How Enzymes Work

From Structure to Function

Haruo Suzuki

• Publisher: Jenny Stanford Publishing
• Year: 2019
• ISBN:
  9781000681437
• Edition: 2
• Topic: Medicine
• Subtopic: Biochemistry in Medicine

The first edition of this book covered the basic treatment of the enzyme reaction using the overall reaction kinetics and stopped-flow method, the general properties of protein and cofactors, the control of enzyme reaction, and the preparation of enzyme protein. These topics are the basis of enzyme research and thus suitable for the beginner in the field. The second edition presents the cofactors produced via the post-translational modification of the enzyme's active site. These cofactors expand the function of enzymes and open a new research field. The carbonyl reagent phenylhydrazine and related compounds have been useful in finding some of the newly discovered cofactors and thus have been discussed in this edition. The topic of the control of enzyme activity through the channel of substrates and products in polyfunctional enzymes has also been expanded in this book.

Chapter 1

Introduction

Foods are digested in the human body to glucose, fatty acids, amino acids, and so on. These are used to produce energy to work and synthesize biomolecules, such as protein, nucleic acids, carbohydrate, and lipids. These changes are performed in cells and called metabolism. The metabolic pathways are composed of chemical reactions, which are catalyzed by enzyme. This chapter describes a brief history of early works on enzyme, fundamental view on the enzyme, and some examples to show its importance.

1.1 General Properties of Enzyme

It seems common that the recognition of enzyme as substance is derived from the observation of Payan and Persoz in 1833. They obtained the substance that converted starch to saccharificate and named it diastase. Then Schwann obtained the substance that digested meat, and named it pepsin in 1836. Berzelius invented the term catalysis in 1835 to describe chemical reactions in which the progress of the reaction is affected by a substance that is not consumed in the reaction. Diastase was used to mean enzyme, but later ferment was used to mean microorganism with the fermentation activity, and also mean the substance like diastase and pepsin. To avoid the confusion, Kühne proposed the term enzyme in 1878 to name the substance like diastase. It means in yeast in Greek. Many enzymes have name with suffix—ase, which originated from Duclaux’s proposal in 1898 [1].

Our life without enzyme could not have been imagined. Our health is maintained by the proper action of various enzymes, and we are surrounded by many things containing enzyme, such as enzyme supplement, detergents, and toothpaste. In this chapter, first, general properties of enzyme are summarized. Then the importance of enzyme is shown by some examples.

1.1.1 Enzyme Specificity

The substance on which an enzyme acts is substrate, which is abbreviated as “S.” Enzyme specificity is classified into substrate specificity and reaction specificity. In other words, an enzyme has “liking” for substrate on which it acts and for the reaction that it catalyzes.

Substrate specificity is that an enzyme acts on its restricted substrate. However, enzymes show a different degree of specificity. For example, alcohol dehydrogenase catalyzes dehydrogenation of ethanol with high efficiency, but alcohol dehydrogenase catalyzes dehydrogenation of methanol with low efficiency. Such an enzyme is considered to have “low or broad substrate specificity.” Urease only catalyzes the hydrolysis of urea to produce ammonia and carbon dioxide; thus, it is called to have high or narrow substrate specificity.

In reaction specificity, an enzyme catalyzes a particular transformation of the substrate. For example, L-amino acid oxidase catalyzes the oxidation of L-amino acid to produce the corresponding keto acid, ammonia, and hydrogen peroxide. However, the racemization of L-amino acid to D-amino acid is catalyzed by the enzyme different from L-amino acid oxidase, that is, amino acid racemase. See Chapter 10 for the example of the reaction specificity.

1.1.2 Rate Enhancement

The prominent nature of the enzyme is the enhancement of a reaction rate. The enhancement is calculated by dividing the enzyme-catalyzed rate by the uncatalyzed rate, and is in the range of 10⁶–10¹⁶ times of the rate of uncatalyzed reaction (Table 1.1) [2]. When substrate changes to product, substrate must pass over an energy barrier (Fig. 1.1). The energy is called activation energy, E_a. Arrhenius (1889) introduced a relationship between a rate of reaction (k) and temperature (T), the Arrhenius equation:

$\frac{d\text{ln}k}{dT}=\frac{E_{\text{a}}}{R{T}^2}$

(1.1)

where E_a and R are the activation energy and the gas constant (8.314 J K⁻¹), respectively. This equation explains our experience that the reaction rate increases with increasing temperature.

Figure 1.1 Energy profiles of uncatalyzed and catalyzed reactions. Substrate (S) passes over the energy barrier (activation energy) to be transformed to product (P) in the presence and absence of enzyme (E). Energy barrier is lower with enzyme.

Determination of the activation energy: Integrating Eq. 1.1,

$k=A\exp \left(\frac{-E_{\text{a}}}{RT}\right)$

(1.2)

where A is pre-exponential factor. Logarithm of Eq. 1.2 results in

$\text{ln}k=\frac{-E_{\text{a}}}{RT}+\text{ln}A$

(1.3)

Table 1.1 Rate enhancement by enzymes

Enzymes	Rate enhancement
Adenosine deaminase	2.1 × 10^12
Alkaline phosphatase	1.6 × 10^16
Alkylsulfatase	2 × 10^26^a
Chorismate mutase	1.9 × 10^6
Peptidase	1.5 × 10^10
Triose phosphate isomerase	6.2 × 10^9
Urease	2.3 × 10^13
Abzyme (amide hydrolysis)	2.5 × 10^5

Source: Adapted from Suzuki [2]. ^aFrom Edwards et al. [3].

Thus, the ln k vs. 1/T plot will give a linear line (Fig. 1.2). The activation energy of a reaction could be estimated from a slope of the plot. A most popular theory to explain the kinetics of reaction is the transition state theory. When a reaction proceeds, a substrate (ground state) passes over the unstable transition state (Fig. 1.1). The energy required passing over the barrier is called activation energy. The enzyme reduces the activation energy and thus increases the rate of reaction. See Chapter 4 for detail.

Figure 1.2 Arrhenius plot. From the slope of the plot, the activation energy can be determined.

1.2 Examples of Enzyme

1.2.1 N...