What Is the Connection Between Enzymes and Substrates?

Enzymes are proteins or RNAs produced by living cells that have a high specificity and catalytic efficiency for their substrates. The catalytic action of enzymes depends on the integrity of the primary structure and the spatial structure of the enzyme molecule. Denaturation or subunit depolymerization of enzyme molecules can lead to loss of enzyme activity. ^[1] Enzymes are biological macromolecules with a molecular mass of at least 10,000 or more, and large ones can reach one million.

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Enzymes are produced by living cells and are highly specific and highly potent in their substrates.

1773 Italian scientist

There are usually two methods of naming conventions and system naming.

Humans and mammals contain at least 5,000 enzymes. They are

1 High efficiency: The catalytic efficiency of the enzyme is higher than that of the inorganic catalyst, which makes the reaction rate faster;

2 Specificity: An enzyme can only catalyze one or one type

The ability of enzymes to catalyze chemical reactions is called

Enzyme biology

In organisms, enzymes play a very wide range of functions. Both signal transduction and regulation of cell activity are inseparable from enzymes,

Enzyme molecular structure and chemical reaction (12 photos)

Especially the involvement of kinases and phosphatases. Enzymes can also produce movement, catalyze the hydrolysis of ATP on myosin to produce muscle contraction, and can participate in the transport of intracellular materials as part of the cytoskeleton. Some ATPases located on the cell membrane participate in active transport as ion pumps. Enzymes are also involved in some of the more peculiar functions in some organisms. For example, luciferase can emit light for fireflies. Viruses also contain enzymes, or participate in infecting cells (such as HIV integrase and reverse transcriptase), or participate in the release of viral particles from host cells (such as neuraminidase of influenza virus).

A very important function of complex enzymes is to participate in the work of the digestive system. Proteases, for example, can degrade the large molecules (starch and protein) entering the digestive tract into small molecules smaller than 15 microns, so that the intestinal capillaries can be fully absorbed. Starch cannot be directly absorbed by the intestine, and enzymes can hydrolyze starch to maltose or further to small molecules that can be absorbed by the intestine, such as glucose. Different enzymes break down different food substrates. There are some bacteria that can produce cellulase in the digestive system of herbivorous ruminants. Cellulase can break down cellulose in the cell wall of plants to provide nutrients that can be absorbed.

In the metabolic pathway, multiple enzymes function in a specific order: the product of the former enzyme is the substrate of the latter; after each enzyme catalyzes the reaction, the product is passed to another enzyme. In some cases, different enzymes can catalyze the same reaction in parallel, allowing more complex regulation: for example, one enzyme can continuously catalyze the reaction with lower activity, while another enzyme can be higher after being induced The activity is catalyzed. The presence of the enzyme determines that the entire metabolism is carried out in the correct way; once there is no enzyme, the metabolism can neither proceed according to the required steps nor complete the synthesis at a sufficient speed to meet the needs of the cell. In fact, without enzymes, metabolic pathways, such as glycolysis, cannot be performed independently. For example, glucose can react directly with ATP so that one or more of its carbon atoms are phosphorylated; in the absence of enzyme catalysis, the reaction proceeds so slowly that it can be ignored; and once hexokinase is added, the carbon at position 6 The atomic phosphorylation reaction has been greatly accelerated. Although the phosphorylation reaction of other carbon atoms is also progressing slowly, after a period of testing, it can be found that most of the products are glucose-6-phosphate. Each cell can then complete the entire reaction network of metabolic pathways through such a set of functional enzymes.

Enzyme kinetics

Enzyme kinetics is the science that studies the ability of enzymes to bind substrates and catalyze reaction rates. Researchers use enzyme assays to obtain reaction rate data for enzyme kinetic analysis.

In 1902, Victor Hendry proposed a quantitative theory of enzyme kinetics; this theory was subsequently confirmed by others and extended to the Mie equation. Henry's greatest contribution is that he first proposed that the enzyme-catalyzed reaction consists of two steps: first, the substrate is reversibly bound to the enzyme to form an enzyme-substrate complex; then, the enzyme completes the catalysis of the corresponding chemical reaction and releases the resulting product .

