Lecture 9 Notes - Enzymology
Lecture 9 Notes - Enzymology BIL 255
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Date Created: 10/18/15
Cell and Molecular Biology Lecture 9 Enzymology Enzymes are catalytic proteins regulating reaction rates They control metabolism 0 Molecules mostly protein vs ribozymes that accelerate enzyme Catalysis is a change in rate of quot enzyme 7 acllernicalreaclioni L O Q 1 CATALYSIS 1 molecule B lplroductl or catalyze chemical reactions in cells by breaking old covalent bonds and forming new ones Biological catalysts have complex structure sequence of molecule A Substrate enzyme substrate complex enzyme product complex aa s and act only upon a specific substrate do not change direction energetics of reaction 0 Catalyst accelerate the rate of a chemical reaction Enzymes convert substrates to products wo changing themselves 0 Ex cAMP protein kinase A PKA group of enzymes that dissolclilaible complex vagina Ms mmm 2th gammawee activated a subunit of stimulatory G protein lG l transfer P from ATP to SER on proteins I Refers to a family of enzymes whose activity is dependent level of cyclic AMP cAMP in the cell low levels inactive I Is a quaternary holoenzyme of 2 Regulatory and 2 Catalytic WWW subunits rm J l l 1 t l 7 7 7quot the activated GPCR ladrenergic receptor activated adenylyl cycliase inactivele I Has several functions in the cell including regulation of glycogen minmsugar and lipid metabolism 77 9 a The first enzyme crystallized was UREASE by James Sumner in m7 395 m39 a 5513 me active glycogen p hosp horylase inactive 1926 tritium O Sumner was first to crystallize a protein fraction with catalytic activity 1000s of enzymes have been purified amp crystallized 0 All are proteins except for ribozymes that also have catalytic activity Important dates in enzyme history 0 1833 Payen amp Peroz alcohol precipitate of malt barley holds heat labile components 1st 45 F inactive glycogen 1 p hosp horylarte GWEOGEH W 1615 Elli llliull HI wow ltht d loam Still NH EREAKDOIWquot enzyme proteins that converted starch to sugars 1878 Wilhelm Kuhne coins term 39enzyme39 Greek quotin leavenquot 1897 Hans amp Eduard Buchner yeast 39juice39 sugars jelly bubbled gas amp ETOH 1898 Emile DucleauX customizes use of suffix quotASE quot for enzyme naming 1900 E Fischer stereospecificity of enzymes is discovered 0000 0 Enzyme Reaction Path enzyme lowers activation energy for activation energy for reaction Var ES 9 ES 9 EP Enzymes catalyze reactions by lowering the energy of activation Ea There is no difference in free energy between an enzyme catalyzed reaction and an uncatalyzed reaction but a nonenzyme catalyzed reaction requires higher energy input than an enzyme catalyzed reaction YIl total energy total energy l uncatalyzed LB reaction pathway Ell39l zym ecata lyze d reaction pathway Fiminn 311 uth Lei Riidlmn39rjllthml f Emlud SliMIEP l ln catalyzed reaction Turnover number number of substrate molecules converted to product per second for a single enzyme molecule 0 Enzyme Terminology 0 Mechanism of Enzyme Action Substrate product enzyme selfexplanatory Cofactors nonprotein compounds required for a protein39s biological activity such as small inorganic ions and many metal ions Cu Mg Mn Fe which act as activators ampor inhibitors of activity Coenzymes small nonprotein ligands that catalyze reactions electrons transfer a group form or break a covalent bond includes vitamins O Lipoic acid oxidative deCOOH of alphaketo acid 0 NAD NADP redox coenzymes dehydrogenations H carrier andor electron transfer 0 FAD another redox coenzyme O CoASH acyl carrier3HCCO via sul aydryl SH Prosthetic group large complex organic molecules b J m r AlD F39 onidiiaedltorm red wced form Oxidized FAD Reduced Fluton quotW quotWetterquot more Hi i 550 rim Flibitol ZIP catalytic Hibitol 45 quotquot1 which may have le acthlty Adenosi he Active Aclenlosine FAD 2 H 2 e a Freon2 site a portion of enzyme which folds to precisely fit the contours of a substrate via weak electrostatic interactions amp facilitates bond reactivity Enzyme substrate complex unique joining of enzyme amp substrate at active site 0 Holds substrate out of aqueous solution 0 Holds substrate in specific orientation close to transition state to allow reaction to occur 0 Reduces ability of free rotation amp molecular collisions with nonreactive atoms 0 Allows amino acid side chains to alter local environment can change ionic strength pH add or remove Hbonds to substrate while precisely holding substrate so that it can be acted upon 0 Analogy a nut amp bolt held in your hand decreases the Entropy of their binding over a random mix of nuts and bolts in a toolbox 39 3 phospha39tegrmurp missing in Mm and mm Figure 334 Essential ICell Itiology 4111 ed lltil Garland Stiente Elli4 The chemical reaction scheme by which an enzyme acts upon its substrate 3 examples 0 Lysozyme an enzyme that cuts polysaccharide glycosidic by hydrolysis adds H20 I Active site is a long groove ehme binds to two substrate molecules and orients them precisely m onceUranus a reaction