Enzymes

Enzymes: Nature's Catalysts

Definition:

  • Enzymes are biological molecules (proteins) that act as catalysts to facilitate and accelerate chemical reactions in living organisms. They play a crucial role in metabolic pathways, allowing cells to carry out essential functions.

Key Characteristics:

  1. Catalytic Activity:

    • Enzymes increase the rate of chemical reactions without being consumed in the process. They lower the activation energy required for reactions to occur, making them occur more rapidly.
  2. Specificity:

    • Enzymes are highly specific, recognizing and binding to specific substrates (reactant molecules). The specificity is due to the unique shape of the enzyme's active site, which fits the substrate molecules.
  3. Substrate and Product:

    • Substrates bind to the enzyme's active site, where the enzyme catalyzes the conversion of substrates into products. The enzyme-substrate complex is a temporary intermediate state in the reaction.
  4. Lock and Key Model:

    • The lock and key model illustrates the specificity of enzymes. The active site of the enzyme is like a lock, and the substrate is like a key. Only the correctly shaped key (substrate) fits into the lock (active site).
  5. Induced Fit Model:

    • The induced fit model suggests that the active site of the enzyme can change its shape slightly to accommodate the substrate more effectively. The enzyme's active site modifies its shape to better fit the substrate, enhancing catalysis.

Enzyme Naming:

  • Enzymes are usually named by adding the suffix "-ase" to the substrate they act upon or the type of reaction they catalyze.
    • Example: Lactase acts on lactose, protease breaks down proteins, and amylase breaks down carbohydrates.

Working of Enzymes

Enzymes are biological catalysts that facilitate and accelerate chemical reactions in living organisms. They do so by lowering the activation energy required for a reaction to occur. The working of enzymes involves several key steps:

1. Substrate Recognition:

  • Enzymes are highly specific and recognize specific molecules called substrates. The substrate is the reactant that will be transformed by the enzyme.
  • The specificity of enzymes is due to the unique shape of their active site, a region where the substrate binds. The active site fits the substrate like a lock and key.

2. Formation of the Enzyme-Substrate Complex:

  • When the substrate encounters the enzyme, it binds to the enzyme's active site. This binding forms the enzyme-substrate complex.

3. Lowering Activation Energy:

  • Enzymes work by stabilizing the transition state of a reaction. The transition state is the point at which the substrate molecules are in an unstable, high-energy state and ready to proceed to the products.
  • Enzymes facilitate this process by providing an alternative reaction pathway that has a lower activation energy. This lowers the energy barrier, making it easier for the reaction to occur.

 

 

Enzymes allow activation energies to be lowered. | Learn Science ...

4. Catalyzing the Reaction:

  • Enzymes can catalyze various types of reactions, such as breaking down or building up molecules, rearranging chemical bonds, or transferring functional groups.
  • During the reaction, the enzyme holds the substrate in a position that allows the reaction to occur more rapidly. It may involve the enzyme stabilizing intermediate reaction states.

5. Product Formation:

  • As the enzyme catalyzes the reaction, the substrate is converted into one or more products.
  • The products have lower energy levels than the substrate, and they are released from the enzyme's active site.

6. Enzyme Regeneration:

  • After the reaction is complete, the enzyme is not consumed. It is free to bind with new substrate molecules and catalyze additional reactions.
  • Enzymes can operate in a continuous cycle, which makes them highly efficient catalysts.

 

 

 

Factor Affecting Enzyme Activity

Enzyme activity is influenced by various factors that can either enhance or inhibit the catalytic function of enzymes. Understanding these factors is essential for controlling and optimizing enzymatic reactions. The main factors affecting enzyme activity include:

  1. Temperature:

    • Enzymes have an optimal temperature at which they function most efficiently. This temperature is often near the normal physiological temperature for the organism (e.g., around 37°C for many human enzymes).
    • At temperatures below the optimal range, enzyme activity decreases because the molecules move more slowly and have less kinetic energy. At higher temperatures, enzymes can denature, losing their shape and activity.
  2. pH (Hydrogen Ion Concentration):

