BIOCHEMISTRY THE ENZYME BY : MISRAN ASROFIL WA ODE SUKMAWATI (F1C1 17 051) (F1C1 17 063) Faculty of Math and Science Haluoleo University CONTENT Introduction Nomenclature of Enzymes and Classification Mechanism of Enzyme Action Factors Affecting Rate of Enzyme Catalyzed Reactions Michaelis-Menten Equation Inhibitor Effect Introduction Enzymes are biological catalysts that speed up the rate of the biochemical reaction. Most enzymes are three dimensional globular proteins (tertiary and quaternary structure). Some special RNA species also act as enzymes and are called Ribozymes e.g. hammerhead ribozyme. globular proteins hammerhead ribozyme. STRUCTURE OF ENZYMES o The active site of an enzyme is the region that binds substrates, co-factors and prosthetic groups and contains residue that helps to hold the substrate. o Apoenzyme (Inactive), Is the protein part of the enzyme, as were attached substrate, are thermolabil (sensitive to high temperatures), and serves to determine the specificity of the enzyme. o Co-factor, It is a non-protein part of the enzyme, is stable at high temperatures, and does not change at the end of the reaction, cofactor consists of: Activator Prosthetic group Coenzyme Nomenclature of Enzyme Substrate Type Types of Chemical Bonds Reaction Type With Classification Substrate Type Substrate + with suffix ase Example : amilase, laktase, sakrase, maltase Problems : enzymes with the same substrate even in different organisms if they look the same TYPES OF CHEMICAL BOND The chemical bond + ase Example : peptidase, esterase Communicative but do not have a sharp distinctive ability The chemical bond is broken up Reaction Type Type reaction + ase Example : glucose oksidase (oxzide of glucose in aerob condition) Glucose dehidrogenase (oxzide of glucose in anaerob condition) Amino transferase (move the amino group) Deskriptif & informatif Nomenclatur Name Enzyme Commission (1961), enzyme divided into six classes depending on the catalyzed reaction. E.C.a.b.c.d a. Enzyme Class b. Enzyme Subclass c. Sub class of enzymes d. Subclasses of enzyme classes Enzyme Class Oksidoreduktase Transferase Hidrolase Liase Isomerase Ligase First Digit EC 1 2 3 4 5 6 The Enzyme Name System According to The International Union of Biochemistry (IUB) Based on Four (IV) Principal Rules 1. According Enzyme Commission (1961), enzyme divided into six classes depending on the catalyzed reaction. Six Class Enzymes (Based on Type Reaction) • • • • • • Oksidoreduktase EC1 Transferase EC2 Hidrolase EC3 Liase EC4 Isomerase EC5 Ligase EC6 2. Enzyme name consist of two (II) Parts The first part shows the substrate, while the second part shows the catalysed reaction type Example: • Enzyme 1.1.1.1 Alcohol: NAD oxsidoreduktase wich catalyzes the following reaction: • Alcohol + NAD+ → aldehid atau keton + NADH + H+ • Alcohol and NAD is a substrate and co-substrate and oxidoreductase indicates the type of reaction based on the previous six class divisions 3. Each enzyme has a code number (EC) consisting of four parts numbering. Example: Enzyme EC 1.1.1.1 Alcohol : NAD Oxsidoreduktase • The first numbering indicates the class of enzyme classes namely: EC 1 oxidoreductase – EC 6 ligase • The second number indicates the subclass of the enzyme • The third number indicates the subsubclass of the enzyme • The fourth number indicates the enzyme it Oxsidoreduktase (EC.1. . ) Second Digit: Hydrogen or electron donor 1. Alcohol 2. Aldehyde or ketone 3. CH-CH 4. Amin primer 5. Amin sekunder 6. NADH atau NADPH Third Digit: Hydrogen or electron acceptor 1. NAD+ or NADP+ 2. Fe 3+ 3. O2 4. acceptors other EC. 1.1.1.1 Sistematic name Trivial name : Alkohol NAD+ oksidoreduktase : Alkohol dehidrogenase Transferase ( EC.2. . ) The second digit is the transferred group 1. One carbon group 2. Aldehyde or ketone group 3. Asil cluster 4. Glycosyl group 7. Phospate group Third digit: clarifycate the transferred group E.C.2.1.1: metiltransferase E.C.2.1.2: hidroksimetiltransferase E.C.2.1.3: karboksil atau karbamoil transferase E.C.2.7.1: fosfotransferase Hidrolase ( EC.3. . ) The Second: The type of bond that is hydrolyzed 1. ester 2. glikosidik 4. peptida 5. C-N beside peptida The Third: further explaining the type of hydrolysed bond E.C.3.1.1. Ester karboksilat E.C.3.1.2. Ester tiol E.C.3.1.3 Monoester fosfat E.C.3.1.4 Diester fosfat Liase (EC.4. . Isomerase (EC.5. . ) The Second Digit: Type of Reaction ) The Second Digit: the broken bond 1. C-C 2. C-O 3. C-N 4. C-S The Third Digit: The removed group. For C-C Liase 1. Carboxyl group 2. Aldehyde group 3. Keto acid group 1. Rasemisasi atau epimerisasi 2. Isomerisasi cis-trans 3. Oxsidoreduktase intramolekul 4. Reaction transfer intramolekul The Third Digit: Types of molecules that undergo Isomerization 1. Amino Acid 2. Hydroxy Acid 3. Carbohydrate Ligase (EC.6. . ) The Second Digit: The type of bond formed 1. C-O 2. C-S 3. C-N 4. C-C The Third Digit: Further explaining the bonds formed E.C. 6.3.1 ammonia acid ligase (amida, sintase) E.C. 6.3.2 amino acid ligase (peptida, sintase) Specific Classification for Certain Enzyme Protein – breaking Enzyme class third IUB Classification System hydrolase peptide endopeptidase • Break peptide bonds that are in the