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Description : Enzyme is the biological macro-molecules that speed up the rate of biochemical reactions without undergoing any change. They are also called biological catalysts. An enzyme is a highly selective catalyst that greatly accelerates both the rate and specificity of metabolic reactions.

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Published on : Dec 12, 2020 | Views : 5917 | Downloads : 27

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UNIVERSITY OF KARACHI Faculty: Faculty of pharmacy and pharmaceutical scienceS Department: Department of pharmacology Course No: PHL-309 COURSE TITLE: PHARMACOLOGY-Biochemistry- I Teacher: DR. AFSHAN SIDDIQ TOPIC: ENZYMES
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First Proff. Section A (Evening) By Group 6: » Fiza Aqeel » Fiza Aslam » Fiza Salman » Gul Naz » Hafiz Abdul Wasay » Hafiza Ayesha Sadiq » Hafsa Ahmed » Hanzala » Hamza Mudassir
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ENZYMES Enzyme are the biological macro-molecules which speed up the rate of biochemical reactions without undergoing any change. They are also called as biological catalysts. An enzyme is a highly selective catalyst that greatly accelerates both the rate and specificity of metabolic reactions.
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PROPERTIES OF ENZYMES The properties of an enzymes can be summarized as: » Catalytic Property: Enzymes have extra ordinary catalytic power. They are active in small quantities. A small amount of enzyme is enough to convert a large quantity of substrates. The enzymes remain unchanged after the reaction. The turnover number of enzymes ranges from 0.5 to 600000. › Turnover number: The number of substrate molecules converted by one molecule of enzyme per second when its active site is saturated with the substrate.
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PROPERTIES OF ENZYMES » Specificity: Enzymes are very specific in their action. Particular enzymes acts on particular substrate only. Enzymes are also specific to a particular type of reaction. Enzymes show different types of specificity such as bond, group, substrate stereoscopic, geometric and cofactor specificity.
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PROPERTIES OF ENZYMES » Reversibility: Most of the enzymes catalyzed reactions are reversible. The reversibility of the reaction depends upon the requirements of the cell. In some cases, there are separate enzymes for forward and reverse reaction. » Sensititiveness to heat and temperature: Enzymes are very sensitive to heat and temperature i.e thermolabile. Correct temperature for the maximum activity is called optimum temperature. At higher temperature the enzyme is denatured or destroyed. The enzymatic activity increases in temperature up to a certain level.
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» Sensitiveness pH: Ezymes are specific for their pH requirements. Some enzymes are active in acidic pH( below7), some in basic pH (above 7) and some others are in neutral pH. The correct pH on an enzyme is denoted as Optimum pH. M
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TYPES OF ENZYMES Enzymes are generally proteinaceous in nature. They may entirely consist of protein i.e amylase or may contain a non-protein part with protein. The enzymes can be divided into following types: » Simple Enzyme: If an enzyme consists only of protein it is called simple enzyme also called proteozyme. » Conjugated Enzyme: Is an enzyme contains another group with protein it is called conjugated enzymes.
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MECHANISM OF ACTION OF ENZYMES » Introduction: Michaelis and Menten have proposed a hypothesis for enzyme action, which is most acceptable. » Hypothesis: According to their hypothesis, the enzyme molecule (E) first combines with a substrate molecule (S) to form an enzyme-substrate (ES) complex which further dissociates to form product (P) and enzyme (E) back. Enzyme once dissociated from the complex is free to combine with another molecule of substrate and form product in a similar way.
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MECHANISM Enzyme is active in catalytic action of biochemical reaction. They act on substrate and forms a complex after interactions with the enzyme is called active center. The enzyme and substrate forms a complex at the active centre. An enzyme attracts substrate to its active site, catalyzes the chemical reaction by which products are formed and, then allows the product to disassociate (separate from the enzyme surface). The combination formed by an enzyme and its substrate is called the enzyme-subtrate complex.
