CHAPTER 11 Mechanism of Enzyme Action
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CHAPTER 11 Mechanism of Enzyme Action 1. General properties of enzymes 2. Activation energy and the reaction coordinate 3. Catalytic mechanism 4. Lysozyme 5. Serine proteases Enzyme act with great speed and precision Introduction 1. Enormous variety of chemical reactions within a cell 2. Mediated by Enzymes 3. Enzymology, the study of enzymes (coined 1878; Greek: en, in; zyme, yeast), fermentation: glucose -> ethanol 12 enzyme-catalyzed steps 4. James Summer, 1926, crystallized urease from jack bean, shown to be a protein 5. Other catalysts, i.e. ribozymes (peptide-bond formation; “RNA-world”), only for units 6. Proteins more versatile, 20 functional units Introduction Enzymes increase the rate of chemical reactions by lowering the free energy barrier that separates the reactants and products 1. General Properties of Enzymes Enzymes differ from ordinary chemical catalysts by: - Higher reaction rates, 106-1012 - Milder reaction conditions (temp, pH, …) - Greater reaction specificity (no side products) - Capacity for regulation Definition catalyst: catalyzes reaction but is not itself consumed during the process Table 11-1 A) Classification of Enzymes - naming: -ase, urease, alcohol dehydrogenase but no rules, - systematic: IUBMB: 6 Classes acc. to the nature of the chemical reaction that is catalyzed (http://expasy.org/enzyme/) B) Enzymes Act on Specific Substrates - Noncovalent forces through which substrates bind to enzymes: van der Waals, electrostatic, hydrogen bonding, hydrophobic intercations - Geometric Complementarity - Electronic Complementarity - Induced fit upon substrate binding - “lock-and-key” model (proposed by Emil Fischer) An Enzyme-Substrate complex Geometric and electrostatic complementarity Enzymes are Stereospecific - Enzymes are highly specific both in binding to chiral substrates and in catalyzing stereo-specific reactions - Enzymes are themselves are chiral, L-amino acids -> active centers = active site is asymmetric/ stereo selective Citrate is prochiral and is stereo- specifically transformed into isocitrate Stereospecificity in substrate binding Enzymes vary in geometric Specificity - Stereoselectivity, right hand into left glove - Geometric specificity is a more stringent requirement than stereoselectivity, old key into modern lock: i.e. alcohol dehydrogenase, oxidation of ethanol (CH3CH2OH) to acetaldehyde (CH3CHO) faster than methanol to formaldehyde or isopropanol to aceton even though they only differ by deletion or addition of one CH2 group ! Some enzymes are very permissive, chymotrypsin, can hydrolyze amide and ester bonds, exception rather than rule ! Some Enzymes Require Cofactors - Can act as enzymes *chemical teeth” to take over chemical reactions that cannot be performed by amino acid side chains… - Required in diet of organisms - for example metal ions, Cu2+, Fe3+, Zn2+ toxicity, Cd2+ and Hg2+ can replace Zn and inactivate the enzyme - organic molecules, coenzymes, can transiently associate with enzyme as cosubstrate, i.e., nicotinamide adenine dinucleotide (NAD+) Types of Cofactors in Enzymes The structure and reaction of NAD+ NAD+ is an obligatory cofactor in The alcohol dehydrogenase (ADH) reaction NADH dissociates from the enzyme to be re-oxidized in an independent reaction Prosthetic groups Permanently associated with enzyme, often by covalent bonds, example heme is bound to proteins called cytochromes Holoenzyme = enzyme+cofactor complex, active Apoenzyme, lacks cofactor, inactive Coenzymes must be regenerated In order to complete the catalytic cycle, the coenzyme must return to its original state i.e. by a different enzyme such as is the case with NADH 2) Activation Energy and the Reaction Coordinate Transition State Theory: developed in 1930s HA-HB + HC -> HA + HB-HC Transition state: HA--HB—HC Transition state = point of highest free energy = most unstable Reactants approach one another along a path of minimal free energy = reaction coordinate Transition state diagram/reaction coordinate diagram: Plot of free energy versus the reaction coordinate Transition State Diagram (Symetrical) Transition State Substrate Product Transition State Diagram (Asymetrical) Free energy of activation Free energy of reaction Activation Energy and the Reaction Coordinate The greater the free energy of activation, the slower the reaction rate If the free energy of the reaction, ∆G<0, then the reaction is spontaneous and releases energy (heat) Transition State Diagram For a Two-Step Reaction Rate-determining “bottleneck” Catalysts Reduce the free energy of activation, ∆G‡ Catalysts act by providing a reaction pathway with a transition state whose free energy is lower than that of the un- catalyzed reaction Effect of a catalyst on the transition