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USM KLE IMP, MD PHASE –I, YEAR-I 2020-21 MOLECULAR BIOLOGY and PHARMACOLOGY COURSE GSL – 1: Chemical Pathology

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USM KLE IMP, MD PHASE –I, YEAR-I 2020-21 MOLECULAR BIOLOGY and PHARMACOLOGY COURSE GSL – 1: Chemical Pathology USM KLE IMP, MD PHASE –I, YEAR-I 2020-21 MOLECULAR BIOLOGY AND PHARMACOLOGY COURSE GSL – 1: Chemical pathology Dr Sadanand B Patil, HOD, Dept. of Biochemistry. Introduction and classification of enzymes Enzymes • Enzymes are defined as ‗biocatalysts‘ synthesized by living cells. They are protein in nature (exception—RNA acting as ribozyme), colloidal and thermo labile in character and specific in their action • Found in all tissues and fluids of the body – Extracellular, intracellular and membrane bound • Biological catalysts i. e., substances of biological origin that accelerate chemical reactions – Catalyze biochemical reactions allowing the metabolism to proceed at a rate optimal to support life – Mammalian enzymes have evolved to catalyze reactions under physiological conditions [i.e., at moderate temperature (37°C), around neutral pH, low concentration in aqueous environment] • Nearly all enzymes are protein macromolecules (Exception: Ribozymes) – Heat labile molecules – Enzymes are subjected to denaturation at high temperature, low pH or High pH – May be present as simple proteins, conjugated proteins or multienzyme complexes • Increase the rate of reaction by providing alternate pathway of lower activation energy to get from reactants to products • They participate in chemical transformation without undergoing any net chemical change during the reaction (= Are regenerated during the course of reaction) • Do not alter equilibrium constant (Keq) of the reaction • Enzymes are highly specific both in the reactions that they catalyze and in their choice of reactants, which are called substrates • Have very high catalytic efficiency • Typically, each enzyme molecule is capable of transforming 100 to 1,000 substrate molecules into product each second • Enzymes are very potent • They remain unchanged at the end of the chemical reaction and can be reused • A small amount of enzyme can bring about a large amount of chemical reaction • Some enzymes require heat stable co-enzymes / co-factors for their activity Apoenzyme + Co-enzyme → Holoenzyme • Enzymes can have multiple forms know as Isoenzymes • Activities of some enzymes regulated . RECOMMENDED NAME: Convenient for everyday use – By adding the suffix ‗–ase‘ to the substrate on which they act – Eg: Maltase, Lactase, amylase, lipases, proteases and urease etc. – By adding the suffix ‗–ase‘ to the type of action performed on the substrate – Eg: Glutamate dehydrogenase, Pyruvate decarboxylase – Some are having trivial names – Eg: pepsin, trypsin, pthalin etc SYSTEMATIC NAME • In 1972, The International Union of Biochemistry and Molecular Biology (IUBMB) developed IUBMB system of nomenclature of enzymes • IUBMB classified enzymes in to six major classes (1 to 6 in that order) based on the types of reaction catalyzed • Each class is further divided in to sub-classes, sub-sub classes, and individual enzymes • The IUBMB names are unambiguous and informative, but are frequently too cumbersome to be of general use IUBMB nomenclature • Individual enzymes are assigned a four digit number preceded by the letters EC for Enzyme Commission – First digit represents the class – Second digit stands for the subclass – Third digit is the sub-sub class (or) sub group – Fourth digit gives the serial number of the particular enzyme in the list • Each enzyme is given a specific name indicating the substrate, coenzyme (if any) and the type of reaction catalyzed by the enzyme IUBMB classification of Enzymes No ENZYME CLASSES (IUBMB) 1 Oxidoreductases 2 Transferases 3 Hydrolases 4 Lyases 5 Isomerases 6 Ligases Class 1. Oxido-reductases: Catalyze oxidation reduction reactions (Transfer of hydrogen, transfer of electrons and addition of oxygen) – Dehydrogenases: Lactate dehydrogenase (LDH), Alcohol dehydrogenase, Succinate dehydrogenase – Oxidases: Cytochrome oxidase, L-amino acid oxidase – Peroxidases Class 2. Transferases: Catalyze transfer functional groups between donor and acceptor molecules – Kinases: Hexokinase, Glucokinase, Creatine kinase (CK) – Aminotransferases: Aspartate transaminase (AST), Alanine transaminase (ALT) Class 3. Hydrolases: They catalyze hydrolysis of substrate by addition of water across a bond (i.e., Hydrolytic reactions) – Peptidases: Pepsin, Trypsin – Gycosidases: Maltase, Lactase – Esterases: Cholinesterase – Phosphatases: Glucose-6-phosphatase All digestive enzymes are hydrolases Class 4. Lyases: Catalyze non-hydrolytic removal of groups from substrates or reverse reactions At times they produce double bonds – Fumarase, Aldolase, Histidase etc – Decarboxylases: Glutamate decarboxylase – Synthases: Citrate synthase Synthases