Che 40 enzymes and nomenclature


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Che 40 enzymes and nomenclature

  1. 1. Written Report on … Enzymes: Nomenclature Molecular Model of Protein Molecular Model of Enzyme Amylase Submitted by: Conrad Vincent V. Vivas BS Chemical Engineering-4 Submitted to: Engr. Christylene S.Balagtas ChE-40 Biotechnology January 12, 2013
  2. 2. ChE 40- Biotechnology Xavier University- Ateneo de CagayanIntroduction In this report the main discussion is all about enzymes and its nomenclature. Enzymesgovern all chemical reactions in living organisms. They are specialized proteins that withfascinating precision and selectivity catalyze biochemical reactions that store and releaseenergy, pigments in our hair and eyes, digest food that we eat, synthesize cellular buildingmaterials, and protect us by repairing cellular damage and clotting our blood. Enzymes aresensitive to their environment, responding quickly in the cell. The deficiency or excess ofparticular enzymes can cause certain disease or signal problems such as heart attack and otherorgan damage.I. Basic Information about Enzymes The name “enzyme” was coined by Wilhelm Kunhne, which means “in yeast”, but the word is now used to mean biological catalyst regardless of their origin.  (Comes from Greek words “en” = in and “zyme” = yeast) Yeast Enzymes  production of breads and alcoholic beverages. (Action of yeast on sugar produces CO2 gas that causes the bread to rise, while fermentation of sugars in fruit juices with the same yeast enzyme produces alcoholic beverages) Enzymes are specialized globular Proteins that acts as biological catalysts, it is used to increase the rate of biochemical reactions taking place within living systems, without themselves undergoing any overall change.  Proteins are polymers of amino acids. (Proteins are major structural component of all tissue of living organisms and are necessary for cell repair and muscular growth.)  Biological catalyst is a substance that mediates or speeds up a specific biochemical (occurs in living organisms) reactions.  As catalyst they are not being destroyed or altered upon completion of the reaction. (Hence it is not consume in the reaction) 1|Page
  3. 3. ChE 40- Biotechnology Xavier University- Ateneo de Cagayan  Enzymes lower the activation energy needed for the reaction to occur or proceed into product. Two structural classes of enzymes: 1. Simple enzymes – enzyme composed only of protein (amino acid chains). 2. Conjugated enzymes –enzymes that have a non-protein part in addition to a protein.Parts of Conjugated Enzyme: a. Apoenzyme - inactive portion of protein b. Cofactor- non-protein component of enzyme c. Coenzyme - enzyme with organic molecule as its cofactor d. Holoenzyme - active enzyme including cofactor Apoenzyme + Cofactor = Holoenzyme Figure 1. parts of conjugated enzyme Deficiency of enzyme in the human body can lead to various complications. Ex. Lactose intolerant  The problem arises because the sugar in milk -- lactose -- does not get broken into its glucose components. Therefore, it cannot be digested.  The intestinal cells of lactose-intolerant people do not produce LACTASE, the enzyme needed to break down lactose. 2|Page
  4. 4. ChE 40- Biotechnology Xavier University- Ateneo de CagayanII. History of Enzymes In 1836, the word “catalyst” was coined by Jon Jakob Berzelius (According to J.J. Berzelius, catalyst refers to materials whose presence would set the reactions to go to which otherwise would be dormant) The concept prevailed until 1926, when Willstaetter first could achieve the isolation of pure enzyme peroxidase  Horseradish Peroxidase (phenols, which are important pollutant, can be removed by enzyme-catalyzed polymerization using horseradish peroxidase.) Almost the same period, +James B. Sumner isolated and crystallize the enzyme Urease from the jack bean. (+His work was to earn him the 1947 Nobel Prize.)  Urease breaks down urea (waste product formed in the liver) into carbon dioxide and ammonia. As time pass by, large number of enzymes has been isolated from time to time. By 1985, as many as 2500 enzymes were known. There needs to be rules for naming!!! *International Union of Biochemistry and Molecular Biology (IUBMB) Named and classified enzymes Figure 2. Discovered Enzymes through time 3|Page