    • Enzymes also have an optimal pH at which they operate most effectively. Changes in pH can alter the enzyme's shape and affect its activity.
    • Extremes of pH (either highly acidic or highly alkaline conditions) can denature enzymes and render them inactive.
  3. Substrate Concentration:

    • Increasing the concentration of substrate molecules initially increases the rate of the enzymatic reaction, as more substrate molecules are available to bind to enzyme active sites.
    • However, once all the enzyme's active sites are occupied (reached saturation), further increases in substrate concentration do not affect the reaction rate. At this point, the enzyme is working at its maximum velocity(Vmax).
  4. Enzyme Concentration:

    • The rate of an enzymatic reaction is directly proportional to the enzyme concentration, assuming that substrate and other factors are not limiting. More enzymes mean more available active sites for substrate binding.
  5. Cofactors and Coenzymes:

    • Many enzymes require cofactors, which are inorganic ions or non-protein molecules, to function properly. For example, metal ions like magnesium (Mg2+) are essential cofactors for certain enzymes.
    • Coenzymes, which are organic molecules (e.g., vitamins), can also assist enzymes in catalyzing reactions.
  6. Inhibitors:

    • Enzyme inhibition is a regulatory mechanism in which the activity of an enzyme is reduced or completely blocked by specific molecules called inhibitors. There are two main types of enzyme inhibition: competitive inhibition and non-competitive inhibition. Here are examples of both types:

      1. Competitive Inhibition:

      • In competitive inhibition, the inhibitor molecule competes with the substrate for binding to the enzyme's active site. When the inhibitor is bound to the active site, the substrate cannot bind, and the reaction is inhibited.

      Example: Malonate Inhibition of Succinate Dehydrogenase

      • Succinate dehydrogenase is an enzyme involved in the citric acid cycle (Krebs cycle) responsible for the oxidation of succinate to fumarate.
      • Malonate is a competitive inhibitor of succinate dehydrogenase. It structurally resembles succinate and can bind to the enzyme's active site.
      • When malonate is present, it competes with succinate for the active site. If malonate binds to the enzyme, succinate cannot bind and the reaction is inhibited.
      • This inhibition is used in biochemical research to study the citric acid cycle and the regulation of metabolic pathways.

      2. Non-Competitive Inhibition:

      • In non-competitive inhibition, the inhibitor binds to a site on the enzyme other than the active site (allosteric site). This binding changes the enzyme's shape and reduces its catalytic activity. Non-competitive inhibitors do not compete with the substrate for the active site.

      Example: Cyanide Inhibition of Cytochrome c Oxidase

      • Cytochrome c oxidase is a crucial enzyme in the electron transport chain involved in cellular respiration.
      • Cyanide (CN-) is a non-competitive inhibitor of cytochrome c oxidase. It binds to a specific site on the enzyme.
      • When cyanide is bound to the enzyme, it changes the enzyme's shape, blocking its ability to transfer electrons during the respiratory chain. This disrupts the electron transport and ATP synthesis.
      • Cyanide poisoning is a well-known example of non-competitive enzyme inhibition. It interferes with the body's ability to use oxygen, which can be fatal.
  7. Activation Energy: Enzymes work by lowering the activation energy of a reaction. Factors that affect the energy required for the transition state, such as the enzyme's stability and substrate positioning, impact enzyme activity.

  8. Enzyme Kinetics:

    • The Michaelis-Menten equation and related enzyme kinetics models describe the relationship between substrate concentration and enzyme activity. These models help quantify enzyme-substrate interactions and reaction rates.

 

 

Classification and Nomenclature of Enzyme

Enzymes are classified and named according to a systematic nomenclature that reflects their functions and substrate specificity. The classification and naming of enzymes follow specific guidelines set by the International Union of Biochemistry and Molecular Biology (IUBMB). Enzymes are generally categorized based on their functions and the reactions they catalyze. Here's an overview of the enzyme classification and nomenclature:

1. Enzyme Classification (Based on Function):

Enzymes are categorized into six main classes based on the type of chemical reaction they catalyze:

  1. Oxidoreductases: These enzymes catalyze oxidation-reduction (redox) reactions, involving the transfer of electrons between molecules. Examples include dehydrogenases and oxidases.

