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Enzymes

An enzyme is a biological catalyst that accelerates chemical reactions in living organisms by lowering activation energy. It is highly specific to its substrates and operates under optimal conditions of temperature and pH.

Key Features of Enzymes:

Specificity: Each enzyme typically acts on a specific substrate.
Catalytic Efficiency: Enzymes greatly increase the reaction rate.
Optimal Conditions: They function best within specific temperature and pH ranges.
Reusability: Enzymes are not consumed in reactions and can be used repeatedly.
Regulation: Enzyme activity can be regulated by inhibitors or activators.
Saturation: Enzyme activity reaches a maximum rate when substrate concentration is high.
Denaturation: Extreme temperatures or pH levels can denature enzymes, losing their functionality.

Enzyme Classification

Understanding the Six Major Classes and Their Functions

Enzymes are systematically classified based on the reactions they catalyze. The International Union of Biochemistry and Molecular Biology (IUBMB) has established a comprehensive classification system, dividing enzymes into six major classes, each with specific subclasses. This system assigns each enzyme a unique Enzyme Commission (EC) number, reflecting its catalytic activity. (PubMed)

The six primary classes of enzymes are:

1. Oxidoreductases (EC 1):

These enzymes facilitate oxidation-reduction reactions, where electrons are transferred between molecules. An example is lactate dehydrogenase, which converts lactate to pyruvate during cellular respiration.

2. Transferases (EC 2):

Enzymes in this class transfer functional groups (e.g., methyl, phosphate) from one molecule to another. For instance, alanine transaminase transfers an amino group from alanine to α-ketoglutarate, forming pyruvate and glutamate.

3. Hydrolases (EC 3):

These enzymes catalyze the hydrolysis of various bonds, breaking molecules into smaller units using water. Proteases, which break down proteins into peptides or amino acids, are a common example.

4. Lyases (EC 4):

Lyases remove groups from substrates without hydrolysis, often forming double bonds or adding groups to double bonds. Adenylate cyclase, which converts ATP to cyclic AMP, is an example.

5. Isomerases (EC 5):

This class includes enzymes that catalyze the rearrangement of atoms within a molecule, converting it into its isomer. Phosphoglucose isomerase, which converts glucose-6-phosphate to fructose-6-phosphate in glycolysis, exemplifies this class.

6. Ligases (EC 6):

Ligases join two molecules together, typically utilizing energy from ATP hydrolysis. DNA ligase, which connects DNA fragments during replication and repair, is a well-known ligase.

Each enzyme's EC number provides a hierarchical classification:

First digit: Indicates the main class (1-6 as listed above).
Second digit: Specifies the subclass, detailing the type of reaction or the group involved.
Third digit: Denotes the sub-subclass, providing more specific information about the reaction.
Fourth digit: A unique identifier for the specific enzyme within its sub-subclass.

For example, the EC number 2.7.1.1 corresponds to hexokinase:

2: Transferase (main class)
7: Transferring phosphorus-containing groups (subclass)
1: Phosphotransferases with an alcohol group as acceptor (sub-subclass)
1: Specific identifier for hexokinase

How Enzyme Works

To understand the difference between reactions with an enzyme and without an enzyme, let's compare the energy profiles of both scenarios in terms of activation energy.

Source: alamy

1. Without an Enzyme:

In a chemical reaction without an enzyme, the reactants (substrates) need to absorb a considerable amount of energy to reach the transition state (see graph-Black Line), which is a high-energy, unstable configuration. This energy is called the activation energy (Eₐ). Reactions without enzymes often proceed very slowly because the required activation energy is too high, and only a few substrate molecules can reach this transition state at any given time.

2. With an Enzyme:

When an enzyme is involved, it binds to the substrates and stabilizes the transition state (see graph-Orange Line), significantly lowering the activation energy required for the reaction. The enzyme provides an alternative reaction pathway, which means that the energy barrier to reach the transition state is much lower. The enzyme-substrate complex achieves this by utilizing binding energy to position the substrate molecules in the optimal orientation and by applying molecular strain, facilitating the transition to the product.

From the above explanation, it is clear that enzymes work by reducing the activation energy required for a chemical reaction to proceed, making the reaction easier and faster. Activation energy is the energy barrier that reactants must overcome to be transformed into products. By lowering this barrier, enzymes facilitate reactions that would otherwise occur very slowly or not at all under normal physiological conditions.

Concept of Activation Energy:

Activation Energy (Eₐ) is the minimum amount of energy required for a chemical reaction to proceed. In a typical reaction without an enzyme, reactants need to absorb energy to reach a high-energy transition state before converting into products.
With an enzyme, the activation energy is lowered, so less energy is needed to reach this transition state. The enzyme provides an alternative pathway with a lower energy barrier, allowing the reaction to proceed more easily.

Concept of Binding Energy:

Binding Energy refers to the energy released when an enzyme binds to its substrate at the active site. This interaction stabilizes the enzyme-substrate complex and contributes to lowering the activation energy.
The binding energy helps in:
- Aligning substrates properly in the active site (facilitating the correct orientation for the reaction).
- Distorting the substrate into a transition state, lowering the energy required to convert it into the product.
- Reducing entropy by bringing substrates together and keeping them in close proximity, which increases the likelihood of a successful reaction.

Together, the activation energy and binding energy enable enzymes to significantly accelerate biochemical reactions in living organisms.

How Enzyme Function

Understanding how enzymes function is crucial for comprehending their role in facilitating biochemical reactions.

Mechanism of Enzyme Action:

Substrate Binding: Enzymes possess an active site—a specific region where substrates bind. This binding forms an enzyme-substrate complex, positioning the substrate optimally for the reaction. [References]
Catalysis: Once the substrate is bound, the enzyme facilitates its conversion into products through various catalytic strategies, such as:
- - Acid-Base Catalysis: Transfer of protons to stabilize intermediates.
  - Covalent Catalysis: Formation of temporary covalent bonds with the substrate.
  - Metal Ion Catalysis: Utilization of metal ions to stabilize charged intermediates.
  - Proximity and Orientation: Bringing substrates into close proximity and correct orientation to enhance reaction rates.
Product Release: After the reaction, the enzyme releases the product(s) and is free to bind new substrate molecules, repeating the catalytic cycle.

Factors Influencing Enzyme Activity:

Temperature and pH: Each enzyme has an optimal temperature and pH at which it functions most effectively. Deviations can reduce activity or denature the enzyme.
Inhibitors and Activators: Molecules that decrease (inhibitors) or increase (activators) enzyme activity by binding to the enzyme and altering its conformation or availability.
Substrate Concentration: Increasing substrate concentration enhances reaction rate up to a saturation point, beyond which additional substrate doesn't further increase the rate.