  5. 5. ChE 40- Biotechnology Xavier University- Ateneo de CagayanIII. Enzyme Nomenclature Enzymes are classified and named (by IUBMB) according to the nature of the chemical reactions they catalyze and not on their structure. (Unlike in organic chemistry, where nomenclature of compounds are mainly based on itsstructures)  suffix -ase indicates an enzymeSome examples:  Urease - hydrolysis of Urea  DNA polymerase - polymerization of nucleotides  Protease - hydrolysis of peptides  suffix –in is also used to name enzyme (Enzymes that were named before the specific reaction they catalyzed were known!) Ex. Pepsin, thrombin and Trypsin Two Naming Systems: 1. Trivial name or Recommended name: everyday use  Gives no idea of source, function or reaction catalyzed by the enzyme.  Ex. Pepsin, thrombin and Trypsin 2. Systematic name: has two parts, a.) substrates b.) name of RxnName of substrate(s) +name of reaction catalyzed (group classification) with –ase suffixEx. Lactate dehydrogenase Suffix -aseSubstrate name of rxn catalyzedSubstrates are reagent molecules upon which enzymes act.The enzyme has spatial binding sites for the attachment of its substrate forming enzyme-substrate. These sites are called activation centers of the enzyme. Substrates bind to thesecenters forming the enzyme-substrate complex. According to IUBMB, Enzymes are grouped into six major classes on the basis of the reaction they catalyzed: 1. Oxidoreductase is an enzyme that catalyzes oxidation-reduction rxn. 4|Page
  6. 6. ChE 40- Biotechnology Xavier University- Ateneo de Cagayan 2. Transferase is an enzyme that catalyzes the transfer of functional group from one molecule to another. 3. Hydrolase is an enzyme that catalyzes hydrolysis reactions in which the addition of water molecule to a bond causes the bond to break. 4. Lyase is an enzyme that catalyzes the addition of a group to a double bond or the removal of a group to form a double bond in a manner that does not involve hydrolysis or oxidation. 5. Isomerase is an enzyme that catalyzes the rearrangement of the functional group within a molecule, converting the molecule into another molecule isomeric with it. 6. A ligase is an enzyme that catalyzes the bonding together of two molecules into one with the participation of ATP. Within each of six main classes of enzymes are subclasses. Table 1 gives further information about enzyme subclass terminology.Main Classes Selected Types of Reaction Catalyzed SubclassesOxidoreductases Oxidases Oxidation of a substrate Reductases Reduction of a substrate Dehydrogenase Introduction of double bond (oxidation) by formal removal of two H atoms from substrate, the H being accepted by coenzyme.Transferases Transminases Transfer of an amino group between substrate Kinases Transfer of phosphate group between substrateHydrolases Lipases Hydrolysis of ester linkages in lipids Proteases Hydrolysis of amide linkages in proteins Nucleases Hydrolysis of sugar-phosphate ester bonds in nucleic acid Carbohydrases Hydrolysis of glycosidic bonds in carbohydrates Phosphatases Hydrolysis of phosphate-ester bondsLyases Dehydratases Removal of H2O from substrate Decarboxylases Removal of CO2 from substrate Deaminases Removal of NH3 from substrate Hydratases Addition of H2O of a substrateIsomerases Racemases Conversion of D to L isomer, or vice versa Mutases Conversion of one constitutional isomer anotherLigases Synthases Formation of new bond between two substrate, with the participation of ATP Carboxylases Formation of a new bond between a substrate and CO2, with the participation of ATPTable 1. Six Major Classification of Enzymes According to Reactions they catalyzed. 5|Page
  7. 7. ChE 40- Biotechnology Xavier University- Ateneo de CagayanIV. Reference(s): Rao, D.G. (2010). Introduction to biochemical engineering. 2nd Edition. Singapore:McGraw-Hill Education Private limited. pg 62-67. Stephen, H.S. 2007. General, organic and biological Chemistry. 4th Edition. New York:wylie&Sons Inc. pg 640-644 6|Page