Biochem Lec Midterms PDF

ENZYMOLOGY B. SECONDARY STRUCTURE ENZYMES...

ENZYMOLOGY B. SECONDARY STRUCTURE ENZYMES twisting of the polypeptide chains large molecules proteins from 12kDa – 1000kDa or more IMPORTANCE: NOTE: The secondary and tertiary structures are the most important the enzymes are responsible for the different reactions in living matter necessary during digestion, metabolism, respiration, structures energy release, and energy transfer in all metabolic reactions CHARACTERISTICS OF AN ENZYME: a) enzymes are invariable complex proteins b) amphoteric – enzymes exist either as Acid or Base, and they do not react with the Acid-Base balance C. TERTIARY STRUCTURE c) easily denatured folding of the chains (interactions among the side chains/group of chains) temperature: the higher the temp, the faster the denaturation optimum temperature: enzymes react best at 37oC D. QUATERNARY STRUCTURE in the enzymatic process, it is active between 30-37oC or 37-40oC relationship between the subunits enzymes denture at 50-60oC d) synthesized in an active state PROPERTIES OF ENZYME e) generally soluble in water, glycerol, and dilute alcohol f) colloidal in nature and are not dialyzable g) usually function with a cofactor 1. COFACTOR h) neither consumed nor produced during the course of reaction non-protein molecule that is necessary for enzyme activity; necessarily needed i) do not cause reactions to take place, they expedite reactions ACTIVATORS – inorganic cofactors (Cl2, Mg, Zn, Ca) (positively charged) j) are highly specific for the reactions they catalyze and produce only the expected products from the given reactants/substrates COENZYME – organic factor (NAD: Nicotinamide Adenine Dinucleotide) (example: salivary amylase – for the breakdown of starch only) k) reactions are frequently reversible 2. PROSTHETIC GROUP a coenzyme bound tightly to the enzyme. The cyst with the enzymatic reaction; not necessarily needed ENZYME STRUCTURE: 3. PROENZYME / ZYMOGEN secreted from the organ production in an inactive form (digestive enzymes) 1. ACTIVE SITE the specific region in enzyme which interacts with its substrate; where the substrates attach forming enzyme-substrate complex 4. APOENZYME both binding and catalytic reaction occur here enzyme portion; can’t exist without the coenzyme 2. SUBSTRATE 5. HOLOENZYME the substance acted upon by an enzyme apoenzyme + coenzyme 3. PRODUCT 6. METALLOENZYME the product derived from a transformed substrate (enzyme + substrate) inorganic activators existing as part of the enzyme molecule 4. ALLOSTERIC SITE a cavity (other than the active site) may bind regulator molecules and thereby be significant to the basic enzyme structure STRUCTURES OF THE ENZYME: A. PRIMARY STRUCTURE the specific amino acid sequence HOW DOES ENZYME CATALYZE A REACTION? 2. HETEROENZYME Activation energy and transition state same enzymatic activity which species are specific for different biological species example: Lactate dehydrogenase (LDH) of rabbits and humans a) In order to react, the molecules involved are distorted, strained, or forced to have an unlikely electronic arrangement b) That is the molecules must pass through a high energy state (transition state) 3. ALLOENZYME c) The energy required to achieve is called the activation energy genetically transmitted enzymes d) Enzymes decrease the energy required to get a reaction started important in defining the biochemical characteristics of an individual e) Enzyme lower energy barrier by forcing the reacting molecules through a different transition state present only in some selected individuals of the same species practical value in forensic medicine and genetics a. If there are enzyme present during enzymatic process, it decreases the energy use, but faster enzymatic reaction ORIGIN OF ENZYMES b. If there are no enzymes present, more energy is used leading A. PLASMA SPECIFIC ENZYMES to a slower enzymatic reaction PLASMA – light-yellow colored of the whole blood, secreted in the liver and released in the plasma contain protein and other constituents other than the exert function in plasma RBC example: Blood clotting mechanism, Fibrinolytic system THROMBIN – enzyme that will convert the fibrinogen to fibrin to create clot ENZYME VARIANTS B. NON-PLASMA ENZYMES no specific function in plasma there are several distinct forms of enzyme THROMBOSIS – too much clot formation these are important in the diagnosis of specificity 2 CLASSES: PLASMIN – dissolves the clot a. Enzyme of secretion – enzymes are directly secreted in the body 1. ISOENZYMES b. Enzymes associated