More about enzymes. Enzymes that speed up chemical reactions without raising the temperature and obtaining energy from outside Proteins enzymes speed up chemical reactions
GENERAL CHARACTERISTICS OF ENZYMES
Enzymes are biological catalysts.
The chemical nature of enzymes. Active site of enzymes.
The mechanism of enzymatic catalysis.
I. Enzymes – biological catalysts of a protein nature, capable of many times accelerating chemical reactions occurring in organism, but they are not part of the final products of the reaction.
The substances that an enzyme acts on are called substrates.
The whole variety of biochemical reactions occurring in microorganisms, plants and animals is catalyzed by the corresponding enzymes. The role of enzymes in food technology is great. The production of any food product is based on either biochemical (enzymatic) or physicochemical processes, or these processes are interrelated.
Unlike inorganic catalysts, enzymes have their own characteristics:
The rate of enzymatic catalysis is several orders of magnitude higher (from 103 to 109) than that of a non-biological catalyst;
the action of each enzyme is highly specific; each enzyme acts only on its own substrate or a group of related substrates;
enzymes catalyze chemical reactions under mild conditions, i.e. at normal pressure, high temperature (20-50С) and at pH values, in most cases close to neutral.
From the point of view of the localization of enzymes in the cell, they are divided into extracellular and intracellular.
Extracellular enzymes are secreted by living cells into the environment, intracellular - are found either in cellular organelles or in complex with supramolecular structures.
A special group of enzymes is made up of polyenzyme complexes, which include a number of enzymes that catalyze successive reactions of the transformation of any substrate. These complexes are localized in intramolecular structures in such a way that each enzyme is located in close proximity to the enzyme that catalyzes the reaction in the chain of this sequence of reactions. Due to this arrangement of enzymes, the process of diffusion of the substrate and reaction products is minimized.
II. Enzymes are high molecular weight protein compounds.
Like other proteins, enzymes have 4 levels of structure, they have all the physicochemical properties of proteins, and only one distinguishing feature is the ability to speed up chemical reactions. Enzymes can be simple - one-component and complex two-component.
Single component enzymes - are built from polypeptide chains and during hydrolysis decompose only to amino acids.
Two-component enzymes - made up of proteins apoforment and non-protein part - cofactor. Both components separately are deprived of enzymatic activity. Only by joining together holoenzyme) they acquire properties characteristic of biocatalysts. The role of a cofactor can be performed by any ion (Zn 2+ , Mg 2+ , Fe 2+ , Cu 2+ , less often K + and Na +) or an organic compound (vitamins, nucleotides). Organic cofactors are called coenzymes.
The type of connection between the cofactor and the apoenzyme can be different. In some cases, they exist separately and are associated only during the course of the reaction; in other cases, the cofactor and apoenzyme are connected permanently, sometimes by strong, covalent bonds.
Active site of enzymes is a local region of the enzyme molecule that is involved in the act of catalysis. AT one-component In enzymes, the active center is formed as a result of a certain orientation of the amino acid residues of the polypeptide chain. Usually a small amount of amino acids takes part in its formation, in the range of 12-16. The functional groups of these amino acids may belong to the links of the polypeptide chain, remote from each other. Their convergence is associated with the formation of the tertiary structure of the enzyme.
AT two-component In enzymes, the active center is a complex of a cofactor and some adjacent amino acid residues.
In the active center there are contact(anchor) a site whose function is to bind the substrate, and catalytic - where the transformation of the substrate into reaction products occurs after its binding by the contact site. The following functional groups take part in the formation of these sites: COOH groups of dicarboxylic amino acids or terminal groups of the polypeptide chain; imidazole group of histidine; OH group of serine; NH 2 - lysine group and end groups of the polypeptide chain; phenolic group of tyrosine and hydrophobic residues of aliphatic amino acids.
III. The rate of any enzymatic reaction is determined energybarrier, which must be overcome by the reacting molecules. According to Arrhenius, a chemical reaction from the point of view of the energy of the process is described by the equation
N \u003d N 0 e - (E act / RT) ,
where N is the number of active molecules; N 0 is the total number of reacting molecules; e is the base of the natural logarithm; R is the gas constant; T is the absolute temperature; E act - activation energy.
Activation energy is the additional amount of energy required for all molecules to overcome the energy barrier of the reaction and enter into it. This energy is the difference between the total energy of the reacting molecules and the energy excited transition state. The higher the activation energy in the reacting system, the higher the energy barrier and the lower the reaction rate.
The most important function of an enzyme is decrease in activation energy catalyzed process. On fig. 1 shows a graph of the change in the energy of non-enzymatic (1) and enzymatic (2) reactions. The enzyme lowers the height of the energy barrier (E act E act).
The mechanism of enzymatic catalysis remains largely unexplained. However, the work of M. Michaelis and M. Menten, who developed the idea of enzyme-substrate complex. The formation of this complex leads to a decrease in the activation energy of the reaction.
