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A.L. Wafa’a sameer 2014 Biochemistry Enzymes … Enzymes Biochemistry : Biochemistry broadly deals with the chemistry of life and living processes .the scope of biochemistry is as vast as life itself . Every aspect of life-birth, growth, reproduction, aging and death, involves biochemistry. For that matter, every moment of life is packed with hundreds of biochemical reactions. Biochemistry is the most rapidly developing and most innovative subject in medicine , these include the application of biochemistry in the laboratory for the diagnosis of diseases . E nzymes : are proteins that act as catalysts, compounds that increase the velocity or the rate of chemical reactions without itself undergoing any change in the overall process. In addition to increasing the speed of reactions, enzymes provide a means for regulating the rate of metabolic pathways in the body.. Enzyme binding sites. An enzyme binds the substrates of the reaction and converts them to products. The substrates are bound to specific substrate binding sites on the enzyme. The spatial geometry required for all the interactions between the substrate and the enzyme makes each enzyme selective for its substrates and ensures that only specific products are formed. (Enzymes act with highly specificity on specific types of molecules ((substrate)) . E + S = ES complex) . Enzymes act under mild conditions (pH and temperature ) . Enzymes found in large number within the cells , and that’s make the cells act like a complex chemical machine . References : Text book (Lippincott’s ) biochemistry A.L. Wafa’a sameer 2014 Biochemistry Enzymes … THE ENZYME-CATALYZED REACTION Enzymes, in general, provide speed, specificity, and regulatory control to reactions in the body. Enzyme-catalyzed reactions have three basic steps: (1) binding of substrate: E + S ↔ ES complex (2) conversion of bound substrate to bound product: ES ↔ EP (3) release of product : EP ↔ E + P An enzyme binds the substrates of the reaction it catalyzes and brings them together at the right orientation to react. The enzyme then participates in the making and breaking of bonds required for product formation, releases the products, and returns to its original state once the reaction is completed. Enzymes do not invent new reactions; they simply make reactions occur faster. The catalytic power of an enzyme (the rate of the catalyzed reaction divided by the rate of the uncatalyzed reaction) is usually in the range of 106 to 1014. Without the catalytic power of enzymes, reactions such as those involved in nerve conduction, heart contraction, and digestion of food would occur too slowly for life to exist. Each enzyme usually catalyzes a specific biochemical reaction. The ability of an enzyme to select just one substrate and distinguish this substrate from a group of very similar compounds is referred to as specificity. The enzyme converts this substrate to just one product. The specificity, as well as the speed, of enzyme catalyzed reactions result from the unique sequence of specific amino acids that form the three-dimensional structure of the enzyme. References : Text book (Lippincott’s ) biochemistry A.L. Wafa’a sameer 2014 Biochemistry Enzymes … Key and lock model Chemical nature and properties of enzymes 1- All the enzymes are invariably proteins. 2- Each enzyme has its own tertiary structure and specific conformation which is very essential for its catalytic activity. 3- The functional unit of the enzyme is known as holoenzyme which is often made up of apoenzyme (the protein part) and a coenzyme (non-protein organic part) . Holoenzyme → Apoenzyme + Coenzyme (active enzyme) (protein part) (non-protein part) 4- The word monomeric enzyme is used if it is made up of a single polypeptide e.g. ribonuclease , trypsin. Some of the enzymes which possess more than one polypeptide (subunit) chain are known as oligomeric enzymes e.g. lactate dehydrogenase, aspartate transcarbamoylase etc. References : Text book (Lippincott’s ) biochemistry A.L. Wafa’a sameer 2014 Biochemistry Enzymes … Nomenclature of enzymes In the early days, the enzymes were given names by their discoverers in an arbitrary manner. For example, the names pepsin, trypsin and chymotrypsin convey no information about the function of the enzyme or the nature of the substrate on which they act. The suffix-ase was added to the substrate for naming the enzymes e.g. lipase acts on lipids; nuclease on nucleic acids; lactase on lactose etc , the suffix – ase also can be added to the name of the reaction that the enzyme react e.g. Oxidases , decarboxylases , dehydrogenases etc . Enzymatic reactions divided in to 6 major classes and each have (4-13) subclasses . The additional information that required to express the nature of the enzymatic reaction . Each enzyme has a specific code number called Enzymatic code (EC) that identified each of class , subclass , sub-subclass , and the last number refers to the name of enzyme itself . e.g.// 2.7.1.1 [ ATP: D-hexose- 6- phosphotransferase] In that 2 refers to the class ( transferase ) . 7 refers to the subclass ( transfer a phosphate group ) . 1 refers to the sub-subclass ( refers that alcohol act like phosphate acceptor ) . 