Visual Animations: Cofactor, vitamins, coenzymes, prosthetic groups, and apoenzymes.

Visual Notes: Cofactors & Coenzymes

Biochemical Coordination, Mechanisms, and Vitamin Precursors

1. The Enzymatic Unit: Apoenzyme and Holoenzyme

Enzymes are highly specific catalysts, but amino acid side chains are chemically limited. To facilitate complex reactions, the protein framework (Apoenzyme) recruits non-protein molecules or metal ions called Cofactors to form the active Holoenzyme.

Apoenzyme (Inactive) + Cofactor ⇌ Holoenzyme (Active)

Figure 1: Mechanism of Holoenzyme Assembly

2. Inorganic Cofactors: Transition Metal Coordination

Transition metals are stabilized within the active site via coordinate covalent bonds donated by the lone pairs of specific amino acid residues.

Example: The Zinc Finger Motif (Cys₂His₂)

The Zn²⁺ ion is coordinated in a strict tetrahedral geometry by the sulfur atoms of two Cysteine residues and the sp² hybridized nitrogen atoms of two Histidine imidazole rings.

Figure 2: Zinc Coordination Sphere

2D Textbook Schematic: Tetrahedral coordination of Zn²⁺ by Cysteine (Thiolate) and Histidine (Imidazole).

3D Crystallographic Model: Zn²⁺ (cyan) secured by the Cys₂His₂ tetrad (PDB: 1ZNF).

3. Organic Cofactors: Prosthetic Groups vs. Coenzymes

Prosthetic Groups: The Permanent Macrocycle

A prosthetic group is tightly bound, making it a permanent part of the enzyme. Heme (Iron Protoporphyrin IX) holds an Fe²⁺/Fe³⁺ ion in the equatorial plane of a porphyrin ring.

Figure 3: Structure of the Heme Prosthetic Group

2D Textbook Schematic: Core Porphyrin ring showing the square planar coordination of Fe²⁺ by four pyrrole nitrogens.

3D Conformation: The planar porphyrin ring (PDB: 1HRC).

Coenzymes (Cosubstrates): The Transient Carriers

Coenzymes bind transiently. They physically carry chemical groups between enzyme systems. Nicotinamide Adenine Dinucleotide (NAD⁺) shuttles hydride (H⁻) ions.

Figure 4: NAD⁺ as a Transient Hydride Carrier

4. Vitamins: The Dietary Precursors

Mammalian metabolism cannot synthesize complex coenzymes de novo. Precursors must be acquired via diet as Vitamins.

Figure 5: Vitamin to Coenzyme Synthesis Pathways

graph LR subgraph "Pathway 1: Niacin" V1["Vitamin B3
(Niacin)"] --> M1["Adenylation"] --> C1["NAD\u207A / NADP\u207A"] --> R1["Hydride (H\u207B) Transfer"] end subgraph "Pathway 2: Pantothenic Acid" V2["Vitamin B5
(Pantothenate)"] --> M2["Cysteine Addition"] --> C2["Coenzyme A
(CoA-SH)"] --> R2["Acyl Group Carrier"] end subgraph "Pathway 3: Riboflavin" V3["Vitamin B2
(Riboflavin)"] --> M3["FAD Synthetase"] --> C3["FAD / FMN"] --> R3["Electron Transfers"] end style V1 fill:#fff3cd,stroke:#856404 style V2 fill:#fff3cd,stroke:#856404 style V3 fill:#fff3cd,stroke:#856404 style C1 fill:#d4edda,stroke:#155724 style C2 fill:#d4edda,stroke:#155724 style C3 fill:#d4edda,stroke:#155724