The process of enzymatic catalysis can be divided into three stages:
Steric binding of the substrate S to the active site of the enzyme E (formation of the enzyme-substrate complex ES).
Transformation of the primary complex ES into an activated transient complex ES ≠ .
Separation of the final product P of the reaction from the enzyme.
The first stage is short in time and depends on the concentration of the substrate and enzyme in the medium, on the rate of diffusion of the substrate to the active site of the enzyme. In the formation of the ES complex, both covalent, coordination, ionic bonds, as well as less strong forms of bonds - electrostatic attraction of polar groups, van der Waals forces of adhesion between non-polar regions of molecules, hydrogen bonds can participate in various combinations. The nature of these bonds is determined by the chemical features of both the substrate and the functional groups that make up the active center of the enzyme.
The second stage is, in fact, an act of catalysis, i.e. an act of rupture or formation of new bonds in the substrate; it is the slowest and limits the rate of a chemical reaction. At this stage, the activation energy of the enzymatic reaction decreases due to formation of an active transition complex ES ≠ .
At the molecular level, a clearer understanding of the mechanism of action of enzymes gives theory of acid-base catalysis. Any reaction that breaks covalent bonds involves the participation of two opposite electronic components. The electrons of the broken bond should be drawn to the electrophilic component and away from the nucleophilic one. The reagents that could cause such an electronic rearrangement are an acid and a base. However, it is impossible to simultaneously create high concentrations of both components in the same solution, since they neutralize each other. In the protein molecule of the enzyme due to consolidation no direct neutralization reaction occurs on the catalytic site of electrophilic and nucleophilic groups. This, in fact, determines the act of catalysis. Being at a certain distance from each other, the electrophilic and nucleophilic groups of the catalytic site of the enzyme not only bind to the reacting groups of the substrate, but also exert a strong polarizing effect on the substrate groups. To this should be added the possibility of charge fluctuations in the ES complex, which creates a high degree of efficiency of this polarization. This is the reason for the decrease in the activation energy during enzymatic catalysis.
According to the theory covalentcatalysis some enzymes interact with their substrates to form unstable, covalently bonded enzyme-substrate complexes. From these complexes in the course of the subsequent reaction, reaction products are formed, and much faster than in the case of non-catalyzed reactions.
Thus, the third stage, which ends with the formation of reaction products, is provided by the processes occurring in the previous stages.
Chapter IV. ENZYMES
§ 11. General ideas about enzymes
enzymes, or enzymes, are biological catalysts that speed up chemical reactions. The total number of known enzymes is several thousand. Almost all chemical reactions occurring in living organisms are carried out with their participation. Enzymes speed up chemical reactions by 10 8 - 10 20 times. They play a decisive role in the most important biological processes: in metabolism, in muscle contraction, in the neutralization of foreign substances that have entered the body, in signal transmission, in the transport of substances, blood coagulation, and many others. For a cell, enzymes are absolutely necessary; without them, the cell, and therefore life, could not exist.
The word enzyme comes from the Latin fermentum - leaven, enzyme translated from Greek means "in yeast". The first information about enzymes was obtained back in the 19th century, but only at the beginning of the 20th century were theories of the action of enzymes formulated, and only in 1926 James Sumner first obtained a purified enzyme in a crystalline form - urease Urease catalyzes the hydrolytic cleavage of urea:
Sumner discovered that urease crystals are made of protein. In the 30s. of the last century, John Norton and colleagues received the digestive enzymes trypsin and pepsin in crystalline form, and also found that they, like urease, are inherently proteins. As a result of these studies, a point of view on the protein nature of enzymes was formed, which was subsequently confirmed many times. It was only much later that the ability to catalyze was discovered in some RNAs; such RNAs are called ribozymes, or RNA enzymes. Ribozymes make up a small part of all enzymes, so we will continue to talk about protein enzymes.
Interesting to know! Ribonuclease P, an RNA-cleaving enzyme, consists of two components, RNA and a polypeptide. At a high concentration of magnesium ions, the presence of the protein component becomes unnecessary. RNA alone can catalyze the reaction.
Similarities and differences between enzymes and non-protein catalysts
Enzymes share a number of properties with chemical non-protein catalysts:
a) are not consumed in the process of catalysis and do not undergo irreversible changes;
b) accelerate both the forward and reverse reactions without shifting the chemical equilibrium;
c) catalyze only those reactions that can proceed without them;
d) increase the rate of a chemical reaction by reducing activation energy(Fig. 26) .
A chemical reaction proceeds because a certain fraction of the molecules of the starting substances has more energy than other molecules, and this energy is sufficient to achieve the transition state. Enzymes, like chemical catalysts, reduce the activation energy by interacting with the initial molecules, in connection with this, the number of molecules capable of reaching the transition state increases, and as a result, the rate of the enzymatic reaction also increases.
