S5

) or small organic molecules. Complex organic cofactors synthesized or derived from vitamins are called coenzymes. When a cofactor is tightly bound (sometimes covalently), it is often called a prosthetic group.

and bicarbonate.

) from substrates.

4.4. Regulation of catalytic activity

Cells regulate enzyme activity to adjust metabolic fluxes to physiological needs. Modulators include:

·         Activators that increase activity.

·         Inhibitors that decrease activity.

·         Allosteric effectors that bind regulatory sites and shift enzyme conformation.

·         Covalent modifications (e.g., phosphorylation), which can switch enzymes on/off or tune activity.

·         Changes in enzyme abundance (gene expression, degradation).

Example:

·         • Phosphofructokinase (PFK) is activated by AMP and inhibited by ATP, linking glycolytic flux to cellular energy status.

5. Enzyme Classification 

The International Union of Biochemistry and Molecular Biology (IUBMB) established a systematic classification (EC numbers). Enzymes are grouped into major classes based on the type of reaction catalyzed.

Each enzyme is assigned an EC number with four digits: the first digit indicates the class, followed by subclass, sub-subclass, and a serial identifier for the specific enzyme.

6. The Enzyme Active Site

The active site is a specialized region—often a pocket or cavity—where substrate binding and catalysis occur. Substrate recognition relies mainly on noncovalent interactions (hydrogen bonds, ionic interactions, van der Waals forces, and hydrophobic effects). These interactions are individually weak but collectively strong and highly specific.

The active site is commonly divided into:

·         Binding (recognition) site: ensures shape and chemical complementarity with the substrate.

·         Catalytic site: contains residues and cofactors directly involved in bond breaking/forming.

Types of amino acids contributing to active-site function (functional view):

·         Structural (contributor) residues: help maintain the correct 3D architecture required for ligand binding.

·         Auxiliary residues: allow mobility and local conformational adjustments near the active site.

·         Contact/catalytic residues: directly participate in catalysis (e.g., acid–base chemistry, nucleophilic attack) and interact with key substrate groups.

Many enzymes stabilize the transition state more strongly than the substrate, which is a major reason they lower activation energy.

7. Enzyme–Substrate Interaction Models

Enzymatic catalysis begins with substrate binding to the active site, forming an enzyme–substrate (ES) complex. Several conceptual models describe how enzymes recognize substrates and achieve catalysis.

7.1. Fischer’s lock-and-key model

In this classical model, the active site is considered pre-formed and complementary in shape to the substrate—like a key fitting into a lock. It highlights specificity but does not fully account for protein flexibility.

7.2. Koshland’s induced-fit model

In the induced-fit model, substrate binding triggers conformational changes in the enzyme. These changes optimize interactions and align catalytic groups for the reaction. This model better explains enzyme flexibility and many cases of high specificity.

7.3. Strain (Jencks) model / transition-state stabilization

This perspective emphasizes that binding can distort (strain) the substrate and/or enzyme toward a transition-state-like geometry, reducing the activation energy. The enzyme effectively ‘pays’ some energetic cost through binding energy to facilitate catalysis.