Biochemistry and Human Nutrition

Module 2. Enzymes

Lesson 9
MECHANISM OF ENZYME ACTION

9.1 Introduction

• Enzymes do two important things: they recognize very specific substrates, and they perform specific chemical reactions on them at fantastic speeds.
• Their role is to make and break specific chemical bonds of the substrates at a faster rate and to do it without being consumed in the process.
• At the end of each catalytic cycle, the enzyme is free to begin again with a new substrate molecule.
• Catalysis is simply making a reaction go faster, it follows that the activation energy of a catalyzed (faster) reaction is lower than the activation energy of an uncatalyzed reaction. Thus enzymes work by lowering the activation energy of the reaction they catalyze.
• The way they accomplish all this can be described by a number of different models, each one of which accounts for some of the behavior that enzymes exhibit. Most enzymes make use of all these different mechanisms of specificity and/or catalysis. (Fig. 9.1 Enzyme catalysis)
  

9.2 Lock-and-Key Model of Enzyme-Substrate Binding

In this model, the active site of the unbound enzyme is complementary in shape to the substrate. As if the key fits in the lock will then open the lock. It accounts for why the enzyme only works on certain substrates. (Fig. 9.2)

9.3 Induced-Fit Model of Enzyme-Substrate Binding

In this model, the enzyme changes shape on substrate binding. The active site forms a shape complementary to the substrate only after the substrate has been bound. The binding of the correct substrate triggers a change in the structure of the enzyme that brings catalytic groups into exactly the right position to facilitate the reaction. In the induced-fit model, the structure of the enzyme is different depending on whether the substrate is bound or not. The enzyme changes the shape (undergoes a conformational change) on binding the substrate. This conformation change converts the enzyme into a new structure in which the substrate and catalytic groups on the enzyme are properly arranged to accelerate the reaction. (Fig. 9.3)

9.4 Multi Substrate Reaction Mechanism

Most reactions in biological systems usually include two substrates and two products and can be represented by the bisubstrate reaction. The majority of such reactions entail the transfer of a functional group, such as a phosphoryl or a hydroxyl group, from one substrate to the other.

There are three general mechanisms which describe multi-substrate enzyme system.

• Ordered mechanism
• Random mechanism
• Ping-Pong mechanism

9.4.1 Ordered mechanism

In this type of reaction all substrates must bind to the enzyme before any product is released. Consequently, in a bisubstrate reaction, a ternary complex of the enzyme and both substrates forms. In ordered mechanism the substrates bind the enzyme in a defined sequence. Many enzymes that have NAD⁺ or NADH as a substrate exhibit the sequential ordered mechanism. Consider lactate dehydrogenase, an important enzyme in glucose metabolism. This enzyme reduces pyruvate to lactate while oxidizing NADH to NAD⁺. In the ordered sequential mechanism, the coenzyme always binds first and the lactate is always released first. (Fig. 9.4 Conversaiton to lactate)

This sequence given above is represented below in fig. 9.3.

Fig. 9.5 Ordered mechanism

9.4.2 Random mechanism

In this mechanism also enzyme exists as a ternary complex: first, consisting of the enzyme and substrates and, after catalysis, the enzyme and products. In the random sequential mechanism, the order of addition of substrates and release of products is random. Sequential random reactions are illustrated by the formation of phosphocreatine and ADP from ATP and creatine, a reaction catalyzed by creatine kinase. Phosphocreatine is an important energy source in muscle. Sequential random reactions can also be depicted as below. Although the order of certain events is random, the reaction still passes through the ternary complexes including, first, substrates and, then, products.

Fig. 9.6 Random mechanism

9.4.3 Double-displacement (Ping-pong) reactions.

In double-displacement, or Ping-Pong, reactions, one or more products are released before all substrates bind the enzyme. The defining feature of double-displacement reactions is the existence of a substituted enzyme intermediate, in which the enzyme is temporarily modified. Reactions that shuttle amino groups between amino acids and α-keto acids are classic examples of double-displacement mechanisms. The enzyme aspartate aminotransferase catalyzes the transfer of an amino group from aspartate to α-ketoglutarate.

The sequence of events can be portrayed as the following diagram.

Fig. 9.7 Double-displacement (ping-pong) reactions

After aspartate binds to the enzyme, the enzyme removes aspartate's amino group to form the substituted enzyme intermediate. The first product, oxaloacetate, subsequently departs. The second substrate, α-ketoglutarate, binds to the enzyme, accepts the amino group from the modified enzyme, and is then released as the final product, glutamate. In this, the substrates appear to bounce on and off the enzyme analogously to a Ping-Pong ball bouncing on a table.