Fig.26. Influence of the enzyme on the activation energy
Enzymes, despite a certain similarity with non-protein chemical catalysts, differ from them in a number of ways:
a) enzymes have a higher efficiency of action, for example, the enzyme catalase, which catalyzes the reaction: 2H 2 O 2 \u003d 2H 2 O + O 2, accelerates it by about 10 12 times, while the efficiency of platinum as a catalyst for this reaction is approximately one million times lower ;
b) enzymes have a higher specificity compared to non-protein catalysts, they accelerate a narrower range of chemical reactions, for example, the already mentioned urease enzyme catalyzes only one reaction - urea hydrolysis, proteases are able to break down only proteins, but do not act on carbohydrates, lipids, nucleic acids acids and other substances. On the other hand, platinum is capable of catalyzing various reactions (hydrogenation, dehydrogenation, oxidation), it catalyzes both the reaction of obtaining ammonia from nitrogen and hydrogen and the hydrogenation of unsaturated fatty acids (this reaction is used to obtain margarine);
c) enzymes work effectively under mild conditions: at a temperature of 0 - 40 ° C, at atmospheric pressure, at pH values close to neutral, under more severe conditions, enzymes denature and do not show their catalytic qualities. Efficient chemical catalysis often requires harsh conditions—high pressure, high temperature, and the presence of acids or bases. For example, the synthesis of ammonia in the presence of catalysts is carried out at 500 - 550 o C and a pressure of 15 - 100 MPa;
d) the activity of enzymes compared to chemical catalysts can be more finely regulated by various factors. There are many substances in the cell, both increasing and decreasing the rate of enzymatic reactions.
Structure of enzymes
The relative molecular weight of enzymes can vary from 104 to 106 or more. Enzymes are usually globular proteins. Some enzymes are simple proteins and consist only of amino acid residues (ribonuclease, pepsin, trypsin), the activity of others depends on the presence of additional chemical components in their composition, the so-called cofactors. Metal ions Fe 2+ , Mn 2+ , Mg 2+ , Zn 2+ or complex organic substances, which are also called coenzymes. Many coenzymes contain vitamins. As an example, in fig. 27 shows the structure of coenzyme A (CoA).
Rice. 27. Coenzyme A
If the coenzyme is strongly associated with the enzyme, then in this case it represents the prosthetic group of the complex protein. Cofactors can perform the following functions:
a) participation in catalysis;
b) the implementation of the interaction between the substrate and the enzyme;
c) stabilization of the enzyme.
The catalytically active enzyme-cofactor complex is called holoenzyme. The separation of the cofactor from the holoenzyme leads to the formation of an inactive apoenzyme:
Holoenzyme apoenzyme + cofactor.
The enzyme molecule contains active center. The active center is the region of the enzyme molecule in which the substrate is bound and converted into a reaction product. The size of the enzyme, as a rule, significantly exceeds the size of their substrates. The active center occupies only a small part of the enzyme molecule (Fig. 28).
Rice. 28. Relative sizes of enzyme and substrate molecules
The active center is formed by the amino acid residues of the polypeptide chain. In two-component enzymes, the active center may also contain a non-protein component. The enzyme molecule contains amino acid residues that are not involved in catalysis and interaction with the substrate. However, they are very significant, since they form a certain spatial structure of the enzyme. Most often, the active center contains polar (serine, threonine, cysteine) and charged (lysine, histidine, glutamic and aspartic acids) amino acid residues. The amino acid residues that form the active center are located at a considerable distance in the polypeptide chain and turn out to be close during the formation of the tertiary structure (Fig. 29).
Rice. 29. Active Center
For example, the active center of chymotrypsin (a digestive enzyme that breaks down proteins) includes histidine residues - 57, aspartic acid - 102, serine - 195 (the numbers indicate the serial numbers in the polypeptide chain). Despite the distance from each other of these amino acid residues in the polypeptide chain, in space they are located side by side and form the active center of the enzyme.
Interesting to know! When animals are immunized with a substance that is an analogue of the transition state of any substrate, antibodies can be obtained that can catalyze the transformation of the substrate, such antibodies are called catalytically x or abzymes . Using this approach, it is possible to obtain catalysts for almost any reaction in a targeted manner.
Some enzymes are synthesized in an inactive form in the form of so-called proenzymes, which are then activated under the influence of certain factors. For example, the digestive enzymes chymotrypsin and trypsin are formed as a result of the activation of chymotrypsinogen and trypsinogen.
Nomenclature and classification of enzymes
Enzyme names are often formed by adding a suffix to the name of the substrate it acts on. For example, the name of the enzyme urease comes from the English word urea - urea, proteases (enzymes that break down proteins) - from the word protein. Many enzymes have trivial names not related to the name of their substrates, such as pepsin and trypsin. There are also systematic names of enzymes, including the names of substrates and reflecting the nature of the catalyzed reaction.