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When two substrate and one enzyme are involved, the complex is called a ternary complex; one substrate and one enzyme are called a binary complex. The substrate are attracted to the active site by electrostatic and hydrophobic forces, which are called non-covalent bonds because they are physical attractions and not chemical bond.
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ENERGY OF ACTIVATION This binding action makes both enzyme and substrate stable. The interaction between substrate and enzyme may be either ionic bonds and hydrogen bonds or Van der Waal forces. The active sites of enzyme have some special groups such as NH2 COOH, -SH etc. which bind the substrate though above bonds to form a transitional (intermediate) compound called enzyme-substrate complex (ES).This reaction is exergonic and releases some energy which raises energy level of the substrate molecule. Thus, activating the substrate molecule and the phenomenon is known as activation energy or energy of activation.
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TYPES OF MECHANISM OF ENZYMES There are two types of mechanisms involved ro explain substrate-enzyme complex formation. » Template or Lock-and-Key Model: This model was originally proposed by Fischer which states that: “The active site already exists in proper conformation even in absence of substrate. Thus the active site by itself provides a rigid, pre-shaped template fitting with the size and shape of the substrate molecule. Substrate fits into the active site of an enzyme as the key fits into the lock and hence it is called the lock-and-key model.
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LOCK-AND-KEY MODEL This model proposes that substrate binds with rigid pre-existing template of the active site, provides additional groups for binding other ligands.
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INDUCED-FIT OR KOSHLAND MODEL » Induced-Fit or Koshland Model: Because of the restrictive nature of lock-and-key model, another model was proposed by Koshland in 1963 which is known as induced-fit model. The important feature of this model is the flexibility of the region of active site. “According to this, active site doesn’t possesses a rigid, performed structure on enzyme to fit the substrate. On the contrary, the substrate during its binding induces conformational changes in the active site to attain the final catalytic shape and form”. This model explains several matters related to enzyme action such as: › Enzymes become inactive on denaturation.
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› Competitive inhibition and Allosteric modulation. › Saturation Kinetics.
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PARTS OF ENZYMES An enzymes consists of › Active Site › Substrate › Co-factor › Co-enzyme › Apo enzyme › Holo enzyme
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ACTIVE SITE
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SUBSTRATE
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CO-ENZYME AND CO-FACTOR
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APO-ENZYME AND HOLO-ENZYME
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CLASSIFICATION OF ENZYMES » CLASSIFICATION OF ENZYMES: According to the type of reactions that the enzymes catalyze, enzymes are classified into seven categories, which include: 1. Oxidoreductases. 2.Transferases. 3. Hydrolases. 4. Lyases. 5. Isomerases. 6. Ligases.
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OXIDOREDUCTASES 1. OXIDOREDUCTASE: Oxidoreductases consist of a large class of enzymes catalyzing the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) molecule, generally taking nicotinamide adenine dinucleotide phosphate (NADP) or nicotinamide adenine dinucleotide (NAD) as cofactors. » REACTION TYPE:
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TRANSFERASES 2. TRANSFERASE: Transferases are a class of enzymes that transfer specific functional groups from one molecule (donor) to another (acceptor). Transferases are implicated in hundreds of different biochemical pathways, and are essential to some of most important processes in lives. Transferases participate in a myriad of cell reactions and are also utilized during translation. Mechanistically, an enzyme catalyzing the following reaction would be considered as a transferase. » REACTION TYPE:
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HYDROLASES HYDROLASES Hydrolase is a class of hydrolytic enzymes that are commonly used as biochemical catalysts utilizing water to break a chemical bond in order to divide a large molecule into two smaller ones. Hydrolases are pivotal for the body since they digest large molecules into fragments for synthesis, excrete waste materials, and provide carbon sources for the production of energy, during which many biopolymers are converted to monomers. Some hydrolases could release energy when they take effect. A number of hydrolases, especially proteases, are connected with biological membranes as peripheral membrane proteins or affixed through a single transmembrane helix. Some others are multi-span transmembrane ones. The names of hydrolases are systematically formed as "substrate hydrolase, while the commonly adopted names are typically in a form of "substratease”.In biochemistry, a hydrolase catalyzes the hydrolysis of a chemical bond like the following reaction: » REACTION TYPE:
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LYASES INTRODUCTION: Lyase is an enzyme catalytically aiding in breaking various chemical bonds by means of an "elimination" reaction, other than hydrolysis and oxidation. This reaction often results in the formation of a new cyclic structure or a new double bond, and a reverse reaction called a "Michael addition" might also possibly happen under the catalysis of lyase. Lyases are different from other enzymes for only one substrate is required for the reaction in one direction, but two substrates are essential for the reverse reaction. Lyases can be commonly observed in the reactions of the Citric Acid Cycle (Krebs cycle) and in glycolysis. Lyases are systematically named as "substrate group-lyase", such as decarboxylase, dehydratase, aldolase, etc. » REACTION: An enzyme that catalyzed this reaction would be a lyase: ATP → cAMP+ Ppi
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Classification of Lyases: In the EC number classification of enzymes, EC 4 could represent lyases, which can be further classified into seven subclasses.
