Enzymes PDF

# ENZYMES ## ENZYMES - Enzymes are protein catalysts that mediate virtually all reactions in the body. - Enzymes catalyze the chemical reactions that make life on the earth possible. - They increase rates of chemical reactions by a hundred thousand to trillion folds. - They lower the energy of act...

# ENZYMES ## ENZYMES - Enzymes are protein catalysts that mediate virtually all reactions in the body. - Enzymes catalyze the chemical reactions that make life on the earth possible. - They increase rates of chemical reactions by a hundred thousand to trillion folds. - They lower the energy of activation. ## ENZYMES - Enzyme is a compound, usually a protein, that acts as a catalyst for a biochemical reaction. - **Substrate:** a molecule acted upon by the enzyme. - **Ligand:** a substance that forms a complex with a biomolecule to serve a biological purpose. ## Properties and Characteristics of Enzyme 1. Catalyze biological and chemical reactions. Enzymes can speed up reactions to go a million or billion times faster. 2. Enzymes are substrate specific. 3. Enzymes are very sensitive to pH and temperature. ## Properties and Characteristics of Enzyme - Enzymes are very specific. One enzyme is to one substrate or one set of substrates, and convert it to one product or one set of products. - As a result, there are virtually and usually no side reactions or by-products. - They can exist as single or multiple subunits. ## Biomedical Importance - Biochemical processes - Assembly of building blocks; muscle contraction - Diagnosis - ALT, AST, GGT, ALP (liver panel) - Pharmacology - Biosynthesis of complex drugs or antibiotics - Food and Industry - Rennin (cheese production); lactase (lactose-intolerant) - Proteases and amylases (dirt/stain removal) ## Enzymes as Highly Specific and Effective Catalysts - Specific for a single substrate or a small set of closely related substrates - Stereospecific - Enhancement of rate of reaction by 10^6 - Neither consumed nor permanently altered - Bind substrates through at least 3 points of attachment ## Nature of Enzymes - Most enzymes are protein in nature. - **Simple Enzyme:** made up of only protein molecules not bound to any nonproteins. - Ex. Pancreatic Ribonuclease ## Parts of an Enzyme - **Apoenzyme:** Protein portion of an enzyme. - **Co-factors:** Non-protein portion of an enzyme (metals, small organic molecules) - Coenzymes that are tightly bound: Prosthetic group - **Holoenzyme:** Protein plus non-protein portion that forms the functional enzyme ## Classification and Nomenclature - Enzymes may be named by adding the suffix " - ase" to the root word. (Lipase, Protease, Carboxylase) - Enzymes may also have trivial or common names (Trypsin, Chymotrypsin, Pepsin) ## Class 1 - Oxidoreductases - Oxidoreductases catalyze oxidation and reduction reactions. - This group includes: Dehydrogenases, Peroxidases, Oxidases - Act as: Electron donor, Electron acceptor ## Class 2 - Transferases - Transferases transfer chemical groups from one molecule to another, or within a single molecule. - These enzyme catalyzes the transfer of groups. - This group includes: Kinases, Transaminases ## Class 3 - Hydrolases - Hydrolases cleave molecules by breaking bonds in the presence of water. - They catalyze hydrolysis of compounds. - This group includes: Lipases, Amylases, Proteases ## Class 4 - Lyases - Lyases split molecules by a nonhydrolytic process cleaving double bonds or alternatively add groups to double bonds. - These enzymes catalyze the nonhydrolytic removal of groups. - This group includes: Decarboxylases, Aldolases ## Class 5 - Isomerases - Isomerases interconvert isomeric molecules by intermolecular rearrangements. - Enzymes in this class catalyze *cis-trans* isomerizations, epimerizations, racemizations, intramolecular transfers, and intramolecular isomerizations. - This group includes: Isomerases, Mutases, Epimerases, Racemases ## Class 6 - Ligases - Join molecules together creating chemical bonds at the expense of a nucleoside triphosphate (e.g. ATP). - Ligases catalyze the coupling together of two molecules with the breaking of a pyrophosphate bond. - This group includes: Synthetases ## Theories - **Lock and Key Theory (Emil Fischer)**: Only the correctly sized key (substrate) fits into the keyhole (active site) of the lock (enzyme). - The active site of an enzyme is complementary to the conformation of the substrate. - **Induced Fit Theory (Daniel Koshland)**: When substrates approach and bind to an enzyme, they induce a conformational change to the enzyme. ## Enzyme Specificity and Efficiency - **Michaelis-Menten Equation:** V = (Vmax[S]) / (Km+[S]) ## Enzyme Kinetics - E + S → ES → E + P - Substrate (S) - Enzyme (E) - Enzyme-substrate complex (ES) - Product (P) ## Michaelis-Menten Kinetics - A particularly useful model for the kinetics of enzyme-catalyzed reactions was devised in 1913 by Leonor Michaelis and Maud Menten. - V = (Vmax[S]) / (Km+[S]) - V = Rate of the enzyme-catalyzed reaction. - Vmax = Maximum velocity. - [S] = Substrate concentration. - Km = Michaelis-Menten constant. ## Michaelis-Menten Equation - **↑Km = ↑ unbound substrate** - **↓Km = ↓ unbound substrate** - Km is a measure of the unbound substrate to the enzyme. ## Michaelis-Menten Plot of Enzyme Kinetics - **Vmax:** Maximum rate or velocity. - **Km:** Michaelis-Menten constant. - Concentration of substrate at which the enzyme potential is 50% of Vmax. ## Michaelis-Menten Equation - **↑Km = ↓ bound substrate** - **↓Km = ↑ bound substrate** - Km measures the affinity of an enzyme for its substrate or the strength of the ES complex. ## Enzyme Inhibition - The rates of enzyme-catalyzed reactions can be decreased by substances called inhibitors. - An enzyme inhibitor is a substance that slows or stops the normal catalytic function of an enzyme by binding to it. - **Irreversible Inhibition:** A molecule that inactivates enzymes by forming a strong covalent bond to an amino acid side-chain group at the enzyme's active site. - **Reversible Competitive Inhibition:** Competitive enzyme inhibitor resembles the substrate enough to compete with the substrate for occupancy of the enzyme's active site. - **Reversible Noncompetitive Inhibition:** Noncompetitive enzyme inhibitor decreases enzyme activity by binding to a site on the enzyme other than the active site. - **Uncompetitive Inhibition:** A rare form of enzyme inhibition characterized by specific binding at the enzyme-substrate complex. ## Lineweaver-Burk Equation - 1 / V = (Km+[S]) / (Vmax[S]) - Obtained by getting the reciprocal of the Michaelis-Menten Equation. ## Lineweaver-Burk Plots for Enzyme Inhibition - **Competitive Inhibition:** Km increases. Vmax is unaffected. - **Noncompetitive Inhibition:** Km is unaffected. Vmax decreases. - **Uncompetitive Inhibition:** Km decreases. Vmax decreases. ## Grapefruit Effect - This enzyme inhibition, known as the "grapefruit effect," leads to increased concentrations of the affected drugs in the bloodstream, which increases the risk of potentially serious side effects from the drugs. - Compounds responsible for the grapefruit effect: bergamottin and one of its metabolites (a dihydroxyderivative of bergamottin) ## Enzyme Induction - **Enzyme Induction:** Stimulates or activates enzyme activity. - **Enzyme Inhibition:** Blocks enzyme activity ## Kinetics in a Multi-Substrate System - In general, reactions fall into two categories: - **Sequential:** Substrates react with the enzyme first before products are released. - **Ping-pong:** Intermediate products are released even before all substrates have reacted. ## Coenzymes - **Coenzymes** are heat-stable. - **Enzymes** are heat-labile. - **Coenzymes** are of low-molecular weight. - **Enzymes** are of high-molecular weight. ## Coenzymes - The active site of the **Holoenzyme** is formed by the coenzyme. - Most coenzymes are derived from vitamins. - Some coenzymes are not derived from vitamins (Tetrahydrobiopterin, Lipoic Acid, Coenzyme Q) ## Coenzymes - NAD+/NADP+ (Transfers electrons and protons in redox reactions) - FAD/FMN (Transfers electrons and protons in redox reactions) - Coenzyme Q (Transfers electrons and protons in redox reactions) - Tetrahydrobiopterin (Transfers electrons and protons in redox reactions especially for the hydroxylation of aromatic amino acids) - Thiamine pyrophosphate (TPP) (Carries acyl groups and active aldehydes) - Lipoic acid (Carries acyl groups and active aldehydes) - Coenzyme A (Carries acyl groups and active aldehydes) - Pyridoxal Phosphate (Transamination, Decarboxylation, Racemization) - Biocytin (Carboxylation) - Tetrahydofolic acid (One carbon group transfer) - Cobamide Coenzyme/Methyl cobamide (Alkyl group transfer) ## Examples of Enzymes in Where They Are Involved - **NAD+:** Lactate dehydrogenase, Malate dehydrogenase, Pyruvate dehydrogenase complex - **NADP+:** Glucose-6-phosphate dehydrogenase - **NADPH:** fatty acid synthase complex - **FAD:** Succinate dehydrogenase, fatty acyl-CoA dehydrogenase - **FMN:** L-amino acid oxidase - **Coenzyme Q:** Complex I (NADH-CoQ oxidoreductase) Complex II (Succinate dehydrogenase) Complex III (CoQ — Cytochrome C reductase) - **Tetrahydrobiopterin:** Phenylalanine Hydroxylase, Tyrosine Hydroxylase, Tryptophan Hydroxylase ## Examples of Enzyme in Where They Are Involved - **Thiamine pyrophosphate (TPP):** Pyruvate decarboxylate complex - **Lipoic acid:** Dihydrolipoyl dehydrogenase of The PDH complex, a-ketoglutaric acid dehydrogenase - **Coenzyme A:** Fatty acyl CoASH synthase - **Pyridoxal Phosphate:** Transaminases (ALT, AST), Amino acid decarboxylases, Amino acid racemases. - **Biocytin:** Acetyl CoA carboxylase, Pyruvate carboxylase, Propionyl carboxylase, Methylmalonyl CoA carboxylase. - **Tetrahydofolic acid:** Serine hydroxymethyl transferase, Thymidylate synthetase, Formyl transferase. - **Cobamide Coenzyme/Methyl cobamide:** Methylmalonyl CoA mutase, Homocysteine-methionine methyl transferase (also known as: methionine synthase)