Interesting to know! An enzyme that catalyzes a reaction
ATP+D-glucoseADP +D-glucose - 6 - phosphate,
is systematically called ATP: hexose 6-phosphotransferase.
In accordance with the catalyzed reaction, all enzymes are divided into 6 classes.
1. Oxidoreductase. Catalyze redox reactions
2. Transferases. Catalyze the reactions of intermolecular transfer of groups:
AB + C = AC + B.
3. Hydrolases. Catalyze hydrolysis reactions:
AB + H 2 O \u003d AOH + BH.
4. Liase. They catalyze the addition of groups to double bonds and reverse reactions.
5. Isomerases. Catalyze isomerization reactions (intramolecular group transfer).
6. Ligases. Catalyze the connection of two molecules, coupled with the hydrolysis of ATP.
In turn, each class is divided into subclasses, subclasses - into subsubclasses. Enzymes forming sub-subclasses are assigned a serial number. As a result, each enzyme has its own four-digit number.
a) a decrease in the activation energy;
b) an increase in the activation energy;
c) an increase in the reaction temperature;
d) lowering the reaction temperature.
18. A change in the conformation of an enzyme in alkalosis is caused by:
19. Enzyme denaturation leads to its inactivation due to:
a) destruction of the active center;
b) destruction of the cofactor;
c) destruction of the allosteric center;
d) destruction of the substrate.
20. With relative specificity, enzymes act on:
a) one substrate;
b) a group of related substrates;
c) for a certain type of connection;
d) on any substrates.
21. According to Fisher's theory:
a) the substrate must absolutely correspond to the conformation of the active center;
b) the substrate may not correspond to the conformation of the active site of the enzyme;
c) the cofactor must absolutely correspond to the conformation of the active site;
d) the cofactor may not correspond to the conformation of the active site.
22. According to Koshland's theory:
a) the active center of the enzyme is finally formed upon binding to the substrate;
b) the active center has the necessary conformation before interaction with the substrate;
c) the active center of the enzyme is finally formed upon binding to the coenzyme;
d) the shape of the active center does not depend on the structure of the cofactor and substrate.
23. To clean purulent wounds, peptidases are used, since they:
a) break down the proteins of destroyed cells and thereby cleanse the wound;
b) break down the glycolipids of destroyed cells and thus clean the wound;
c) cleave nucleic acids and thereby cleanse the wound;
d) break down carbohydrates of destroyed cells and thus clean the wound.
24. Adding trypsin to enzymes:
a) will not change their activity;
b) lead to the loss of their activity;
c) will lead to an increase in their activity;
d) will lead to the destruction of the cofactor.
25. Direct evidence of the protein nature of the enzyme is:
a) decrease in activation energy;
b) acceleration of forward and reverse reactions;
c) acceleration of reaching the equilibrium position of the reversible reaction;
d) termination of the catalytic action when a substance that destroys peptide bonds is added to the solution.
26. To preserve the sweet taste, freshly harvested corn cobs are placed in boiling water for several minutes in order to:
a) they become soft;
b) denature the enzymes that convert glucose to starch;
c) it was easy to release the grains;
d) break peptide bonds.
27. The change in the conformation of the enzyme in acidosis is caused by:
a) destruction of hydrogen and ionic bonds;
b) destruction of disulfide bonds;
c) destruction of peptide bonds;
d) destruction of hydrophobic bonds.
28. With absolute specificity, enzymes act on:
a) one substrate;
b) to a certain type of bond in the substrate;
c) for a certain type of connection in the product;
d) on any substrates.
29. Enzyme denaturation is caused by:
a) substrates;
b) salts of heavy metals;
c) products;
d) cofactors.
30. Enzyme denaturation is caused by:
a) substrates;
b) products;
c) trichloroacetic acid;
d) cofactors.
31. Enzyme denaturation is caused by:
a) substrates;
b) high temperatures;
c) products;
d) cofactors.
32. Apoenzyme is:
a) a complex of protein and cofactor;
b) the protein part of the enzyme;
c) metal ions;
d) vitamins.
33. The common property of an enzyme and an inorganic catalyst is:
a) controllability;
b) is not consumed in the reaction process;
c) operates in mild conditions;
d) high specificity.
34. The common property of an enzyme and an inorganic catalyst is:
a) controllability;
b) decrease in activation energy;
c) molecular weight;
d) high specificity.
35. Competitive Inhibitor:
a) similar in structure to the substrate;
b) is not similar in structure to the substrate;
c) similar in structure to the product;
d) is similar in structure to a cofactor.
36. Allosteric inhibitors:
a) act reversibly;
b) act irreversibly;
d) compete with the substrate.
