Enzymes Part 1 PDF

ENZYMES PART 1 OBJECTIVES 1. Describe enzyme and its molecular structure. 2. Discuss the properties of enzymes 3. Classify the different enzyme according to their reactions. ENZYMES Greek word en, means “in”, and zyme, which means “yeast” an organic compound that act as a catalyst for a b...

ENZYMES PART 1 OBJECTIVES 1. Describe enzyme and its molecular structure. 2. Discuss the properties of enzymes 3. Classify the different enzyme according to their reactions. ENZYMES Greek word en, means “in”, and zyme, which means “yeast” an organic compound that act as a catalyst for a biochemical reaction; increases rate of reaction but are not changed in the process water-soluble, globular proteins  Features: a) Enhance reaction rates (pH 7.4 and 37°C). An enzyme catalyzed reaction can be 106 to 1012 times faster than uncatalyzed reaction b) Enzymes are very specific. STRUCTURE OF ENZYME simple enzyme – an enzyme composed only of protein. conjugated enzyme – an enzyme that has a nonprotein part in addition to the protein part. CONJUGATED ENZYME apoenzyme is the protein part of a conjugated enzyme cofactor is the nonprotein part of a conjugated enzyme holoenzyme is the biochemically active conjugated enzyme produced from an apoenzyme and a cofactor Apoenzyme + cofactor = holoenzyme Why do apoenzymes need cofactors? A cofactor is a non-protein chemical compound that is required for the protein's biological activity. Cofactors can be considered "helper molecules" that assist enzymes in their action. Cofactors can be ions or organic molecules (called coenzymes).  Coenzyme is a small organic molecule that serves as a cofactor in a conjugated enzyme. Inorganic ion cofactors include zinc, magnesium, manganese, and iron; chloride occasionally acts as a cofactor Role of Metal Ions in Enzymes - activity of many enzymes depends on the presence of potassium, magnesium, calcium, zinc and copper ions Metal activated enzymes: - metals form a loose and easily dissociable complex. - The metal ion can be removed by dialysis or any other such method from the enzyme without causing any denaturation of apoenzyme.  Metallo-enzymes: - It is bound tightly to the enzyme and is not dissociated even after several extensive steps of purification. Metal play a variety roles such as: a) Help in either maintaining or producing (or both) active structural conformation of the enzyme. b) Formation of enzyme-substrate complex. c) Making structural changes in substrate molecule. d) Accept or donate electrons e) Activating or functioning as nucleophiles f) Formation of tertiary complexes with enzyme or substrate. Nomenclature and Classification of Enzymes Naming provides the function of the enzyme rather than the structure; type of reaction catalyzed and substrate are the focal points for nomenclature. substrate is the reactant in an enzyme-catalyzed reaction; it is the substance upon which the enzyme “acts” 1) Suffix –ase identifies an enzyme (urease, lipase….); suffix – in in some names of digestive enzymes (trypsin, chymotrypsin, and pepsin) 2) The type of reaction catalyzed by an enzyme is often noted with a prefix. (oxidase, hydrolase…) 3) The identity of the substrate is often noted in addition to the type of reaction. (glucose oxidase, pyruvate carboxylase, and succinate dehydrogenase) - Few enzymes exist in their inactive form called proenzymes or zymogens. - Zymogens become active after prior modification in its structure by certain agents. Many times the active form of enzyme acts on zymogen and catalyzes its conversion into active form – process called autocatalysis PROPERTIES OF ENZYMES A. Active sites - special pocket or cleft within the enzyme molecule - contains amino acids side chains that participate in substrate binding and catalysis B. Catalytic efficiency - Highly efficient (103- 108) times faster than uncatalyzed reactions C. Specificity - highly specific, interacting only with one or a few substrates and catalyzing only one type of chemical reaction D. Holoenzymes - some enzymes require molecules other than proteins for enzymatic activity - Holoenzymes refers to the active enzymes with its nonprotein component, whereas the enzyme without its nonprotein moiety is termed an apoenzyme and is inactive. - If the nonprotein is a metal ion (Zn2+ or Fe2+ ), it is called a cofactor If it is a small organic molecule, it is termed as coenzyme. - Coenzymes that only transiently associate with the enzyme are called cosubstrates. - Cosubstrates dissociate from the enzyme in an altered state. (ex. NAD+) - Coenzymes frequently are derived from vitamins. (ex. NAD+ contains niacin and FAD contains riboflavin) E. Regulation - Enzyme activity can be regulated, that is, increased or decreased, so that the rate of product formation responds to cellular need. F. Location within the cell - Many enzymes are localized in specific organelles within the cell. Such compartmentalization serves to isolate the reaction substrate or product from other competing reactions. This provides a favorable environment for the reaction, and organizes the thousands of enzymes present in the cell into purposeful pathways Classes of Enzymes (Based on the Type of Reaction) 1. Oxidoreductase - requires a coenzyme that is oxidized or reduced as the substrate is reduced or oxidized. - Lactate dehydrogenase is an oxidoreductase that removes hydrogen atoms from a molecule. ✓ An organic oxidation reaction is an oxidation that increases the number of C-O bonds and/or decreases the number of C-H bonds. ✓ An organic reduction reaction is a reduction that decreases the number of C-O bonds and/or increases the number of C-H bonds. 2. Transferase an enzyme that catalyzes the transfer of a functional group from one molecule to another. Two subtypes: Transaminase catalyzes the transfer of an amino group from one molecule to another;  Kinases - catalyze the transfer of a phosphate group from adenosine triphosphate (ATP) to give adenosine diphosphate (ADP) and a phosphorylated product (a product containing an additional phosphate group) 3. Hydrolase - an enzyme that catalyzes a hydrolysis reaction in which the addition of a water molecule to a bond causes the bond to break. Hydrolysis are central to the process of digestion. 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. Dehydratase – effects the removal of the components of water from a double bond Hydratase – effects the addition of the components of water to a double bond 5. Isomerase ▪ an enzyme that catalyzes the isomerization (rearrangement of atoms) of a substrate in a reaction, converting it into a molecule isomeric with itself. ▪ There is only one reactant and one product in reactions where isomerases are operative. 6. Ligase is an enzyme that catalyzes the bonding together of two molecules into one with the participation of ATP. MAIN CLASSES AND SUBCLASSES OF ENZYMES Main Classes Selected Subclasses Type of Reaction Catalyzed Oxidoreductases Oxidases Oxidation of a substrate Reductases Reduction of a substrate Dehydrogenases Introduction of double bond (oxidation) by formal removal of two H atoms from a substrate, with one H being accepted by a coenzyme Main Classes Selected Subclasses Type of Reaction Catalyzed Transferases Transaminases Transfer of an amino group between substrate Kinases Transfer of a phosphate group between substrate Hydrolases Lipases Hydrolysis of ester linkages in lipids Proteases Hydrolysis of amide linkage in proteins Nucleases Hydrolysis of sugar-phosphate ester bonds in nucleic acids Carbohydrases Hydrolysis of glycosidic bonds in carbohydrates Phosphatases Hydrolysis of phosphate-ester bonds Main Classes Selected Subclasses Type of Reaction Catalyzed Lyases Dehydratases Removal of H2O from a substrate Decarboxylases Removal of CO2 from a substrate Deaminases Removal of NH3 from a substrate Hydratases Addition of H2O to a substrate Isomerase Racemases Conversion of D-isomer to L-isomer or vice versa Mutases Tranfer of a functional group from one position to another in the same molecule Ligases Synthetases Formation of a new bond between two substrates, with participation of ATP Carboxylases Formation of a new bond between substrate and CO2 with participation of ATP.