Lecture 1 - Enzyme Features and Classes PDF

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COMMONWEALTH OF AUSTRALIA Copyright Regulations 1969 WARNING This material has been reproduced and communicated to you by or on behalf of La Trobe University pursuant to Part VB of the Copyright Act 1968 (the Act). The material in this communication may be subject to copyright under the Act. Any further reproduction or communication of this material by you may be the subject of copyright protection under the Act. Do not remove this notice. Slide 1  Lecture 1 – Enzyme features and classes Module 1 - Enzymes Dr Sebastien Desbois Slide 2 Intended Learning Outcomes (ILOs) After this lesson students will be able to: Recognise that enzymes are catalysts by explaining their function and significance in biochemical reactions Identify some of the basic features of enzymes Describe the major classes of enzymes Explain that enzymes lower the activation energy of a reaction but do not change the equilibrium Slide 3 Enzymes are biological catalysts Catalyst: a substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change Enzymes accelerate the rate of a reaction Enzymes are NOT consumed during the reaction Most enzymes are proteins, some catalytic RNA molecules called ribozymes Enzymes have optimal environments in which they function (most human enzymes at pH 7.4, 37°C) Slide 4 Enzymatic equation Generally speaking, an enzymatic reaction can be written with the following equation: E + S ⇌ ES ⇌ EP ⇌ E + P where E = enzyme, S = substrate, P = product Substrate: molecule on which an enzyme can act Product: molecule produced by the chemical reaction of an enzyme Slide 5 Rate of reaction vs equilibrium Reaction rate: speed at which the concentration of product and substrate change Equilibrium: concentrations of substrate and product which no longer evolve over time (in a closed system) Equilibrium does not mean equal concentrations Enzymatic equations usually get the sign ⇌ which signifies the reversibility of the reaction Slide 6 Enzymes increase rate of reaction Enzymes increase the rate of reaction, they do not change the equilibrium Slide 7 Enzymes lower activation energy Enzymes lower activation energy by providing an alternate route for the reaction Slide 8  Changes in transition state S⇌P E + S ⇌ ES ⇌ EP ⇌ E + P without enzyme with enzyme Transition state: Highly unstable More stable Requires high activation energy Requires less activation energy Slow reaction Requires formation of intermediates Slide 9 How much faster is faster? Enzyme Non-enzymatic Uncatalysed Catalysed Rate ½ life rate (s-1) rate (s-1) enhancement OMP decarboxylase 78 000 000 28 x 10-16 39 1.4 x 1017 (pyrimidine biosynthesis) years 140 quadrillion Staphylococcal nuclease 130 000 years 1.7 x 10-13 95 5.6 x 1014 560 trillion Carboxypeptidase 7.3 years 3.0 x 10-9 578 1.9 x 1011 (Cleaves peptide bond at 190 billion C-terminus of a protein) Ketosteroid isomerase 7 weeks 1.7 x 10-17 66 000 3.9 x 1011 390 billion Triose phosphate 1.9 days 4.3 x 10-6 4 300 1.0 x 109 isomerase 1 billion Carbonic anhydrase 5 seconds 1.3 x 10-1 1 x 106 7.7 x 106 7 million Slide 10 What do enzymes need to work? Although a lot of enzymes can function without the help of other compounds, some do need other molecules to catalyse their reaction Coenzymes provide additional functional groups Vitamin derivatives (NADH) Cofactors can provide a change in conformation of the enzyme to facilitate function Metal ions (Mg2+, Fe2+, Zn2+…) Slide 11 Some recap of definitions Enzyme: protein (or the occasional RNA) that acts as a catalyst for a specific biochemical reaction Coenzyme: compound derived from a vitamin that assists an enzyme in facilitating a reaction Cofactor: Inorganic ion that assists an enzyme in facilitating a reaction Apoenzyme: Protein only part of an enzyme that requires an additional coenzyme Holoenzyme: combination of apoenzyme and coenzyme Slide 12 Enzyme classifications There are 6 major classes of enzymes Class Class name Reaction catalysed Example(s) # 1 Oxidoreductase Reduction/oxidation Alcohol dehydrogenase (ADH): alcohols ⇌ aldehydes 2 Transferase Group transfer between 2 Aminotransferases different molecules Kinases (such as MAPK) 3 Hydrolase Hydrolysis reaction Lipases from break down of fats, Proteases to digest proteins 4 Lyase Creation/removal of double Decarboxylase or dehydratase bonds such carbonic anhydrase 5 Isomerase Group transfer within 1 Phosphoglucose isomerase molecule converts G6P to F6P 6 Ligase Joins 2 molecules together DNA ligase joins together 2 DNA (coupled with ATP hydrolysis) molecules (Okazaki fragments) Slide 13 Summary An enzyme increases the rate of reaction by lowering the activation energy An enzyme does not change the equilibrium of the reaction catalysed Some enzymes require other elements to function properly such as specific cofactors or coenzymes There are 6 classes of enzymes classified by the reaction they catalyse Slide 14 Resources Lehninger Principles of Biochemistry Seventh Edition (2017), W. H. Freeman and Company, Chapter 6 Slide 15