Enzymes PDF

ENZYMES COMPILED AND ARRANGED BY JUSTIN RACHELLE P. DIMAGUIBA LEARNING OUTCOMES Identify the chemical nature, classification, and nomenclature of enzymes. Describe typical enzymes Discuss different enzyme activities Describe factors affecting enzyme activities  General Characteristics...

ENZYMES COMPILED AND ARRANGED BY JUSTIN RACHELLE P. DIMAGUIBA LEARNING OUTCOMES Identify the chemical nature, classification, and nomenclature of enzymes. Describe typical enzymes Discuss different enzyme activities Describe factors affecting enzyme activities  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 Importance of Enzymes Digestion Importance of Enzymes Construction of macromolecules from smaller precursor Importance of Enzymes Conservation and transformation of chemical energy 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 These enzymes were the first ones to be studied type of reaction they catalyze and/or their substrate Prefix denotes the type of reaction the enzyme catalyzes – Oxidase: redox reaction – Hydrolase: Addition of water to break one Substrate = the reactant upon component into two parts which the specific enzyme acts Substrate identity is often used together – Enzyme physically binds to the with the reaction type substrate – Pyruvate carboxylase, lactate dehydrogenase Enzyme Substrate Enzyme/substrate Classes of Enzymes  6 Major Classes of Enzymes Enzyme Class 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. Hexokinase catalyzing the phosphorylation of glucose by ATP to glucose-6-P. Hydrolase Hydrolysis reaction Lipases catalyze the hydrolysis of lipids, and proteases catalyze the hydrolysis of proteins 6 Enzyme Major Classes of Class Enzyme Reaction Catalyzed Examples in Metabolism Lyase Addition / removal ofsatoms 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. Ligase Synthesis reaction (Joining of 2 Synthetases link two smaller molecules into one, forming a new molecules are form a larger one. chemical bond, coupled with ATP hydrolysis) Definition of terms 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 Structure SIMPLE ENZYMES Composed only of protein CONJUGATED ENZYMES Composed of: – Apoenzyme Conjugate enzyme without its cofactor The apoenzyme can’t catalyze its reaction Protein part of a without its cofactor. conjugated enzyme – 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.  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 Stoker 2014, Table 21-7 p780 Mechanism of Enzyme Action  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 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 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 Stoker 2014, Figure 21-4 p751  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  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: Stoker 2014, Figure 21-11 p758  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. 11 and 12, p.634  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, p759 Stoker 2014, p760  Allosteric Enzymes Allosteric enzymes have a Binding of a regulator molecule to quaternary structure its regulatory site causes changes – Are composed of 2 or more protein chains in 3-D structure of the enzyme & – Possess 2 or more binding sites the active site 2 types of binding sites: – Binding of a Positive regulator up-regulates enzyme activity – One binding site for the substrate Enhances active site, more able Active site to accept substrate – Second binding site for a regulator molecule 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 & Compromises active site, less able to accept substrate location  Different effects of Positive & Negative regulators on an Allosteric enzyme Stoker 2014, Figure 21-13 p762  Example: Feedback Control The degradation of glucose through a metabolic pathway A process in which activation or inhibition of one of the earlier can be regulated in several reaction steps in a reaction sequence is controlled by a product of ways this reaction sequence. The enzyme PFK is allosterically inhibited by – One of the mechanisms in which allosteric enzymes are the product ATP regulated – Most biochemical processes proceed in several steps & each step Glycolysis (makes ATP) is catalyzed by a different enzyme is slowed when cellular The product of each step is the substrate for the next step / ATP is in excess Observe animation enzyme. of feedback control http://highered.mheducation.com/sites/0072507470/student_view0/chapter2/animation feedback_in hibition_of_biochemical_pathways.html Reaction 1: converts reagent Reaction 2: converts reagent Reaction 3: converts reagent A into product B B into product C C into product D Proteolytic Enzymes Most digestive & blood-clotting enzymes are proteolytic & Zymogens – Blood clotting enzymes break down proteins within the blood so that they can form the clot 2nd mechanism of allosteric enzyme regulation Platelets interspersed with tangled – Production of an enzyme in an inactive form protein (collagen and thrombin) Activation of a zymogen requires the – Activated when required (right time & place) removal of a peptide fragment from the Activated aka “turned on” zymogen structure – Changing the 3-D shape & affecting the Proteolytic enzymes catalyze breaking of active site peptide bond in proteins E.g. Pepsiongen (zymogen) >>> Pepsin (active proteolytic enzyme) – To prevent these enzymes from destroying the tissues, that produced them, they are released in an inactive form = ZYMOGENS  Covalent Modification of Enzymes Covalent modifications are the 3rd mechanism of enzyme activity regulation – A process of altering enzyme activity by covalently modifying the structure of the enzyme Adding / removing a group to / from the enzyme Most common covalent modification = addition & removal of phosphate group: – Phosphate group is often derived from an ATP molecule Addition of phosphate = phosphorylation is catalyzed by a Kinase enzyme Removal of phosphate = dephosphorylation is catalyzed by a Phosphatase enzyme – Glycogen synthase: involved in synthesis of glycogen Deactivated by phosphorylation – Glycogen phosphorylase: involved in breakdown of glycogen Activated by phosphorylation.  