Enzymes PDF - Biochemistry for Medical Laboratory Science

CHEM 113 LECTURE: BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE WEEK 5: ENZYMES 1st SEMESTER | PRELIMS | A.Y. 2023-2024 TRANSCRIBED BY: ANNE JUSTINE KATIMBANG PROFESSOR: SIR JOSEPH DEUEL S. CASINSINAN, RMT...

CHEM 113 LECTURE: BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE WEEK 5: ENZYMES 1st SEMESTER | PRELIMS | A.Y. 2023-2024 TRANSCRIBED BY: ANNE JUSTINE KATIMBANG PROFESSOR: SIR JOSEPH DEUEL S. CASINSINAN, RMT ENZYMES - Combined apoenzyme and cofactor entity. It is a compound, usually a protein, that acts as a ○ Coenzymes catalyst for a biochemical reaction. Serves as a cofactor in a conjugated ○ Each cell in a human body contains a thousand enzyme. different enzymes. ○ Catalysts speed up the chemical reaction. Proteins are one of the components of our cell; within the ○ Speeds up or accelerates the biochemical cell we have an enzyme. reaction. Enzymes are important, because “No Enzymes = No NOMENCLATURE AND CLASSIFICATION OF ENZYMES - Metabolic Reactions”. Enzymes are selective in what they do or process. Named about the: ○ E.g Glycolysis → Glucose to another substance. ○ Function of the enzyme Most of the enzymes are proteins but aren’t purely ○ Type of reaction catalyzed proteins. ○ The substrate identity. There are 6 functional classes of enzymes which are Substrate - reactant in an enzyme–catalyzed reaction classified based on the type of reaction in which they are used to catalyze. 3 Important Aspects In The Naming Process Of Ezymes: Enzymes are very sensitive to the environment as they respond quickly. 1. Suffix Enzyme comes from the Greek word “en” which means a. Most enzymes end in the suffix “ase” in and “zyme” which means yeast. i. Ex. Urease, Sucrase, Lipase ○ Yeast speeds up the process of bread b. Exception: Digestive enzymes fermentation. i. Ex. Trypsin, chymotrypsin, pepsin Cause cellular reactions to occur millions of times 2. Prefix faster. a. Type of reaction catalyzed by an enzyme ○ Not consumed during the reaction but merely i. Ex. Oxidase - oxidation reaction & helps the reaction occur more rapidly. Hydrolase - hydrolysis reaction Enzymes are completely soluble in water. 3. Identity of substrate and type of reaction catalyzed Mostly, they are globular proteins (glob means a. Ex. Glucose oxidase, pyruvate carboxylase, spherical). succinate dehydrogenase ENZYME STRUCTURE - CLASSIFICATION OF ENZYMES 1. SIMPLE ENZYME OXIDOREDUCTASE Composed only of protein. Consist entirely of amino acid chains. Catalyzes an oxidation – reduction reaction. ○ Oxidation 2. CONJUGATED ENZYME Increases the number of carbon to oxygen bonds and decreases the Has a non –protein part in addition to a protein part. number of carbon to hydrogen They contain additional chemical components in line bonds. with their reaction. ○ Reduction ○ Apoenzyme Decreases the number of carbon to Protein of the conjugated enzyme. oxygen bonds and increases the Needs cofactor. number of carbon to hydrogen bonds ○ Cofactor Requires a coenzyme that is oxidized or reduced as Non –protein part of the conjugated the substrate is reduced or oxidized. enzyme. They are providing additional chemical TRANSFERASE reactions on that particular functional group. Catalyzes the transfer of a functional group from one Beside those present in the molecule to another. amino acid chain of the ○ Transaminases apoenzyme. Catalyzes the transfer of amino ○ Holoenzyme group from one molecule to another Biochemically active conjugated ○ Kinases enzyme produced from an apoenzyme and a cofactor. OUR LADY OF FATIMA UNIVERSITY  Catalyzes the transfer of phosphate ISOMERASE groups from ATP to give ADP and a phosphorylated product. Catalyzes the isomerisation of a substrate in a Donation of the substrate. reaction converting it to a molecule isomeric with Will gain a phosphate group itself. and the high energy ATP One reactant and one product in reactions. molecule will become