Enzymes Introduction PDF

Enzymes Biochemistry Diploma  Defination == Enzymes are organic catalysts produced by living cells. == They accelerate a wide variety of chemical reactions which occur in biological systems. == Thus, enzymes are biocatalysts.  Nomenclature of Enzymes...

Enzymes Biochemistry Diploma  Defination == Enzymes are organic catalysts produced by living cells. == They accelerate a wide variety of chemical reactions which occur in biological systems. == Thus, enzymes are biocatalysts.  Nomenclature of Enzymes Recommended name --- The common name have the suffix ase attached to the substrate of the reaction: Urea: remove -a, replace with -ase = urease Lactose: remove -ose, replace with -ase = lactase --- Other enzymes are named for the substrate and the reaction catalyzed Lactate dehydrogenase Pyruvate decarboxylase --- Some names are historical - no direct relationship to substrate or reaction type Catalase Pepsin Chymotrypsin Trypsin  Systematic name --- In the systematic naming system, enzymes are divided into six major classes  Enzymes properties Present in Converts substrates Made of protein into products all living cells Enzymes Affected by cellular conditions any condition that affects protein structure temperature, pH.  1- Active sites === Enzyme molecules contain a special pocket or cleft called the active site. === The active site contains amino acid side chains that create a three dimensional surface complementary to the substrate. === The substrate binds the enzyme, forming an enzyme– substrate (ES) complex. === ES is converted to enzyme-product (EP) complex that dissociate to enzyme and product.  2- Catalytic efficiency === Enzyme-catalyzed reactions are highly efficient, proceeding from 103–108 times faster than uncatalyzed reactions. === Typically, each enzyme molecule is capable of transforming 100 to 1000 substrate molecules into product each second. === The number of molecules of substrate converted to product per enzyme molecule per second is called the turnover number, or kcat.  3- Specificity === Enzymes are highly specific, interacting with one or a few substrates and catalyzing only one type of chemical reaction. === The set of enzymes made in a cell determines which metabolic pathways occur in that cell.  4- Holoenzymes === Some enzymes require molecules other than proteins for enzymic activity. === The term holoenzyme refers to the active enzyme with its non-protein component, whereas the enzyme without its non-protein moiety is termed an apoenzyme and is inactive. === If the non-protein moiety is a metal ion such as Zn2+ or Fe2+, it is called a cofactor. === If it is a small organic molecule, it is termed a coenzyme as NAD and FAD. === === Coenzymes frequently are derived from vitamins. For example, NAD+ contains niacin and FAD contains riboflavin.  5- Regulation === Enzyme activity can be regulated, that is, increased or decreased, so that the rate of product formation responds to cellular need.  6- Location within the cell === Many enzymes are localized in specific organelles within the cell. === Such compartmentalization serves to isolate the reaction substrate or product from other competing reactions. === This provides a favorable environment for the reaction, and organizes the thousands of enzymes present in the cell into purposeful pathways.  Theories of enzyme action === There are two theories that describe the binding of enzymes: 1) Lock and Key Theory and 2) Induced Fit Theory.  1) Lock and Key Theory === The shape of the enzyme's active site is complementary to that of its substrate  2) Induced Fit Theory === The active site has a flexibility of shape, thus when an appropriate substrate comes in contact with the enzyme's active site, the shape of the active site would change to fit with the substrate.  Factors affecting enzyme activity === Different enzymes show different responses to changes in substrate concentration, temperature, and pH.  A. Substrate concentration === The rate or velocity of a reaction (v): is the number of substrate molecules converted to product per unit time; velocity is usually expressed as μmol of product formed per minute. === The rate of an enzyme-catalyzed reaction increases with substrate concentration until a maximal velocity (Vmax) is reached. === The leveling off of the reaction rate at high substrate concentrations reflects the saturation with substrate of all available binding sites on the enzyme molecules present.  B. Temperature === Generally, the rate of enzyme reaction would increase as temperature increase; however, if the optimal temperature—usually around 40°C-- is reached the enzyme would denatured and loss its ability to react with the substrate. human enzymes = 35°- 40°C  C. pH 1. Effect of pH on the ionization of the active site: --- The concentration of H+ affects reaction velocity in several ways. --- First, the catalytic process usually requires that the enzyme and substrate have specific chemical groups in either an ionized or un- ionized state in order to interact. --- For example, catalytic activity may require that an amino group of the enzyme be in the protonated form (–NH3+). --- At alkaline pH, this group is deprotonated, and the rate of the reaction, therefore, declines.  2. Effect of pH on enzyme denaturation: --- Extremes of pH can also lead to denaturation of the enzyme, because the structure of the catalytically active protein molecule depends on the ionic character of the amino acid side chains.  3. The pH optimum varies for different enzymes: ===The pH at which maximal enzyme activity is achieved is different for different enzymes, and often reflects the [H+] at which the enzyme functions in the body. === For example, pepsin, a digestive enzyme in the stomach, is maximally active at pH=2, whereas other enzymes, designed to work at neutral pH, are denatured by such an acidic environment  Inhibition of enzyme activity === Any substance that can diminish the velocity of an enzyme- catalyzed reaction is called an inhibitor. === In general, irreversible inhibitors bind to enzymes through covalent bonds. === Reversible inhibitors typically bind to enzymes through non-covalent bonds, thus dilution of the enzyme–inhibitor complex results in dissociation of the reversibly bound inhibitor, and recovery of enzyme activity. === The two most commonly encountered types of reversible inhibition are competitive and noncompetitive.  A. Competitive inhibition === This type of inhibition occurs when the inhibitor binds reversibly to the same site that the substrate would normally occupy and, therefore, competes with the substrate for that site. === The effect of a competitive inhibitor is reversed by increasing [S]. === At a sufficiently high substrate concentration, the reaction velocity reaches the Vmax observed in the absence of inhibitor.  B. Noncompetitive inhibition === This type of inhibition is recognized by its characteristic effect on Vmax. === Noncompetitive inhibition occurs when the inhibitor and substrate bind at different sites on the enzyme. === The noncompetitive inhibitor can bind either free enzyme or the ES complex, thereby preventing the reaction from occurring. === Noncompetitive inhibition cannot be overcome by increasing the concentration of substrate. === Thus, noncompetitive inhibitors decrease the apparent Vmax of the reaction.