Enzymes 2023-2024 PDF

Biochemistry Enzyme and Coenzyme Lebanese University - Faculty of Medical Sciences Dr. Eva Chaalan Hamade Year 2023-2024 Session Plan General Characteristics of Enzymes Enzyme Structure Enzyme Nomenclature...

Biochemistry Enzyme and Coenzyme Lebanese University - Faculty of Medical Sciences Dr. Eva Chaalan Hamade Year 2023-2024 Session Plan General Characteristics of Enzymes Enzyme Structure Enzyme Nomenclature Enzyme Function Enzyme Specificity Factors Affecting Enzyme Activity Enzyme Inhibition Regulation of Enzyme Activity Medical Uses of Enzymes General Characteristics of Enzymes ENZYME – Usually a protein, acting as catalyst in specific biochemical reaction Each cell in the human body contains 1,000s of different enzymes – Every reaction in the cell requires its own specific enzyme Most enzymes are globular proteins – A few enzymes are made of RNA Catalyze biochemical reactions involving nucleic acids Enzymes undergo all the reactions of proteins – Enzymes denaturation due to pH or temperature change A person suffering high fever runs the risk of denaturing certain enzymes General Characteristics of Enzymes  Nomenclature / enzyme classification IUBMB has recommended system of nomenclature for enzymes & according to them each enzyme is assigned with two names: ✓Trivial name (common name, recommended ✓name). ✓Systemic name ( official name ).  Systemic name Each enzyme is characterized by a code no.called Enzyme Code no. or EC number and contain four Figure (digit) separated by a dot. e.g. EC m. n. o. p First digit represents the class; Second digit stands for subclass ; Third digit stands for the sub-sub class or subgroup; Fourth digit gives the serial number of the particular enzyme in the list. e.g. EC 2.7.1.1 for hexokinase. Systemic name……… According to the IUBMB system of enzyme nomenclature enzymes are grouped into 6 major classes EC 1 OXIDOREDUCTASES EC 2 TRANSFERASES EC 3 HYDROLASES EC 4 LYASES EC 5 ISOMERASES EC 6 LIGASES - Nomenclature / enzyme classification Enzyme Structure SIMPLE ENZYMES Composed only of protein CONJUGATED ENZYMES Composed of: – Apoenzyme Conjugate enzyme without its cofactor Protein part of a The apoenzyme can’t catalyze its reaction conjugated enzyme without its cofactor. – The combination of the apoenzyme with the cofactor makes the conjugated enzyme functional. – Coenzyme (Cofactor) Holoenzyme = apoenzyme + cofactor Non-protein part of a – The biochemically active conjugated enzyme. conjugated enzyme Coenzymes and cofactors Coenzymes provide additional chemically reactive functional groups besides those present in the amino acids of the apoenzymes – Are either small organic molecules or inorganic ions Metal ions often act as additional cofactors (Zn2+, Mg2+, Mn2+ & Fe2+) – A metal ion cofactor can be bound directly to the enzyme or to a coenzyme COENZYME – A small organic molecule, acting as a cofactor in a conjugated enzyme Coenzymes are derived from vitamins or vitamin derivatives – Many vitamins act as coenzymes, esp. B-vitamins  Enzyme definitions Term Definition Enzyme Protein only enzyme that facilitates a chemical reaction (simple) Coenzyme Compound derived from a vitamin (e.g. NAD+) that assists an enzyme in facilitating a chemical reaction Cofactor Metal ion (e.g. Mg2+) that that assists an enzyme in facilitating a chemical reaction Apoenzyme Protein only part of an enzyme (e.g. isocitrate dehydrogenase) that requires an additional coenzyme to facilitate a chemical reaction (not functional alone) Holoenzyme Combination of the apoenzyme and coenzyme which together facilitating a chemical reaction (functional) Enzyme Nomenclature Suffix of an enzyme –ase – Lactase, amylase, lipase or protease Denotes an enzyme Enzymes are named according to the Some digestive enzymes have the suffix –in – Pepsin, trypsin & chymotrypsin type of reaction they These enzymes were the first ones to be studied catalyze and/or their substrate Prefix denotes the type of reaction the enzyme catalyzes – Oxidase: redox reaction Substrate = the reactant upon – Hydrolase: Addition of water to break one which the specific enzyme acts component into two parts – Enzyme physically binds to the Substrate identity is often used together substrate with the reaction type – Pyruvate carboxylase, lactate dehydrogenase Enzyme Substrate Enzyme/substrate complex 6Enzyme MajorClass Classes of Enzymes Reaction Catalyzed Examples in Metabolism Oxidoreductase Redox reaction (reduction & Examples are dehydrogenases oxidation) catalyse reactions in which a substrate is oxidised or reduced Transferase Transfer of a functional group Transaminases which catalyze from 1 molecule to another the transfer of amino group or kinases which catalyze the transfer of phosphate groups. 