Enzymes | PDF

Aya Daghash Enzymes  Lecture out lines : Introduction to enzymes General properties of enzymes Definition of enzyme terms and nomenclature Description of general properties of enzymes Enzyme Catalyzed Reactions Enzyme Specificity Theories Enzymes catalytic mech...

Aya Daghash Enzymes  Lecture out lines : Introduction to enzymes General properties of enzymes Definition of enzyme terms and nomenclature Description of general properties of enzymes Enzyme Catalyzed Reactions Enzyme Specificity Theories Enzymes catalytic mechanisms  What is Catalyst : Catalyst is a substance that causes or accelerate a chemical reaction without itself being affected. With a catalyst, reactions occur faster and with less energy. ❖ENZYMES : are effective & high specific biological catalyst that catalyze the conversion of one or more compounds (substrates) into one or more different compounds (products). ❖Enzymes are involved in all essential body reactions & found in all body tissues ❖Like all catalysts, enzymes are neither consumed nor permanently altered as a consequence of their participation in a reaction.  Enzymes as Biological Catalysts Enzymes are proteins that increase the rate of reaction by lowering the energy of activation Like other catalysts, enzymes lower activation energy by bringing the reactants closer together, aligning reactants, and/or weakening chemical bonds so reactions proceed faster.  General Properties of Enzyme ❖Unlike most catalysts used in synthetic chemistry, enzymes are specific both for: 1. The type of reaction catalyzed 2. A single substrate or a small set of closely related substrates 3. Stereospecific catalysts and typically catalyze reactions of only one stereoisomer of a given compound -Example, D- but not L-sugars, L- but not D-amino acids. Since they bind substrates through at least "three points of attachment.  ENZYMES Nomenclature Each enzyme is assigned two names: 1. The first is its short, Recommended Name, convenient for everyday use. 2. The second is the more complicated Systematic Name, which is used when an enzyme must be identified without ambiguity.  Recommended Name Recommended Name : The commonly used names for most enzymes describe the type of reaction catalyzed, followed by the suffix -ase. For example: Dehydrogenases remove hydrogen atoms Proteases hydrolyze proteins Isomerases catalyze rearrangements in configuration. Modifiers may precede the name to indicate: The substrate (xanthine oxidase) The source of the enzyme (pancreatic ribonuclease) Its regulation (hormone-sensitive lipase) Alphanumeric designators are added to identify multiple forms of an enzyme (eg, RNA polymerase III; protein kinase C ).  Systematic name The International Union of Biochemists (IUB) developed a clear system of enzyme nomenclature in which each enzyme has a unique name and code number that identify the type of reaction catalyzed and the substrates involved. Despite the clarity of the IUB system, the names are relatively difficult, so we generally continue to refer to enzymes by their traditional names. In this system enzymes are grouped into the following six classes.  Enzymes class 1. Oxidoreductases:enzymes that catalyze oxidations and reductions. 2. Transferase:enzymes that catalyze transfer of moieties such as methyl, or phosphoryl groups. 3. Hydrolases: enzymes that catalyze hydrolytic cleavage of C—C, C—O, C—N and other covalent bonds. 4. Lyases : enzymes that catalyze cleavage of C—C, C—O, C—N and other covalent bonds by atom elimination, generating double bonds. 5. Isomerases:enzymes that catalyze geometric or structural changes within a molecule. 6. Ligases:enzymes that catalyze the joining together (ligation) of two molecules in reactions coupled to the hydrolysis of ATP. The IUB name for hexokinase illustrates both the clarity of the IUB system and its complexities. The IUB name of hexokinase is : ATP:D-hexose 6-phosphotransferase E.C.2.7.1.1. This name identifies hexokinase as a member of class 2 (transferases) Subclass 7 (transfer of a phosphoryl group) Subsubclass 1 (alcohol is the phosphoryl acceptor) "hexose-6" indicates that the alcohol phosphorylated is on carbon six of a hexose In addition to the previous nomenclature systems ✓ Some enzymes retain their original trivial names, which give no hint of the associated enzymic reaction, for example, trypsin and pepsin  Definitions and Related Terms Holoenzyme & Apoenzyme Some enzymes need molecules other than protein for enzymic activity Holoenzyme refer to the complete, catalytically active enzyme with its non protein components. Apoenzyme (zymogen) is the protein portion of a holoenzyme (i.e. the enzyme yet in an inactive form) The active site is a region within an enzyme that fits the shape of substrate molecules. Amino acid side-chains align to bind the substrate through H-bonding, salt-bridges, and hydrophobic interactions, etc. Products are released when the reaction is complete (they no longer fit well in the active site)  Non-active site May interact with other substances resulting in overall enzyme shape change & inhibition or regulation. When a substrate (S) fits properly in an active site, an enzyme-substrate (ES) complex is formed: E + S  ES Within the active site of the ES complex, the reaction occurs to convert substrate to product (P): ES → E + P The products are then released, allowing another substrate molecule to bind the enzyme - This cycle can be repeated millions (or even more) times per minute The overall reaction for the conversion of substrate to product can be written as follows: E + S  ES → E + P The reaction for the sucrase catalyzed hydrolysis of sucrose to glucose and fructose can be written as follows: E + S  ES → E + P1 + P2 where E = sucrase, S = sucrose, P1 = glucose and P2 = fructose  Two models are proposed : 1- The Lock-and-Key Mode 2- The Induced Fit Model In the lock-and-key model of enzyme action: - The active site has a rigid shape - Only substrates with the matching shape can fit - The substrate is a key that fits the lock of the active site This is an older model, however, and does not work for all enzymes In the induced-fit model of enzyme action: - The active site is flexible, not rigid - The shapes of the enzyme, active site, and substrate adjust to maximumize the fit, which improves catalysis - There is a greater range of substrate specificity This model is more consistent with a wider range of enzymes Isoenzymes are different forms of an enzyme that catalyze the same reaction in different tissues in the body. They have slight variations in the amino acid sequences of the subunits of their quaternary structure Different isoenzymes may arise from different tissues and their specific detection may give clues to the site of pathology.  Pyruvate Lactate (anaerobic glycolysis) o lactate dehydrogenase (LDH), which converts lactate to pyruvate, during anaerobic glycolysis o It is a tetrameric protein and made of two types of subunits namely : H = Heart, M = skeletal muscle o It exists as 5 different isoenzymes with various combinations of H and M subunits o LDH is elevated in myocardial infarction, blood& liver disorders LACTATE DEHYDROGENASE ISOENZYMES  Creatine + ATP phosphocreatine + ADP (Phosphocreatine – serves as energy reserve during muscle contraction) o Creatine kinase is a dimer made of 2 monomers: M subunit, & B subunits o Three different isoenzymes are formed Isoenzyme Composition Present in Elevated in Name CK-1 BB Brain CNS diseases Myocardium/ Acute myocardial CK-2 MB Heart infarction Skeletal CK-3 MM muscle, Myocardium 1. The ability to assay the activity of specific enzymes in blood aids in the diagnosis and prognosis of disease. 2. Deficiencies in the quantity or catalytic activity of key enzymes can result from genetic defects, nutritional deficits, or toxins. 3. The absolute specificity of enzymes is of a particular value for using them as catalysts for specific reactions in the synthesis of a drug or antibiotic. 4. Enzymes also can be employed in the clinical laboratory as tools for determining the concentration of critical metabolites. For example, glucose oxidase is frequently utilized to measure plasma glucose concentration. 5. Enzymes are also used for the treatment of injury and disease. 6. Tissue plasminogen activator (tPA) or streptokinase is used in the treatment of acute MI, while trypsin has been used in the treatment of cystic fibrosis 30  An enzyme useful for diagnostic enzymology should be relatively specific for the tissue or organ under study, should appear in the plasma or other fluid at a time useful for diagnosis (the "diagnostic window"), and should be amenable to automated assay. The enzymes used to confirm a myocardial infarction (MI) illustrate the concept of a "diagnostic window," and provide a historical perspective on the use of different enzymes for this purpose. 1. Detection of an enzyme must be possible within a few hours of an MI to confirm a preliminary diagnosis and permit initiation of appropriate therapy. 2. Enzymes that only appear in the plasma 12 h or more following injury are thus of limited utility. 3. The first enzymes used to diagnose MI were aspartate aminotransferase (AST), alanine aminotransferase (ALT), and lactate dehydrogenase. - AST and ALT proved less than ideal, however, as they appear in plasma relatively slowly and are not specific to heart muscle. -LDH also is released relatively slowly into plasma, it offered the advantage of tissue specificity as a consequence of its quaternary structure. o Myocardial muscle is the only tissue that contains CK2 (MB) isoenzyme. o Appearance of this isoenzyme in plasma is virtually specific for infarction of the myocardium o Following an acute myocardial infarction, this isoenzyme appears approximately four to eight hours following onset of chest pain, and reaches a peak of activity at approximately 24 hours. [Note: Lactate dehydrogenase activity is also elevated in plasma following an infarction, peaking 36 to 40 hours after the onset of symptoms. LDH activity is, thus, of diagnostic value in patients admitted more than 48 hours after the time when plasma CK2 may provide equivocal results.]