1 refers to the enzyme ( hexoxinase ) . Which is the enzyme that help in the transferring of phosphate group from ATP to the hydroxyl group on the 6th carbon atom of glucose . References : Text book (Lippincott’s ) biochemistry A.L. Wafa’a sameer 2014 Biochemistry Enzymes … Classification of Enzymes Enzymes are sometimes considered under two broad categories : (a) Intracellular enzymes- They are functional within cells where they are synthesized. (b) Extracellular enzymes – These enzymes are active outside the cell; all the digestive enzymes belong to this group. The International Union of Biochemistry (lUB) appointed an Enzyme Commission in 1961.This committee made a thorough study of the existing enzymes and devised some basic principles for the classification and nomenclature of enzymes. Enzymes are divided into six major classes in that order . Each class on its own represents the general type of reaction brought about by the enzymes of that class . The six classes of the enzymes are as in the table below : References : Text book (Lippincott’s ) biochemistry A.L. Wafa’a sameer 2014 Biochemistry Enzymes … 1- Oxidoreductases : Oxidation-reduction reactions are very common in biochemical pathways and are catalyzed by a broad class of enzymes called oxidoreductases. Whenever an oxidation-reduction reaction occurs, at least one substrate gains electrons and becomes reduced, and another substrate loses electrons and becomes oxidized. a- One subset of reactions is catalyzed by dehydrogenases, which accept and donate electrons in the form of hydride ions (H:-) or hydrogen atoms. Usually an electron-transferring coenzyme, such as NAD_/NADH, acts as an electron donor or acceptor b- In another subset of reactions, O2 donates either one or both of its oxygen atoms to an acceptor (for example, see xanthine oxidase,). When this occurs, O2 becomes reduced, and an electron donor is oxidized. Enzymes participating in reactions with O2 are called * hydroxylases and oxidases when one oxygen atom is incorporated into a substrate and the other oxygen atom into water, or both atoms are incorporated into water. They are called *oxygenases when both atoms of oxygen are incorporated into the acceptor. Most hydroxylases and oxidases require metal ions, such as Fe-2, for electron transfer. 2- Transferases : Transferases catalyze group transfer reactions—the transfer of a functional group from one molecule to another. If the transferred group is a high-energy phosphate, the enzyme is a kinase; if the transferred group is a carbohydrate residue, the enzyme is a *Glycosyltransferase; if it is a fatty acyl group, the enzyme is an *acyltransferase. Another subset of group transfer reactions consists of transaminations . In this type of reaction, the nitrogen group from an amino acid is donated to an alpha - keto acid, forming a new amino acid and the alpha - keto acid corresponding to the donor amino acid. Enzymes catalyzing this References : Text book (Lippincott’s ) biochemistry A.L. Wafa’a sameer 2014 Biochemistry Enzymes … last type of reaction are called *transaminases or aminotransferases. The coenzyme pyridoxal phosphate is required for all transaminases . When the physiologically important aspect of the reaction is the compound synthesized, the transferase may be called a synthase. For example, the enzyme commonly called glycogen synthase transfers a glucosyl residue from UDP-glucose to the end of a glycogen molecule. Its systematic name is UDP-glucose-glycogen glycosyltransferase. 3- Hydrolases: In hydrolysis reactions, C-O, C-N, or C-S bonds cleaved by the addition of H2O in the form of OH- and H+ to the atoms forming the bond . The enzyme class names specify the group being cleaved (e.g., the enzyme commonly named chymotrypsin is a protease, a hydrolase that cleaves peptide bonds in proteins). 4- Lyases. The lyase class of enzymes consists of a diverse group of enzymes cleaving C-C, C-O, and C-N bonds by means other than hydrolysis or oxidation. Some of the enzymes catalyzing C-C bond cleavage are called *aldolases, *decarboxylases (when carbon dioxide is released from a substrate), and *thiolases (when the sulfur-containing nucleophile of cysteine or CoASH is used to break a carbon-carbon bond) . This broad class of enzymes also includes *dehydratases and many *synthases. Dehydratases remove the elements of water from two adjacent carbon– carbon bonds to form a double bond. Certain enzymes in this group, such as certain group transferases, are commonly called synthases when the physiologically important direction of the reaction favors the formation of a carbon–carbon bond (e.g., citrate synthase). 5- Isomerases : Many biochemical reactions simply rearrange the existing atoms of a molecule, that is, create isomers of the starting material . Enzymes rearranging the bond structure of a compound are called isomerases, whereas References : Text book (Lippincott’s ) biochemistry A.L. Wafa’a sameer 2014 Biochemistry Enzymes … enzymes catalyzing movement of a phosphate from one atom to another are called mutases. 6- Ligases : Ligases synthesize C-C, C-S, C-O, and C-N bonds in reactions coupled to the cleavage of a high-energy phosphate bond in ATP or another nucleotide. Carboxylases, for example, add CO2 to another compound in a reaction requiring ATP cleavage to provide energy . Most carboxylases require the coenzyme biotin. Other ligases are named synthetases (e.g., fatty acyl CoA synthetase). Synthetases differ from the synthases mentioned under “lyases” and group “transferases” in that synthetases derive the energy for new bond formation from cleavage of high-energy phosphate bonds, and synthases use a different source of energy. References : Text book (Lippincott’s ) biochemistry