Enzymes

Enzymes

Definition and Characteristics of Enzymes

  • Enzymes are biological catalysts produced by living cells that catalyze various reactions in the body.
  • Nature of Enzymes:
    • Enzymes are primarily composed of proteins.
    • They exhibit specificity in their action, meaning each enzyme can catalyze only one type of reaction.
    • Enzymes function in very small quantities.
    • They lose catalytic activity when exposed to heat, strong acids, bases, or organic solvents.

Functions of Enzymes

  • Enzymes facilitate metabolic pathways within the body.
  • Deficiency of specific enzymes can lead to inborn errors of metabolism.
  • Most enzymes are produced by the cells of specific tissues and function within those cells; these are referred to as intracellular enzymes (e.g., enzymes involved in glycolysis, TCA cycle, and fatty acid synthesis).
  • Conversely, some enzymes are produced in a particular tissue and released into other tissues, known as extracellular enzymes (e.g., proteolytic enzymes like Trypsin and Chymotrypsin from the gastrointestinal tract).

Mechanism of Enzymatic Reactions

  • Enzymes bind with their specific substrates to form an enzyme-substrate complex.
  • This complex facilitates the conversion of substrates into products, allowing the enzymes to remain unchanged after the reaction.
  • Enzymatic reactions are initiated from substrate molecules that convert to products.
  • Enzymes are necessary for nearly all chemical reactions within biological cells.

Catalytic Activity

  • Similar to all catalysts, enzymes lower the activation energy required for reactions, thereby increasing the rate of the reactions.
  • As a result, enzyme-catalyzed reactions produce products quicker and reach equilibrium states more rapidly.
  • The reaction rates of enzymes are often millions of times faster compared to non-catalyzed reactions.
  • Enzymes are not consumed during the reactions they facilitate, and they do not alter the reaction equilibrium.
  • Enzymes are known to catalyze around 4,000 biochemical reactions.

Ribozymes

  • Certain RNA molecules function as catalysts, known as ribozymes. An important example is found in ribosomal components.

Factors Affecting Enzyme Activity

  • Enzyme activity can be modulated by various molecules:
    • Inhibitors: Decrease enzyme activity.
    • Activators: Increase enzyme activity.
    • Many drugs and poisons act as enzyme inhibitors.
  • Environmental factors affecting enzyme activity include:
    • Temperature
    • pH
    • Concentration of substrates

Applications of Enzymes

  • Enzymes have commercial uses, such as:
    • Synthesis of antibiotics.
    • Ingredients in household products:
    • Biological washing powders utilize enzymes to break down protein or fat stains on clothes.
    • Meat tenderizers utilize enzymes to decompose proteins into smaller molecules, enhancing tenderness.

Historical Perspective of Enzymes

  • In 1926, James B. Sumner demonstrated that urease is a pure protein and crystallized it.
  • Sumner also crystallized catalase in 1937.
  • The work on digestive enzymes (pepsin, trypsin, chymotrypsin) by Northrop and Stanley in 1930s led to their Nobel Prize in Chemistry in 1946.

Chemical Nature of Enzymes

Basic Composition

  • Primarily, enzymes are proteins.
  • Some enzymes require additional organic or inorganic substances and are classified as conjugated proteins.
  • Such enzymes are termed holoenzymes, where:
    • The protein part is called apoenzyme.
    • The non-protein component is called prosthetic group.

Role of Cofactors

  • Certain apoenzymes require the presence of metal ions (e.g., Mg extsuperscript{2+} for Hexokinase, Zn extsuperscript{2+} for carboxypeptidase) termed cofactors.
  • If a metal ion is integral to the structure of the enzyme, such enzymes are referred to as metalloenzymes.

Enzyme Activation Processes

Forms of Activation

  1. Proteolytic Activation:

    • Example: Pepsinogen (inactive) + HCl → Pepsin (active)
    • Other examples include transformations from fibrinogen to thrombin and angiotensinogen.

