Notes on Enzymology from Dr. Sedoud's Lectures at University of Health Sciences

HEALTH SCIENCES

This document pertains to the field of Health Sciences, specifically focusing on the study of Enzymology within the Faculty of Medicine at the University of Health Sciences under Dr. Sedoud.Z for the academic year 2025/2026.

INTRODUCTION

Enzymology is the study of enzymes, which are biocatalysts facilitating biochemical reactions. Enzymes are proteins that have crucial metabolic roles. Notably, while highly complex chemical reactions in vitro can be challenging, they often proceed easily in vivo due to the catalytic properties of enzymes. Biocatalysts or enzymes allow for rapid and efficient chemical reactions.

1. GENERAL INFORMATION AND DEFINITIONS

1.1 Enzymes

  • Enzymes are characterized as biological catalysts (biocatalysts) crucial for biochemical reactions.
  • Most enzymes are globular (spherical) proteins, and their activity relies on several factors: temperature, pressure, and substrate concentration.
  • Major properties of enzymes include:
    • Catalysts: Speed up chemical reactions without changing the end products and work effectively at low concentrations. They remain unchanged after reactions.
    • Biological origin: Enzymes are primarily produced by cells in the form of proteins, except for ribozymes, which are RNA molecules that possess catalytic activity.
    • Specificity: Enzymes exhibit substrate specificity and are subject to regulatory mechanisms.

1.2 Substrate and Product

  • Substrate: A molecule acted upon by an enzyme to undergo transformation.
  • Product: A molecule resulting from a reaction catalyzed by an enzyme.

1.3 Ligands

  • Ligand: A molecule that reversibly binds to a macromolecule, typically a protein.

1.4 Cofactor

  • Cofactor: A non-protein chemical that assists in enzymatic reactions, involved in substrate transport or communication, and can take forms such as:
    • Ions: e.g., zinc for carbonic anhydrase.
    • Water: A general cofactor in various biochemical reactions.
    • Complex molecules: Synthesized by cells, such as coenzymes.

1.5 Coenzyme

  • A specific type of cofactor essential for enzyme catalysis.
  • Coenzymes can be free or bound (prosthetic groups):
    • Free coenzymes: Bind during the enzymatic reaction and dissociate afterward, usually present in concentrations similar to the substrate.
    • Bound coenzymes: Permanently attached to the enzyme, always catalytically active, and exhibit concentrations equal to that of the enzyme.

1.6 Examples of Coenzymes

Some Coenzymes that transfer specific atoms or groups include:

  • Coenzyme A
  • Flavin adenine dinucleotide (FAD)
  • Nicotinamide adenine dinucleotide (NAD)
  • Pyridoxal phosphate
    etc.

1.7 Apoenzyme and Holoenzyme

  • Apoenzyme: The protein part of an enzyme.
  • Holoenzyme: The complete and catalytically active enzyme formed by the apoenzyme and its cofactor.

2. ENZYME STRUCTURE

2.1 Primary Structure

  • Refers to the linear sequence of amino acids that form the enzyme.

2.2 Secondary Structure

  • Structural motifs formed by amino acids, prominently α-helices and β-sheets.

2.3 Tertiary Structure

  • The overall 3D shape of the enzyme, influenced by interactions among side chains of amino acids, where polar amino acids are located on the outer surface and non-polar ones in a hydrophobic internal zone, particularly the active site.

2.4 Quaternary Structure

  • Involves multiple polypeptide chains (oligomers) associated together, important in regulatory enzymes.

2.5 Active Site

  • The active site is a specific region on the enzyme where substrate binding and catalysis occur, featuring binding sites for substrate recognition and catalytic actions producing products.

2.6 Amino Acid Types in Enzymes

  • Contributing amino acids: Assist in the enzyme's spatial conformation for ligand binding.
  • Auxiliary amino acids: Support the movement of regions near the active site.
  • Contact amino acids: Direct involvement in the enzymatic reaction.

2.7 Enzyme Types

  • Monomeric enzymes: Single subunit (e.g., ribonuclease).
  • Oligomeric enzymes: Multiple subunits (e.g., lactate dehydrogenase).
  • Multi-enzyme complexes: Include several enzymes maintaining substrates bound during product transformation (e.g., pyruvate dehydrogenase).
  • Proenzymes or zymogens: Inactive precursors of enzymes activated by proteolysis (e.g., pepsinogen to pepsin).

