Enzymes 1 (2023) PDF - University of Sunderland

WEEK 13 MPharm Programme Enzymes 1 Dr Gabriel Boachie-Ansah [email protected] Dale 113 ext. 2617 MPharm PHA112 Enzymes WEEK Outline of Lectures 13 What enzymes are, and why they do Enzyme structure & classification, and enzyme co-factors Enzymes & cellular metabolism...

WEEK 13 MPharm Programme Enzymes 1 Dr Gabriel Boachie-Ansah [email protected] Dale 113 ext. 2617 MPharm PHA112 Enzymes WEEK Outline of Lectures 13 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 PHA112 Enzymes Learning Outcomes WEEK 13 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 MichaelisMenten & Lineweaver-Burk Plots Describe the various types of enzyme inhibition Appreciate the relevance of enzymes & enzyme inhibition in medicine Slide 3 of 69 MPharm PHA112 Enzymes Enzymes WEEK 13 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 PHA112 Enzymes Enzymes WEEK 13 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 1. Oxidoreductases 2. Transferases 3. Hydrolases 4. Lyases 5. Isomerases 6. Ligases Slide 5 of 69 Type of Reaction Catalysed Oxidation–reduction reactions Transfer of functional groups Hydrolysis reactions Group elimination to form double bonds Isomerization Bond formation coupled with ATP hydrolysis MPharm PHA112 Enzymes WEEK 13 International Classification of Enzymes Slide 6 of 69 MPharm PHA112 Enzymes Enzymes WEEK 13 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 PHA112 Enzymes Enzymes WEEK 13 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’ – it’s 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 PHA112 Enzymes WEEK 13 Slide 9 of 69 Enzyme Cofactors MPharm PHA112 Enzymes WEEK Enzyme Cofactors 13 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 PHA112 Enzymes WEEK Enzyme Cofactors 13 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 PHA112 Enzymes WEEK 13 Slide 12 of 69 Examples of Coenzymes MPharm PHA112 Enzymes WEEK Enzyme & Cofactors 13 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 PHA112 Enzymes Enzymes WEEK 13 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 PHA112 Enzymes Enzymes WEEK 13 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 PHA112 Enzymes WEEK Enzymes & Cellular Metabolism 13 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 PHA112 Enzymes WEEK Enzymes & Cellular Metabolism 13 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 PHA112 Enzymes WEEK 13 Slide 18 of 69 Cellular Metabolism MPharm PHA112 Enzymes WEEK 13 Enzyme-catalysed Metabolic Reactions Anabolic - dehydration synthesis (synthesis) enzyme Catabolic - hydrolysis (digestion) enzyme Slide 19 of 69 MPharm PHA112 Enzymes WEEK Enzymes & Cellular Metabolism 13 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 PHA112 Enzymes WEEK 13 Endergonic Slide 21 of 69 MPharm Exergonic PHA112 Enzymes WEEK 13 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 PHA112 Enzymes WEEK 13 Enzyme-catalysed Metabolic Reactions Slide 23 of 69 MPharm PHA112 Enzymes WEEK 13 Enzyme-catalysed Metabolic Reactions Slide 24 of 69 MPharm PHA112 Enzymes WEEK 13 Enzyme-catalysed Metabolic Reactions Slide 25 of 69 MPharm PHA112 Enzymes WEEK How Do Enzymes Work? 13 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 shape of substrate Slide 26 of 69 MPharm Active site forms a complementary shape of substrate after binding substrate PHA112 Enzymes WEEK How Do Enzymes Work? 13 ‘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 PHA112 Enzymes WEEK How Do Enzymes Work? 13 ‘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 PHA112 Enzymes WEEK How Do Enzymes Work? 13 ‘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 PHA112 Enzymes Enzymes WEEK 13 What Are The Factors That Affect Enzyme Function? Enzyme concentration Substrate concentration Temperature pH Salinity Slide 30 of 69 MPharm PHA112 Enzymes WEEK Factors That Affect Enzyme Function 13 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 Reaction rate substrate concentration becomes the limiting factor not all enzyme molecules can find a substrate Enzyme concentration Slide 31 of 69 MPharm PHA112 Enzymes WEEK Factors That Affect Enzyme Function 13 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 Reaction rate all enzyme active sites become engaged (saturated) maximum rate of reaction has been reached Substrate concentration Slide 32 of 69 MPharm PHA112 Enzymes WEEK Factors That Affect Enzyme Function 13 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 PHA112 Enzymes WEEK 13 Effect of Temperature on Enzyme Function Optimum Enzyme Activity Increasing number of collisions (Q10) 0 10 20 Denaturation 30 40 50 Temperature (C) Slide 34 of 69 MPharm PHA112 Enzymes WEEK 13 Effect of Temperature on Enzyme Function Optimum Temperature hot spring bacteria enzyme Reaction rate human enzyme 37°C 70°C Temperature Slide 35 of 69 MPharm PHA112 Enzymes