state diagram of a reaction Catalysts Reduce the free energy of activation, ∆G‡ Reaction rate is proportional to e-∆G‡/RT ∆∆G‡ of 5.7kJ/mol (1/2 of one hydrogen bond) gives 10-fold rate enhancement ∆∆G‡ of 34kJ/mol (small fraction of a covalent bond) give 106-fold enhancement Note: the catalyst enhances rate of forward and that of the back reaction by the same magnitude, but ∆Greaction determines whether forward or back reaction is favored 3) Catalytic Mechanisms Enzymes lower the free energy of the transition state (∆G‡) by stabilizing the transition state Learn about enzymatic reactions mechanisms by examining the corresponding non-enzymatic reactions of model compounds Catalytic Mechanisms Curved arrow convention to trace electron pairs At all times, rules of chemical reasons apply to the system, i.e. never five bonds on C, or 2 on H etc. Types of Catalytic Mechanisms 1. Acid-base catalysis 2. Covalent catalysis 3. Metal ion catalysis 4. Proximity and orientation effects 5. Preferential binding of the transition state A) Acid-Base Catalysis occurs by Proton Transfer General acid catalysis: Proton transfer from an acid lowers the free energy of a reaction’s transition state Example, keto-enol tautomerization (a) Enhanced by proton donation (b) or proton abstraction (c) (general base catalyzed) Concerted Acid-Base Catalysis Asp, Glu, His, Cys, Tyr, Lys have pK’s in or near the physiological range The ability of enzymes to arrange several catalytic groups around their substrates makes concerted acid-base catalysis a common enzymatic mechanism Effects of pH on Enzyme Activity Most enzymes are active only within a narrow pH range of 5-9. Reaction rates exhibit bell-shaped curves in dependence of pH (reflects ionization state of important residues) pH optimum gives information about catalytically important residues, if 4/5 -> Glu, Asp; 6->His, 10->Lys pK of residues can vary depending on chemical environment +/- 2 pH Optimum of Fumarase RNase A is an acid-base catalyst Bovine pancreatic RNase A: Digestive enzyme secreted by pancreas into the small intestine 2’,3’ cyclic nucleotides isolated as intermediates pH-dependence indicates 2 important His, 12, 119 that act in a concerted manner as general acid and base catalysts to catalyze a two-step reaction X-ray structure of bovine pancreatic RNase S UpcA substrate in active site The RNase A mechanism B) Covalent Catalysis Usually Requires a Nucleophile Covalent Catalysis accelerates reaction rates through the transient formation of a catalyst-substrate covalent bond Usually, nucleophilic group on enzyme attacks an electrophilic group on the substrate = nucleophilic catalysis Example: decarboxylation of acetoacetate Decarboxylation of acetoacetate Three stages of Covalent Catalysis 1. Nucleophilic attack of enzyme on substrate 2. Withdrawal of electrons 3. Elimination of catalysts by reversion of step 1 (not shown above). Nucleophilicity of a substance is related to its basicity: Important aspect of covalent catalysis The more stable the covalent bond formed, the less easily it can be decomposed in the final step of a reaction Good covalent catalysis must be (i) highly nucleophile and (ii) form a good leaving group. These are imidazole and thiol groups, i.e. Lys, His and Cys, Asp, Ser, some coenzymes (thiamine pyrophosphate, pyridoxal phosphate) C) Metal Ion Cofactors Act as Catalysts 1/3 of known enzymes require metal ions for catalysis Metalloenzymes contain tightly bound metal ion (Fe2+, Fe3+, Cu2+, Mn2+, Co2+), Na+, K+, or Ca2+ play structural rather than catalytic roles Mg2+, Zn2+ may be either structural or catalytic Metal Ion Cofactors Act as Catalysts Metal ions participate in the catalytic process: 1. By binding to substrate to orient them properly for reaction 2. By mediating oxidation-reduction reactions through reversible changes in the metal ions oxidation state 3. By electrostatically stabilizing or shielding negative charges Often: Metal ion acts similar to a proton, or polarizes water to generate OH- The role of Zn2+ in carbonic anhydrase - + CO2 + H2O <-> HCO3 + H 2+ Zn polarizes water, which then attacks CO2 D) Catalysis can occur through proximity and orientation effects Enzymes are much more efficient catalysts than organic model compounds Due to proximity and orientation effects Reactants come together with proper spatial relationship Example: p-nitrophenylacetate intramolecular reaction is 24 times faster Inter- versus intramolecular reaction 24-times faster Catalysis can occur through proximity and orientation effects Enzymes are usually much bigger than their substrates By oriented binding and immobilization of the substrate, enzymes facilitate catalysis by four ways 1. bring substrates close to catalytic residues 2. Binding of substrate in proper orientation (up to 102-fold) 3. Stabilization