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ISOMERASES INTRODUCTION: An enzyme that catalyzes the isomerization changes in a molecule, thereby aid in the conversion of a chemical compound from one isomeric form to another. Isomers present in many varieties can generally be divided into structural isomers and stereoisomers. Structural isomers have a different sequence and/or different connectivity of bonds from one another. Stereoisomers with the same ordering of individual bonds and the same connection type differ in the three-dimensional arrangement of bonded atoms. » REACTION: The general form of such a reaction is as follows: A–B → B–A Example:
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CLASSIFICATION OF ISOMERASES CLASSIFICATION OF ISOMERASES Isomerases have been assigned EC number of EC 5 and are further classified into six Subclasses. a. Racemases, epimerases: Isomerases in EC 5.1 include racemases and epimerases, both of which invert stereochemistry at the target chiral carbon. Racemases mainly act upon molecules with only one chiral carbon for stereochemical inversion, whereas epimerases target molecules with multiple chiral carbons by acting on one of them. b. Cis-trans isomerases: Isomerases in EC 5.2 are enzymes that catalyze the isomerization of cis trans isomers, which are not distinguished by absolute configuration but rather by the position of substituent groups with respect to a plane of reference, like a double bond or a ring structure. Molecules with substituents on the same side belong to cis isomers, while trans isomers have groups on opposite sides. c. Intramolecular oxidoreductases: Intramolecular oxidoreductases are categorized into EC 5.3 and they catalyze the transfer of electrons from one part of the molecule to another, meaning that the oxidation of one part of the molecule and the reduction of another part are concurrently catalyzed by this type of enzymes.
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d. Intramolecular transferases: Intramolecular transferases (mutases) in EC 5.4 accelerate the transfer of functional groups from one part of a molecule to another. According to the functional groups the enzyme transfers, they can be further classified into five groups. e. Intramolecular lyases: Isomerases in EC 5.5 are intramolecular lyases that catalyze reactions where a group can be regarded as eliminated from one part of a molecule, leaving a double bond, while keeping covalently attached to the molecule. Some of these types of reactions involve the destruction of a ring structure. » MECHANISM OF ISOMERASES: Different types of isomerases have different action modes, mainly including ring expansion and contraction via tautomers, epimerization, intramolecular transfer, and intramolecular oxidoreduction.
