* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Lecture 21 Enzyme mechanisms
Survey
Document related concepts
Fischer–Tropsch process wikipedia , lookup
Enantioselective synthesis wikipedia , lookup
Woodward–Hoffmann rules wikipedia , lookup
Marcus theory wikipedia , lookup
Ring-closing metathesis wikipedia , lookup
Diels–Alder reaction wikipedia , lookup
Asymmetric induction wikipedia , lookup
Wolff–Kishner reduction wikipedia , lookup
Hofmann–Löffler reaction wikipedia , lookup
Hydroformylation wikipedia , lookup
Physical organic chemistry wikipedia , lookup
Ene reaction wikipedia , lookup
Baylis–Hillman reaction wikipedia , lookup
Strychnine total synthesis wikipedia , lookup
Transcript
Lecture 21 Enzyme mechanisms - I Enzyme binds with the substrate with the help of various interactions like covalent bonding, hydrogen bonding, ionic interactions, ion-dipole and dipole-dipole interactions, charge transfer interactions, hydrophobic interactions, and van der Waals interactions. After binding of the substrate with the active site, the enzyme converts the substrate into the product by employing various types of catalytic mechanisms. These mechanisms are classified as: 1. Acid–base catalysis. 2. Covalent catalysis. 3. Metal ion catalysis. 4. Electrostatic catalysis. 5. Proximity and orientation effects. 6. Preferential binding of the transition state complex. 1. Acid–Base Catalysis In general acid catalysis process, lowering of free energy of the transition state occurs via partial proton transfer from a Brønsted acid. For example, keto–enol tautomerization reaction occurs quite slowly when it is uncatalysed. The carabanionlike transition state of this reaction, being high energy slows down the reaction rate. In the presence of acid, donation of proton to the oxygen atom reduces carbanion character of the transition state and hence increases the reaction rate. Few reactions also may be catalyzed by a Brønsted base. Also there are some reactions where simultaneous catalysis by acid and base occur. The RNase A Reaction Incorporates General Acid–Base Catalysis An example of enzymatic acid–base catalysis is Hydrolysis of RNA to its component nucleotides by Bovine pancreatic ribonuclease A (RNase A). This digestive enzyme cleaves RNA using the following reaction sequence: Mechanism of RNA (Image hasCleaving: to be drawn later) Active site of RNase A comprises of two His residues (His 12 and His 119) and Lys 41 which act in a concerted manner as general acid and base catalysts. RNase A cleaves RNA by following the two-step process: 1. In the first step, His 12 behaves as a general base. It abstracts a proton from 2ʹ-OH group of RNA. The newly generated 2ʹ-O-, being a good nucleophile promptly attack on the adjacent phosphorous atom. In the concerted way His 119 acts as an acid by protonating the oxygen atom of the leaving group which promotes the bond scission between phosphorous and 5ʹ oxygen. As a result of this step a 2ʹ,3ʹ-cyclic intermediate is formed. 2. In the second step, actually reverse of the first step take place. Here, His 12 acts as a general acid and His 119 as a general base. His 119 abstract a proton from a water molecule and facilitate the nucleophilic attack to the phosphorous atom of the 2ʹ,3ʹ-cyclic intermediate. His 12 protonate the 2ʹ-oxygen atom of the cyclic intermediate and helps to cleave the bond between phosphorous and 2ʹ-oxygen atom. 2. Covalent Catalysis In the covalent catalysis process a transient catalyst–substrate covalent bond is formed. An example of such a process is decarboxylation of acetoacetate which is chemically catalyzed by primary amines. In the uncatalyzed decarboxylation process the enolate transition state is very unstable. Whereas in the catalytic process, the high-energy enolate character of the transition state is stabilized as the protonated nitrogen atom of the covalent intermediate acts as an electron sink. The steps of Schiff base formation as well as its decomposition are very fast, so that these steps are not rate determining in this reaction sequence. Covalent catalysis is the summation of three successive three stages: 1. The nucleophilic reaction between the catalyst and the substrate to form a covalent bond. 2. The withdrawal of electrons from the reaction center by the now electrophilic catalyst. 3. The elimination of the catalyst, a reaction that is essentially the reverse of stage 1. D. Electrostatic Catalysis When substrate binds with the enzyme it generally excludes water from the active site. Due to the presence of substrate at the active site, the local dielectric constant of the active site is similar to that as found in an organic solvent. As a result the electrostatic interactions are much stronger than they are in aqueous solutions. Here, the distribution of charge is present in a medium of low dielectric constant which greatly influences chemical reactivity. Due to the presence of charge group near the active site, the pK’s of amino acid side chains in proteins may vary by several units from their nominal values. Distributions of charge near the active sites of enzymes are arranged in such a way that it can stabilize the transition states of the catalyzed reactions which in turn increase the rate of the reaction. Enhancement of enzymatic reaction rate due to the stabilization of transition state by the charge distribution is termed electrostatic catalysis. In case of few enzymatic reactions these charge distributions acts as a guide of a polar substrates to reach toward their binding sites. As a result rate of these reactions is higher than that of their apparent diffusion-controlled limits. Catalysis through Proximity and Orientation Effects Catalytic mechanisms of enzymatic reaction are similar to that of organic model reactions. In spite of this, enzymatic reactions are far more catalytically efficient than these models. Higher efficiency of enzymatic reaction is due to the specific physical conditions at enzyme catalytic sites that promote the corresponding chemical reactions. Proximity and proper orientation of the substrate and active site of an enzyme are the two most obvious specific physical conditions. For a reaction to occur, reactants must come together with the proper spatial relationship. For example, bimolecular reaction of imidazole with p-nitrophenylacetate. The progress of the reaction is monitored by the formation of the intensely yellow p-nitrophenolate ion. But if the reaction proceeds intramolecularly, the first-order rate constant k2 = 24 k1, when concentration of imidazole is 1M. Thus, due to the attachment of the imidazole catalyst with the the reactant, it is 24-fold more effective than when it is free in solution. So, in the case intramolecular reaction the imidazole group behaves as if its concentration is 24M. Both proximity and orientation contribute to this rate enhancement. Catalysis by Preferential Transition State Binding The catalytic mechanisms so far discussed for an enzyme is not the enough reason for the enormous rate enhancements effected by enzymes. One of the most important mechanisms of enzymatic catalysis is not considered yet i.e., the binding of the transition state to an enzyme with greater affinity than the corresponding substrates or products. If both of them i.e. the previously described catalytic mechanisms and preferential transition state binding are consider together that will rationalizes the observed rates of enzymatic reactions. The concept of transition state binding is based on rack mechanism. The concept proposed that enzymes mechanically strained their substrates toward the transition state geometry through binding sites into which undistorted substrates did not properly fit. Model (organic reaction) example: The reaction occurs at 315 times faster rate when R is CH3 rather than when it is H due to the greater steric repulsions between the CH3 groups and the reacting groups. Another example of reaction rate enhancement due to strain is the ring opening reaction where a strained ring such as cyclopropane opens at faster rate compared to the unstained ring such as cyclohexane. In case of both of the mentioned example the strained reactant is more close to the transition state of the reaction in terms of energy than does the corresponding unstrained reactant.