Enzymes 1 & 2 (2024-25) PDF

WEEK 14 MPharm Programme Enzymes 1 Dr Gabriel Boachie-Ansah [email protected] Dale 113 ext. 2617 MPharm PHA115 Enzymes WEEK 14 Outline of Lectures Wha...

WEEK 14 MPharm Programme Enzymes 1 Dr Gabriel Boachie-Ansah [email protected] Dale 113 ext. 2617 MPharm PHA115 Enzymes WEEK 14 Outline of Lectures What enzymes are, and why they do Enzyme structure & classification, and enzyme co-factors Enzymes & cellular metabolism How enzymes work, and the factors that affect enzyme function How enzymes interact with their substrates Enzyme kinetics Enzyme inhibition Slide 2 of 69 MPharm PHA115 Enzymes  Learning Outcomes WEEK 14 At the end of this lecture, you should be able to: Describe the structure, classification & function of enzymes Describe the metabolic processes that are catalysed by enzymes, and why enzyme catalysis is needed Describe the nature of the interaction between enzymes & their substrates Describe enzyme kinetics & the associated Michaelis- Menten & Lineweaver-Burk Plots Describe the various types of enzyme inhibition Appreciate the relevance of enzymes & enzyme inhibition in medicine Slide 3 of 69 MPharm PHA115 Enzymes  Enzymes WEEK 14 What Are Enzymes? Specialised, catalytically active biological macromolecules Act as specific, efficient and active catalysts of chemical reactions in aqueous solution Most enzymes are Globular proteins Some are RNA – e.g. ribozymes and ribosomal RNA Slide 4 of 69 MPharm PHA115 Enzymes  Enzymes WEEK 14 How Are Enzymes Named and Classified? Enzymes are named by adding the suffix “-ase” to: the name of their substrate or a word or phrase describing their catalytic action Classification based on the type of reaction catalysed Classification Type of Reaction Catalysed 1. Oxidoreductases Oxidation–reduction reactions 2. Transferases Transfer of functional groups 3. Hydrolases Hydrolysis reactions 4. Lyases Group elimination to form double bonds 5. Isomerases Isomerization 6. Ligases Bond formation coupled with ATP hydrolysis Slide 5 of 69 MPharm PHA115 Enzymes  International Classification of Enzymes WEEK 14 Slide 6 of 69 MPharm PHA115 Enzymes  Enzymes WEEK 14 Naming of Enzymes Each enzyme is assigned a ‘four-part classification number’ and ‘a systematic name’, which identifies the reaction it catalyses – e.g. for hexokinase: Formal name: ATP:glucose phosphotransferase Enzyme Commission number is 2.7.1.1 2 = the class name (transferase) 7 = the subclass (phosphotransferase) 1 = phosphotransferase with a hydroxyl group as acceptor 1 = D-glucose as the phosphoryl group acceptor Slide 7 of 69 MPharm PHA115 Enzymes  Enzymes WEEK 14 What Are The Key Structure-Function features of Enzymes? Enzymes are protein They have a globular shape & a complex 3-D structure They have an ‘active site’ – its unique shape & chemical environment determine which substrate(s) will bind Some enzymes require additional non-protein chemical component(s), called cofactor(s), in order to function properly Cofactors act as non-protein "helper" molecules – may be metal ions or organic / metallo-organic molecules Slide 8 of 69 MPharm PHA115 Enzymes  Enzyme Cofactors WEEK 14 Slide 9 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme Cofactors Metal ion cofactors small inorganic ions – Mg++, K+, Ca++, Zn++, Cu++, Co, Fe may be free (e.g. Na+, K+) or held in coordination complexes with the enzyme protein (e.g. Zn++, Ca++) assist with enzyme catalysis Slide 10 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme Cofactors Organic / metallo-organic cofactors Coenzymes – organic cofactors that are loosely bound and easily released from the enzymes Prosthetic groups – organic cofactors that are tightly bound to the enzymes Coenzymes usually