37. Allosteric inhibitors:
a) they are irreversible;
b) join the allosteric center;
c) join the active center;
d) compete with the cofactor.
38. Limited proteolysis is:
a) attaching the oligo- or polypeptide to the enzyme;
b) cleavage of the oligo- or polypeptide from the enzyme;
c) attachment of the oligo- or polypeptide to the allosteric center of the enzyme;
d) cleavage of the oligo- or polypeptide from the allosteric center of the enzyme.
ChapterIV.3.
Enzymes
Metabolism in the body can be defined as the totality of all chemical transformations undergone by compounds coming from outside. These transformations include all known types of chemical reactions: intermolecular transfer of functional groups, hydrolytic and non-hydrolytic cleavage of chemical bonds, intramolecular rearrangement, new formation of chemical bonds, and redox reactions. Such reactions proceed in the body at an extremely high rate only in the presence of catalysts. All biological catalysts are substances of a protein nature and are called enzymes (hereinafter F) or enzymes (E).
Enzymes are not components of reactions, but only accelerate the achievement of equilibrium by increasing the rate of both direct and reverse transformations. The acceleration of the reaction occurs due to a decrease in the activation energy - the energy barrier that separates one state of the system (the initial chemical compound) from another (the reaction product).
Enzymes speed up a wide variety of reactions in the body. So, quite simple from the point of view of traditional chemistry, the reaction of splitting off water from carbonic acid with the formation of CO 2 requires the participation of an enzyme, because without it, it proceeds too slowly to regulate the pH of the blood. Thanks to the catalytic action of enzymes in the body, it becomes possible to carry out such reactions that would go hundreds and thousands of times slower without a catalyst.
Enzyme Properties
1. Influence on the rate of a chemical reaction: enzymes increase the rate of a chemical reaction, but they themselves are not consumed.
The reaction rate is the change in the concentration of the reaction components per unit time. If it goes in the forward direction, then it is proportional to the concentration of the reactants; if it goes in the opposite direction, then it is proportional to the concentration of the reaction products. The ratio of the rates of forward and reverse reactions is called the equilibrium constant. Enzymes cannot change the values of the equilibrium constant, but the state of equilibrium in the presence of enzymes comes faster.
2. The specificity of the action of enzymes. In the cells of the body, 2-3 thousand reactions take place, each of which is catalyzed by a certain enzyme. The specificity of the action of an enzyme is the ability to accelerate the course of one particular reaction without affecting the rate of others, even very similar ones.
Distinguish:
Absolute– when F catalyzes only one specific reaction ( arginase- breakdown of arginine)
Relative(group special) - F catalyzes a certain class of reactions (eg hydrolytic cleavage) or reactions involving a certain class of substances.
The specificity of enzymes is due to their unique amino acid sequence, which determines the conformation of the active center that interacts with the reaction components.
A substance whose chemical transformation is catalyzed by an enzyme is called substrate ( S ) .
3. The activity of enzymes is the ability to accelerate the reaction rate to varying degrees. Activity is expressed in:
1) International units of activity - (IU) the amount of the enzyme catalyzing the conversion of 1 μM of the substrate in 1 min.
2) Katalakh (cat) - the amount of catalyst (enzyme) capable of converting 1 mol of substrate in 1 s.
3) Specific activity - the number of units of activity (any of the above) in the test sample to the total mass of protein in this sample.
4) Less often, molar activity is used - the number of substrate molecules converted by one enzyme molecule per minute.
activity depends on temperature . This or that enzyme shows the greatest activity at an optimum temperature. For F of a living organism, this value is within +37.0 - +39.0° C, depending on the type of animal. With a decrease in temperature, Brownian motion slows down, the diffusion rate decreases and, consequently, the process of complex formation between the enzyme and the reaction components (substrates) slows down. In case of temperature increase above +40 - +50° With the enzyme molecule, which is a protein, undergoes a process of denaturation. At the same time, the rate of the chemical reaction drops noticeably (Fig. 4.3.1.).
Enzyme activity also depends on medium pH . For most of them, there is a certain optimal pH value at which their activity is maximum. Since the cell contains hundreds of enzymes and each of them has its own opt pH limits, the change in pH is one of the important factors in the regulation of enzymatic activity. So, as a result of one chemical reaction with the participation of a certain enzyme, the pH opt of which lies in the range of 7.0 - 7.2, a product is formed, which is an acid. In this case, the pH value shifts to the region of 5.5 - 6.0. The activity of the enzyme sharply decreases, the rate of product formation slows down, but another enzyme is activated, for which these pH values are optimal, and the product of the first reaction undergoes further chemical transformation. (Another example about pepsin and trypsin).
