Question

Metallic elements are essential components of many important enzymes operating within our bodies. Carbonic anhydrase, which contains \(\mathrm{Zn}^{2+}\), is responsible for rapidly interconverting dissolved \(\mathrm{CO}_{2}\) and bicarbonate ion, \(\mathrm{HCO}_{3}^{-} .\) The zinc in carbonic anhydrase is coordinated by three nitrogen-containing groups and a water molecule. The enzyme's action depends on the fact that the coordinated water molecule is more acidic than the bulk solvent molecules. Explain this fact in terms of Lewis acid-base theory (Section 16.11).

Short answer

In conclusion, the increased acidity of the coordinated water molecule in carbonic anhydrase can be explained using Lewis acid-base theory. The water molecule donates an electron pair to the Zn2+ ion (a Lewis acid), forming a coordinate covalent bond. This interaction results in the water molecule acquiring a partially positive charge, increasing its tendency to lose a proton (H+) and making it more acidic than bulk solvent water molecules.

Step-by-step solution

Recall the Lewis acid-base theory

According to the Lewis acid-base theory, Lewis acids are electron pair acceptors, and Lewis bases are electron pair donors. In this problem, we will be looking at how the coordinated water molecule's acidity is affected by its interaction with the Zn2+ ion, a Lewis acid.

Understand the interaction between Zn2+ and the water molecule

In carbonic anhydrase, the Zn2+ ion is coordinated by three nitrogen-containing groups and a water molecule. The water molecule acts as a Lewis base by donating an electron pair to the Zn2+ ion, which acts as a Lewis acid by accepting the electron pair. This interaction forms a coordinate covalent bond between the Zn2+ ion and the water molecule.

Analyze the effect of the interaction on the acidity of the water molecule

When the water molecule donates its electron pair to the Zn2+ ion, it is left with a partially positive charge, making it more prone to lose a proton (H+). According to the Brønsted-Lowry acid-base theory, an acid is a proton donor. Therefore, the water molecule coordinated to the Zn2+ ion becomes more acidic than bulk solvent water molecules, which have not donated an electron pair and are not coordinated to a Lewis acid.

Conclusion

In conclusion, the coordinated water molecule in carbonic anhydrase is more acidic than bulk solvent water molecules due to its interaction with the Zn2+ ion. According to Lewis acid-base theory, the water molecule donates an electron pair to the Zn2+ ion (a Lewis acid), forming a coordinate covalent bond. This interaction leads to the water molecule having a partially positive charge, increasing its tendency to lose a proton (H+) and making it more acidic.

Key concepts

Enzymes in Chemistry

Enzymes are biological catalysts predominantly composed of proteins whose action is essential in speeding up the rate of chemical reactions in biological systems. They accomplish this by lowering the activation energy required for a reaction to take place, thus enhancing the rate at which products are formed.

Each enzyme is specific to a particular reaction or group of reactions, much like a lock and key, with the enzyme's active site being the 'lock' and the substrate—the molecule upon which the enzyme acts—being the 'key'. This specificity is due to the unique three-dimensional shape of the enzyme, allowing it to stabilize the transition state more effectively than the substrate alone could.

Zinc, in enzymes such as carbonic anhydrase, plays a critical role by acting as a cofactor—a non-protein chemical compound that is required for the protein's biological activity. These metal ions provide a distinct environment that facilitates the electron shifts during a reaction, which often involves the formation and breakage of covalent bonds.

Zinc in Biochemistry

Within the field of biochemistry, zinc is a vital trace element, intricately involved in various enzymatic functions. It serves as a catalytic, structural, or regulatory cofactor in many enzymes. Zinc stabilizes the molecular structure of enzymes and participates in catalysis through its physical and chemical properties.

As a d-block element, zinc can accept electron pairs from Lewis bases such as nitrogen from amino acids or a water molecule, which participates directly in the catalytic processes. In the case of carbonic anhydrase, zinc's role is to facilitate the conversion of carbon dioxide and water into bicarbonate and protons, which is fundamental to many physiological processes, including respiration and pH regulation.

Furthermore, the interaction with zinc affects the chemical characteristics of the molecules bound to it. For instance, a water molecule coordinated to zinc will have different acid-base properties compared to a free water molecule, a concept explained further by the Lewis acid-base theory.

Coordinate Covalent Bond

A coordinate covalent bond, also known as a dative bond, is a type of covalent bond in which both electrons shared in the bond come from the same atom. In traditional covalent bonds, each atom contributes one electron to the bond. In contrast, in a coordinate bond, a Lewis base donates a pair of electrons to a Lewis acid.

This form of bonding is crucial in biochemistry. For example, the zinc ion in carbonic anhydrase forms a coordinate covalent bond with a water molecule. The water molecule donates a lone pair of electrons to the empty orbitals of the zinc ion, creating a bond that is essential for the enzyme's activity. This type of interaction has far-reaching implications as it greatly impacts the reactivity and acidity of the molecules involved.

Brønsted-Lowry Acid-Base Theory

The Brønsted-Lowry acid-base theory broadens the understanding of acids and bases beyond the original concepts proposed by Lewis. According to this theory, an acid is a substance that can donate a proton (H+), and a base is a substance that can accept a proton.

In the context of the zinc-bound water molecule in carbonic anhydrase, the interaction with the zinc ion increases the water molecule's acidity, making it more prone to donating a proton. From the Brønsted-Lowry perspective, the coordinated water molecule is 'activated' as an acid because the bond with zinc creates a situation where it is more favorable for the water to release a proton. This theory, when combined with the Lewis acid-base concept, provides a comprehensive explanation of the changes in the water molecule’s behavior within the enzyme's active site.