enzymes 1

Enzymology

  • Professor: Prof. Dr. Esam Abd El-Mohsen Afifi

  • Enzymes are crucial biological catalysts, referred to as the "tools of life."

Enzyme Nomenclature

A. Recommended Names

  • Enzymes generally have names ending in "-ase" derived from substrates (e.g., glucosidase, urease) or actions performed (e.g., lactate dehydrogenase).

  • Some enzymes retain trivial names (e.g., trypsin, pepsin) without relation to substrate or action.

B. Systematic Names

  • Developed by the International Union of Biochemistry and Molecular Biology (IUBMB), enzymes are classified into six major classes.

  • Example: Hexokinase is systematically named ATP: D-hexose 6-phosphotransferase (E.C. 2.7.1.1).

Major Classes of Enzymes

  1. Oxidoreductases

    • Involve oxidation-reduction reactions.

    • Example: Lactate dehydrogenase facilitating the conversion of lactate to pyruvate.

  2. Transferases

    • Transfer functional groups (C-, N-, P-containing).

    • Example: Serine hydroxy methyl transferase.

  3. Hydrolases

    • Cleave bonds with water addition.

    • Example: Urease catalyzes urea to ammonia and carbon dioxide.

  4. Lyases

    • Catalyze bond cleavage without hydrolysis or oxidation.

    • Example: Pyruvate decarboxylase.

  5. Isomerases

    • Catalyze isomerization (geometric and optical).

    • Example: Methylmalonyl CoA isomerization.

  6. Ligases

    • Form bonds between C and O, S, or N atoms with ATP hydrolysis.

    • Example: Pyruvate carboxylase.

Properties of Enzymes

  • Enzymes are:

    • Protein catalysts, except for ribozymes (catalytic RNA).

    • Not consumed or permanently changed by the reaction.

    • Highly efficient (up to 10^8 times faster than non-catalyzed reactions).

    • Specific for substrates and reactions, contributing to selective catalysis.

Active Sites

  • The active site is a 3D region made up of amino acid side chains that provides specificity for substrate binding.

  • Notable models:

    • Lock and Key Model

    • Induced Fit Model

Catalytic Efficiency

  • Enzymes can convert 100-1,000 substrate molecules to product per second, defined as the turnover number (kcat).

Cofactors

  • Cofactors are non-protein molecules aiding enzyme reactions.

    • Organic Cofactors: Non-metal (e.g., coenzymes like NAD+).

    • Inorganic Cofactors: Metal ions (e.g., Zn2+, Fe2+).

Holoenzymes

  • Holoenzymes consist of an apoenzyme and its associated cofactor (inorganic or organic).

    • Coenzyme: Transiently associated organic molecules.

    • Prosthetic Group: Permanently bound organic molecules.

Cell Locations

  • Enzymes may be compartmentalized to optimize conditions for their respective reactions while isolating substrates/products from competing reactions.

Mechanism of Action

1. Thermodynamic Changes

  • Enzymes lower the activation energy barrier, enhancing the reaction velocity.

2. Active Site Processes

  • The active site stabilizes the transition state and provides catalytic groups, facilitating substrate conversion.

Factors Affecting Enzyme Activity

  1. Temperature

    • Reaction velocity peaks at optimal temperature (35-40°C for human enzymes).

  2. pH

    • Optimal pH varies by enzyme (e.g., pepsin at pH 2).

  3. Substrate Concentration

    • Reaction velocity increases until saturation (Vmax).

    • Kinetics can be first-order or zero-order based on substrate concentration relative to Km.

Michaelis-Menten Kinetics

  • Describes the reaction rate based on substrate concentration.

  • Michaelis-Menten Equation:

    • Vo = (Vmax[S]) / (Km + [S]).

  • Km reflects the enzyme's affinity towards its substrate alluding to reaction rates across three substrate concentration conditions.

Enzyme Inhibition

  1. Competitive Inhibition

    • Inhibitor resembles substrate; affects Km but not Vmax.

  2. Noncompetitive Inhibition

    • Inhibitor binds separately; affects Vmax, not Km.

  3. Uncompetitive Inhibition

    • Inhibitor binds to ES complex; lowers both Km and Vmax.

Clinical Application of Enzymes

1. Diagnosis via Plasma Enzyme Activity

  • Functional enzymes: Secreted by living cells (e.g., liver).

  • Non-functional enzymes: Released during cell turnover; increased levels indicate tissue damage (e.g., ALT in liver damage).

2. Isoenzymes

  • Different physical properties due to genetic variance; help localize tissue damage.

Key Enzymes in Myocardial Infarction

  • Troponin T/I and CK-MB markers critical for diagnosing myocardial infarction (MI).

  • Timing of elevation after MI: Troponin T/I appears after 4-6 hours; CK-MB within 4-8 hours.

High-Sensitivity Cardiac Troponin Test

  • Detects low troponin levels to expedite heart attack diagnosis and rule out coronary artery disease.

Q&A on Enzymology

  • Discusses various concepts including enzyme inhibitors, effects of pH and substrate concentration, and importance of structural properties in enzyme functionality.