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Enzyme Class 1 Download Enzymes General Introduction MI 201 Unit:2 By: Dr. MohammedAzim Bagban Assistant Professor C. U. Shah Institute of Science Ahmedabad What is an enzyme? globular protein which functions as a biological catalyst, Active speeding up reaction site rate by lowering activation energy without being affected by the reaction it catalyse Enzymes are protein in nature (?) Globular protein. Ribozymes are RNA molecule with enzymatic activity. Catalytic behaviour of any enzyme depends upon its primary, secondary, tertiary or quaternary structure. Enzymes of digestive tract and those found in blood are present in inactive form called zymogen or proezymes. Etymology and history • French chemist Anselme Payen was the first to discover an enzyme, diastase, in 1833. • A few decades later, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that this fermentation was caused by a vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms. • The conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley, who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry. Enzyme Nomenclature . An enzyme's name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase. Examples are lactase, alcohol dehydrogenase and DNA polymerase. Different enzymes that catalyze the same chemical reaction are called isozymes. The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers; each enzyme is described by a sequence of four numbers preceded by "EC", which stands for "Enzyme Commission". The first number broadly classifies the enzyme based on its mechanism. Enzyme Nomenclature The top-level classification is: . EC 1, Oxidoreductases: catalyze oxidation/reduction reactions . EC 2, Transferases: transfer a functional group (e.g. a methyl or phosphate group) . EC 3, Hydrolases: catalyze the hydrolysis of various bonds . EC 4, Lyases: cleave various bonds by means other than hydrolysis and oxidation . EC 5, Isomerases: catalyze isomerization changes within a single molecule . EC 6, Ligases: join two molecules with covalent bonds. Active site Enzymes are composed of long chains of amino acids that have folded into a very specific three-dimensional shape which contains an active site. An active site is a region on the surface of an enzyme to which substrates will bind and catalyses a chemical reaction. Enzymes are highly specific for the type of the reaction they catalyze and for their substrate. Co-factor (Prosthetic group) A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's activity as a catalyst, a substance that increases the rate of a chemical reaction. Cofactors can be considered "helper molecules" that assist in biochemical transformations. Cofactors can be divided into two types: inorganic ions and complex organic molecules called coenzymes. Coenzymes are further divided into two types. The first is called a "prosthetic group", which consists of a coenzyme that is tightly or even covalently, and permanently bound to a protein. he second type of coenzymes are called "cosubstrates", and are transiently bound to the protein. Cosubstrates may be released from a protein at some point, and then rebind later. Coenzyme examples Cofactor examples Distribution of Enzyme in cells Enzyme Intracellular Extracellular Enzyme Enzyme Soluble Particulate Periplasmic Enzymes Enzymes Enzymes Extracellular Enzymes An exoenzyme, or extracellular enzyme, is an enzyme that is secreted by a cell and functions outside that cell. Exoenzymes are produced by both prokaryotic and eukaryotic cells and have been shown to be a crucial component of many biological processes. Most often these enzymes are involved in the breakdown of larger macromolecules. The breakdown of these larger macromolecules is critical for allowing their constituents to pass through the cell membrane and enter into the cell. For humans and other complex organisms, this process is best characterized by the digestive system which breaks down solid food. Bacteria and fungi also produce exoenzymes to digest nutrients in their environment, and these organisms can be used to conduct laboratory assays to identify the presence and function of such exoenzymes. Some pathogenic species also use exoenzymes as virulence factors to assist in the spread of these disease-causing microorganisms. Intracellular Enzymes An endoenzyme, or intracellular enzyme, is an enzyme that functions within the cell in which it was produced and the majority of enzymes fall within this category. Soluble Enzymes: Found within the cytoplasm and associated with metabolic activity of cytoplasm. Particulate enzymes: Found within embedded in cell membrane. Associated with metabolic activity leading to ATP generation. Periplasmic enzymes: Located in the periplasmic regions and associated with biosynthesis of cell wall constituents. Mechanism of enzyme action The enzymatic reactions takes place by binding of the substrate with the active site of the enzyme molecule by several weak bonds. E + S ‹--------› ES --------› E + P Formation of ES complex is the first step in the enzyme catalyzed reaction then ES complex is subsequently converted to product and free enzyme. "Lock and key" or Template model Induced-fit model References o Stryer L, Berg JM, Tymoczko JL (2002). Biochemistry (5th ed.). San Francisco: W.H. Freeman. ISBN 0-7167-4955-6.open access o Murphy JM, Farhan H, Eyers PA (2017). "Bio-Zombie: the rise of pseudoenzymes in biology". Biochem Soc Trans. 45 (2): 537–544. doi:10.1042/bst20160400. PMID 28408493. o Murphy JM, et al. (2014). "A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties". Biochemical Journal. 457 (2): 323–334. doi:10.1042/BJ20131174. PMC 5679212. PMID 24107129. o adzicka A, Wolfenden R (January 1995). "A proficient enzyme". Science. 267 (5194): 90–931. Bibcode:1995Sci...267...90R. doi:10.1126/science.7809611. PMID 7809611. S2CID 8145198. o Holmes FL (2003). "Enzymes". In Heilbron JL (ed.). The Oxford Companion to the History of Modern Science. Oxford: Oxford University Press. p. 270. ISBN 9780199743766. o Nomenclature Committee. "Classification and Nomenclature of Enzymes by the Reactions they Catalyse". International Union of Biochemistry and Molecular Biology (NC-IUBMB). School of Biological and Chemical Sciences, Queen Mary, University of London. Archived from the original on 17 March 2015. Retrieved 6 March 2015. o Nomenclature Committee. "EC 2.7.1.1". International Union of Biochemistry and Molecular Biology (NC-IUBMB). School of Biological and Chemical Sciences, Queen Mary, University of London. Archived from the original on 1 December 2014. Retrieved 6 March 2015. o Anfinsen CB (July 1973). "Principles that govern the folding of protein chains". Science. 181 (4096): 223–30. Bibcode:1973Sci...181..223A. doi:10.1126/science.181.4096.223. PMID 4124164. o Dunaway-Mariano D (November 2008). "Enzyme function discovery". Structure. 16 (11): 1599–600. doi:10.1016/j.str.2008.10.001. PMID 19000810. o Hasim, Onn (2010). Coenzyme, Cofactor and Prosthetic Group – Ambiguous Biochemical Jargon. Kuala Lumpur: Biochemical Education. pp. 93–94. o "coenzymes and cofactors". Retrieved 2007-11-17. o "Enzyme Cofactors". Archived from the original on 2003-05-05. Retrieved 2007-11-17. o Crane FL (December 2001). "Biochemical functions of coenzyme Q10". Journal of the American College of Nutrition. 20 (6): 591–8. doi:10.1080/07315724.2001.10719063. PMID 11771674. Archived from the original on 16 December 2008. Thank You….. Write me on: [email protected] [email protected] .
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