Essential Elements of Biochemistry BCHM 3050 Dr Srikripa Chandrasekaran Dr Sri Lecture Notes 1 30 15 Enzymes Part 1 Properties and Classification Enzyme biological catalyst normally a protein rarely RNA that functions to speed up the rate of a biological reaction but is not altered or consumed in the reaction Substrates the substances upon which an enzyme acts reactants The substrates bind at the active site Products the substances produced by chemical modification of substrates Active site the specific region on in an enzyme where substrates bind and where the catalytic reaction occurs Transition state the unstable energized intermediate formed in an enzymic reaction that has properties of both the substrate and the product The point in a reaction where reactants and products have the highest energy Transition state refers to the intermediate form Transition state has properties of both the reactants and the products Enzymes stabilize the transition state Activation energy the threshold energy required to produce a chemical reaction the amount of energy required to active the substrate Models for enzyme action The Lock Key Model The Induced Fit Model o Proposed by Emil Fischer 1894 o The enzyme active site i e lock perfectly matches the shape of the substrate i e key o The enzyme thus allows only one substrate to bind to the active site and be converted to product o Enzyme action is not actually as stiff as a lock and key it has some wiggle room to move around it is flexible o Proposed by Daniel Koshland 1958 o Substrates fit into active site like a flexible hand in glove after putting the glove on you can still change the conformation of the glove on your hand because it is flexible o Enzyme Substrate binding interactions changes the shape of both enzyme and substrate to fit snugly o Enzymes are not as rigid as once thought Lock Key they are much more flexible and dynamic Induced Fit o The Induced Fit Model has been confirmed by X ray crystallography Energy changes during the progress of a reaction 1 Products and reactants have different amounts of energy Enzymes lower the activation energy DG but not the free energy DG Activation Energy vs Free Energy Significance of DG G2 G1 Reactants pass through a transition state as they form products Activation energy is the amount of energy required to reach the transition state threshold for a chemical reaction Free energy is the difference in energy between the products vs reactants Refer to graph on PowerPoint This graph measures how fast a reaction goes We would probably still get by without enzymes all reactions would just G represents free energy take longer and require more energy the cells would get overworked In exothermic reactions the product has lower energy than the substrate Activation energy the amount of energy required to get the reactants to the transition state this is much lesser for reactions that are catalyzed by enzymes Enzymes lower the activation energy Enzymes do not do anything to alter the free energy The difference in free energy between the substrate and the product is not changed by enzymes Reactions will happen regardless of the presence or absence of enzymes the presence or absence of enzymes just alter the time in which is takes to complete the reaction Six Classes of Enzymes 1 Oxidoreductases catalyze oxidation reduction reactions add remove electrons protons from its substrate Includes dehydrogenases oxidases reductases peroxidases etc Example Alcohol dehydrogenase Acetaldehyde is toxic damages the liver Acetaldehyde dehydrogenase produces acetyl CoA LEO says GER lose electrons oxidation gain electrons reduction reduction Most oxidation reduction reactions have cofactors the cofactors get reduced while something else gets oxidized Oxidoreductases Always an oxidation is preceded by a Oxidoreductase is the enzyme in the body that breaks down alcohol Asians have less oxidoreductase than the average person so they have to be very careful when they drink alcohol because they can get drunk much easier and off less alcohol than many others since they have less oxidoreductase enzymes Asians typically can not tolerate alcohol consumption very well because they have a more active form of alcohol deydrogenase and a mutated less active form of acetaldehyde dehydrogenase which leads to a more rapid and prolonged buildup of 2 acetaldehyde In other words they will experience a hangover more quickly and longer than caucasians americans 2 Transferases transfer a functional group from one molecule to another amino phosphoryl methyl acyl Includes transaminases transmethylases acyl transferases etc Example Hexokinase 3 Hydrolases cleave bonds by adding a water molecule Includes esterases phosphatases peptidases lipases glycosidases Example Phospholipase A2 Water is involved water comes in and chops a molecule into different parts it breaks down one molecule into multiple Hydrolases are present in the venom of many snakes Some snake venoms can block neurotransmitters which causes harmful effects 4 Lyases remove functional groups via non hydrolytic reactions Often result in formation of a double bond Includes decarboxylases deaminases dehydratases Example Phenylalanine Ammonia Lyase Phenylalanine ammonia lyase is important in plants because it is the regulatory enzyme that controls synthesis of phenylpropane monomers of lignin Lyase removes part of the molecule in the absence of water similar to hydrolase but acts without the help of water Example Isocitrate Lyase Isocitrate Lyase is the first unique enzyme of the glyoxylate cycle i e unique from the TCA cycle The glyoxylate cycle is important in gluconeogenesis in plants 5 Isomerases catalyze rearrangements of functional groups within a molecule converts a molecule into its isomer Mutases transfer functional groups from one position to another Epimerases invert functional groups about asymmetric carbons Two compounds with a double sided arrow inbetween Examples Triose Phosphate Isomerase Bisphosphoglycerate 6 Ligases use the energy from ATP hydrolysis to form bonds between two Mutase substrate molecules 2 ester bonds Form C C C S C O PO3 Includes synthetases carboxylases Example Acetyl CoA Carboxylase Ligase is the opposite of lyase Ligase joins things together most cases involve the presence of ATP which provides energy ATP is broken down into ADP and a phosphate group Cofactor loosely bound non protein components of enzymes that assist in catalytic reactions enzymes
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