act as ‘co-substrates’ or as transient carriers of specific functional groups Most are derived from vitamins – organic nutrients that are required in small amounts in the diet Examples include: NAD (niacin; B3) FAD (riboflavin; B2) Coenzyme A Slide 11 of 69 MPharm PHA115 Enzymes WEEK 14 Examples of Coenzymes Slide 12 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme & Cofactors The complete, catalytically active enzyme together with its bound coenzyme and/or metal ion is called a holoenzyme The protein part of such an enzyme is called the apoenzyme or apoprotein Slide 13 of 69 MPharm PHA115 Enzymes  Enzymes WEEK 14 Why Are Enzymes So Important? They catalyse (accelerate) biochemical reactions in the body – by speeding up chemical reactions Most biochemical & physiological reactions in the body proceed at very slow pace Enzymes act to speed up these so-called ‘chemical reactions of life’ Without enzymes, most chemical reactions of life would proceed so slowly (or not at all) that life could not exist Slide 14 of 69 MPharm PHA115 Enzymes  Enzymes WEEK 14 What Are These ‘Chemical Reactions of Life’ That Are Catalysed By Enzymes? Enzymes catalyse cellular metabolic reactions Metabolism is the sum of the chemical reactions that take place in an organism Two types of metabolism or metabolic reactions Anabolism or Anabolic reactions – involve the formation of bonds between molecules Catalysed by Anabolic enzymes Catabolism or Catabolic reactions – involve the breaking of bonds between molecules Catalysed by Catabolic enzymes Slide 15 of 69 MPharm PHA115 Enzymes WEEK 14 Enzymes & Cellular Metabolism Anabolism or Anabolic reactions Biosynthetic – building of complex molecules from simpler ones Involve the formation of bonds between molecules Energy-utilising processes / reactions Involve dehydration synthesis reactions (reactions that release water) – e.g. carbohydrate/protein synthesis Endergonic – consume more energy than they produce Slide 16 of 69 MPharm PHA115 Enzymes WEEK 14 Enzymes & Cellular Metabolism Catabolism or Catabolic reactions Degradative – breakdown of complex molecules into simpler ones Involve the breaking of bonds between molecules Energy-releasing processes / reactions Involve hydrolytic reactions (use water to break chemical bonds) – e.g. digestion of carbohydrates Exergonic – produce more energy than they consume Slide 17 of 69 MPharm PHA115 Enzymes WEEK 14 Cellular Metabolism Slide 18 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme-catalysed Metabolic Reactions Anabolic - dehydration synthesis (synthesis) enzyme Catabolic - hydrolysis (digestion) enzyme Slide 19 of 69 MPharm PHA115 Enzymes WEEK 14 Enzymes & Cellular Metabolism So, Why Do Cellular Metabolic Reactions Require The Intervention of Enzymes? All chemical/metabolic reactions require the initial input of energy (Activation Energy, EA) in order to proceed EA is needed to increase collisions between reactant molecules to shift the reactant molecules into a ‘transition state’, where existing bonds can be broken & new ones formed EA is usually too high for the metabolic reactions to proceed significantly at ambient temperature Enzymes, as catalysts, help to lower the EA and enable metabolic reactions to proceed at a faster rate Slide 20 of 69 MPharm PHA115 Enzymes WEEK 14 Endergonic Exergonic Slide 21 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme-catalysed Metabolic Reactions How Do Enzymes Work? They act as catalysts – speed up metabolic/biochemical reactions without being consumed or chemically altered they provide an alternative pathway or mechanism for the reaction & lower the activation energy, EA they bind to & form an intermediate with the reactant (substrate), which