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Chem 352 - Lecture 6 Enzymes: Biological Catalysts

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Chem 352 - Lecture 6 Enzymes: Biological Catalysts 1 Chem 352 - Lecture 6 Enzymes: Biological Catalysts Question for the Day: Describe how to easily determine the number of reactions that one enzyme molecule is capable catalyzing in one second. Outline 2 8.1 Enzymes as Biological Catalysts 8.2 The Diversity of Enzyme Function 8.3 Chemical Reaction Rates and the Effects of Catalysts 8.4 How Enzymes Act as Catalysts : Principles and Examples 8.5 Coenzymes, Vitamins, and Essential Metals 8.6 The Kinetics of Enzymatic Catalysts 8.7 Enzyme Inhibition 8.8 The Regulation of Enzyme Activity 8.9 Covalent Modifications Used to Regulate Enzyme Activity Chem 352, Lecture 6 - Enzymes 2 3 8.1 Enzymes as Biological Catalysts Enzymes as Catalysts 4 Enzymes are biological catalysts catalyst |ˈkatl-ist| noun a substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change. • figurative a person or thing that precipitates an event : the governor's speech acted as a catalyst for debate. ORIGIN early 20th cent.: from catalysis , on the pattern of analyst. (New Oxford American Dictionary) Chem 352, Lecture 6 - Enzymes 4 Enzymes as Catalysts 5 Enzyme are biological catalysts ✦ Nearly every reaction in a living cell is catalyzed by an enzyme. ✦ Most enzymes are proteins. ✦ The reactants in an enzyme-catalyzed reaction are called substrates. ✦ Enzymes are incredibly efficient at what they do, so capable of increasing the rates of chemical reactions a million to as much as a billion times over an uncatalyzed reaction! Chem 352, Lecture 6 - Enzymes 5 Enzymes as Catalysts 6 Enzymes can exhibit: ✦ High specificity • High substrate specificity • High reaction specificity • Stereospecificity ✦ They can couple energetically unfavorable reactions with those that are favorable. ✦ They serve as control points in metabolic pathways. Question: Explain why it should be a relatively simple task for an enzyme to distinguish between L-alanine and D-alanine. Chem 352, Lecture 6 - Enzymes 6 Enzymes as Catalysts 7 Enzymes are often the target for drug therapies. Chem 352, Lecture 6 - Enzymes 7 Enzymes as Catalysts 8 In this lecture will discuss ✦ The classification and nomenclature of enzymes ✦ The analysis of the kinetics of enzyme-catalyzed reactions • and learn what this can tell us about the mechanisms of enzyme catalyzed reactions. ✦ The regulation of enzyme activity by inhibitors and activators ✦ A case study: Serine Proteases Chem 352, Lecture 6 - Enzymes 8 9 8.1 The Diversity of Enzyme Function Enzyme Classes and Nomenclature 10 Common names use the suffix -ase |ˈnōmənˌklā ch ər| nomenclature✦ The common name often describes the substrate as well as noun the reaction that the enzyme catalyzes. the devising or choosing of names for things, esp. in a science or other ✦ discipline.For example: • the body• pyruvate or system kinase of such - catalyzenames in thea particular transfer field of a: thephosphate nomenclature group of chemical compounds.(kinase) from/to pyruvate and ATP • formal the term or terms applied to someone or something : “customers” was preferred• toalcohol the original dehydrogenase nomenclature “passengers.” - removes an equivalent of a DERIVATIVEShydrogen molecule, H2, from an alcohol such as ethanol. nomenclatural |ˌnōmənˈklā ch ərəl| |ˈˈnoʊmənˈˈkleɪtʃ(ə)rəl| |- ˈklatʃ(ə)r(ə)l| |-kləˈtʃʊər(ə)l| adjective ORIGIN early 17th cent.: from French, from Latin nomenclatura, from nomen ‘name’ + clatura ‘calling, summoning’ (from calare ‘to call’ ). Chem 352, Lecture 6 - Enzymes 10 Enzyme Classes and Nomenclature 11 There is also a systematic nomenclature that names of enzymes using numbers ✦ The numbers describes • the class of reaction • the substrates used in the reaction • the products produced in the reaction ✦ Then numbers are called Enzyme Commission (E.C.) numbers. ✦ The scheme for deriving these number is defined by the International Union of Biochemistry and Molecular Biology (IUBMB) ✦ The SwissProt Enzyme Database provides an example of how the EC numbers are used. Chem 352, Lecture 6 - Enzymes 11 Enzyme Classes and Nomenclature 12 Chem 352, Lecture 6 - Enzymes 12 Enzyme Nomenclature 13 Systematic names use numbers ✦ pyruvate kinase - EC 2.7.1.40 ✦ alcohol dehydrogenase - EC 1.1.1.1 Chem 352, Lecture 6 - Enzymes 13 Enzyme Classes 14 Oxidoreductases (1.) ✦ Catalyze oxidation-reduction reactions ✦ For example • lactate dehydrogenase ✦ lactate:NAD oxidoreductase (EC 1.1.1.27) Distinguishing features: ✦ Many (dehydrogenases) involve addition or removal of H2 as H:- + H+ Chem 352, Lecture 6 - Enzymes 14 Enzyme Classes 15 Transferases (2.) ✦ Catalyze the transfer of a group from one molecule