  2. Cofactors:

    • Inorganic components aiding substrate binding at the active site; examples include Zn extsuperscript{2+}, Ca extsuperscript{2+}, Mg extsuperscript{2+}, Cu extsuperscript{2+}.
    • Specific examples include:
      • Zn extsuperscript{2+} in carbonic anhydrase and alcohol dehydrogenase.
      • Cu extsuperscript{2+} in cytochrome oxidase.
      • K extsuperscript{+} and Mg extsuperscript{2+} in pyruvate phosphokinase.

  3. Coenzymes:

    • Small organic molecules that accept and transfer electrons between enzymatic reactions (e.g., NAD extsuperscript{+}) and often come from vitamins or nucleotide derivatives.
    • Apoenzymes are inactive without their cofactors, while holoenzymes are complete and catalytically active.

Structure of the Active Site

  • The active site is a specific region in the enzyme where substrate molecules attach and undergo reaction, usually located in a three-dimensional groove or pocket composed of various amino acid residues, crucial for substrate recognition.
  • Active sites are reusable after the reaction has occurred.

Enzyme Action Mechanisms

  • Enzymes lower the Gibbs free energy of activation (ΔG‡) needed by stabilizing the transition state.
  • Transition state stabilization reduces the energy required for reactants to transition into products.

Models of Enzyme-Substrate Interaction

  1. Lock and Key Model:

    • Proposed by Emil Fischer in 1894, suggesting that enzymes and substrates have specific complementary shapes that fit perfectly.
    • This model explains specificity but does not adequately explain how enzymes stabilize the transition state.

  2. Induced Fit Model:

    • The preferred model, suggesting initial weak interactions lead to conformational changes in the enzyme that strengthen binding to the substrate.

Michaelis-Menten Kinetics

  • Enzyme-catalyzed reactions saturate, illustrating that the rate of catalysis does not linearly respond to increased substrate concentrations.
  • As substrate concentration ext{[S]} increases, the rate of reaction (v) initially rises until it reaches a maximum rate (Vmax) when the enzyme is saturated.
  • The Michaelis constant (Km) is defined as the substrate concentration at which the reaction rate is half of Vmax.

Enzyme Classification

  • The International Union of Biochemistry (IUB) categorizes enzymes into six groups:
    1. Oxidoreductases (EC1): Catalyze oxidation-reduction reactions.
    • Examples: Lactate dehydrogenase, Glyceraldehyde-3-phosphate dehydrogenase.
    1. Transferases (EC2): Transfer groups from one substrate to another.
    • Example: Alanine aminotransferase.
    1. Hydrolases (EC3): Hydrolyze substrates by adding water.
    • Examples: Glucose 6-phosphatase, Amylase, Pepsin.
    1. Lyases (EC4): Remove small molecules from large substrates without adding water.
    • Examples: Fumarase, Enolase.
    1. Isomerases (EC5): Catalyze isomerization processes.
    2. Ligases (EC6): Join two substrates, using energy.
    • Example: Glutamine synthetase.

Enzyme Commission Number (EC Number)

  • An enzyme's numerical classification is termed the EC number, correlating with the reaction type it catalyzes.
  • Each EC number consists of the prefix "EC" followed by four numerical digits, indicating progressively specific classifications.
  • Example: The enzyme aminopeptidase with the code "EC 3.4.11.4" indicates its classification as a hydrolase acting on peptide bonds.

Factors Influencing Enzyme Activity

  1. Effect of pH:
    • Each enzyme functions optimally at a specific pH; for instance:
      • Pepsin: Optimum pH 1-2
      • Amylase: Optimum pH 6.8
      • Alkaline Phosphatase (ALP): Optimum pH 9.0
      • Acid Phosphatase (ACP): Optimum pH 5.0
  2. Effect of Temperature:
    • The optimal temperature for enzyme function is typically around 37°C (body temperature). Activity doubles with every 10°C increase until maximum velocity is reached; activity declines thereafter, denaturing at 100°C.
  3. Effect of Substrate Concentration:
    • At low substrate concentration, enzyme activity is proportional to substrate availability, but increases in substrate lead to saturation at high concentrations where activity plateaus.
  4. Effect of Enzyme Concentration:
    • The rate of reaction is directly proportional to enzyme concentration.
  5. Enzyme Activators and Inhibitors: - Activity can also be modulated by activators, which enhance activity, and inhibitors, which decrease activity.