with cellular metabolism – there are specific organs that will secrete this types of enzymes different molecular forms of enzymes that may be isolated from the same or different tissues are of similar activity C. BASED ON DISTRIBUTION Example: 1. UNILOCULAR released by either cell sap (vacuoles present in the cell) or one location only 2. BILOCULAR released by mitochondria and cell sap NOMENCLATURE AND CLASSIFICATIONS OF ENZYMES a. CK-MB most important sub-unit, for the heart and skeletal muscle I. EMPIRICAL NAMES more specific and sensitive than CK-MM not specific; based on organ / observation (such as characteristic) / experiences (such as type of chemical reaction) Disease: Acute Myocardial Infarction – for the first 12 hours 1. ARBITRARY – (not specific; all of these 4 are not specific) Ptyalin CHARACTERISTICS OF ISOENZYMES Trypsin ELECTROPHORESIS Pepsin classifies the different sub-units of isoenzymes Rennin charged molecules functions to be able to see the mobility of ions II. ATTACHING THE SUFFIX -ASE TO THE made up of Ion Exchange Resin name of the substrate or group acted upon by the enzyme response to activation and inactivation process reaction catalyzed (example: ACP isoenzymes [ACP-RBC + 2% Formaldehyde = active, and ACP-Prostate + 2% formaldehyde = inactivation]) not all enzymes have the -ase response to inhibitors we use plasma for enzymes ex: collection of blood either using fluoride, heparin, or oxalic, it can inhibit ACP EXAMPLES: 2. TRANSFERASE catalyze the transfer of an intact group of atoms (amine or phosphate group) from one substrate to another 1. OXIDASE - oxygen most of these enzymes are important in assessing liver damage and myocardial infarction 2. DECARBOXYLASE – carbon dioxide Aminotransferase, Kinase, Phosphorylase, Methyltransferase 3. TRANSAMINASE – AST/ALT 4. HYDROLASE – esterase, glycosidases, peptidases 3. HYDROLASES 5. HYDRASE/DEHYDRASE – CO2, HCO3, H2O catalyze hydrolysis of variety of bonds; presence of water for reaction to proceed 6. UREASE – urea Phosphatase (Esterase), Phosphodiesterase, Protease 7. MALTASE – maltose, glucose 8. CELLULASE – cellulose 4. LYASES 9. AMYLASE – starch catalyze removal of groups from substrates without hydrolysis (lysis = splitting of molecules, leads to double bonds) 10. LIPASE – lipids most are assayed in skeletal muscle disorders Decarboxylases, Aldolases, Synthases III. STANDARDIZED NAMING Example of bonds: C-C, C-O, C-N complete naming of the enzyme 4 numerical-digit 5. ISOMERASE catalyze the interconversion of one isomer to another by molecular arrangements 1. SYSTEMATIC NAME (EC of the IUB) Cis = trans, L-D forms; Aldehyde – Ketone define the substrate acted upon Racemases, Mutases describe the nature of the reaction catalyzed No clinical significance possibly the name of the coenzyme involved in the reaction associated unique numerical code designation 6. LIGASES catalyze the joining of 2 substrate molecules usually with the presence of energy supplied by the cleavage of an ATP 2. TRIVIAL OR PRACTICAL NAME Carboxylases, Synthetases simplification of naming by using acronyms and uppercase abbreviation of enzymes example: Aminoacyl-tRNA synthetase suitable for everyday use Ex: Lactate dehydrogenase (LDH) ENYZME KINETICS 3. EC NUMERICAL CODE with 4 digits separated by decimal points FIRST DIGIT – class of the enzyme (1-6) SECOND AND THIRD DIGIT – subclass (2), sub-sub-class (3) FOURTH DIGIT – serial number that is specific to each enzyme in a sub-class EXAMPLE: I. FACTORS AFFECTING THE BINDING CLASSIFICATIONS OF ENZYME 1. ENERGY – activation energy 1. OXIDOREDUCTASE Catalyze oxidation (addition of H ion) and reduction reactions (removal of H ion) between two substances 2. MOLECULAR COMPATIBILITY – commonness / sameness of enzyme and substrate Oxidases; Dehydrogenases: Oxygenase; Peroxidase most of these enzymes are important in assessing heart attacks (ex. CK) and liver problems (ex. LDH) 3. SPACE AVAILABILITY – number of enzymes or substrates that can be reacted 4. SPECIFICITY – the particular enzyme catalyzing a specific substrate II. SPECIFICITY OF ENZYME ACTION 1. LOCK AND KEY THEORY the active site of the enzyme is always complementary to the substrate, so that the enzyme and the substrate recognize one another postulated by Emil Fischer 2. INDUCED FIT THEORY the enzyme changes its shape upon binding the substrate, so that the conformation of substrate and enzyme protein are only complimentary upon the binding reaction (binding with the substrate) postulated by Daniel Koshland TITLE SUBTITLE SUBSUBTITLE NOTES SPECIAL ELEMENTS ∗ → >