Vitamins as Coenzymes Many enzymes require B vitamins as coenzymes – Allow the enzyme to function Coenzymes serve as temporary carriers of atoms or functional groups – Coenzymes provide chemical reactivity that the apoenzyme lacks – Important in metabolism reactions to release energy from foods E.g. redox reactions where they facilitate oxidation or reduction B vitamins don’t remain permanently bonded to the apoenzyme – After the catalytic action the vitamin is released & can be repeatedly used by various enzymes – This recycling reduces the need for large amounts of B vitamins Stoker 2014, Figure 21-20 p779 Stoker 2014, Table 21-7 p780  Why is an enzyme active site important to the function of the enzyme? Why is the enzyme regulatory binding site important for controlling the activity of the enzyme? Why are coenzymes (derived from vitamins) important to the function of some enzymes? G  Drugs Inhibiting Enzyme Activity Prescription drugs that inhibit enzymes ACE Inhibitors – Inhibit Angiotensin-Converting Enzyme Lowers blood pressure Sulfa drugs – Antibiotics acting as competitive inhibitors of bacterial enzymes Involved in conversion of PABA to Folic acid – Deficiency of folic acid retards bacterial growth, eventually killing them Penicillin's – β-lactam antibiotics inhibit transpeptidase Transpeptidase enzyme strengthens the cell wall – Forms peptide cross links between polysaccharides strands in bacterial cell walls – Without transpeptidase enzyme (inhibited by Penicillin) >>> weakened cell wall, bacteria  Medical Uses of Enzymes Enzymes can be used in diagnosis & treatment of certain diseases Lactate dehydrogenase (LDH) is normally not found in high levels in blood, as it is produced in cells – Increased levels of LDH in the blood indicate myocardial infarction (MI) (Heart attack) – Tissue plasminogen activator (TPA) activates the enzyme plasminogen that dissolves blood clots Used in the treatment of MI There is no direct test to measure urea in the blood – Urease converts urea into ammonia, which is easily measured & is used as urea indicator Blood Urea Nitrogen (BUN) is used to measure kidney function – High urea levels in the blood indicate kidney malfunction  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]  Stoker 2014, Figure 21-6 p753 Temperature (t) 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)  Stoker 2014, Figure 21-7 p753 pH 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  Substrate Concentration 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 Stoker 2014, Figure 21-8 p754 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 Stoker 2014, Figure 21-9 p755 Enzymes can be reused many times Stoker 2014, p756 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  Medical Uses of Enzymes Enzymes can be used in diagnosis & treatment of certain diseases Lactate dehydrogenase (LDH) is normally not found in high levels in blood, as it is produced in cells – Increased levels of LDH in the blood indicate myocardial infarction (MI) (Heart attack) – Tissue plasminogen activator (TPA) activates the enzyme plasminogen that dissolves blood clots Used in the treatment of MI There is no direct test to measure urea in the blood – Urease converts urea into ammonia, which is easily measured & is used as urea indicator Blood Urea Nitrogen (BUN) is used to measure kidney function – High urea levels in the blood indicate kidney malfunction Stoker 2014, Table 21-3 p768  Aldolase an enzyme that helps convert glucose (sugar) into energy found throughout your body but is primarily found in high levels in muscle tissue Aldolase levels in the blood rise when a person has muscle damage. aldolase blood test may be ordered to diagnose and monitor certain conditions related to skeletal muscle.  Aldolase specifically catalyzes the reversible reaction of converting fructose 1,6-bisphosphate into dihydroxyacetone phosphate (DHAP) and glyceraldehydes 3-phosphate.  Isoenzymes Isoenzyme catalyze the same reaction in different tissues in the body – e.g. lactate dehydrogenase (LDH) consists of 5 isoenzymes Each isoenzyme of LDH has the same function – Converts lactate to pyruvate LDH1 isoenzyme is more prevalent in heart muscle LDH5 form is found in skeletal muscle & liver Isoenzymes can be used to identify the damaged or diseased organ or tissue It is a marker for a particular location If LDH1 isoenzyme was found in the blood >>> indicates heat muscle damage Readings & Resources Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn, Brooks/Cole, Cengage Learning, Belmont, CA. Stoker, HS 2004, General, Organic and Biological Chemistry, 3rd edn, Houghton Mifflin, Boston, MA. Timberlake, KC 2014, General, organic, and biological chemistry: structures of life, 4th edn, Pearson, Boston, MA. Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter P 2008, Molecular biology of the cell, 5th edn, Garland Science, New York. Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7th edn, W.H. Freeman, New York. Dominiczak, MH 2007, Flesh and bones of metabolism, Elsevier Mosby, Edinburgh. Tortora, GJ & Derrickson, B 2014, Principles of Anatomy and Physiology, 14th edn, John Wiley & Sons, Hoboken, NJ. https://healthjade.net/aldolase/ https://scienceworld2103.blogspot.com/2020/07/enzyme-and-their-functions.html © Endeavour College of Natural Health www.endeavour.edu.au 45