  2. Transferases: Transferases catalyze the transfer of functional groups, such as a methyl or phosphate group, from one molecule to another. Examples include kinases and methyltransferases.

  3. Hydrolases: Hydrolases catalyze the hydrolysis (breakdown) of substrates by adding water molecules. Examples include lipases and proteases.

  4. Lyases: Lyases catalyze the removal of specific groups from a substrate, leading to the formation of double bonds or the addition of groups to a double bond. Examples include decarboxylases and synthases.

  5. Isomerases: Isomerases catalyze the rearrangement of atoms within a molecule, converting it into an isomer with the same molecular formula but different structural arrangement. Examples include epimerases and mutases.

  6. Ligases: Ligases catalyze the joining of two molecules through the formation of a covalent bond. They are also known as synthetases or synthases. Examples include DNA ligase and RNA ligase.

2. Enzyme Nomenclature:

Enzymes are named following the recommendations of the IUBMB. The names are typically formed by combining the name of the substrate or type of reaction with the suffix "-ase." The name reflects the enzyme's function and, to some extent, its substrate. For example:

  • Enzyme: Lactase

    • Function: Catalyzes the hydrolysis of lactose (a sugar found in milk) into glucose and galactose.
    • Suffix: "-ase" denotes that it is an enzyme.
  • Enzyme: DNA polymerase

    • Function: Catalyzes the synthesis of DNA by adding nucleotide units to a growing DNA chain.
    • Suffix: "-ase" denotes that it is an enzyme.
  • Enzyme: Superoxide dismutase

    • Function: Catalyzes the dismutation of superoxide radicals into molecular oxygen and hydrogen peroxide.
    • Suffix: "-ase" denotes that it is an enzyme.

In addition to the systematic name, enzymes may also have common names that are widely recognized, especially for frequently studied enzymes.

 

Co-factor

A cofactor is a non-protein chemical compound or ion that is required for the activity of an enzyme. Cofactors play an essential role in enzyme function by assisting enzymes in catalyzing specific chemical reactions. Cofactors can be broadly categorized into two main types: inorganic cofactors and organic cofactors, also known as coenzymes.

  1. Inorganic Cofactors:

    • Inorganic cofactors are typically metal ions that are required for the activation of certain enzymes. These metal ions may act as Lewis acids, helping to facilitate enzymatic reactions by stabilizing reaction intermediates and participating in electron transfer processes.
    • Examples of inorganic cofactors include:
      • Magnesium ions (Mg²+): These ions are essential for the activity of many enzymes, particularly those involved in ATP hydrolysis and nucleic acid metabolism.
      • Zinc ions (Zn²+): Zinc is a cofactor for a wide range of enzymes, including those involved in DNA replication and protein digestion.
      • Iron ions (Fe²+ and Fe³+): Iron ions are crucial for enzymes involved in electron transport and oxygen binding, such as cytochrome c and hemoglobin.
  2. Organic Cofactors (Coenzymes):

    • Organic cofactors, often referred to as coenzymes, are small organic molecules that are required for the function of certain enzymes. Coenzymes participate in the enzyme's catalytic mechanism by serving as carriers of specific functional groups or electrons.
    • Examples of coenzymes include:
      • NAD+ (Nicotinamide adenine dinucleotide): NAD+ is a coenzyme involved in redox reactions. It can accept and carry electrons during various metabolic processes.
      • FAD (Flavin adenine dinucleotide): FAD is another coenzyme that plays a role in redox reactions, shuttling electrons in a manner similar to NAD+.
      • Coenzyme A (CoA): CoA plays a critical role in fatty acid metabolism, serving as a carrier for acetyl groups.

Cofactors, both inorganic and organic, are indispensable for enzyme activity. They expand the versatility and efficiency of enzymes, enabling them to catalyze a wide range of biochemical reactions. Cofactors are often tightly bound to the enzyme's active site or directly interact with the enzyme during the catalytic process, and their presence is essential for the enzyme to function properly.