The chemical nature of enzymes. The structure of the enzyme. Active and allosteric centers
All enzymes are proteins with a molecular weight of 15,000 to several million Da. According to the chemical structure, they are simple enzymes (consist only of AA) and complex enzymes (have a non-protein part or a prosthetic group). The protein portion is called apoenzyme, and non-protein, if it is covalently linked to an apoenzyme, then it is called coenzyme, and if the bond is non-covalent (ionic, hydrogen) - cofactor . The functions of the prosthetic group are as follows: participation in the act of catalysis, contact between the enzyme and the substrate, stabilization of the enzyme molecule in space.
Inorganic substances usually act as a cofactor - ions of zinc, copper, potassium, magnesium, calcium, iron, molybdenum.
Coenzymes can be considered as an integral part of the enzyme molecule. These are organic substances, among which there are: nucleotides ( ATP, UMF, etc.), vitamins or their derivatives ( TDF- from thiamine ( IN 1), FMN- from riboflavin ( IN 2), coenzyme A- from pantothenic acid ( AT 3), NAD, etc.) and tetrapyrrole coenzymes - hemes.
In the process of catalysis of the reaction, not the entire enzyme molecule comes into contact with the substrate, but a certain part of it, which is called active center. This zone of the molecule does not consist of a sequence of amino acids, but is formed when the protein molecule is twisted into a tertiary structure. Separate sections of amino acids approach each other, forming a certain configuration of the active center. An important structural feature of the active center is that its surface is complementary to the surface of the substrate; AA residues of this zone of the enzyme are able to enter into chemical interaction with certain groups of the substrate. It can be imagined that the active site of the enzyme matches the structure of the substrate like a key and a lock.
AT active center two zones are distinguished: binding center, responsible for the attachment of the substrate, and catalytic center responsible for the chemical transformation of the substrate. The composition of the catalytic center of most enzymes includes such AAs as Ser, Cys, His, Tyr, Lys. Complex enzymes in the catalytic center have a cofactor or coenzyme.
In addition to the active center, a number of enzymes are equipped with a regulatory (allosteric) center. Substances that affect its catalytic activity interact with this zone of the enzyme.
The mechanism of action of enzymes
The act of catalysis consists of three successive stages.
1. Formation of an enzyme-substrate complex during interaction through the active center.
2. The binding of the substrate occurs at several points of the active center, which leads to a change in the structure of the substrate, its deformation due to a change in the bond energy in the molecule. This is the second stage and is called substrate activation. When this occurs, a certain chemical modification of the substrate and its transformation into a new product or products.
3. As a result of such a transformation, the new substance (product) loses its ability to be retained in the active center of the enzyme and the enzyme-substrate, or rather, the enzyme-product complex, dissociates (disintegrates).
Types of catalytic reactions:
A + E \u003d AE \u003d BE \u003d E + B
A + B + E \u003d AE + B \u003d ABE \u003d AB + E
AB + E \u003d ABE \u003d A + B + E, where E is an enzyme, A and B are substrates, or reaction products.
Enzymatic effectors - substances that change the rate of enzymatic catalysis and thereby regulate metabolism. Among them are distinguished inhibitors - slowing down the rate of reaction and activators - accelerating the enzymatic reaction.
Depending on the mechanism of inhibition of the reaction, competitive and non-competitive inhibitors are distinguished. The structure of the competitive inhibitor molecule is similar to the structure of the substrate and coincides with the surface of the active center like a key with a lock (or almost coincides). The degree of this similarity may even be higher than with the substrate.
If A + E \u003d AE \u003d BE \u003d E + B, then I + E \u003d IE¹
The concentration of the enzyme capable of catalysis decreases and the rate of formation of reaction products drops sharply (Fig. 4.3.2.).
A large number of chemicals of endogenous and exogenous origin (i.e., formed in the body and coming from outside - xenobiotics, respectively) act as competitive inhibitors. Endogenous substances are regulators of metabolism and are called antimetabolites. Many of them are used in the treatment of oncological and microbial diseases, maybe. they inhibit key metabolic reactions of microorganisms (sulfonamides) and tumor cells. But with an excess of the substrate and a low concentration of a competitive inhibitor, its action is canceled.
The second type of inhibitors is non-competitive. They interact with the enzyme outside the active site, and an excess of substrate does not affect their inhibitory ability, as is the case with competitive inhibitors. These inhibitors interact either with certain groups of the enzyme (heavy metals bind to the thiol groups of Cys) or most often with the regulatory center, which reduces the binding ability of the active center. The actual process of inhibition is the complete or partial suppression of enzyme activity while maintaining its primary and spatial structure.
There are also reversible and irreversible inhibition. Irreversible inhibitors inactivate the enzyme by forming a chemical bond with its AA or other structural components. Usually this is a covalent bond with one of the sites of the active center. Such a complex practically does not dissociate under physiological conditions. In another case, the inhibitor disrupts the conformational structure of the enzyme molecule - causing its denaturation.
