme must be complementary to the reaction transition state The free energy released by the formation of these interactions pays for the energy required to reach the top of the energy hill Weak binding interactions between the enzyme and the substrate provide a substantial driving force for enzymatic catalysis o The requirement for weak interactions is why so many enzymes are reaction large Binding Energy Contributes to Reaction Specificity and Catalysis specificity a competing molecule the ability of an enzyme to discriminate between a substrate and o derived from the formation of many weak interactions between the enzyme and its specific substrate molecule physical and thermodynamic factors that contribute to the activation energy might include o the entropy of the molecules in solution o the solvation shell of hydrogen bonded water that surrounds and helps to stabilize most biomolecules in aqueous solution o the distortion of substrates that must occur in many reactions o the need for proper alignment of catalytic functional groups on the enzyme o binding energy can be used to overcome all of these barriers a large restriction in the relative motions of two Entropy reduction substrates that are to react o Benefit of binding to an enzyme formation of weak bonds between substrate and enzyme results in desolvation o Enzyme substrate interactions replace most or all of the hydrogen bonds between the substrate and water Binding energy involving weak interactions formed only in the reaction transition state helps to compensate thermodynamically for any distortion that the substrate must undergo to react The enzyme undergoes a change in conformation when the substrate binds induced fit the reaction o Brings specific functional groups into the proper position to catalyze Specific Catalytic Groups Contribute to Catalysis There is a variety of mechanisms by which bonds are catalytically cleaved and formed o Acid base catalysis o Covalent catalysis o Metal ion catalysis General Acid base Catalysis o Specific acid base catalysis present in water transfers are mediated by other classes of molecules o General acid base catalysis when water is not enough proton catalysis that only uses H or OH ions o a number of amino acid side chains can act as proton donors and acceptors in the active site of an enzyme o A transient covalent bond is formed between the enzyme and the Covalent Catalysis substrate o A number of amino acid side chains and the functional groups of some enzyme cofactors can serve as nucleophiles Metal Ion Catalysis o Ionic interactions between an enzyme bound metal and a substrate can help orient the substrate for reaction or stabilize charged reaction transition states o Metals can also mediate oxidation reduction reactions by reversible changes in the metal ion s oxidation state Most enzymes combine several catalytic strategies