Question

(a) Explain the importance of enzymes in biological systems. (b) What chemical transformations are catalyzed (i) by the enzyme catalase, \((i i)\) by nitrogenase? (c) Many enzymes follow this generic reaction mechanism, where \(\mathrm{E}\) is enzyme, \(\mathrm{S}\) is substrate, ES is the enzyme-substrate complex (where the substrate is bound to the enzyme's active site), and \(\mathrm{P}\) is the product: 1\. \(\mathrm{E}+\mathrm{S} \rightleftharpoons \mathrm{ES}\) 2\. \(\mathrm{ES} \longrightarrow \mathrm{E}+\mathrm{P}\) What assumptions are made in this model with regard to the rate of the bound substrate being chemically transformed into bound product in the active site?

Short answer

Enzymes are crucial in biological systems as they act as biological catalysts, accelerating chemical reactions and allowing vital cellular processes to occur efficiently. Catalase decomposes hydrogen peroxide into water and oxygen, while nitrogenase reduces atmospheric nitrogen to ammonia for incorporation into essential molecules. The given enzyme reaction model assumes a reversible formation of the enzyme-substrate complex and that the rate-limiting step is the chemical transformation of the substrate into the product within the active site.

Step-by-step solution

a) Importance of enzymes in biological systems

Enzymes are biological catalysts that accelerate chemical reactions in living organisms without being consumed in the process. They play an essential role in almost every biochemical process that takes place within cells and are crucial for maintaining life. These proteins allow reactions to occur at a faster rate and under milder conditions than would otherwise be necessary, enabling metabolism and other cellular processes to happen efficiently. Some examples of important enzyme functions include breaking down food molecules, repairing damaged cell structures, and helping in the production of energy.

b) Chemical transformations catalyzed by (i) catalase and (ii) nitrogenase

(i) Catalase is an enzyme that catalyzes the decomposition of hydrogen peroxide (H2O2) into water (H2O) and oxygen (O2). The chemical transformation can be represented as follows: \[2 H_{2}O_{2} \xrightarrow{Catalase} 2 H_{2}O + O_{2}\] (ii) Nitrogenase is an enzyme that reduces atmospheric nitrogen (N2) to ammonia (NH3) through the process of nitrogen fixation. This reaction is crucial for incorporating nitrogen into molecules essential for life, such as proteins and nucleic acids. The chemical transformation can be represented as follows: \[N_{2} + 8 H^{+} + 8 e^{-} \xrightarrow{Nitrogenase} 2 NH_{3} + H_{2}\]

c) Assumptions in the given enzyme reaction model

The given enzyme reaction model describes a simple two-step process involving the formation of an enzyme-substrate complex (ES) and the subsequent generation of products. 1. E + S ↔ ES 2. ES → E + P There are two main assumptions made in this model with regard to the rate of the bound substrate being chemically transformed into bound product in the active site: 1. The model assumes that the initial binding of the enzyme (E) to the substrate (S) to form the enzyme-substrate complex (ES) is reversible. This means the complex can dissociate back into separate enzyme and substrate molecules if the reaction conditions change. 2. The model also assumes that the rate-limiting step is the second step (ES → E + P) where the enzyme-substrate complex is being converted into the product (P) and the free enzyme (E). This implies that the chemical transformation of the substrate into the product within the active site is the slowest step of the overall reaction, which determines the overall reaction rate. This is known as the "steady-state assumption".

Key concepts

Enzyme Catalysis

Enzymes are essential biological catalysts that enhance the speed of chemical reactions in cells. They achieve this without undergoing any permanent changes themselves. This ability to accelerate reactions is critical as it allows the numerous biochemical reactions necessary for life to occur at rates suitable for the needs of the organism.

Enzyme catalysis is unique because:

• Enzymes are highly specific, often facilitating only one type of reaction or acting on a single substrate.
• They function under mild conditions, such as normal body temperature and pH, which is adaptive for living organisms.
• Enzymes can increase the reaction rate by several orders of magnitude, making processes like metabolism fast and efficient.

This specificity and efficiency come from the enzyme's unique three-dimensional structures. These structures enable the formation of an enzyme-substrate complex, where the substrate fits into the enzyme’s "active site," akin to a key fitting into a lock.
Without enzymes, reactions required for cellular functions would be too slow, undermining essential processes like digestion, energy production, and DNA replication.

Biochemical Processes

Biochemical processes are a vast array of chemical reactions that occur in living organisms. These processes allow organisms to grow, reproduce, and maintain their structures and respond to environmental changes.

For example, the enzyme catalase facilitates a key biochemical process by decomposing hydrogen peroxide, a potentially harmful byproduct of metabolism, into harmless water and oxygen. Similarly, nitrogenase catalyzes the conversion of atmospheric nitrogen into ammonia, a vital component for the biosynthesis of amino acids and nucleotides.

Biochemical processes are highly controlled and integrated, allowing for efficient energy usage and waste elimination, and are integral in processes such as:

• Metabolism, which includes catabolic pathways that break down molecules to produce energy, and anabolic pathways that require energy to synthesize complex molecules.
• Signal transduction, where cells respond to external stimuli through a series of reaction pathways.
• Gene expression, which involves the transcription and translation processes to form proteins needed for cellular function.

In summary, enzymes facilitate these processes by reducing the energy barrier, ensuring the reactions occur accurately and swiftly to meet the cell's demands.

Reaction Mechanisms

Understanding enzyme reaction mechanisms is important to comprehend how enzymes work at the molecular level. Reaction mechanisms describe the detailed step-by-step processes by which chemical reactions occur.

The generic enzyme reaction model provided includes two key steps:

• First is the reversible formation of the enzyme-substrate complex (ES) from the enzyme (E) and substrate (S).
• Second is the conversion of the enzyme-substrate complex into the product (P) and free enzyme (E), which is typically the rate-limiting step.

This model assumes the steady-state condition, where the formation of the ES complex and its conversion to product and freed enzyme reach a balance.
Analyzing reaction mechanisms helps in designing drugs and manipulating enzyme activity for industrial processes. It reveals crucial insights into how the rates of reactions are controlled and how catalytic properties are conferred through the structure of the enzyme.
Ultimately, reaction mechanisms are central to biochemistry and molecular biology as they provide a framework for understanding the dynamic nature of life at the molecular level.