The action of reversible inhibitors can be removed by an excess of the substrate or by the action of substances that change the chemical structure of the inhibitor. Competitive and non-competitive inhibitors are in most cases reversible.
In addition to inhibitors, activators of enzymatic catalysis are also known. They are:
1) protect the enzyme molecule from inactivating effects,
2) form a complex with the substrate, which more actively binds to the active center of F,
3) interacting with an enzyme having a quaternary structure, they separate its subunits and thereby open access for the substrate to the active center.
Distribution of enzymes in the body
Enzymes involved in the synthesis of proteins, nucleic acids and energy metabolism enzymes are present in all cells of the body. But cells that perform special functions also contain special enzymes. So the cells of the islets of Langerhans in the pancreas contain enzymes that catalyze the synthesis of the hormones insulin and glucagon. Enzymes that are peculiar only to the cells of certain organs are called organ-specific: arginase and urokinase- liver, acid phosphatase- prostate. By changing the concentration of such enzymes in the blood, the presence of pathologies in these organs is judged.
In the cell, individual enzymes are distributed throughout the cytoplasm, others are embedded in the membranes of mitochondria and the endoplasmic reticulum, such enzymes form compartments, in which certain, closely related stages of metabolism occur.
Many enzymes are formed in cells and secreted into the anatomical cavities in an inactive state - these are proenzymes. Often in the form of proenzymes, proteolytic enzymes (break down proteins) are formed. Then, under the influence of pH or other enzymes and substrates, their chemical modification occurs and the active center becomes available to the substrates.
There are also isoenzymes - enzymes that differ in molecular structure, but perform the same function.
Nomenclature and classification of enzymes
The name of the enzyme is formed from the following parts:
1. the name of the substrate with which it interacts
2. the nature of the catalyzed reaction
3. the name of the enzyme class (but this is optional)
4. suffix -aza-
pyruvate - decarboxyl - aza, succinate - dehydrogen - aza
Since about 3 thousand enzymes are already known, they must be classified. Currently, an international classification of enzymes has been adopted, which is based on the type of catalyzed reaction. There are 6 classes, which in turn are divided into a number of subclasses (in this book they are presented only selectively):
1. Oxidoreductases. Catalyze redox reactions. They are divided into 17 subclasses. All enzymes contain a non-protein part in the form of heme or derivatives of vitamins B 2, B 5. The substrate undergoing oxidation acts as a hydrogen donor.
1.1. Dehydrogenases remove hydrogen from one substrate and transfer it to other substrates. Coenzymes NAD, NADP, FAD, FMN. They accept the hydrogen cleaved off by the enzyme, turning into the reduced form (NADH, NADPH, FADH) and transfer it to another enzyme-substrate complex, where it is given away.
1.2. Oxidase - catalyzes the transfer of hydrogen to oxygen with the formation of water or H 2 O 2. F. Cytochromoxysdase respiratory chain.
RH + NAD H + O 2 = ROH + NAD + H 2 O
1.3. Monooxidases - cytochrome P450. According to its structure, both hemo- and flavoprotein. It hydroxylates lipophilic xenobiotics (by the mechanism described above).
1.4. Peroxidasesand catalase- catalyze the decomposition of hydrogen peroxide, which is formed during metabolic reactions.
1.5. Oxygenases - catalyze the reactions of oxygen addition to the substrate.
2. Transferases - catalyze the transfer of various radicals from the donor molecule to the acceptor molecule.
BUT a+ E + B = E a+ A + B = E + B a+ A
2.1. Methyltransferase (CH 3 -).
2.2 Carboxyl- and carbamoyltransferases.
2.2. Acyltransferases - Coenzyme A (acyl group transfer - R-C=O).
Example: synthesis of the neurotransmitter acetylcholine (see chapter "Protein metabolism").
2.3. Hexosyl transferases catalyze the transfer of glycosyl residues.
Example: the splitting of a glucose molecule from glycogen under the action of phosphorylase.
2.4. Aminotransferases - transfer of amino groups
R 1- CO - R 2 + R 1 - CH - NH 3 - R 2 \u003d R 1 - CH - NH 3 - R 2 + R 1 - CO - R 2
They play an important role in the transformation of AK. The common coenzyme is pyridoxal phosphate.
Example: alanine aminotransferase(AlAT): pyruvate + glutamate = alanine + alpha-ketoglutarate (see chapter "Protein metabolism").
2.5. Phosphotransferesis (kinase) - catalyze the transfer of a phosphoric acid residue. In most cases, ATP is the phosphate donor. Enzymes of this class are mainly involved in the process of glucose breakdown.
Example: Hexo (gluco) kinase.
3. Hydrolases - catalyze hydrolysis reactions, i.e. splitting of substances with addition at the place of breaking the bond of water. This class includes mainly digestive enzymes, they are one-component (do not contain a non-protein part)
R1-R2 + H 2 O \u003d R1H + R2OH
3.1.
