Enzyme catalysis mechanisms involved
- 2. ENZYME CATALYSIS Enzymes achieve their enormous rate accelerations via the same catalytic mechanisms used by chemical catalysts. Enzymes have simply been better designed through evolution. Enzymes, like other catalysts, reduce the free energy of the transition state (ΔG); that is, they stabilize the transition state of the catalysed reaction. 2
- 3. FREE ENERGY Free energy (G) is the most valuable thermodynamic function for determining whether a reaction can take place and for understanding the energetics of catalysis A reaction can occur spontaneously only if the change in free energy (∆ G) is negative. Enzymes do not alter reaction equilibria; rather, they increase reaction rates. 3
- 4. ENZYME CATALYSIS- LOWERING FREE ENERGY 4
- 5. BIOCHEMICAL MECHANISMS The types of catalytic mechanisms that enzymes employ have been classified as: 1. Acid–base catalysis 2. Covalent catalysis 3. Metal ion catalysis 4. Proximity and orientation effects 5. Catalysis by approximation. 5
- 6. ACID–BASE CATALYSIS General acid catalysis is a process in which proton transfer from an acid lowers the free energy of a reaction’s transition state. The ionisable functional groups of amino acyl side chains and (where present) of prosthetic groups contribute to catalysis by acting as acids or bases. The ability of enzymes to arrange several catalytic groups around their substrates makes concerted acid–base catalysis a common enzymatic mechanism. 6
- 7. ACID–BASE CATALYSIS CONTD. The catalytic activity of these enzymes is sensitive to pH, since the pH influences the state of protonation of side chains at the active site. RNase A Is an Acid–Base Catalyst. Bovine pancreatic RNase A provides an example of enzymatically mediated acid–base catalysis. This digestive enzyme is secreted by the pancreas into the small intestine, where it hydrolyzes RNA to its component nucleotides. 7
- 8. RNase A has two essential His residues, His 12 and His 119, that act in a concerted manner as general acid and base catalysts. Evidently, RNase A catalyzes a two-step reaction . 8 BOVINE PANCREATIC RNASE
- 9. COVALENT CATALYSIS The process of covalent catalysis involves the formation of a covalent bond between the enzyme and one or more substrates. Covalent catalysis accelerates reaction rates through the transient formation of a catalyst– substrate covalent bond. Usually, this covalent bond is formed by the reaction of a nucleophilic group on the catalyst with an electrophilic group on the substrate, and hence this form of catalysis is often also called nucleophilic catalysis. 9
- 10. COVALENT CATALYSIS CONTD. Covalent catalysis can be conceptually decomposed into 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 10
- 11. COVALENT CATALYSIS CONTD. Functional groups in proteins that act in this way include: the unprotonated amino group of Lysine, the imidazole group of Histidine, the thiol group of Cysteine, the carboxyl group of Aspartic acid , and the hydroxyl group of Serine. 11
- 12. Examples of enzymes that participate in covalent catalysis include the proteolytic enzyme chymotrypsin and trypsin in which the nucleophlie is the hydroxyl group on the serine. 12
- 13. METAL ION CATALYSIS Nearly one-third of all known enzymes require metal ions for catalytic activity. This group of enzymes includes the metalloenzymes. Most common transition metal ions include Fe2+, Fe3+, Cu2+, Mn2+ or, Co2+ Ionic interactions between an enzyme-bound metal and a substrate can help orient the substrate for reaction or stabilize 13
- 14. METAL ION CATALYSIS Metal ions participate in the catalytic process in three major ways: 1. By binding to substrates to orient them properly for reaction. 2. By mediating oxidation–reduction reactions through reversible changes in the metal ion’s oxidation state. 3. By electrostatically stabilizing or shielding negative charges. 14
- 15. An excellent example of this phenomenon occurs in the catalytic mechanism of carbonic anhydrase a widely occurring enzyme that catalyzes the reaction: CO2 + H2O ⇌ HCO− 3 + H+ 15
- 16. PROXIMITY AND ORIENTATION Enzyme-substrate interactions align the reactive chemical groups and hold them close together in an optimal geometry, which increases the rate of the reaction. This reduces the entropy of the reactants and thus makes addition or transfer reactions less unfavorable, since a reduction in the overall entropy when two reactants become a single product. 16
- 17. CATALYSIS BY APPROXIMATION Many reactions include two distinct substrates. In such cases, the reaction rate may be considerably enhanced by bringing the two substrates together along a single binding surface on an enzyme. NMP kinases bring two nucleotides together to facilitate the transfer of a phosphoryl group from one nucleotide to the other. This strategy takes advantage of binding energy and positions the substrates in the correct orientation for the reaction to proceed. 17
- 18. An example of catalysis by approximation is when NMP kinases bring two nucleotides together to facilitate the transfer of a phosphoryl group from one nucleotide to the other. 18