7 Key excerpts on "Classes of Enzymes"

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  eBook - ePub

  Medical Biochemistry

  • Antonio Blanco, Gustavo Blanco(Authors)
  • 2017(Publication Date)
  • Academic Press

    (Publisher)

  e ) (see p. 152). Enzymes are more effective than most inorganic catalysts; moreover, enzymes show a greater specificity of effect. Usually inorganic catalysts function by accelerating a variety of chemical reactions, whereas enzymes catalyze only a specific chemical reaction. Some enzymes act on different substances, but generally, these are compounds with similar structural characteristics and the catalyzed reaction is always of the same type.

  The substances that are modified by enzymes are called substrates .

  The specificity of enzymes allows them to have high selectivity to distinguish among different substances and even between optical isomers of a compound. For example, glucokinase, an enzyme that catalyzes d -glucose phosphorylation, does not act on l -glucose.

  Nomenclature and classification of enzymes

  Enzymes are often named by adding the suffix -ase to the name of the substrate that they modify. For example, amylase, urease, and tyrosinase are enzymes that catalyze reactions involving starch, urea, and tyrosine, respectively. Enzymes are also designated by the type of reaction catalyzed, for example, dehydrogenases and decarboxylases catalyze hydrogen and carboxyl removal from different substrates, respectively.

  Certain enzymes have arbitrary names; among them are saliva ptyalin, gastric pepsin, and pancreatic trypsin and chymotrypsin.

  The confusion created by the use of names according to different criteria, led the International Union of Biochemistry and Molecular Biology (IUBMB) to propose a classification system, to assign each enzyme a descriptive name and a number that allows its unequivocal identification. In this classification, six main Classes of Enzymes are considered according to the type of reaction catalyzed. Each class is divided into subclasses and sub-subclasses. The numeric code used to identify the enzyme consists of four components: the first number corresponds to the main enzyme class, the second refers to the subclass, the third denotes the sub-subclass (these numbers are assigned taking into account the nature of the atom groups involved in the reaction), and the fourth represents the enzyme order number in its sub-subclass. Periodically the IUBMB publishes the nomenclature of enzymes giving their systematic name, type of substrates used, and reaction catalyzed; the common or recommended trivial name and the code number is also indicated. To accurately identify an enzyme, the code number must be mentioned. In this book, the trivial name recommended by the IUBMB will be used, except for cases, in which the use has imposed another denomination.

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  Medical Biochemistry

  Human Metabolism in Health and Disease

  • Miriam D. Rosenthal, Robert H. Glew(Authors)
  • 2011(Publication Date)
  • Wiley

    (Publisher)

  CHAPTER 2

  ENZYMES

  2.1 THE NATURE OF ENZYMES

  Enzymes are catalysts that greatly increase the rate of chemical reactions and thus make possible the numerous and diverse metabolic processes that occur in the human body. Catalysts increase the rate of a reaction without affecting its equilibrium. Enzymes can increase the rate of physiological reactions by as much as 1010 -fold. They accomplish this feat by decreasing the amount of energy required for activation of the initial reactants (substrates), thereby increasing the percentage of substrate molecules that have sufficient energy to react (Fig. 2-1) .

  FIGURE 2-1

  Activation energy of a chemical reaction.

  With the exception of a few ribonucleic acid (RNA) molecules (ribozymes) that catalyze reactions involving nucleic acids, enzymes are proteins. Every enzyme has an active site that is composed of specific amino acid side chains which are brought into close proximity when the enzyme is folded into its active conformation. During the course of the reaction that it catalyzes, the enzyme’s active site stabilizes the transition state, which is an intermediate conformation between substrates and products. The interaction between active site and substrate(s) is thus responsible for the catalytic efficiency of the enzyme as well as its substrate specificity. After the reaction occurs, the products are released from the enzyme and the active site is available to bind additional substrate molecules.

  2.2 TYPES OF ENZYMES

  There are more than 2500 different enzymes in the human body. It is useful to group them into six major classes based on the type of reaction they catalyze.

  2.2.1 Oxidoreductases

  Oxidative reactions remove electrons, usually one or two electrons per molecule of substrate, while reductive reactions accomplish the converse. The substrate in an oxidation–reduction reaction may be a metal, as in the case of the one-electron oxidation of the ferrous ion of hemoglobin to the ferric ion of methemoglobin, or an organic compound as illustrated by the two-electron, reversible oxidation of lactate to pyruvate.

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  Biochemistry

  An Organic Chemistry Approach

  • Michael B. Smith(Author)
  • 2020(Publication Date)
  • CRC Press

    (Publisher)

  ry 1986, 261, 14313–14320.