3. CHARACTERISTICS OF ENZYMES

3.1 Specificity

  • Enzymes are specific catalysts for particular reactions and substrates. Two types of specificity include:
    • Action specificity: One enzyme catalyzes one type of reaction.
    • Substrate specificity: Can be absolute (single substrate) or broad (similar substrates).

3.2 Efficiency

  • Enzymes significantly lower activation energy, allowing for effective catalysis even at low concentrations. The active site enhances reactant proximity and orientation, lowering the activation energy ( riangle G^#).

3.3 Thermolability

  • Enzymes are sensitive to temperature changes, impacting their structure and catalytic activity, potentially leading to denaturation.

3.4 Regulation

  • Enzymes can undergo regulatory mechanisms to modify their activity, including feedback inhibition and cofactor availability.

3.5 Molecular Variety

  • Isoenzymes: Different structural variations of the same enzyme with distinct physical or binding properties.

4. NOMENCLATURE AND CLASSIFICATION OF ENZYMES

Enzymes possess systematic and common names based on their properties and substrate. Classifications by the Enzyme Commission (EC) are based on the type of reaction catalyzed. The six main classes are:

  1. Oxidoreductases: Catalyze oxidation-reduction reactions.
  2. Transferases: Transfer functional groups between substrates.
  3. Hydrolases: Catalyze hydrolysis reactions.
  4. Lyases: Remove groups or add to substrates without hydrolysis.
  5. Isomerases: Rearrange molecular structure.
  6. Ligases: Join substrates together forming bonds.

5. APPLICATION OF ENZYMOLOGY

5.1 Diagnostic Applications

  • Enzymes can act as diagnostic markers, identifying specific tissues during injury or dysfunction.

5.2 Industrial Applications

  • Assessing food quality, verifying sterilization processes, and synthetic applications in drug creation.

5.3 Therapeutic Applications

  • Application of enzyme inhibitors in therapy (e.g., statins for cholesterol management).

5.4 Analytical Applications

  • Enzymes are key tools in bioanalysis for quantifying biomolecules through various methods (e.g., colorimetric, immunoassays).

5.5 Genetic Applications

  • Enzymes are involved in gene manipulation and modification techniques such as PCR.

6. ENZYMATIC KINETICS

6.1 Definition

  • The study of reaction rates of enzymes and variations under different conditions.

6.2 Reaction Rate

  • The speed of reaction expressed as a change in concentration over time.

6.3 Phases of Enzymatic Reaction

  • Pre-stationary: Initial increase in reaction velocity.
  • Stationary: Stable state where the rate of substrate and product concentrations stabilize.

6.4 Concepts of Velocity

  • Initial Velocity (Vi): The rate of product formation with negligible substrate concentration.

6.5 Enzyme Concentration Effects

  • Initial rate is impacted by enzyme concentration, illustrating saturation points.

7. FACTORS INFLUENCING ENZYMATIC REACTION

7.1 Physicochemical Factors

7.1.1 pH
  • Alters enzyme conformation affecting activity; extreme values can lead to denaturation.
7.1.2 Temperature
  • Temperatures accelerate enzymatic reactions but can damage protein structures if excessive.
7.1.3 Ionic Strength
  • Influences solubility and binding affinity; metal ions can boost enzyme activity.
7.1.4 Radiation Effects
  • Ionizing radiation causes free radical formation, which can negatively affect reactions.

7.2 Chemical Effectors

7.2.1 Inhibitors
  • Two main types:
    • Reversible: Competitive, non-competitive, and non-competitive inhibitors alter reaction rates without permanent changes to the enzyme.
    • Irreversible: Covalently bind to active sites hindering activity permanently.
7.2.2 Activators
  • Enhance enzyme activity, including metal ions and covalent modifications.

8. ALLOSTERIC ENZYMES

8.1 Definitions

  • Allostery: Changes in enzyme activity due to conformational changes upon effector binding at non-active sites.

8.2 Structure of Allosteric Enzymes

  • Typically quaternary proteins with multiple subunits, allowing for cooperative effects in substrate binding.

8.3 Kinetics of Allosteric Enzymes

  • Allosteric enzymes display sigmoidal kinetics differing from traditional Michaelis-Menten kinetics due to cooperative binding of substrates.