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LIGASE INTRODUCTION: In biochemistry, ligase, also called synthetase, is an enzyme catalyzing the joining of two large molecules through the formation of a new chemical bond such as C-O, C-S, C-N, or the linking together of two compounds, usually accompanied with the hydrolysis of a small attached chemical group to one of the larger molecules. This procedure usually assimilates the needed energy from the cleavage of an energy-rich phosphate bond, involves the conservation of chemical energy and offers a linkage between energy-requiring synthetic processes and energy-yielding breakdown reactions. In most cases, the simultaneous conversion of ATP to adenosine ADP functions as a source of energy. »REACTION: The ligase catalyzed reaction has a general formulation as following:
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» NOMENCLATURE: The common names of ligases often contain the word "ligase", like DNA ligase, a frequently used enzyme in molecular biolaboratory to link DNA fragments together. Synthetase is another commonly adopted name for ligases since they are applied in the synthesis of new molecules. Synthetases sometimes are distinguished from synthases and sometimes treated as synonym of synthases. From the view of definition, nucleoside triphosphates such as ATP, GTP, CTP, TTP, and UTP, are employed by synthetases to produce energy, whereas synthases do not use nucleoside triphosphates. » CLASSIFICATION: Ligases are classified as EC 6 in the EC number classification of enzymes. Ligases can be further classified into six subclasses: EC 6.1 includes ligases used to form carbon-oxygen bonds EC 6.2 includes ligases used to form carbon-sulfur bonds EC 6.3 includes ligases used to form carbon-nitrogen bonds (including argininosuccinate synthetase) EC 6.4 includes ligases used to form carbon-carbon bonds EC 6.5 includes ligases used to form phosphoric ester bonds EC 6.6 includes ligases used to form nitrogen-metal bonds, as in the chelatases
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ENZYME COMMISSION SYSTEM The Enzyme Commission Number (E.C Number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. The chemical reaction catalyzed is the specific property that distinguishes one enzyme from another. E.C number specify enzyme-catalyzed reactions. As a system of enzyme nomenclature, every E.C number is associated with a recommended name for the respective enzyme. EC numbers donot specify enzymes but enzyme-catalyzed reactions. If different enzymes (for instance from ddifferent organisms) catalysed the same reaction, then they receive the same EC number.
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HISTORY OF ENZYME COMMISSION SYSTEM The enzyme nomenclature scheme was developed starting in 1955, when the International Congress of Biochemistry on Brussels set up an Enzyme Commission. The first version was published in 1961. The current sixth edition, published by the International Union of Biochemistry and Molecular Biology in 1992. Supplements 1-4 were published 1993-1999. Subsequent Supplements have been published electronically, at the website of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. In August 2018, the Enzyme Commission reorganized the nomenclature by adding the top-level EC 7 category describing translocation.
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FORMAT OF EC NUMBERS Every enzyme code consists of the letters “EC” followed by four numbers separated by periods. Those numbers represent a progressively finer classification of the enzyme. Preliminary EC numbers exist and have an n as part of the fourth (serial) digit (e.g. EC 3.5.1.n3) FOR EXAMPLE, the tripeptide aminopeptidases have the code. » “EC 3.4.11.4”, whose components indicate the following groups of enzymes: » EC 3 enzymes are hydrolases ( enzymes that use water to break up some other molecules. » EC 3.4 are hydrolases that act on peptide bonds. » EC 3.4.11 are those hydrolases that cleave up the amino-terminal amino acid from a polypeptide. » EC 3.4.11.4 are those that cleave off the aminoaminoterminal amnio termianl end from a acid tripeptide.
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EXAMPLES OF EC COMMISSION NUMBERS OXIDOREDUCTASES (EC 1) Oxidoreductases are classified as EC1 in the EC number classification of enzymes. › This class can be further divided into 22 sub-classes which include E.C 1.1 to E.C 1.97. To this class belong all enzymes catalysing oxidoreduction reactions. The second figure in the code number of the oxidoreductases, unless it is 11, 13, 14 or 15, indicates the group in the hydrogen (or electron) donor that undergoes oxidation: 1 denotes a -CHOH- group, 2 a -CHO or -CO-COOH group or carbon monoxide. › The third figure, except in subclasses EC 1.11, EC 1.13, EC 1.14 and EC 1.15, indicates the type of acceptor involved: 1 denotes NAD(P)+, 2 a cytochrome, 3 molecular oxygen, 4 a disulfide, 5 a quinone or similar compound, 6 a nitrogenous group, 7 an iron-sulfur protein and 8 a flavin. › In subclasses EC 1.13 and EC 1.14 a different classification scheme is used and sub-subclasses are numbered from 11 onwards.