Enzyme Inhibitors

Classification of Inhibitors

  1. Reversible Inhibitors:

    • Bind through non-covalent interactions (H-bonds, hydrophilic, and ionic interactions) without undergoing reactions. Can be removed via dilution/dialysis.
    • Types:
      • Competitive Inhibition:
      • Inhibitor competes with the substrate for the active site on the enzyme, increasing Km but Vmax remains constant.
      • Example: Malonate competes with succinate for succinate dehydrogenase.
      • Non-competitive Inhibition:
      • Inhibitor binds to the enzyme irrespective of substrate binding and decreases Vmax without impacting Km since substrate binding retains functionality.

  2. Irreversible Inhibitors:

    • Form covalent modifications of the enzyme, rendering the inhibition permanent. Often target specific classes of enzymes without destroying overall protein structure but by altering the active site directly.

Cofactors

  • Cofactors assist in biotransformations and can be organic (e.g., flavin, heme) or inorganic (e.g., metal ions such as Mg extsuperscript{2+}, Cu extsuperscript{+}, Mn extsuperscript{2+}).
  • They may be loosely-bound (coenzymes) or tightly-bound (prosthetic groups).
  • An inactive enzyme without a cofactor is termed an apoenzyme; the complete and functional enzyme with its cofactor is termed a holoenzyme.

Types of Cofactors

  • Organic Cofactors:
    • Small molecules often derived from vitamins, can be loosely or tightly bound.
    • Examples include NAD and coenzyme A, which carry acyl groups.
  • Inorganic Cofactors:
    • Examples such as Mg extsuperscript{2+}, Cu extsuperscript{+}, and various metal ion associations with different enzymes.

Isoenzymes and Allosteric Modulation

Isoenzymes

  • Isoenzymes (or isoforms) differ in amino acid sequences but catalyze the same chemical reactions.
  • They may exhibit different kinetics (e.g., varying Km values) and regulatory properties, while serving identical functions.

Allosteric Modulation

  • Allosteric sites allow non-substrate molecules to bind, causing conformational changes that affect the active site and subsequently the enzyme's reaction rate.
  • Allosteric modulation can either activate or inhibit enzyme activity, representing a common mechanism for enzyme regulation in biological systems.
Definition and Characteristics of Enzymes
  • Enzymes are biological catalysts produced by living cells that catalyze various reactions in the body.
  • Nature of Enzymes:
    • Enzymes are primarily composed of proteins.
    • They exhibit specificity in their action, meaning each enzyme can catalyze only one type of reaction.
    • Enzymes function in very small quantities.
    • They lose catalytic activity when exposed to heat, strong acids, bases, or organic solvents.
Functions of Enzymes
  • Enzymes facilitate metabolic pathways within the body.
  • Deficiency of specific enzymes can lead to inborn errors of metabolism.
  • Most enzymes are produced by the cells of specific tissues and function within those cells; these are referred to as intracellular enzymes (e.g., enzymes involved in glycolysis, TCA cycle, and fatty acid synthesis).
  • Conversely, some enzymes are produced in a particular tissue and released into other tissues, known as extracellular enzymes (e.g., proteolytic enzymes like Trypsin and Chymotrypsin from the gastrointestinal tract).
Mechanism of Enzymatic Reactions
  • Enzymes bind with their specific substrates to form an enzyme-substrate complex.
  • This complex facilitates the conversion of substrates into products, allowing the enzymes to remain unchanged after the reaction.
  • Enzymatic reactions are initiated from substrate molecules that convert to products.
  • Enzymes are necessary for nearly all chemical reactions within biological cells.
Catalytic Activity
  • Similar to all catalysts, enzymes lower the activation energy required for reactions, thereby increasing the rate of the reactions.
  • As a result, enzyme-catalyzed reactions produce products quicker and reach equilibrium states more rapidly.
  • The reaction rates of enzymes are often millions of times faster compared to non-catalyzed reactions.
  • Enzymes are not consumed during the reactions they facilitate, and they do not alter the reaction equilibrium.
  • Enzymes are known to catalyze around 4,000 biochemical reactions.