is released later on during the product formation step Enzymes accelerate the rate of the reaction without shifting or changing the equilibrium of the reaction!!! equilibrium is reached faster with enzyme!!! Slide 22 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme-catalysed Metabolic Reactions Slide 23 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme-catalysed Metabolic Reactions Slide 24 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme-catalysed Metabolic Reactions Slide 25 of 69 MPharm PHA115 Enzymes WEEK 14 How Do Enzymes Work? Enzymes bind their substrates with high specificity Binding specificity is governed by 3D arrangement of atoms ‘Lock and Key’ Model ‘Induced-Fit’ Model (E. Fisher, 1890) (D.E. Koshland, 1958) Active site is complementary to Active site forms a complementary shape shape of substrate of substrate after binding substrate Slide 26 of 69 MPharm PHA115 Enzymes WEEK 14 How Do Enzymes Work? ‘Lock and Key’ Model Simplistic model of enzyme action Substrate fits into 3-D structure of enzyme active site weak chemical bonds formed between substrate & enzyme like a “key fits into lock” Slide 27 of 69 MPharm PHA115 Enzymes WEEK 14 How Do Enzymes Work? ‘Induced Fit’ Model More accurate model of enzyme action Substrate binding causes the enzyme to change shape (‘conformational change), leading to a tighter fit this brings chemical groups in position to catalyse reaction Slide 28 of 69 MPharm PHA115 Enzymes WEEK 14 How Do Enzymes Work? ‘Induced Fit’ Model More accurate model of enzyme action Substrate binding causes the enzyme to change shape (‘conformational change), leading to a tighter fit this brings chemical groups in position to catalyse reaction Hexokinase (a) without (b) with glucose substrate Slide 29 of 69 MPharm PHA115 Enzymes  Enzymes WEEK 14 What Are The Factors That Affect Enzyme Function? Enzyme concentration Substrate concentration Temperature pH Salinity Slide 30 of 69 MPharm PHA115 Enzymes WEEK 14 Factors That Affect Enzyme Function Effect of Enzyme Concentration Initially, as  enzyme concentration   reaction rate more enzymes  more frequent collisions with substrate Then, reaction rate levels off with further increase in enzyme concentration substrate concentration becomes the limiting factor not all enzyme molecules can find a substrate Reaction rate Enzyme concentration Slide 31 of 69 MPharm PHA115 Enzymes WEEK 14 Factors That Affect Enzyme Function Effect of Substrate Concentration Initially, as  substrate concentration   reaction rate more substrate  more frequent collisions with enzyme Then, reaction rate levels off with further increase in substrate concentration all enzyme active sites become engaged (saturated) maximum rate of reaction has been reached Reaction rate Substrate concentration Slide 32 of 69 MPharm PHA115 Enzymes WEEK 14 Factors That Affect Enzyme Function Effect of Temperature  temperature   reaction rate molecules move faster   collisions between enzyme & substrate  temperature   reaction rate molecules move slower   collisions between enzyme & substrate Optimum T° – peak effect on enzyme-catalysed reaction greatest number of molecular collisions of enzyme & substrate  temperature beyond optimum T°  enzyme denaturation disrupts bonds in enzyme & between enzyme & substrate enzymes lose their 3D shape (3° structure) Slide 33 of 69 MPharm PHA115 Enzymes WEEK 14 Effect of Temperature on Enzyme Function Optimum Increasing number of Denaturation collisions (Q10) Enzyme Activity 0 10 20 30 40 50 Temperature (C) Slide 34 of 69 MPharm PHA115 Enzymes WEEK 14 Effect of Temperature on Enzyme Function Optimum Temperature hot spring human enzyme bacteria enzyme Reaction rate 37°C 70°C Temperature Slide 35 of 69 