ADP. Rearrangement of atoms. LIGASE Catalyzes the bonding together of two molecules into one with the participation of ATP. HYDROLASE Catalyzes the hydrolysis reaction. MAIN CLASSES SELECTED TYPE OF REACTION Central to the process of digestion. SUBSTANCES CATALYZED Carbohydrases ○ Break down glycosidic linkages Oxidases Oxidation of a substrate Proteases ○ Break down peptide bonds Reductases Reduction of a Lipases substrate ○ Break down ester bonds Dehydrogenases Introduction of double OXIDOREDUCTASES bond (oxidation) by They are connected with the lipid metabolism, lipid formal removal of two synthesis, and fat breakdown. H atoms from substrate, the H being LYASE accepted by a coenzyme. Catalyzes the addition of a group to a double bond or Transaminases Transfer of an amino the removal of a group to form a double bond in a group between manner that does not involve hydrolysis or oxidation. substrates. ○ Hydratase Effect TRANSFERASES Addition reaction of the component Kinases Transfer of a phosphate of water to double bond. group between substrates. ○ Dehydratase Removal reaction of the component Lipases Hydrolysis of ester of water to double bond. linkages in lipids. Proteases Hydrolysis of amide linkages in proteins. Nucleases Hydrolysis of sugar-phosphate ester HYDROLASES bonds in nucleic acids. Carbohydrases Hydrolysis of glycosidic bonds in carbohydrates. Phosphatases Hydrolysis of phosphate-ester bonds. Dehydratases Removal of H2O from substrate. LYASES Decarboxylases Removal of CO2 from OUR LADY OF FATIMA UNIVERSITY  substrate. INDUCED–FIT MODEL Deaminases Removal of NH3 from Enzyme’s active site is not rigid and static. substrate. There’s a constant change in shape Hydratases Addition of H2O from Allows for changes in the shape or geometry of the substrate. active site of an enzyme to accommodate a substrate. Result of the enzyme’s flexibility; it adapts the Racemases Conversion of D to L incoming substrate. isomer, or vice versa. ISOMERASES Mutases Transfer of a functional group from one position to another in the same molecule. Synthetases Formation of a new bond between two substrates, with participation of ATP. LIGASES Carboxylases formation of new bond between a substrate and CO2, with participation of ATP, MODELS OF ENZYME REACTION Enzyme Active Site ○ Small part of an enzyme’s structure that is actually involved in catalysis. ○ A three –dimensional entity formed by groups that come from different parts of the protein chains. ENZYME SPECIFICITY ○ Area where the substrate will bind; explains how the enzyme functions in the biochemical Extent to which an enzyme’s activity is restricted to: system. ○ A specific substrate ○ Crevice-like Locatio ○ A specific group of substrate Location where the substrate will ○ A specific type of chemical bond or a specific bind. type of chemical reaction. Enzyme–Substrate Complex Degree of specificity is determined by the active site. ○ The intermediate reaction species that is formed when a substrate binds to the active TYPES OF ENZYME SPECIFICITY site of an enzyme. ○ There is a specific enzyme product complex. ABSOLUTE SPECIFICITY Catalyze only one reaction. Most restrictive of all specificities. Catalase ○ Enzyme with absolute specificity. Urease ○ For bacterial inhibition; only for bacterial inhibition GROUP SPECIFICITY LOCK–AND–KEY MODEL Act only on molecules that have a specific functional Enzyme group, such as hydroxyl, amino or phosphate groups. specificity to Carboxylpeptidase is group specific. its substrate. The amino acid group; they are cleaving the amino Active site in acid one at a time and they will see that particular the enzyme amino acid from the carboxyl from the peptide chain. has the fixed, rigid LINKAGES SPECIFICITY geometrical conformation. Act on the particular type of bond, irrespective of the Substrates rest of the molecular structure. with a Phosphatases hydrolyze phosphate –ester bonds in complementary geometry can be accommodated. all