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TRANSFERASES (EC 2) Transferases are enzymes transferring a group. A methyl group or a glycosyl group, from one compound (generally regarded as donor) to another compound (generally regarded as acceptor). The systematic names are formed according to the scheme donor: acceptor grouptransferase. The common names are normally formed according to acceptor grouptransferase or donor grouptransferase. The donor is a cofactor (coenzyme) charged with the group to be transferred. The second figure in the code number of transferases indicates the group transferred; a one-carbon group in EC 2.1, an aldehydic or ketonic group in EC 2.2, an acyl group in EC 2.3 and so on.The third figure gives further information on the group transferred. Subclass EC 2.1 is subdivided into methyltransferases (EC 2.1.1), hydroxymethyl- and formyltransferases (EC 2.1.2) and so on; only in subclass EC 2.7, does the third figure indicate the nature of the acceptor group.
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HYDROLASES (EC 3) These enzymes catalyse the hydrolytic cleavage of C-O, C-N, C-C and some other bonds, including phosphoric anhydride bonds. Although the systematic name always includes hydrolase, the common name is, in many cases, formed by the name of the substrate with the suffix -ase. The second figure in the code number of the hydrolases indicates the nature of the bond hydrolysed; EC 3.1 are the esterases; EC 3.2 the glycosylases, and so on.The third figure normally specifies the nature of the substrate. In the esterases the carboxylic ester hydrolases (EC 3.1.1), thiolester hydrolases (EC 3.1.2), phosphoric monoester hydrolases (EC 3.1.3); in the glycosylases the O-glycosidases (EC 3.2.1), N-glycosylases (EC 3.2.2). Exceptionally, in the case of the peptidyl-peptide hydrolases the third figure is based on the catalytic mechanism.
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LYASES (EC 4) Lyases are enzymes cleaving C-C, C-O, C-N, and other bonds by elimination, leaving double bonds or rings, or conversely adding groups to double bonds. The systematic name is formed according to the pattern substrate group-lyase. The second figure in the code number indicates the bond broken: EC 4.1 are carbon-carbon lyases, EC 4.2 carbon-oxygen lyases and so on.The third figure gives further information on the group eliminated (e.g. CO2 in EC 4.1.1, H2O in EC 4.2.1).
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ISOMERASES (EC 5) These enzymes catalyse geometric or structural changes within one molecule. According to the type of isomerism, they may be called racemases, epimerases, cis-trans-isomerases, isomerases, tautomerases, mutases or cycloisomerases.The subclasses are formed according to the type of isomerism, the sub-subclasses to the type of substrates.
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LIGASES (EC 6) Ligases are enzymes catalysing the joining together of two molecules coupled with the hydrolysis of a diphosphate bond in ATP or a similar triphosphate. The systematic names are formed on the system X:Y ligase (ADP-forming). In a few cases in Group 6, where the reaction is more complex or there is a common name for the product, a synthase name is used (e.g. EC 6.3.2.11 and EC 6.3.5.1).The second figure in the code number indicates the bond formed: EC 6.1 for C-O bonds (enzymes acylating tRNA), EC 6.2 for C-S bonds (acyl-CoA derivatives). Sub-subclasses are only in use in the C-N ligases.In a few cases it is necessary to use the word other in the description of subclasses and sub-subclasses.
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Ligases are classified as EC 6 in the EC number classification of enzymes. Ligases can be further classified into six subclasses: EC 6.1 includes ligases used to form carbon-oxygen bonds EC 6.2 includes ligases used to form carbon-sulfur bonds EC 6.3 includes ligases used to form carbon-nitrogen bonds (including argininosuccinate synthetase) EC 6.4 includes ligases used to form carbon-carbon bonds EC 6.5 includes ligases used to form phosphoric ester bonds EC 6.6 includes ligases used to form nitrogen-metal bonds, as in the chelatases
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