MPharm PHA115 Enzymes WEEK 14 MPharm Programme Enzymes 2 Dr Gabriel Boachie-Ansah [email protected] Dale 113 ext. 2617 MPharm PHA115 Enzymes WEEK 14 Factors That Affect Enzyme Function Effect of pH Changes in pH add or remove H+  small changes in the charges on the enzyme & substrate molecules (altered critical ionization states) affect the binding of the substrate with the enzyme active site Optimum pH – peak effect on enzyme-catalysed reaction pH 6-8 for most human enzymes – depends on localised conditions e.g. pepsin (stomach) = pH 2-3; trypsin (small intestines) = pH 8 Extreme pH levels  enzyme denaturation disrupt attraction between charged amino acids disrupt bonds & the enzyme’s 3D shape active site is distorted  loss of substrate fit Slide 37 of 69 MPharm PHA115 Enzymes WEEK 14 Effect of pH on Enzyme Function Optimum pH pepsin trypsin Reaction rate pepsin trypsin 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 pH Slide 38 of 69 MPharm PHA115 Enzymes WEEK 14 Factors That Affect Enzyme Function Effect of Salinity (Salt Concentration) Changes in salinity add or remove cations & anions Extreme salinity  enzyme denaturation Enzymes are intolerant of extreme salinity disrupts attraction between charged amino acids disrupts bonds & the enzyme’s 3D shape affects 2° & 3° enzyme structure Reaction rate Salt concentration Slide 39 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme Kinetics Enzyme kinetics is the study of the rates of chemical reactions that are catalysed by enzymes It provides insight into the mechanisms of enzyme catalysis & their role in metabolism how the activity of enzymes is controlled in the cell how drugs and poisons can inhibit or modulate the activity of enzymes In 1913, Michaelis and Menten proposed the model known as Michaelis-Menten Kinetics to account for & explain how enzymes can increase the rate of metabolic reactions how the reaction rates depend on the concentration of enzyme & substrate Slide 40 of 69 MPharm PHA115 Enzymes WEEK 14 Michaelis-Menten Kinetics All enzymes show a ‘saturation effect’ with their substrates At low substrate concentration [S], the reaction rate or velocity, V, is proportional to [S] However, as [S] is increased, the reaction rate falls off, and is no longer proportional to [S] On further increase in [S], the reaction rate or velocity becomes constant and independent of [S] At this stage, the enzyme is saturated with substrate A plot of initial reaction velocity, V, against substrate concentration, [S], gives a rectangular hyperbola The Michaelis-Menten equation or kinetics model was developed to explain or account for this ‘saturation effect’ Slide 41 of 69 MPharm PHA115 Enzymes WEEK 14 Relationship between Reaction Velocity & Substrate Concentration Slide 42 of 69 MPharm PHA115 Enzymes WEEK 14 Michaelis-Menten Kinetics Michaelis and Menten proposed the following mechanism for a saturating enzyme-catalysed single substrate reaction: According to this postulate/scheme In an enzyme-catalysed reaction, a free enzyme, E, binds its substrate, S, to form an enzyme-substrate complex, ES ES either undergoes further transformation to yield a final product, P, and the free enzyme, E, or breakdowns via a reverse reaction to form the free enzyme, E and substrate, S Slide 43 of 69 MPharm PHA115 Enzymes WEEK 14 Michaelis-Menten Kinetics Rate of formation of ES = k1[E][S] Rate of breakdown of [ES] = k-1[ES] + k2[ES] = (k-1 + k2)[ES] At equilibrium, k1[E][S] = (k-1 + k2)[ES] Re-arranging, [ES] = [E][S]/{(k-1 + k2)/k1} But (k-1 + k2)/k1 = KM (Michaelis constant) Therefore, [ES] = [E][S]/KM Slide 44 of 69 MPharm PHA115 Enzymes WEEK 14 Michaelis-Menten Equation By re-arranging the equations, and making several assumptions, they