middle or in the substrate protein molecule eksopeptidase • Peptidase enzymes that act on peptide bonds in the outermost part of the substrate protein molecule MECHANISM OF ENZYME ACTION Enzymes catalyze the reaction by increasing the reaction rate. Enzymes increase the rate of reaction by reducing activation energy (the energy needed for reaction) How the enzyme works, can be explained by the following two theories: Induced Fit Model Lock and Key Theory MECHANISM OF ENZYME ACTION Induced Fit Theory • proposed by Daniel Koshland in 1958 • This theory states that the enzyme has an active side which readily adjusts to the shape of the substrate Lock and Key Model Proposed by EMIL FISCHER in 1894. Lock and key hypothesis assumes the active site of an enzymes are rigid in its shape. There is no change in the active site before and after a chemical reaction. This model has been proven to be inaccurate because it failed to explain the stabilization of the transition state achieved by the enzyme Factors Affecting Rate of Enzyme Catalyzed Reactions Temperature Hydrogen ion concentration (pH) Substrate concentration Effect of Temperature Raising the temperature increases the rate of enzyme catalyzed reaction by increasing kinetic energy of reacting molecules. Enzymes work maximum over a particular temperature known as optimum temperature. Enzymes for humans generally exhibit stability temperature up to 35-45 ᵒC. Very low temperatures affect the active side of the enzyme which is part of binding to the substrate. Can experience coagulation due to a temperature that is too low, the function of the enzyme cannot run even if the enzyme is not damaged. Temperature Each temperature increases 10 oC, the speed of the enzyme will be doubled, to a certain temperature limit. Enzymes and proteins are generally deactivated by high temperatures Warm-blooded enzymes and humans work most efficiently at 37 oC, while coldblooded animal enzymes at 25 oC. 5- 40 oC Increase in Activity <5 oC - inactive 40oC - denatures Effect of pH o Rate of almost all enzymes catalyzed reactions depends on pH o Most enzymes exhibit optimal activity at pH value between 5 and 9 o High or low pH value than optimum value will cause ionization of enzyme which result in denaturation of enzyme Michaelis-menten Model & Effects of Substrate Concentration Michaelis-Menten Model: “According to this model the enzyme reversibly combines with substrate to form an ES complex that subsequently yields product, regenerating the free enzyme” E + S k₁ k ₋₁ where: S is the substrate E is the enzyme ES-is the enzyme substrate complex P is the product K1,K-1 and K2 are rate constants ES k2 E + P Michaelis-Menten Equation Michaelis-Menten Equation: “It is an equation which describes how reaction velocity varies with substrate concentration.” Where : Vo is the initial reaction velocity. Vmax is the maximum velocity. Km is the Michaelis constant = (k₋₁+k₂)/k₁. [S] is the substrate concentration. SUBSTRATE CONCENTRATION • In an enzymatic reaction, an increase in substrate concentration will reach a maximum speed, where the addition of the next substrate will not increase the reaction speed. Inhibition INHIBITORS: o o o Any substance that can diminish the velocity of an enzyme catalyzed reaction is called an inhibitor. The inhibitor will bind to the enzyme to form an enzyme-inhibitor complex Obstacles to enzyme activity in a chemical reaction are also mechanisms for regulating the reactions that occur in our bodies. Types Of Inhibition Inhibition Reversible Competitive Uncompetitive Irreversible Mixed Noncompetitive Reversible Inhibition o It is an inhibition of enzyme activity in which the inhibiting molecular entity can associate and dissociate from the protein‘s binding site. TYPES OF REVERSIBLE INHIBITION o There are three types : Competitive inhibition. Uncompetitive inhibition. Mixed inhibition. Competitive inhibition Competitive inhibitors have a chemical structure similar to the substrate and bind the enzyme to the same active site as the substrate (catalytic site) The effect of competing inhibitors does not depend on solely inhibitor concentrations, but also on substrate concentration In competitive inhibition, inhibitors and substrates compete to bind to enzymes Uncompetitive inhibition Non-competitive inhibitions have no competition between substrates and inhibitors In this reaction, the substrate and inhibitor each bind to the enzyme in a different place Inhibitors can bind either free enzyme molecules or ES complexes. The EIS complex that is formed then becomes inactive Mixed Inhibition Mixed inhibition This type of inhibition is similar to noncompetitive inhibition, besides the EIS complex has residual enzymatic activity Inhibitor may bind E or ES better In mixed inhibition, the inhibitor binds to an allosteric site, i.e. a site different from the active site where the substrate binds. However, not all inhibitors that bind at allosteric sites are mixed inhibitors Irreversible Inhibition o This type of inhibition involves the covalent attachment of the inhibitor to the enzyme. o The catalytic activity of enzyme is completely lost. o It can only be restored only by synthesizing molecules. Thank You L/O/G/O
