Enzymes_Mechanism of Action.2023-2024.pdf

Enzymes: Mechanism of Action Dr. Sebnem GARIP USTAOGLU  Enzymes ‘Biological Catalysts’ All biochemical reactions are enzyme catalyzed rxn’s in the living organism. They accelerate the rate of chemical reaction by lowering the energy of activation without altered o...

Enzymes: Mechanism of Action Dr. Sebnem GARIP USTAOGLU  Enzymes ‘Biological Catalysts’ All biochemical reactions are enzyme catalyzed rxn’s in the living organism. They accelerate the rate of chemical reaction by lowering the energy of activation without altered or being consumed in the reaction Reusable All enzymes are protein in nature except ribozymes (RNA in nature).  Chemical Nature of Enzymes 2 types of Protein enzymes: Simple Protein enzymes Complex (conjugated) Protein They are formed of They are formed of protein part protein only. and non protein part. 1) Protein part: called apoenzyme 2) Non- protein: called cofactor The whole enzyme is called holoenzyme. The cofactor may be coenzyme or prosthetic group; Coenzyme: Is organic, thermo-labile , loosely attached to enzyme. They are mainly vitamin B derivatives e.g. FAD, NAD. Prosthetic group: Is inorganic, thermo-stable, tightly attached to enzyme. They are usually metal ions e.g. Ca, Zn. The enzymes with metal prosthetic groups are called metalloenzymes.  General Terms Active Site (Catalytic Site): A restricted region of an enzyme which binds to the substrate. Substrate: reactant which binds to enzyme and form temporary association as an enzyme-substrate complex Product: end result of reaction  Enzymatic Reaction Steps 1. Substrate approaches active site 2. Enzyme-substrate complex forms 3. Substrate transformed into products 4. Products released 5. Enzyme recycled  Enzyme-Substrate Binding 1) Lock and Key model: Proposed by Fischer in 1894 the active sites of the unbound enzyme is complementary in shape to the substrate  Enzyme-Substrate Binding con’t. 2) Induced fit theory: It is a more flexible model, where the catalytic site is not fully formed. The catalytic site of the enzyme is not complementary to the substrate. Binding of the substrate to the enzyme induces changes in the shape of the catalytic site making it more fit for substrate.  Enzymes are grouped into 6+1 classes 1. Oxidoreductases: enzymes that catalyze oxidations and reductions (the transfer of electrons from one molecule to another) A– + B → A + B– 2. Transferases: enzymes that catalyze transfer of moieties such as glycosyl, 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. 7. Translocase: general term for a protein that assists in moving another molecule, usually across a cell membrane. enzymes catalyze the movement of ions or molecules across membranes or their separation within membranes.  Enzyme Nomenclature The word enzyme is formed from two Greek words: ‘en’ means inside and ‘zyme’, which means yeast i.e., the word ‘enzyme’ means inside yeast. There are many methods for naming enzymes: 1- The old trivial name as pepsin and trypsin. 2- The name of substrate and the suffix – ase added to it as lactase acting on lactose and sucrase acting on sucrose. 3- Two words, one for the substrate and the other for the type of reaction e.g. Succinate dehydrogenase, pyruvate decarboxylase and glutamine synthetase.  the appearance of multiple names for the same enzyme and duplication in the naming of enzymes exhibiting similar catalytic capabilities To address these problems, the International Union of Biochemistry and Molecular Biology (IUBMB) developed an unambiguous 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.  Enzyme Commission (EC) Number Each enzyme has a numerical code which is formed of four digits separated by dots: – The first digit denotes the class (reaction type) of the enzyme. – The second digit denotes the functional group upon which the enzyme acts. – The third digit denotes the substrate/acceptor. – The fourth digit denotes the serial number of the enzyme (individual enzyme number).  For example 1.1.1.1 enzyme, – 1 means oxidoreductase, – 1.1 means that the functional group is hydroxyl group (-OH), – 1.1.1 means alcohol is the substrate and CH3CH2OH + NAD+ → CH3CHO + NADH + H+ So, 1.1.1.1 means alcohol dehydrogenase enzyme.  Hexokinase - 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), – sub-subclass 1 (alcohol is the phosphoryl acceptor) and – Individual enzyme number is 1, “hexose-6” indicates that the alcohol phosphorylated is on carbon six of a hexose. Hexose-CH2OH + MgATP2− → Hexose-CH2O-PO2−3 + MgADP−+ H+  THE CATALYTIC ACTIVITY OF ENZYMES FACILITATES THEIR DETECTION Assays of the catalytic activity of enzymes are frequently used in research and clinical laboratories. Under appropriate conditions, the rate of the catalytic reaction being monitored is proportionate to the amount of enzyme present, which allows its concentration to be inferred.  THE ANALYSIS OF CERTAIN ENZYMES AIDS DIAGNOSIS The analysis of enzymes in blood plasma has played a central role in the diagnosis of several disease processes. Many enzymes such as lipoprotein lipase and components of the cascades that trigger blood clotting are functional constituents of blood. Other enzymes are released into plasma following cell death or injury and can be used as biomarkers. The appearance or levels of these enzymes can assist in the diagnosis and prognosis of diseases and injuries affecting specific tissues. Following injury, the plasma concentration of a released enzyme may rise early or late and may decline rapidly or slowly. Principal Serum Enzymes Used in Clinical Diagnosis  Quantitative analysis of the activity of released enzymes or other proteins, typically – in plasma or serum – in urine or – in various cells, provides information concerning – diagnosis, – prognosis, and – response to treatment. THANK YOU