types of phosphate esters. Most general of the common species. OUR LADY OF FATIMA UNIVERSITY  STEREOCHEMICAL SPECIFICITY Operates in the small intestines, function best at pH 8.0 Act on a particular isomer. NOTE: Enzymes are acidic because of zwitterion. ENZYME ACTIVITY Enzymes are pH sensitive because neutral pH is what it prefers. Measures the rate at which an enzyme converts Acidic - goes up fast. substrate to products in a biochemical reaction. Basic - goes down slow FACTORS THAT AFFECT ENZYME ACTIVITY SUBSTRATE CONCENTRATION TEMPERATURE Increased concentration of Measure of kinetic substrate will obtain the energy of enzyme activity. molecules. Turnover Number More than 37 deg C ○ Number of (body temperature) substrate will cause the molecules enzyme to transformed per denature. minute by one Higher molecule of temperatures mean enzyme under optimum conditions of molecules are temperature, pH and saturation. moving faster and Higher substrate = High enzyme activity colliding more frequently. When the temperature increases beyond a certain point, the increased energy begins to cause disruption to the tertiary structure of enzymes. ENZYME CONCENTRATION ○ It will result in denaturation of the enzyme. Optimum temperature ○ Temperature at which an enzyme exhibits Kept in a low number maximum activity. because enzymes are not consumed in the reaction. pH The greater the enzyme concentration, the greater the The charge on acidic reaction rate. and basic amino acids located at the active site depends on pH Small pH changes can result in enzyme denaturation and EXTREMOZYMES subsequent loss of catalytic activity. A microbial enzyme active at a condition that would Biochemical buffers inactivate human enzymes as well as enzymes present in help maintain the other types of higher organisms. optimum pH for an enzyme. Extremophile Microorganisms that thrives in Can also affect extreme environments substrate, causing either protonation or deprotonation of groups on the Acidophile Optimal growth at pH levels of substrate. 3.0 or below. Optimum pH ○ pH at which an enzyme exhibits maximum Alkaliphile Optimal growth at pH levels of activity 9.0 or above. ○ Physiological pH ranges from 7.0 – 7.5 ○ Pepsin Hyperthermophile Temperature between 80C and Active in the stomach, functions best 122C needed to thrive at pH 2.0 ○ Trypsin Halophile Includes bacteria, Archaebacteria and some OUR LADY OF FATIMA UNIVERSITY  eukaryotic – chain group at the enzymes active site. Hyper saline in environment ○ Do not have structures similar to that of the enzyme’s normal substrate. Other term is psychrophile It cannot bring back the original function. They are categorized as Locks onto the active site and permanently changes extremophilic organisms its shape. Cryophile Growth in lower temperature From -20C to 10C REGULATION OF ENZYME ACTIVITY - Places that are permanently cold such as polar regions and deep 1. A cell that continually produces a large amount of areas of the sea enzyme for which substrate concentration is always very low is wasting energy. a. The production of the enzyme needs to be “ ENZYME INHIBITION turned off”. 2. A product of an enzyme – Catalyzed reaction that is Enzyme Inhibitor present in plentiful amounts in a cell is a waste of energy ○ Substance that slows or stops the normal if the enzyme continues to catalyze the reaction that catalytic function of an enzyme by binding to produces the product. it. a. The enzyme needs to be turned off. REVERSIBLE COMPETITIVE INHIBITION Body will run out of energy if enzymes do not shut off Competitive Enzyme Inhibitor ○ Molecules that sufficiently ALLOSTERIC ENZYME resemble an enzyme substrate in shape and 1. Have Quaternary Structure charge distribution that it a. 2 or more protein chains. can compete with the 2. Have 2 kinds of binding sites substrate for occupancy of a. For substrates and for regulators the enzyme's active site. 3. Active and regulatory binding sites