  16 Escribano, J.; Grubb, A.; Mendez, E. Biochemical and Biophysical Research Communications 1988 , 1 55, 1424–1429.

  17 Escriano, J.; Lopex-Otin, C.; Hierpe, A.; Grubb, A.; Mendez, E. FEBS Letters 1990 , 2 66, 167–170.

  There are many enzymes that facilitate myriad chemical transformations. Once the activity in specific transformation has been confirmed, the enzyme is assigned an EC number : Enzyme Commission Number .18 The EC number is a numerical classification scheme based on the chemical reactions that are catalyzed. The name of an enzyme often refers to the chemical reaction it catalyzes: oxidases, reductases, aldolases, decarboxylases, etc. Two or more different enzymes that catalyze the same chemical reaction are called isozymes . There are six “top-level” (main) categories of enzymes, EC 1-EC 6. Oxidoreductases catalyze oxidation/reduction reactions (EC 1 ); transferases catalyze the transfer of a specific group from one molecule to another [donor to acceptor] (EC 2 ); hydrolases catalyzed the hydrolysis of a chemical bond (EC 3 ); lyases cleave chemical bonds by mechanisms other than hydrolysis or oxidation (EC 4 ); Isomerases catalyze the isomerization of one molecule to an isomer of that molecule (EC 5 ); and, ligases, which catalyze the formation of a covalent bond between two molecules EC 6). The actual EC number for a specific enzyme has four numbers that take the form 1.X.X.X, all beginning with the “top-level” categories 1–6. The second-level subclass and third-level sub-subclass indicate the specific bonds or functional groups involved in the reaction, and the fourth-level serial number defines the specific chemical reaction.

  18 (a) Webb, E.C. Enzyme Nomenclature 1992: Recommendation of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes , San Diego, 1992 ; (b) Also see Nath, N.; Mitchel J.B.O. BMC Bioinformati cs 20

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  eBook - ePub

  Chemistry of Biomolecules, Second Edition

  • S. P. Bhutani(Author)
  • 2019(Publication Date)
  • CRC Press

    (Publisher)

    3  

  Enzymes

  Learning Objectives In this chapter we will study •  Enzymes – Nomenclature and Classification •  Characteristics of Enzymes – Catalytic Power, Enzyme Specificity and Stereo-specificity •  Factors Influencing Enzyme Activity – Effect of Temperature and pH on Enzyme Activity; Effect of Substrate and Enzyme Concentration •  Cofactors and Coenzymes

  •  Some Important Coenzymes – NAD+ , NADP+ , Coenzyme A, Pyridoxal-5-phosphate, FMN, FAD, TPP

  •  Enzyme Inhibitors •  Mechanism to Enzyme Catalysis – Lock and Key Model •  Alcoholic Fermentation •  Glycolysis •  Citric Acid Cycle •  Introduction to Green Chemistry •  Biocatalysis–Importance in Green Chemistry and Chemical Industry

  3.1    INTRODUCTION

  We consume various food ingredients - carbohydrates, proteins and fats - any time we take our meals. These are digested and give us energy for performing the various metabolic functions in our body. The secret ingredient in living organisms is catalysis. The catalysts in living cells which facilitate the metabolic reactions are called enzymes. The miracle of life is that chemical reactions in the cell occur with great accuracy and at astonishing speed. Without the proper enzymes to process the food we eat, it might take us years to digest our breakfast or lunch.

  With the exceptions of some RNAs that have catalytic activity, all enzymes are proteins or their derivatives and vary in molecular weight from 10,000 up to 5,00,000. Of all the functions of proteins, catalysis is probably the most important. In the absence of catalysis, most reactions in biological systems would take place too slowly to provide products at an adequate speed for a metabolising organism. A number of enzymes have been isolated and obtained in a crystalline form. Other enzymes are derivatives of proteins formed by combination with some other group such as a metal. Enzymes containing a wide range of metals including iron, copper, zinc, manganese and magnesium are known. In other cases, the protein is combined with a non-proteinous organic molecule. We shall study these under cofactors.

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  Environmental Microbiology for Engineers

  • Volodymyr Ivanov(Author)
  • 2020(Publication Date)
  • CRC Press

    (Publisher)

  The trivial name of an enzyme includes the type of the substrate and the type of catalyzed reaction, and ends with “ase.” For example, an enzyme catalyzing the oxidation of alcohol by removal of hydrogen has the trivial name “alcohol dehydrogenase.” To identify thousands of enzymes, the enzyme classification (EC) numbers and names are used. Seven Classes of Enzymes are described in the following:

  1. 1. Oxidoreductases catalyze oxidation–reduction reactions. Oxidoreductases are important enzymes for environmental engineering because they catalyze oxidation, which is commonly used for the biodegradation of organic substances. Some subclasses of oxidoreductases important for environmental engineering are shown in Table 3.1 .
  2. 2. Transferases catalyze transfers of different chemical groups. They are most important in the biosynthesis of cellular substances and the regulation of cellular processes.
  3. 3. Hydrolases catalyze hydrolysis reactions where a molecule is split into two or more smaller molecules by the addition of water. These enzymes are important for environmental engineering because they catalyze the breakdown of biopolymers into monomers. Some subclasses of hydrolases are shown in Table 3.2 .
  4. 4. Lyases

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  Biotechnology for Beginners

  • Reinhard Renneberg, Vanya Loroch(Authors)
  • 2016(Publication Date)
  • Academic Press

    (Publisher)

  biological catalysts —turning substances into other products without undergoing any change themselves.