create new bond, (ATP independent) Class 5. Isomerases: Interconversion of isomers by intramolecular rearrangements – Isomerases: Phosphohexose isomerase – Epimerases: Phosphopentose epimerase Class 6. Ligases: Catalyze reactions in which two chemical groups are joined (or ligated) with the use of energy from ATP – Carboxylases: Pyruvate carboxylase – Synthetases: Glutamine synthetase CHEMICAL NATURE OF ENZYMES All enzymes are invariably protein macromolecules (Exception: Ribozymes) • Monomeric enzymes: Made up of single polypeptide chain E.g., Trypsin, Ribonuclease etc • Oligomeric enzymes: Made up of two or more polypeptide chains (subunits) E.g., Lactate dehydrogenase (4 subunits), Creatine kinase (dimer) Multienzyme complex: Several enzyme activities catalyzing different consecutive reactions are located at different sites of the same macromolecule E.g., Pyruvate dehydrogenase complex (Contains 3 enzyme activities), Fatty acid synthase complex (has 6 enzyme activities) • The catalytic activity of many enzymes depends on the presence of small molecules— additional non-protein chemical component for enzymic activity The enzyme without its nonprotein moiety is termed an apoenzyme and is inactive The complete, catalytically active enzyme with its nonprotein component is called a holoenzyme • If the nonprotein moiety is a metal ion such as Zn2+or Fe2+, it is called a cofactor – For example, the enzyme carbonic anhydrase, requires Zn2+ for its activity • If the nonprotein moiety is a small organic molecule, it is termed a coenzyme – Mostly they are derivatives of water soluble vitamines • For example, NAD+ contains niacin, coenzyme A contains pantothenic acid and FAD contains riboflavin – They bind to the active site of the enzyme and participate in catalysis • Coenzymes can be either tightly or loosely bound to the enzyme – If tightly bound, they are called— prosthetic groups (FAD is an example) • Remain associated with their enzymes even between reaction cycles, and returned to its original form – Loosely associated coenzymes are called— cosubstrates (NAD+ is an example) • They bind to and are released from the enzyme just as substrates and products. • Isoenzymes • Isoenzymes – are are multipal forms of (isomers) of the same enzymes that differ in amino acid sequence but catalyze the same chemical reaction. • They have similar catalytic activity, but are different biochemically or immunologically. • Different forms may be differentiated from each other based on certain physical properties – electrophoretic mobility, – differences in absorption properties – or by their reaction with a specific antibody – kinetic properties. References: 1. Pankaja Naik, Test Book Of Biochemistry, 3rd edition. 2. Lippincott‘s Illustrated Reviews : Biochemistry, 6th edition. 3. Textbook of Biochemistry, DM Vasudevan, 7th edition. USM KLE IMP, MD PHASE –I, YEAR-I MOLECULAR BIOLOGY AND PHARMACOLOGY COURSE GSL – 1: Chemical pathology Avinash A K Math, Dept. of Biochemistry. Principles & Methods of Biomolecule Separation Principles of Purification Aim : One particular biomolecule form a mixture of biomolecules/ Isolate one particular protein from a mixture of proteins Different properties of protein or biomolicules are used: Eg; Charge differences, Solubility differences, Size differences, Affinity to any particular substance etc Centrifugation A centrifuge is used to separate particles or macromolecules like : -Cells -Sub-cellular components -Proteins -Nucleic acids Basis of separation: -Size -Shape -Density Methodology: -Utilizes density difference between the particles/macromolecules and the medium in which these are dispersed (solid from liquid) -Dispersed systems are subjected to artificially induced gravitational fields Principle of centrifugation In a solution, particles whose density is higher than that of the solvent sink (sediment), and particles that are lighter than it float to the top. To take advantage of even tiny differences in density to separate various particles in a solution, gravity can be replaced with the much more powerful―centrifugal force‖ provided by a centrifuge. Centrifuges are classified into two categories: • Laboratory centrifuges • Preparative centrifuges • Used commonly for the separation of plasma, serum from blood cells • To separate a supernatant from a precipitate during analytic reaction • To separate two immiscible liquids Laboratory centrifuges • Used for small-scale separation and particle free sample preparations • The material to be centrifuged is distributed in centrifuge tubes • Tubes are attached rotor in a symmetric manner • Two types of rotors: fixed rotors and swing out rotors • Induced gravitational field move particles towards the bottom of the tubes • Typical rotation speeds:1,000 – 15,000 rpm • Induced gravitational field is measured in terms of the G value • G value depends on the rotation speed as well as the
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