are distinct from ○ Remains in changed as it each other in both location and shape. binds to the enzyme's 4. Binding of a molecule at the regulatory site causes active site. changes in the overall three – dimensional structure It can bring back function. of the enzyme, including structural changes at the Duct tape mouth analogy. active site. Reversible process because it is maintained but weak interactions. Can be reduced by increasing the concentration of the substrate. REVERSIBLE NON-COMPETITIVE INHIBITION Non-competitive Enzyme Inhibitor ○ Molecule that decreases enzyme activity by binding to a site on an enzyme other than the active site. ○ Presence of this causes a change in the structure of the enzyme sufficient to prevent the catalytic groups at the active site from properly affecting their catalyzing action. Choking analogy. It changes the shape of the active site so that the substrate cannot be processed. IRREVERSIBLE INHIBITION Irreversible Enzyme Inhibitor ○ Molecule that inactivates enzymes by forming a strong covalent bond to an amino acid side OUR LADY OF FATIMA UNIVERSITY ENZYME WITH TWO OR MORE PROTEIN CHAINS AND 2 COVALENT MODIFICATION OF ENZYME KINDS OF BINDING SITES Process in which enzyme activity is altered by Regulators covalently modifying the structure of the enzyme ○ Substances that bind at the regulatory sites of through attachment of a chemical group or removal of allosteric enzymes. a chemical group from a particular amino acid within the enzyme structure. A. Positive Regulator a. Increase enzyme activity Phosphorylation Process of addition of the b. The shape of the active site is changed phosphate group to the enzyme by such that it can more readily accept protein kinases. substrates. c. Positive Catalysis Dephosphorylation Removal of the phosphate group B. Negative Regulator from the enzyme by phosphatases. a. Decrease enzyme activity b. Changes to the active site are such that MEDICAL USES OF ENZYMES - substrate is less readily accepted. c. Negative Catalysis 1. Used to diagnose certain diseases. 2. Appearance of these enzymes in the blood often indicates that there is tissue damage in an organ and FEEDBACK CONTROL that cellular contents are spilling out into the bloodstream. A process in which activation or inhibition of the first 3. Used in the treatment of disease. reaction in a reaction sequence is controlled by a product of reaction sequence. NOTE: Negative Feedback Plasminogen - enzyme that breaks down clots. ○ Product turns into a regulatory substance and shuts down enzyme 1 by attaching to the regulatory site. ENZYME CONDITION INDICATED BY ABNORMAL LEVEL Lactate dehydrogenase (LDH) Heart disease; Liver disease Creatinine phosphokinase Heart disease PROTEOLYTIC ENZYMES (CPK) Aspartate transaminase (AST) Heart disease; Liver Catalyzes the breaking of peptide bonds that disease; Muscle damage maintain the primary structure of protein. Generated in an inactive form and converted to active Alanine transaminase (ALT) Heart disease; Liver form when they are needed. disease; Muscle damage Regulate enzymes. Inactive form of enzyme that turns into active when Gamma-glutamyl Heart disease; Liver needed to stop another enzyme. transpeptidase (GGTP) disease ZYMOGEN Alkaline phosphatase (ALP) Bone disease; Liver disease Inactive precursor of a proteolytic enzyme. Requires another enzyme to turn active. AST, ALT, GGPT, & ALP - are used for liver profile tests. Activation of a zymogen requires an enzyme – Serum Glutamic Pyruvic Transaminase (SGPT) & controlled reaction that moves some part of the Serum Glutamic-Oxaloacetic Transaminase (SGOT) - zymogen structure which changes the 3 – are two most common types of liver enzymes, dimensional structure of zymogen, which affects ○ Besides the liver, SGOT is found in the kidney, active site conformation. muscles, heart and even the brain. On the contrary, SGPT is predominantly found in the liver only. OUR LADY OF FATIMA UNIVERSITY