derived the Michaelis-Menten Equation Vmax S v= K M + S Where, Vmax = the maximum velocity or rate of reaction, at maximum (saturating) concentrations of the substrate KM = (k-1 + k2)/k1 = substrate concentration at which the reaction velocity is 50% of the Vmax (Michaelis constant) [S] = concentration of the substrate, S Slide 45 of 69 MPharm PHA115 Enzymes WEEK 14 Michaelis-Menten Kinetics A graph of initial reaction velocity, V0, against substrate concentration, [S], results in a rectangular curve, where Vmax represents the maximum reaction velocity Slide 46 of 69 MPharm PHA115 Enzymes WEEK 14 Linear Transformations of Michaelis-Menten Equation It is not easy to accurately determine Vmax at high substrate concentrations from the Michaelis-Menten curve Algebraic transformation of the Michaelis-Menten equation into linear forms for plotting experimental data Lineweaver-Burk Plot (also called Double Reciprocal plot) Eadie-Hofstee Plot Slide 47 of 69 MPharm PHA115 Enzymes WEEK 14 Lineweaver-Burk Plot Also called the Double Reciprocal Plot – derived by taking the reciprocal of both sides of the Michaelis-Menten equation, and separating out the components of the numerator on the right side of the equation: 1 1  KM  1 = +  v vmax  vmax  [ S ]0 Slide 48 of 69 MPharm PHA115 Enzymes WEEK 14 Eadie-Hofstee Plot Derived by inverting the Michaelis-Menten equation, and multiplying both sides of the equation by Vmax A plot of V against V/[S] yields Vmax as the y-intercept, Vmax/Km as the x-intercept, and Km as the negative slope v v = −KM + vmax [S ]0 Slide 49 of 69 MPharm PHA115 Enzymes WEEK 14 Significance of KM (Michaelis Constant) It has same unit as the substrate concentration (M) The substrate concentration [S] at which the reaction proceeds at half maximal velocity (50%), i.e. KM = [S] at ½ Vmax A measure of an enzyme’s affinity for its substrate – the lower the KM value, the higher the enzyme’s affinity for the substrate and vice versa Provides an idea of the strength of binding of the substrate to the enzyme molecule – the lower the KM value, the more tightly bound the substrate is to the enzyme for the reaction to be catalysed Indicates the lowest concentration of the substrate [S] the enzyme can recognise before reaction catalysis can occur Describes the substrate concentration at which half the enzyme's active sites are occupied by substrate Slide 50 of 69 MPharm PHA115 Enzymes WEEK 14 Significance of KM (Michaelis Constant) KM Values for Some Key Enzymes Slide 51 of 69 MPharm PHA115 Enzymes WEEK 14 Significance of Vmax Gives an idea of how fast the reaction can occur under ideal circumstances Reveals the turnover number of an enzyme, i.e. the number of substrate molecules being catalysed per second Magnitude varies considerably – from  10 in the case of lysozyme to 600,000 in the case of carbonic anhydrase Slide 52 of 69 MPharm PHA115 Enzymes WEEK 14 Significance of Vmax Turnover Numbers of Some Key Enzymes Slide 53 of 69 MPharm PHA115 Enzymes WEEK 14 Enzyme Inhibition Enzymes are required for most of the processes required for life They catalyse biological reactions by reducing the activation energy needed for the reactions to occur They bind to specific substrates in the reaction pathway & speed up the reaction, but are released unchanged to be used again Activity of enzymes needs to be tightly regulated to maintain homeostasis Regulation is accomplished via enzyme inhibition Enzyme inhibition is widely exploited in clinical therapeutics Slide 54 of 69 MPharm PHA115 Enzymes WEEK 14 Types of Enzyme Inhibition Two types of inhibition Irreversible Reversible Reversible inhibition Competitive Non-competitive Uncompetitive Mixed Slide 55 of 69 MPharm PHA115 Enzymes