to another ✦ For example • L-alanine amino transferase ✦ L-alanine:2-oxyglutarate aminotransferase (EC 2.6.1.2) Distinguishing features: ✦ Look for double-replacement reactions Chem 352, Lecture 6 - Enzymes 15 Enzyme Classes 16 Hydrolases (3.) ✦ Catalyze a special case of transfer reactions, where water is the acceptor of the group being transferred. The reactions lead to the splitting of molecules in two. ✦ For example • pyrophosphatase ✦ diphosphate phosphohydrolase (EC 3.6.1.1) ✦ Distinguishing features: • Look for water splitting in conjunction with another molecule splitting Chem 352, Lecture 6 - Enzymes 16 Enzyme Classes 17 Lyases (4.) ✦ Catalyze a lysis of a subtrate, which is nonoxidative, nonhydrolytic and generates a double bond. ✦ For example • pyruvate decarboxylase ✦ pyruvate decarboxylase, 2-oxo-acid carboxy-lyase (EC 4.1.1.1) ✦ Distinguishing features: • Look for addition and elimination reactions involving the loss or formation of a double bond Chem 352, Lecture 6 - Enzymes 17 Enzyme Classes 18 Isomerase (5.) ✦ Catalyze a conversion between two isomers. • Sometimes referred to as an rearrangement reaction. ✦ For example • alanine racemase ✦ alanine racemase (EC 5.1.1.1) ✦ Distinguishing features: • Look for reactions that have only a single substrate and a single product. Chem 352, Lecture 6 - Enzymes 18 Enzyme Classes 19 Ligase (6.) ✦ Catalyze the ligation or joining of two molecules. • This reaction usually requires a source of chemical energy, which is often provided by the hydrolysis of ATP to ADP and Pi ✦ For example • glutamine synthetase ✦ L-glutamate:ammonia ligase (EC 6.3.1.2) ✦ Distinguishing features: • Look for a combination of two reactions Chem 352, Lecture 6 - Enzymes 19 Enzyme Classes 20 ClickerQuestion: Question: O Which class does the enzyme that catalyzes the following reactionO H triosephosphate CH2 O P O C belong to? O isomerase C O OH H C OH O CH OH CH O P O 2 2 O CH2 OH CH2 O P O C O A.phoOxidoreductasesphofructokinase C O OH O CH O P OO A. Oxidoreductase 2 dihydroxyacetone glyceraldehyde OH ATP ADP CH OaldoPlaseO HO C H B. TransferaseHO C H CH2 2OH phosphate C COH2 OH P O 3-phosphate C O OH O+ H C OH C. LyaseHydrolaseH C OH C O CH2 C OH O OH CH OH ? C H H2O C H ? O H dihydroxyacetone D. Isomerase HO C H HO C H H C OH OD. Isomerase H C OH O ? phosphate C C H O C O OH + ATP CH OH O+ + ADP E. LigaseLyase H C OH H C OH CH2 O P O CH2 O P O CH2H OC POH OO H C CH2OH O O P O H C OH O O H HC OH O OH OH CH OHO P O OCH 2 CH2 O P O CH2 O P O CH2 O P O OH H C OH O fructose frucdtihosyedroxyacetone glyceraldOehHyde OH OH 6-phosphate 1,6-bisphospphaostpehate 3-phosphateCH O P O fructose 2 1,6-bisphosphate fructose glyceraldehyde frOuHctose 6-phosphate 3-phosphate 1,6-bisphosphate glyceraldehyde 3-phosphate Chem 352, Lecture 6 - Enzymes 20 21 8.3 Chemical Reaction Rates and Effects of Catalysts Reaction Rates and Catalysts 22 Observing the kinetics of a reaction can reveal details about the mechanism of the reaction Starting with the kinetics of non-catalyzed reactions ✦ The rate, or velocity, v, of a reaction, is monitored by observing the change in the concentration of either the substrate (reactant) or the product of the reaction. A → B change in concentration of A or B Rate = v = change in time dB dA v = = − dt dt Chem 352, Lecture 6 - Enzymes 22 Reaction Rates and Catalysts 23 Kinetics of non-catalyzed reactions ✦ Typically it is the substrate dependence of the initial rate, vo, that is determined. d[B] v = at t = 0 o dt [B] Chem 352, Lecture 6 - Enzymes 23 Reaction Rates and Catalysts 24 The rate equation for this relationship can take on different forms with respect to the substrate or product concentrations, for example: d[B] d[A] v = = − = k [A]n dt dt 1 ✦ where k1 is the rate constant ✦ and n is the order of the reaction • n = 1, first order, • n = 2, second order • n = 0, zero order Chem 352, Lecture 6 - Enzymes 24 Reaction Rates and Catalysts 25 Kinetics of non-catalyzed reactions ✦ For first-order reactions, vo is proportional to [A]. vo = k1[A] [A] ✦ In this case, k1 is called the first order rate constant and has dimension of s-1. Chem 352, Lecture 6 - Enzymes 25 Reaction Rates and Catalysts 26 Kinetics of non-catalyzed reactions ✦ Deriving an expression that gives [A] as function of time for a first order reaction. d[A] − = k [A] ln([A]t) − ln([A]o) = − k1t dt 1 d[A] [A]t = − k1dt ln = − k1t [A] ( [A]o ) [A]t d[A] t = − k dt [A] = [A] e−k1t ∫ 1 ∫ t o [A]o [A] 0 Chem 352, Lecture 6 - Enzymes 26 Reaction Rates and Catalysts 27 Kinetics of non-catalyzed reactions ✦ For a second order reaction, vo has a quadratic dependence on [A]. A + A → C 2 vo = k1[A] or A + B → C vo = k1[A][B] • vo is the second order rate constant and has units of M-1s-1.
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