Esterases - break down essential bonds. This is a large subclass of enzymes that catalyze the hydrolysis of thiol esters, phosphoesters.
Example: NH 2 ).
Example: arginase(urea cycle).
4. Liases - catalyze the reactions of cleavage of molecules without the addition of water. These enzymes have a non-protein part in the form of thiamine pyrophosphate (B 1) and pyridoxal phosphate (B 6).
4.1. C-C bond lyases. They are commonly referred to as decarboxylases.
Example: pyruvate decarboxylase.
5.Isomerases - catalyze isomerization reactions.
Example: phosphopentose isomerase, pentose phosphate isomerase(enzymes of the non-oxidative branch of the pentose phosphate pathway).
6. Ligases catalyze the synthesis of more complex substances from simple ones. Such reactions proceed with the expenditure of ATP energy. Synthetase is added to the name of such enzymes.
LITERATURE TO THE CHAPTER IV.3.
1. Byshevsky A. Sh., Tersenov O. A. Biochemistry for a doctor // Ekaterinburg: Ural worker, 1994, 384 p.;
2. Knorre D. G., Myzina S. D. Biological chemistry. - M .: Higher. school 1998, 479 pp.;
3. Filippovich Yu. B., Egorova T. A., Sevastyanova G. A. Workshop on general biochemistry // M.: Prosveschenie, 1982, 311 pp.;
4. Lehninger A. Biochemistry. Molecular bases of the structure and functions of the cell // M.: Mir, 1974, 956 p.;
5. Pustovalova L.M. Workshop on biochemistry // Rostov-on-Don: Phoenix, 1999, 540 p.
Enzymes - biological catalysts, without whose participation not a single life process can do. Boni are characterized by the ability to: react with a certain re substance - the substrate; speed up biochemical reactions, which usually go very slowly; act at the same insignificant concentrations of the substrate, while not requiring energy from outside; the functioning of cotton wool depending on the temperature and pH of the medium.
biological catalysis extremely< высокой эффективностью и способностью ферментов четкие < выделять вещество, с которой они взаимодействуют.
The enzyme molecule contains a group of especially active amino acids that form the active center of the enzyme (129), which is capable of rapidly interacting only with the corresponding substance, the substrate (130). At the same time, the substrate is specific for a certain enzyme and is suitable, both in its structure and physico-chemical properties, to the active center “like a key to a lock”, and therefore the course of the reaction of the substrate with the active center is instantaneous. As a result of the reaction, an enzyme arises - a substrate complex, which then easily decomposes, forming new products. The substances formed are immediately separated from the enzyme, which restores its structure and becomes able to carry out the same reaction again. In a second, the enzyme reacts with millions of substrate molecules and does not itself break down.
Thanks to the enzyme biochemical reactions are possible at a very low concentration of a substance in the cell, which is extremely important, especially in cases where the body gets rid of harmful substances with the help of enzymes. The enzyme catalase, already known to you, destroys as many hydrogen peroxide molecules in one second as it takes 300 years under normal conditions.
Each enzyme catalyzes only a specific reaction. It should be noted that it does not determine the very possibility of the reaction, but only accelerates it millions of times, making its speed "cosmic". Further transformation of the substance formed as a result of one enzymatic reaction is carried out by the second enzyme, then the third, etc. The cells of animals and plants contain thousands of different enzymes, so they not only accelerate thousands of chemical reactions, but also control their course.
The rate of action of the enzyme depends on the temperature (effective - about +40 ° C) and certain pH values of the solution, specific to a particular enzyme. For most enzymes, the pH value ranges from 6.6 to 8.0, although there are exceptions. (Remember at what pH values certain enzymes work best.)
Raising the temperature to +50 ° C leads to the destruction of the active center of the enzyme and it permanently loses the ability to perform its functions. This is due to the fact that an irreversible violation of the tertiary structure of the protein occurs, and after cooling, the enzyme molecule does not restore its structure. This explains why even a short exposure to high temperature kills living beings. However, there are organisms whose enzymes have adapted to high temperatures. For example, in Africa, in hot springs with a water temperature of about +60 ° C, a representative of the thermosbena class of crustaceans lives and breeds, and some bacteria live even in water bodies where the water temperature is more than 70 ° C.
Destruction of the structure of the enzyme can cause poisons that enter the body even in very small quantities. These substances, called inhibitors (from lat. Ingibio - hold back), are irreversibly combined with the active center of the enzyme and thus block its activity.
One of the most powerful poisons, as you know, is cyanides (salts of hydrocyanic acid HCN), blocking the work of the respiratory enzyme cytochrome oxidase. Therefore, even a small amount of this substance, once in the body, causes death by suffocation. Inhibitors are heavy metal ions (Hg2 +, Pb2 +), as well as arsenic compounds, which form compounds with amino acids that are part of the active center of the enzyme.
