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Enzyme Mechanisms
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Oxidoreductases catalyze oxidation-reduction reactions.
Transferases catalyze transfer of functional groups from one molecule to another. Hydrolases catalyze hydrolytic cleavage. Lyases catalyze removal of a group from or addition of a group to a double bond, or other cleavages involving electron rearrangement. Isomerases catalyze intramolecular rearrangement. Ligases catalyze reactions in which two molecules are joined. Types of Enzymes
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Two Models for Enzyme-Substrate Interaction
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Induced Conformational Change in Hexokinase
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Coenzymes
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Example of a Coenzyme Involved in Oxidation/Reduction Reactions
Hydride (H:-) transfer (nicotinamide adenine dinucleotide)
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Stereospecificity of Yeast Alcohol Dehydrogenase
ethanol acetaldehyde pro-S pro-R pro-R pro-S Vennesland and Westheimer, 1950
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Stereospecificity Conferred by an Enzyme
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Catalytic Mechanisms Acid-base catalysis Covalent catalysis
Metal ion catalysis Electrostatic catalysis Proximity and orientation effects Preferential binding to transition state (transition state stabilization)
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Acid-Base Catalysis
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Keto-Enol Tautomerism: Uncatalyzed vs. Acid- or Base-Catalyzed
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Example of Acid-Base Catalysis: Bovine Pancreatic RNase A
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Covalent Catalysis: Nucleophiles and Electrophiles
Protonated
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Example of Covalent Catalysis: Decarboxylation of Acetoacetate
Lysine side chain e-amino group on enzyme is nucleophile in attack on substrate. Electrophilic “electron sink”
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Example of Metal Ion Catalysis: Carboxypeptidase A
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Example of Metal Ion Catalysis: Carbonic Anhydrase
Carbonic anhydrase catalyzes the reaction: CO2 + H2O HCO3− + H+
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Enolase Mechanism
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Entropic and Enthalpic Factors in Catalysis
Proximity and orientation effects Transition state stabilization through preferential binding of transition state
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Proximity and Orientation Effects
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Enzymes Are Complementary to Transition State
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Serine Protease Mechanism: Multiple Catalytic Mechanisms at Work
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Structure of the Serine Protease Chymotrypsin
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Serine Protease Substrate Specificity and Active-Site Pockets
Trypsin cleaves amide bond immediately C- terminal to basic amino acid residues. Substrate specificity in serine proteases through active-site binding of side chain of amino acid residue adjacent to amide bond that will be cleaved. Chymotrypsin cleaves amide bond immediately C-terminal to hydrophobic amino acid residues.
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Serine Nucleophile in Serine Proteases
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The Pre-Steady State in Chymotrypsin-Catalyzed Hydrolysis of p-Nitrophenyl Acetate
H2O k1 E + S ES EP2 E + P2 k-1 k k3 vo = kcat[E]t[S]/(KM + [S]) Steady-state velocity, where kcat = k2k3/(k2 + k3) KM = KSk3/(k2 + k3) KS = k-1/k1 For chymotrypsin with ester substrates: k2 >> k3 Release of P1 faster than EP2 breaks down to E + P2
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Serine Protease Mechanism
Catalytic triad: Acid-base catalysis Covalent catalysis Proximity/orientation effects Also (not depicted here) - electrostatic catalysis and transition state stabilization
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carboxylic acid,
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The Oxyanion Hole In Serine Proteases
Role of oxyanion hole in serine protease mechanism: Electrostatic catalysis Preferential binding of transition state
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Trypsin/Bovine Pancreatic Trypsin Inhibitor (BPTI) Complex
Trypsin-BPTI complex resembles tetrahedral transition state.
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Transition State in Proline Racemase Reaction and Transition State Analogs
Proline racemase preferentially binds transition state, stabilizing it, and is potently inhibited by transition state analogs.
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RNA-Based Catalysts (Ribozymes)
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Cleavage of a Typical Pre-tRNA by Ribonuclease P
Ribonuclease P is a ribonucleoprotein (RNA- and protein-containing complex), and the catalytic component is RNA. An even more complex example of an RNA- and protein-containing enzyme system is the ribosome. The central catalytic activity of the ribosome (peptide bond formation) is catalyzed by an RNA component. tRNA substrate of ribonuclease P
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Catalysis by the Intervening Sequence in Tetrahymena Preribosomal RNA
RNA by itself without any protein can be catalytic.
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Enzyme Regulation
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Effect of Cooperative Substrate Binding on Enzyme Kinetics
Cooperative enzymes do not obey simple Michaelis-Menten kinetics.
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Effect of Extreme Homoallostery
Homotropic allosteric regulation by substrate: S at one active site affects catalysis of S P at other sites on enzyme complex. Extreme positive cooperativity depicted here [S]c = critical substrate concentration
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Heteroallosteric Control of an Enzyme
(positive allosteric effector) Heterotropic allosteric regulation: non-S effectors modulate catalysis of S P. (negative allosteric effector)
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A Model for Enzyme Regulation: Aspartate Transcarbamoylase (Aspartate Carbamoyltransferase) in Pyrimidine Synthesis
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Aspartate Transcarbamoylase (ATCase)-Catalyzed Reaction
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Feedback Inhibition of ATCase by CTP
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Regulation of ATCase by ATP and CTP
ATP is a positive heterotropic allosteric effector of ATCase, while CTP is a negative heterotropic allosteric effector.
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Detailed Structure of One Catalytic Subunit and Adjacent Regulatory Subunit of ATCase
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Quaternary Structure of ATCase in T State and R State
CTP and ATP bind at regulatory site, but CTP preferentially binds in T state, while ATP preferentially binds R state.
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X-Ray Structure of Aspartate Transcarbamoylase
T State T State “top” view “side” view R State “side” view
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