Study Notes on Enzymatic Catalysis

Chapter 11: Enzymatic Catalysis

General Properties of Enzymes

  • Enzyme Nomenclature:

    • Enzymes are named by adding ‘-ase’ to the substrate or by using a phrase that describes their catalytic action.

    • Examples:

    • Urease: Catalyzes the hydrolysis of urea.

    • Alcohol dehydrogenase: Catalyzes the oxidation of alcohols to their corresponding aldehydes.

  • Substrate Specificity:

    • Enzymes exhibit a high degree of specificity toward substrates, often achieving this through geometric and electrostatic complementarity.

    • The “lock and key” model describes how specific substrates fit into the active sites of enzymes.

    • Some enzyme-substrate binding pockets undergo conformational changes to adapt to the substrate, known as the “induced fit” model.

  • Cofactors and Coenzymes:

    • Cofactors: Non-protein molecules or ions that assist enzymes. For example, metals like Cu²⁺, Fe³⁺, Zn²⁺.

    • Coenzymes: Organic molecules that serve as cofactors, e.g., NAD⁺, heme, pyridoxal phosphate.

    • Cosubstrates: Temporary enzyme-associated coenzymes.

    • Prosthetic groups: Permanently attached coenzymes.

    • Holoenzyme: An active enzyme-bound cofactor complex.

    • Apoenzyme: An inactive enzyme that lacks its cofactor.

Activation Energy and the Reaction Coordinate

  • The reaction coordinate illustrates the energy changes during a chemical reaction, determined by the activation energy (G^‡)

  • Transition States: High-energy states that reactants must overcome to form products.

Catalytic Mechanisms

  • Various mechanisms enable enzymes to perform catalysis:

    • Acid-base catalysis

    • Covalent catalysis

    • Metal ion catalysis

    • Electrostatic catalysis

    • Proximity and orientation effects

    • Preferential binding of the transition state complex

Enzymes: The Workers of the Cell

  • Enzymes are proteins that facilitate biochemical reactions, acting as catalysts to increase reaction rates greatly compared to uncatalyzed reactions, enhancing them between $10^6$ to $10^{12}$ times.

General Properties of Enzymes

  • Higher Reaction Rates:

    • Enzymes accelerate reactions significantly compared to both uncatalyzed reactions and chemical catalysts.

  • Milder Reaction Conditions:

    • Operate under near-neutral pH, at temperatures below $100^{ ext{o}}C$, and at atmospheric pressure, contrasting with chemical reactions that often require extreme conditions.

  • Greater Reaction Specificity:

    • Enzymes generally have high specificity for substrates, leading to minimal side product formation.

  • Capacity for Regulation:

    • Enzymatic activity can be modulated through allosteric control, covalent modifications, and variations in protein expression.

Catalytic Power of Some Enzymes


  • Table 11-1: Catalytic Power of Some Enzymes

    Enzyme

    Nonenzymatic Reaction Rate (s⁻¹)

    Enzymatic Reaction Rate (s⁻¹)

    Rate Enhancement


    Carbonic anhydrase

    1.3imes10−11.3 imes 10^{-1}

    1imes1061 imes 10^6

    7.7imes1067.7 imes 10^{6}


    Chorismate mutase

    2.6imes10−52.6 imes 10^{-5}

    5050

    1.9imes1061.9 imes 10^{6}


    Triose phosphate isomerase

    4.3imes10−64.3 imes 10^{-6}

    43004300

    1.0imes1091.0 imes 10^{9}


    Carboxypeptidase A

    3.0imes10−93.0 imes 10^{-9}

    578578

    1.9imes10111.9 imes 10^{11}


    AMP nucleosidase

    1.0imes10−111.0 imes 10^{-11}

    6060

    6.0imes10126.0 imes 10^{12}


    Staphylococcal nuclease

    1.7imes10−131.7 imes 10^{-13}

    9595

    5.6imes10145.6 imes 10^{14}

    Enzyme-Specific Interactions

    • Enzymes exhibit stereospecificity, as demonstrated by the action of aconitase in the citric acid cycle, converting pro-chiral citrate into chiral isocitrate through selective binding of enantiomers.

    Enzyme Stereospecificity

    • Aconitase:

      • Converts pro-chiral citrate to the chiral product isocitrate, illustrating selective binding and transforming geometries in enzyme catalysis.

    • Preferentially binds a single enantiomer and ensures stereospecific reactions occur even if the substrate lacks chirality.

    Catalytic Mechanisms In Detail

    Acid-Base Catalysis

    • Enzymes catalyze reactions through proton transfer mechanisms, facilitating the registration of reactants and products.

    • General Acid-Base Catalysis:

      • The role of amino acids such as Asp, Glu, Lys, His, Cys, and Tyr plays a pivotal role where the ionization state affects catalytic efficacy.

    Covalent Catalysis

    • Involves the transient formation of a covalent bond between the enzyme and substrate to facilitate reaction progression.

    • Example: The decarboxylation of acetoacetate by primary amines where nucleophilic attack leads to Schiff base (imine bound) formation.

    • Covalent catalysis can be described in three steps:

      1. Nucleophilic reaction forming a covalent bond.

      2. Withdrawal of electrons from the reaction center, making the catalyst electrophilic.

      3. Elimination of the catalyst, followed by the reverse of step one, ensuring optimal nucleophile and leaving group qualities.

    Metal Ion Catalysis

    • Metal ions like Zn²⁺ serve as vital components in enzymatic activity, for instance, human carbonic anhydrase.

      • Metal ions stabilize negative charges, orient substrates, and mediate oxidation-reduction reactions, enhancing catalytic efficiency.

    • In carbonic anhydrase, the enzyme facilitates the conversion between CO₂ and HCO₃⁻ through water molecules and stabilized hydroxide ions for nucleophilic attacks.

    Electrostatic Catalysis

    • The active site environment often excludes bulk water, enhancing electrostatic interactions crucial for catalysis.

      • The charge distribution in these active sites preferentially stabilizes transition states, hastening reaction progress and lowering activation energy.

    Catalysis through Proximity and Orientation Effects

    • Enzymes position substrates closely together with correct orientation essential for reaction occurrence, significantly increasing effective collision rates.

    • This spatial arrangement amplifies reaction kinetics, providing a significant rate enhancement, with movement restrictions earning up to $10^7$ times the rate of free solution systems.

    Transition State Stabilization

    • Enzymes stabilize the transition states of reactions more effectively than that of reactants or products, leading to higher reaction rates.

      • This concept forms the basis for understanding how transition-state analogs can act as competitive inhibitors for drug design.

    Transition State Analogs as Competitive Inhibitors

    • A theory posits that enzymes have a greater affinity for transition states over substrates, encouraging drug designs that mimic these states.