Enzymology - BMS 23110C Lecture Notes PDF

Enzymology - BMS 23110C Dr. Amel Hamdi Fall Semester 2024 - 2025 The mechanism of enzyme action Define the mechanism of an enzyme-catalyzed reaction Describe catalysis  An enzyme (E) is typically a protein molecule that promotes a reaction of another molecule, its substrate (S). This...

Enzymology - BMS 23110C Dr. Amel Hamdi Fall Semester 2024 - 2025 The mechanism of enzyme action Define the mechanism of an enzyme-catalyzed reaction Describe catalysis  An enzyme (E) is typically a protein molecule that promotes a reaction of another molecule, its substrate (S). This binds to the active site of the enzyme to produce a transition enzyme-substrate complex ES, and to from a product P.  Overall reaction is composed of two elementary reactions in which the substrate forms a complex with the enzyme that subsequently decomposes to products and enzymes How do enzymes work?  To deduce the mechanism of an enzyme-catalyzed reaction, we should determine: The sequence of the enzyme containing complexes as substrate (s) is (are) converted to product (s) The rates at which these complexes are interconverted The structures of these complexes  Kinetic and structural techniques have made major contributions to our understanding of enzyme mechanisms.  Various factors contribute to the enhancement of the rate of reactions  The “Energy profile” for a typical reaction shows that in order to proceed from reactant (s) to product (s) an energy​ barrier (∆G) must be surmounted. Reaction Coordinate (progress of reaction). (A) Uncatalyzed (B) Catalyzed (C) Catalyzed with discrete intermediates (transition states) In order to speed up the rate of a reaction at constant temperature, the value of ∆G must be reduced  Enzymes  Enzymes reduce the free energy of activation of the reactions they catalyze  Transition state: intermediate formed between the initial chemical reactant and the product  For substrate (reactant) to become product (catalyzed or not), the substrate must pass through the transition state  Stabilization of transition state is the mechanism of enzyme action The highest point of the energy profile designated the transition state of the reaction  Example of Carbonic anhydrase, which is found within red blood cells, catalyzes a reaction converting CO2 and water into carbonic acid https://www.youtube.com/watch?v=ie_7Y7HJlps  The function of a catalyst is to provide an alternative reaction pathway so that a lowered energy barrier has to be surmounted https://www.youtube.com/watch?v=m_9bpZep1QM Various factors contribute to the enhancement of the rate of reactions: Proximity and orientation effects Acid-base catalysis Covalent catalysis Changes in environment Proximity and orientation effects:  The higher the concentration of enzymes and substrates, the more frequently they will encounter one another  It seems obvious that an enzyme could increase the rate of a reaction involving more than one substrate by binding the substrates at adjacent sites and therefore bringing them into close proximity with each other. Proximity and orientation effects:  A close proximity between a substrate and an enzyme active site does not mean that a catalysis reaction will occur. The enzyme must guide or steer the substrate into the active site in a specific orientation to make the reaction actually occur, which is called orientation. Proximity effects and orientation effects on reaction rates.  Acid-base catalysis:  Anything that can stabilize the charges on the intermediate and hence the developing charges in the transition states will lower the energy of the transition state and catalyze the reaction.  Many reactions of the type catalyzed by enzymes are known to be catalyzed by acids and / or bases.  The acid is the proton (hydrogen ion, H+) donor and the base is the proton acceptor. Typical reactions catalyzed by proton transfer are esterifications and aldol reactions Covalent Catalysis (intermediate formation):  Catalysis which involves substrates forming transient covalent bond with the residues present in the active site is referred to as covalent catalysis  If the catalysis involves participation of small organic molecules, co-factors and amino-acids side chains from the enzyme, the catalysis is referred to lock and key model  If the catalysis involves water molecules for proton donation or acceptance, the catalysis is referred to acid base catalysis Changes in environment: The rates of many organic reactions are highly sensitive to the nature of the solvents in which they occur. Strain or distortion: The bonds in a substrate may be distorted on binding to the appropriate enzyme. This would speed up the reaction if the distortion (or strain) lowered the free energy of activation by making the geometry and electronic structure of the substrate more closely resemble to that of the postulated transition state. The catalytic cycle of an enzyme The target substrate molecules bind to active site of the enzyme transforming into products through a series of steps known as the ____________ a) enzyme kinetics b) enzymatic mechanism c) chemical kinetics d) zero order reaction kinetics If the catalysis involves participation of small organic molecules, cofactors, and amino-acid side chains from the enzyme; it is termed as ____________ a) specific acid base catalysis b) general acid base catalysis c) substrate collision theory d) lock and key model ________________ involves substrates forming transient covalent bond with the residues present in the active site a) Covalent catalysis b) Specific acid-base catalysis c) General acid-base catalysis d) Substrate catalysis