WEEK 14 Competitive Inhibition The inhibitor (I) is structurally similar to the substrate (S) The inhibitor (I) competes with the substrate (S) for the substrate binding site The inhibitor has virtually no affinity for the enzyme- substrate complex (ES), since the substrate (S) already occupies the inhibitor binding site when bound In the presence of an effective concentration of inhibitor the apparent KM is increased there is no change in the Vmax The inhibition can be reversed by increasing the concentration of the substrate (S) Slide 56 of 69 MPharm PHA115 Enzymes WEEK 14 Competitive Inhibition Slide 57 of 69 MPharm PHA115 Enzymes WEEK 14 Competitive Inhibition Slide 58 of 69 MPharm PHA115 Enzymes WEEK 14 Non-competitive Inhibition The inhibitor has similar affinity for both the free enzyme (E) and the enzyme-substrate complex (ES) The inhibitor may bind with the free enzyme as well as the enzyme-substrate complex The inhibitor binds with the enzyme at a site which is distinct from the substrate binding site The binding of the inhibitor does not affect the substrate binding, and vice versa However, the inhibitor binding to enzyme or enzyme- substrate complex prevents enzyme from forming its product there is no effect on, or change, in the KM the Vmax for the reaction is decreased Slide 59 of 69 MPharm PHA115 Enzymes WEEK 14 Non-competitive Inhibition Slide 60 of 69 MPharm PHA115 Enzymes WEEK 14 Non-competitive Inhibition Slide 61 of 69 MPharm PHA115 Enzymes WEEK 14 Uncompetitive Inhibition The inhibitor has affinity for the enzyme-substrate complex (ES), but not the free enzyme (E) The inhibitor binds only the enzyme-substrate complex (ES), but not the free enzyme (E) An inactive ESI complex is formed when the inhibitor reversibly binds to the enzyme-substrate complex The inactive ESI complex does not form a product (P) the apparent KM is decreased – due to the selective binding of the inhibitor to the enzyme-substrate complex (ES) the Vmax for the reaction is also decreased inhibition cannot be reversed by increasing the substrate concentration Slide 62 of 69 MPharm PHA115 Enzymes WEEK 14 Uncompetitive Inhibition Slide 63 of 69 MPharm PHA115 Enzymes WEEK 14 Uncompetitive Inhibition Slide 64 of 69 MPharm PHA115 Enzymes WEEK 14 Slide 65 of 69 MPharm PHA115 Enzymes WEEK 14 Summary of the Effect of Enzyme Inhibition on the KM and Vmax Type of Inhibition Apparent KM Apparent Vmax Competitive Increased Unchanged Non-competitive Unchanged Decreased Uncompetitive Decreased Decreased Slide 66 of 69 MPharm PHA115 Enzymes WEEK 14 The Inhibitor Constant (Ki) A measure of the affinity of an inhibitor drug for an enzyme Ki values are used to characterize and compare the effectiveness of inhibitors relative to KM Useful and important in evaluating the potential therapeutic value of inhibitor drugs for a given enzyme reaction In general, the lower the Ki value, the tighter the binding, and hence the more effective an inhibitor is Slide 67 of 69 MPharm PHA115 Enzymes WEEK 14 Graphical Determination of the Inhibitor Constant (Ki) Non-competitive inhibitor Competitive inhibitor Slide 68 of 69 MPharm PHA115 Enzymes WEEK 14 Enzymes as Important Drug Targets Disease Enzyme Drug Mechanism Hypertension Angiotensin Converting Lisinopril Inhibitor Enzyme (ACE) Alzheimer’s Acetylcholinesterase Donepezil Inhibitor Disease (AChE) Parkinson’s Dopamine β-hydroxylase L-DOPA Substrate Disease Inflammation Cyclooxygenase 2 (COX 2) NSAIDs, e.g. aspirin, Inhibitors ibuprofen, naproxen, celecoxib Gout Xanthine oxidase Allopurinol Inhibitor Parkinson’s Monoamine oxidase Selegiline Inhibitor Disease Moclobemide Cardiovascular HMG CoA reductase Statins Inhibitor disease Slide 69 of 69 MPharm PHA115 Enzymes