6 Major Classes Hydrolase Hydrolysis reaction Lipases catalyze the hydrolysis of Enzymes of lipids, and proteases catalyze the hydrolysis of proteins Based on the type of reaction they catalyze Lyase Addition / removal of atoms to / Decarboxylases catalyze the from double bond removal of carboxyl groups Isomerase Isomerization reaction Isomerases may catalyze the conversion of an aldose to a ketose, and mutases transfer functional group from one atom to another within a substrate. The table explains Synthesis reaction Synthetases link two smaller the functions of Ligase (Joining of 2 molecules into one, molecules are form a larger one. enzymes and how forming a new chemical bond, they are classified coupled with ATP hydrolysis) and named. Enzyme Active Site Active site – The specific portion of an enzyme (location) where the substrate binds while it undergoes a chemical reaction The active site is a 3-D ‘crevice-like’ cavity formed by secondary & tertiary structures of the protein part of the enzyme – Crevice formed from the folding of the protein Aka binding cleft – An enzyme can have more than only one active site – The amino acids R-groups (side chain) in the active site are important for determining the specificity of the substrate Stoker 2014, Figure 21-2 p750  Enzyme – Substrate Complex When the substrate binds to the enzyme active site an Enzyme-Substrate Complex is formed temporarily – Allows the substrate to undergo its chemical reaction much faster Timberlake 2014, Figure 4, p.738 Timberlake 2014, Figure 3, p.737 Lock & Key Model of Enzyme Action The active site is fixed, with a rigid shape (LOCK) The substrate (KEY) must fit exactly into the rigid enzyme (LOCK) Complementary shape & geometry between enzyme and substrate – Key (substrate) fits into the lock (enzyme) Upon completion of the chemical reaction, the products are released from the active site, so the next substrate molecule can bind Stoker 2014, Figure 21-3 p750  Stoker 2014, Figure 21-4 p751 Induced Fit Model of Enzyme Action Many enzymes are flexible & constantly change their shape – The shape of the active site changes to accept & accommodate the substrate Conformation change in the enzyme’s active site to allow the substrate to bind Analogy: a glove (enzyme) changes shape when a hand (substrate) is inserted into it Induced Fit Model of Enzyme Action Enzyme Specificity Absolute Specificity – An enzyme will catalyze a particular reaction for only one substrate – Most restrictive of all specificities Not common – Catalase has absolute specificity for hydrogen peroxide (H2O2) – Urease catalyzes only the hydrolysis of urea Group Specificity – The enzyme will act only on similar substrates that have a specific functional group Carboxypeptidase cleaves amino acids one at a time from the carboxyl end of the peptide chain Hexokinase adds a phosphate group to hexoses Enzyme Specificity Linkage Specificity – The enzyme will act on a particular type of chemical bond, irrespective of the rest of the molecular structure – The most general of the enzyme specificities Phosphatases hydrolyze phosphate–ester bonds in all types of phosphate esters Chymotrypsin catalyzes the hydrolysis of peptide bonds Stereochemical Specificity – The enzyme can distinguish between stereoisomers – Chirality is inherent in an active site (as amino acids are chiral compounds) L-Amino-acid oxidase catalyzes reactions of L-amino acids but not of D-amino acids Factors Affecting Enzyme Activity Enzyme activity Measure of the rate at which an enzyme converts substrate to products in a biochemical reaction 4 factors affect enzyme activity: Temperature pH Substrate concentration: [substrate] Enzyme concentration: [enzyme]  Temperature (t) Stoker 2014, Figure 21-6 p753 With increased t the EKIN increases – More collisions – Increased reaction rate Optimum temperature (tOPT) is the t, at which the enzyme exhibits maximum activity – The tOPT for human enzymes = 370C When the t increases beyond tOPT – Changes in the enzyme’s tertiary structure occur, inactivating & denaturing it (e.g. fever) Little activity is observed at low t  Effect of(t) Temperature Increasing Temperature and Reaction Rates Effect of Increasing Temperature and Reaction Rates  pH Stoker 2014, Figure 21-7 p753 Optimum pH (pHOPT) is the pH, at which the enzyme exhibits maximum activity Most enzymes are active over a very narrow pH range – Protein & amino acids are properly maintained – Small changes in pH (low or high) can result in enzyme denaturation & loss of function Each enzyme has its characteristic pHOPT, which usually falls within physiological pH range 7.0 - 7.5 Digestive enzymes are exceptions: – Pepsin (in stomach) – pHOPT = 2.0 – Trypsin (in SI) – pHOPT = 8.0 pH Effect of Varying pH and Enzymatic Re Effect of Varying pH and Enzymatic Reaction Rates action Rates Lysozyme Lysozyme: kills bacteria Works at pH 4-5 Why?  