The relationship between the initial enzyme reaction rate (expressed as "V") and the substrate concentration (expressed as "[S]"). With increasing substrate concentration, the reaction rate of the enzyme also tends to the maximum reaction rate (denoted as "V _max "). Enzymes can catalyze millions of reactions in a second. For example, the reaction catalyzed by orotic acid nucleoside 5-phosphate decarboxylase requires 78 million years to convert half of the substrate to the product without enzymes; and the same reaction process, if this decarboxylation is added For enzymes, it takes only 25 milliseconds. The rate of enzyme catalysis depends on the reaction conditions and substrate concentration. If there are factors that can melt the protein in the reaction conditions, such as high temperature, extreme pH and high salt concentration, the enzyme activity will be destroyed; and increasing the substrate concentration in the reaction system will increase the enzyme activity. In the case of constant enzyme concentration, as the substrate concentration continues to increase, the reaction rate catalyzed by the enzyme also continues to accelerate and tends to the maximum reaction rate (V _max ). The reason for this phenomenon is that when the substrate concentration in the reaction system increases, more and more enzyme molecules in the free state bind to the substrate to form an enzyme-substrate complex; when the active sites of all enzyme molecules are Substrate saturation binding, that is, when all enzyme molecules form an enzyme-substrate complex, the catalytic reaction rate reaches a maximum. Of course, V _{max is} not the only kinetic constant of the enzyme, and the substrate concentration required to reach a certain reaction rate is also an important kinetic index. This kinetic index, the Mie constant (K _m ), refers to the substrate concentration required to reach a reaction rate that is half the value of V _max . For a specific substrate, each enzyme has its characteristic K _m value, which indicates the strength of the binding between the substrate and the enzyme (the lower the K _m value, the stronger the binding, the higher the affinity). Another important kinetic indicator is the catalytic constant, which is defined as the number of substrates catalyzed by an enzyme's active site within one second. It is used to indicate the ability of an enzyme to catalyze a specific substrate.

The catalytic efficiency of an enzyme can be measured in terms of catalytic constant / Mie index. This expression is also known as the specificity constant, which contains the reaction constants for all steps in the catalytic reaction. Since the specificity constant reflects both the affinity and catalytic ability of the enzyme for the substrate, it can be used to compare the catalytic efficiency of different enzymes for a specific substrate or the catalytic efficiency of the same enzyme for different substrates.

Each collision between the enzyme and the substrate will cause the substrate to be catalyzed, so the rate of product formation is no longer dominated by the reaction rate, and the diffusion rate of the molecules plays a decisive role. This property of the enzyme is called "catalytic perfection" or "kinetic perfection". Examples of related enzymes are triose phosphate isomerase, carbonic anhydrase, acetylcholinesterase, catalase, fumarate, -lactamase and superoxide dismutase.

The Mie equation is based on the law of mass action, which is based on the assumptions of free diffusion and thermodynamically driven collisions. However, due to the high concentration and phase separation of enzymes / substrates / products or one-dimensional / two-dimensional molecular motion, many biochemical or cellular processes deviate significantly from the assumptions of the law of mass action. In these cases, a fractal Mie equation can be applied.

There are some enzymes whose catalytic product kinetic rate is even higher than the molecular diffusion rate. This phenomenon cannot be explained by the currently accepted theories. Various theoretical models have been proposed to explain this phenomenon. Among them, part of the situation can be explained by the additional effect of enzymes on substrates, that is, some enzymes are believed to capture substrates through a double dipole electric field and place the substrates at the catalytically active site in the correct orientation. Another theoretical model introduces a tunneling effect based on quantum theory, that is, protons or electrons can pass through the activation energy barrier (just like tunneling), but there are more controversies about tunneling effects. There are reports of quantum tunneling effects in protons in tryptamine. Therefore, some researchers believe that there is also a tunneling effect in enzyme catalysis, which can directly pass through the energy barrier of the reaction, instead of reducing the energy barrier to achieve the catalytic effect in a manner similar to the traditional theoretical model. Related experimental reports suggest that there is a tunneling effect in the catalytic reaction of an alcohol dehydrogenase, but whether the tunneling effect is widespread in the enzyme-catalyzed reaction is inconclusive.

Enzyme thermodynamics

Like other catalysts, the enzyme does not change the equilibrium constant of the reaction, but accelerates the reaction rate by reducing the activation energy of the reaction. Generally, the reaction direction is the same in the presence or absence of the enzyme, but the former reacts faster. However, it must be pointed out that in the absence of enzymes, substrates can generate different products through other uncatalyzed "free" reactions, because these different products form faster.

Enzymes can link two or more reactions, so you can use one reaction that is more thermodynamically easier to "drive" another reaction that is less easily thermodynamically. For example, cells often drive other chemical reactions through the energy produced by ATP's enzymatic hydrolysis.

Enzymes can catalyze forward and reverse reactions equally without changing the chemical equilibrium of the reaction itself. For example, carbonic anhydrase can catalyze the following two reciprocal reactions. Which one is catalyzed depends on the reactant concentration.

Of course, if the reaction equilibrium tends to a certain direction, such as a reaction that releases high energy, and the reverse reaction cannot occur effectively, then the enzyme does not actually catalyze the direction allowed by thermodynamics, but only its reverse reaction.