  Due to enzymes, chemical reactions reach their equilibrium much faster and may be speeded up by a factor of up to 10 12 . It is the activity of enzymes that makes life possible at all. Turning sugar into alcohol and carbon dioxide is a matter of seconds for the enzymes in yeast cells, but without them it would take hundreds of years and be virtually impossible. Enzymes are highly effective, high-performing biocatalysts .

  In cells ranging in size between a tenth and a thousandth of a millimeter, thousands of coordinated enzymatic reactions take place every second (See Figs. 4.5 and 4.6 in Chapter 4 ).

  This can only work because each of the molecular catalysts involved recognizes its specific substrate among thousands of other compounds within a cell and turns it to a specific product. This process, called biocatalysis, takes place in the active site of the enzyme.

  Nearly all biological catalysts are proteins. However, RNA (ribonucleic acid) can also act as a biocatalyst (see Chapter: The Wonders of Gene Technology ). These ribozymes often break down other RNA molecules. RNA can also be used to build artificial aptamers that bind to designated compounds (see Chapter: Analytical Biotechnology and the Human Genome ).

  As early as 1894, the German chemist Emil Fischer (1852–1919), who was later awarded the Nobel Prize (Fig. 2.4 ), postulated that enzymes recognize their substrates on a lock-and-key principle . If the active site of an enzyme lies in a dimple (cavity, crevice) on the molecule’s surface, the substrate molecule must fit accurately, just like a key into its lock. Even slightly modified molecules will no longer interact with the enzyme. Lock-and-key is a viable preliminary explanation for the high substrate specificity of enzymes. It also explains why the shape of competing enzyme inhibitors (e.g., penicillin) strongly resembles that of the original substrate. Like a skeleton key, they block the active site of an enzyme (competitive inhibition

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  Pharmaceutical Biotechnology

  A Focus on Industrial Application

  • Adalberto Pessoa, Michele Vitolo, Paul Frederick Long, Adalberto Pessoa, Michele Vitolo, Paul Frederick Long(Authors)
  • 2021(Publication Date)
  • CRC Press

    (Publisher)

  The quantitative phase, which refers to the establishment of mathematical models for quantifying enzyme activity, began at the end of 19th century, with the first quantitative model – known as Michaelis-Menten’s model – established in 1913 and improved by Briggs and Haldane in 1926. In the same year, Sumner crystallized urease and concluded that it was a protein. The protein character of enzymes became clear during the 20th century as new enzymes were discovered, described and chemically characterized.

  The applied with planning phase, in spite of its beginning in the first decade of the 20th century – with the use of amylase and invertase for the hydrolysis of starch and sucrose, respectively – had renaissance during the 1940s when new enzymes appeared in the market and basic knowledge about them was improving.

  It must be borne out that all known enzymes are of protein in nature, but not all protein has catalytic capability. Recently, it was discovered that some ribonucleic acids, the so-called ribozymes, also have catalytic capacity. Their role is circumvented to the modification of some kinds of mRNA before translation of proteins at the ribosome. Ribozymes can be employed in gene therapy (Purich, 2010).

  Like all proteins, enzymes are polymers of amino acids linked through peptic bonds. The interactions amongst chemical groups present as side chains of the amino acids that constitute the enzyme can lead the protein to acquire higher order tertiary structure, which allows the enzyme to interact with some other molecules (substrates, co-factors and alike), whose structures are modified to allow the biochemical reaction to proceed.

  15.2   Enzyme Specificity

  In enzyme-catalyzed reactions, enzymes, in general, specifically accept one substance as the substrate. Even when an enzyme catalyzes the conversion of more than one substrate, the reaction rates are different. For instance, glucoamylase catalyzes the breakdown of maltose at maximum rate whereas the activity of this enzyme on nigerose and isomaltose is only 7% and 4%, respectively (Kulp, 1975).

  Substrate specificity is linked to a region of the enzyme molecule called the active site. The substrate – a reagent which will be modified by the enzyme – fits into the active site, and it is transformed into another compound (called the product). There are two theories explaining enzyme-substrate interactions. One of them – the Key-Lock theory proposed by Fisher at the beginning of the 20th century– states that the substrate (key) enters the active site (lock) following its modification. This theory requires that two conditions must be met, i.e., complementarily between the substrate and the active site and that the substrate and the active site must have compatible polarity and size. The other theory proposed by Koshland during the 1960s is called the Theory of Induced Fitting – proposes that the structure of the active site would be a region of the enzyme molecule susceptible to conformational modification as the substrate nears it, so facilitating the interaction between them. Essentially, both theories only differ on the particular characteristics attributed to the active site, i.e., rigid envisaged by Fisher or flexible as pictured by Koshland.

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