Substrate Concentration Stoker 2014, Figure 21-8 p754 If [enzyme] is kept constant & the [substrate] is increased – The reaction rate increases until a saturation point is met At saturation the reaction rate stays the same even if the [substrate] is increased – At saturation point substrate molecules are bound to all available active sites of the enzyme molecules Reaction takes place at the active site – If they are all active sites are occupied the reaction is going at its maximum rate Each enzyme molecule is working at its maximum capacity – The incoming substrate molecules must “wait their turn”  Stoker 2014, Figure 21-9 p755 Enzyme Concentration If the [substrate] is kept constant & the [enzyme] is increased – The reaction rate increases – The greater the [enzyme], the greater the reaction rate RULE: – The rate of an enzyme-catalyzed reaction is always directly proportional to the amount of the enzyme present In a living cell: – The [substrate] is much higher than the [enzyme] Enzymes are not consumed in the reaction Enzymes can be reused many times Stoker 2014, p756  Key concept: function of an enzyme What is the function of an enzyme in a chemical reaction? What happens to the enzymes when the body temperature rises from 37ᵒC to 42ᵒC? If an enzyme has broken down and is non-functional, what would happen to the chemical reaction normally facilitated by the enzyme? Explain. G Enzyme Inhibition ENZYME INHIBITOR – A substance that slows down or stops the normal catalytic function of an enzyme by binding to the enzyme Three types of inhibition: – Reversible competitive inhibition – Reversible non-competitive inhibition – Irreversible inhibition Reversible Competitive Inhibition A competitive inhibitor resembles the substrate – Inhibitor competes with the substrate for binding to the active site of the enzyme – If an inhibitor is bound to the active site: Prevents the substrate molecules to access the active site – Decreasing / stopping enzyme activity The binding of the competitive inhibitor to the active site is a reversible process – Add much more substrate to outcompete the competitive inhibitor Many drugs are competitive inhibitors: – Anti-histamines inhibit histidine decarboxylase, which converts histidine to histamine Stoker 2014, Figure 21-11 p758  Stoker 2004, Figure 21.11, p.634 Reversible Noncompetitive Inhibition A non-competitive inhibitor decreases enzyme activity by binding to a site on the enzyme other than the active site – The non-competitive inhibitor alters the tertiary structure of the enzyme & the active site Decreasing enzyme activity Substrate cannot fit into active site – Process can be reversed only by lowering the [non-competitive inhibitor] Example: – Heavy metals Pb2+ & Hg2+ bind to –SH of Cysteine, away from active site Disrupt the secondary & tertiary structure Stoker 2004, Figure 21.12, p.634  Stoker 2014, p759 Irreversible Inhibition An irreversible inhibitor inactivates an enzyme by binding to its active site by a strong covalent bond – Permanently deactivates the enzyme – Irreversible inhibitors do not resemble substrates Addition of excess substrate doesn’t reverse this process – Cannot be reversed Chemical warfare (nerve gases) Organophosphate insecticides Stoker 2014, p760 Allosteric Enzymes Allosteric enzymes have a quaternary structure – Are composed of 2 or more protein chains – Possess 2 or more binding sites Binding of a regulator molecule to its regulatory site causes 2 types of binding sites: changes in 3-D structure of the enzyme & the active site – One binding site for the substrate – Binding of a Positive regulator Active site up-regulates enzyme activity Enhances active site, more able – Second binding site for a regulator molecule to accept substrate Regulatory site – Binding of a Negative regulator (non-competitive inhibitor) Active & regulatory binding sites are down-regulates enzyme activity distinct from each other in shape & location Compromises active site, less able to accept substrate The different effects of Positive & Negative regulators on an Allosteric enzyme Stoker 2014, Figure 21-13 p762 Positive allosteric regulators Helps enzyme work better promotes/stabilizes an “active” conformation