Enzymes 1 2024 PDF

Cellular Biology & Homeostasis ENZYMES - Part 1 VP 2024 Clara Camargo, DVM Learning Objectives  Define enzyme and the key-lock mechanism.  List some industrial applications of enzymes, give some examples.  How enzymes work, what is activation energy and the transition state  Understand enzyme no...

Cellular Biology & Homeostasis ENZYMES - Part 1 VP 2024 Clara Camargo, DVM Learning Objectives  Define enzyme and the key-lock mechanism.  List some industrial applications of enzymes, give some examples.  How enzymes work, what is activation energy and the transition state  Understand enzyme nomenclature, give some examples  Understand apoenzyme, holoenzyme and cofactors  List and explain the properties of the enzymes Enzymes Part 1 RECALL: SUMMARY OF DIGESTIVE ENZYMES Where secreted Salivary glands Stomach Pancreas Small intestine brush border What enzyme RECAP Product of digestion α –amylase (Ptyalin) Amylose (polysaccharide)  disaccharides Lingual lipase Lipids (TAG, cholesterol)  DAG, MAG, FFA, glycerol Pepsin (protease) Proteins  peptides Gastric lipase Lipids  DAG, MAG, FFA, glycerol Pancreatic amylase Polysaccharides  disaccharides Trypsin (protease) Proteins  peptides Chymotrypsin (protease) Proteins  peptides Acid lipases Lipids  DAG, MAG, FFA, glycerol Peptidases Polypeptides  amino acids Nucleotidases, nucleases DNA, RNA  nucleotides, ribose Lactase Disaccharides  monosaccharides Maltase Disaccharides  monosaccharides Sucrase Disaccharides  monosaccharides RECAP Most all diseases in animals are manifestations of abnormalities in: biomolecules chemical reactions biochemical pathways Veterinary Physiological Chemistry – Larry R. Engelking ENZYMES General concepts Enzymes are proteins that act as biological catalysts by accelerating chemical reactions. Generally, a small amount of enzyme will The molecules upon which enzymes may act substrate. influence a large amount of reactive are called substrates, and the enzyme converts the substrates into different Act as mediators for virtually all chemical molecules known as products. reactions in biological systems, playing They have a high degree of specificity for their substrates, and they accelerate chemical reactions tremendously, without being changed or used up during the process (reversible binding). fundamental roles in metabolic events, signal transduction and cell regulation. General Enzymes concepts Part 1 ENZYMES The binding is very specific, small changes in the shape of the ligand/substrate (key) can cause major change in protein (lock) behavior. Complementary shape: recognition function, plays a major role in information transfer General Enzymes concepts Part 1 ENZYMES Allostery: the ability of a protein to change shape, resulting in a change in binding affinity at a different binding site. “shape influences binding, and in turn, binding can influence shape” Allosteric enzymes: have the active site, as well as an additional site (allosteric site) From the Greek 'allo', which means 'other'. LIFE DEPENDS ON A COMPLEX NETWORK OF CHEMICAL REACTIONS Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. FAST!!! Catalyzed E + S ↔ ES  EP  E + P Spontaneous S SLOW!!! P Binding sites are usually very specific for a particular ligand/substrate and the binding is reversible. Enzymes Part 1 INDUSTRIAL FIELDS ALSO BENEFITS FROM ENZYMES Biofuel production (biodiesel, alcohol from sugar cane) Agricultural (animal feed additives, fertilizers…) Fermentations: transformation of raw materials such as sugar, starch, etc. in industrial mixtures such as liquors, brewing Biotransformations: transformation of defined precursors to a desired target product o Environmentally friendly processes to treat waste Pharmaceutical industry: synthesis & modification of antibiotics & medicines Diagnosis of disease: increased or decreased concentrations of enzyme activity in the target system (liver, kidney, muscle) Treatment of disease: i.e. use of streptokinase to dissolve blood clots, exocrine pancreatic insufficiency… Enzymes Part 1 ENZYMES IN INDUSTRIAL APPLICATIONS Enzymes Part 1 FYI SOME INDUSTRIAL ENZYMES AND THEIR USES Enzyme Application Enzymes Part 1 Sector Protease Degradation of proteins Detergents Cellulase Degradation of cellulose Detergents Lipase Degradation of lipids Detergents Amylase Conversion of starch to glucose Starch processing Glucose Isomerase Production of High Glucose Syrup Starch processing Phytase Improve nutrient availability Animal feed Xylanase Removal of lignin ‘bio bleaching’ Paper and pulp Amylase Removal of fruit starch haze Fruit/vegetable processing Hydrolase Breakers for biopolymer gels Petrol and Gas Chymosin Clotting in cheese manufacture Dairy Pectinase Increased yields Wine HOW ENZYMES WORK? Chemical reactions have an energy barrier separating the reactants and the products. Energy is needed to get them started = Activation energy Enzymes greatly reduce the activation energy barriers that block chemical reactions. Enzymes Part 1 HOW ENZYMES WORK? https://www.youtube.com/watch?v=Dd1yi2aVoOc Enzymes Part 1 HOW ENZYMES WORK? Enzymes direct substrate molecules through a specific reaction pathway allowing a reaction to proceed rapidly by providing an alternate reaction pathway in the cell which has a lower activation energy. Enzymes show a high selectivity and usually catalyze only one specific reaction, or a set of closely related reactions; directing a particular reaction pathway. Enzymes Part 1 Enzymes Part 1 THE TRANSITION STATE The active site acts as a molecular template that binds the substrate and initiates its conversion to the transition state. The transition state is the form the substrate must take before it becomes product. What is: It is the highest energy point of the reaction.  ∆G♯ uncat?  ∆GM  ∆G♯ THE TRANSITION STATE Enzymes Part 1 Stabilizing the transition state (T*) an enzyme can greatly increase the concentration of the reactive intermediate that can be converted to product accelerating the reaction. NOMENCLATURE Enzymes Part 1 Recommended name: short name, most used, has the suffix ‘-ase’ attached to the substrate of the reaction: i.e., Glucokinase (found mostly in liver and pancreas, phosphorylation of glucose) the description of the reaction performed: i.e., Lactate dehydrogenase NOMENCLATURE Nomenclature Systematic name: more complete, complex; is used when an enzyme must be identified without ambiguity. The suffix -ase is attached to a more complete description of the chemical reaction catalyzed, including the names of all substrates: LDH (lactate dehydrogenase): Lactate, NAD+oxidoreductase The systematic names are unambiguous and informative, but often too big for general use NOMENCLATURE Enzymes Part 1 Some enzymes retain their original, trivial names, which give no hint of the associated enzymatic reaction. THE MAJOR CLASSES OF ENZYMES Enzymes Part 1 Oxidoreductases: catalyze reactions in which one molecule is oxidized while the other is reduced, transfer of electrons (e-) and hydrogens H+ oxidases, reductases, dehydrogenases, peroxidases + + Classes of Enzymes Transferases: transfer carbon, nitrogen or phosphate groups methyltransferases, aminotransferases, kinases, phosphorylases COO- + COO- + Classes of enzymes Hydrolases: enzymes that catalyze a hydrolytic cleavage reaction (use water to break a chemical bond) *most digestive enzymes are hydrolases nucleases, proteases, phosphatases, amylase, lipase Classes of enzymes Lyases: catalyze the cleavage of C-C, C-S, and C-N bonds (catalyzes the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure) decarboxylases, aldolases, synthases, polymerases Classes of enzymes Isomerases: catalyze the rearrangement of bonds within a single molecule, transfer of groups within molecules to yield isomeric forms mutases, racemases =O =O l Classes of enzymes Ligases: Join two molecules in an energy-dependent process Catalyze formation of bonds between carbon and O, S, and N coupled to hydrolysis of high energy phosphates Classes of enzymes and Nomenclature Enzymes Part 1 POTENTIALLY CONFUSING ENZYME NOMENCLATURE: Synthetase: requires ATP Synthase: no ATP required Dehydrogenase: catalyze oxidation/reduction reactions (i.e., transferring hydrogen to NAD⁺/NADPH⁺) Phosphatase: remove phosphates Phosphorylase: add phosphates (cleave bonds by orthophosphate - phosphorolysis) Oxidase: O2 is the acceptor of electrons or hydrogen, and oxygen atoms are not incorporated into substrate Oxygenase: catalyze the incorporation of molecular O2 to a substrate. CLASSES OF ENZYMES mostly discussed in our lectures Polymerases: catalyze polymerization reactions such as the synthesis of DNA and RNA Proteases: break down proteins by hydrolyzing bonds between amino acids Kinases: Catalyze the addition of phosphate groups to molecules (protein kinases are very common in physiology) ATPases: Hydrolyze ATP (Na, K- ATPase) Synthases: synthesize molecules in anabolic reactions by condensing two smaller molecules together without using ATP Phosphatase: catalyze the hydrolytic removal of a phosphate group from a molecule PROPERTIES and CHARACTERISTICS OF ENZYMES Active sites: enzymes contain a special pocket called the ‘active site’ which has a high specificity  Contains amino acid side chains that participate in substrate binding and catalysis “Reusable” Sensitive to pH changes Denatured by high heat Inhibited by poison From: Harvey. Biochemistry Enzymes Part 1 PROPERTIES and CHARACTERISTICS OF ENZYMES Catalytic Efficiency: reactions Presence of Cofactor and coenzymes catalyzed by enzymes are 103-108 times faster than uncatalyzed reactions. Specificity: enzymes interact with one or very few substrates and catalyze only one type of chemical reaction. *Coenzymes and Cosubstrates are often the metabolically active form of the vitamins. PROPERTIES and CHARACTERISTICS OF ENZYMES Location in the cell: Many enzymes are in specific organelles in the cell (compartmentalization) and in specific cells  some reactions are isolated from others (avoiding competition for the substrate or enabling more favorable conditions, like pH) Recall: protein sorting importance to maintain this compartmentalization. o Glycolysis o PP pathway o Fatty acid synthesis SERUM BIOQUEMISTRY - Enzymatic diagnosis Testing for specific enzymes provides information about the organs and tissues in the body as well as the metabolic state of the animal. Enzymes P1 FYI Liver Enzymes ALT alanine aminotransferase (typically found when the cells of the liver are stressed or damaged) ALP alkaline phosphatase (increased when bile flow in the liver is reduced) Pancreatic Enzymes Amylase Lipase PLI (pancreatic lipase immunoreactivity) Muscle Enzymes CK (creatine kinase) enzyme most frequently measured to assess injury (trauma, inflammation). AST (aspartate aminotransferase) and ALT (alanine aminotransferase) also used to assess liver function, lesser importance during muscle injury. PROPERTIES and CHARACTERISTICS OF ENZYMES Regulation: enzyme activity can be regulated (it can be increased or decreased) so that the rate of product (biochemical reactions) responds to cellular needs  recall: insulin and glucagon regulating several enzymatic activities on metabolic map pathways Picture: ResearchGate How enzymes work https://www.youtube.com/watch?v=yk14dOOvwMk&t=1s Enzymes by Amoeba sisters https://www.youtube.com/watch?v=qgVFkRn8f10 HAPPY STUDYING Clara Camargo, DVM [email protected] ©2021 Ross University School of Veterinary Medicine. All rights reserved.