to occur between them binding of substrate to onetime roarrang as electrons in the substrate creating partial negative anti positive charges that favor a reaction onetime strains the bound on narrate molecule lowing it toward a transition state to favor a reaction bonds Flinn 135 H V 39 WJ hu f f f T I39 Figure 434 Essential tell Biology tilt ed U Gatiandl Science 1mm holding six sugar units has 2 acidic side chains GLU amp ASP hold substrate I Breaks glycosidic bond C OC via bond strain amp distortion of glu amp asp A 5 E h ES 1 EP Schematic View of the enzyme lysoznme E which catalyzes the cutting of a polysaccharide substrate molecule 5 The enzyme rst binds to the polysaccharide to form an enzyme substrate complex ES then it catalyzes the cleavage of a speci c covalent bond iri the backbone of the polysaccharide The resulting enzymeproduct complex EP rapidly dissociates releasing the products P and leaving le enzyme free to act on another substrate molecule B A spacetitling model of lysozyme bound to a short length olfrpolysaccharlde chain prior to cleavage I Enzyme binding of substrate bends bonds from a stable state lowering Ea I Acidic side group of GLU provides a proton to attack glycosidic bond and ASP favors hydrolysis of glycosidic bond 0 Protease hydrolysis of peptide bonds I serine proteases catalytic sites hold ser195 asp102 amp his57 OH of ser195 attacks CO of peptide bond amp transition state is held by Hbonds I E s break peptide bond amp release part of protein HOH is split amp other half released 0 Catalytic action of cAMP dependent Protein Kinase A e39s of ATP delocalized by LYS amp Mg2 new bond forms between SEROH amp VP bond between SPVP broken ADP Pprotein 0 Classification of Enzymes Enzyme commission IUBMB International Union Biochemistry amp Molecular Biology 4 digit Numbering System 1234 by Enzyme Commission 1958 0 1st one of 6 Major Classes of Enzyme Activity 0 2nd a subclass type of bond acted upon 0 3rd a subclass group acted upon cofactor required etc 0 4th a serial number order in which enzyme was added to list Examples of major classes of enzymes 1 Oxidoreductases dehydrogenases catalyzes oxidation reduction reactions often using coenzyme as NADFAD Transferases catalyzes the transfer of functional group Hydrolases catalyzes hydrolytic reactions adds water across CC bonds Lyases cleaves CC CO CN amp other bonds often generating a CC bond or ring Isomerases mutases catalyze isomerations Ligases condensation of 2 substrates with splitting of ATP 99 TABLE 4il SOME COMMON FUNCTIONAL CILASSEE S OF ENZYMES Hydrolase 3 General term For enzymes that catalyze a hydrolytic cleavage reaction Nuclease 3 Breaks clown nucleic acids by hydrolyzing bonds between nucleotides Protease 3 Breaks down proteins by hydrolyzing peptide bonds between amino acids Ligase 6 Jioins two molecules together DNA ligase joins two DNA strands together endtoend lsornerase 5 Catalyzes the rearrangement of bonds within a single molecule Polymerase 2 Catalyzes polymerization reactions such as the synthesis of DNA and RNA Kinase 2 Catalyzes the addition of phosphate groups to molecules Protein kinases are an important group of kinases that attach phosphate groups to proteins Phosphatase 3 Catalyzes the hydrolytic removal of a phosphate group irom a molecule Oxidoreductase General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is 1 reduced Enzymes of this type are often called midiases reductases or dehydrOQenases ATPase 3 Hydrolyzes ATP Many proteins have an energyharnessing AT Fase activity as part of their function including motor proteins such as myosin discussed in Chapter 17 and membrane transport proteins such as the sodium pump discussed in Chapter i2 Enzyme names typically end in quotasequot with the exception oil some enzymes such as pepsin trypsin thrombin lysozyme and so on which were discovered and named beFore the convention became generallyr accepted at the end at the nineteenth century The name of an enzyme usually indicates the nature of the reaction catalyzed For example citrate Synthase catalyzes the synthesis of citrate by a reaction between acetyi Cork and oxaloacetate a EirrmWma 0 Enzyme Kinetics Defines the physical amp chemical properties of enzyme by mathematical andor graphical expression of the reaction rates of enzyme catalyzed reactions Observed enzyme kinetic reaction curves 0 Rate 08ml OZmin vs E a classical 1st order linear plot 0 Rate vs pH 0 Rate vs temperature 0 Rate vs S Vim I Most characteristic curve 1 I Defines a rectangular hyperbola g I At low S rate is directly proportional ml to 12 Vmax o I At h1gher S rate dec11nes g1v1ng a 3 rectangular hyperbola I 1 st amp 2nd order reaction kinetics are ii Lures2t Essential EEIII lBiol Antidl39icGa ainMniente Mint NOT suff1c1ent to descr1be the 5 0 KM substrate concentration I rectangular hyperbola of enzyme M t a W is reached At this point all substratebinding sites on the enzyme molecules are fully occupied and the rate of the reaction depends h w fast 5 can be Cl averted D P Fm WDSE enzymes the cancentrstlon 01f substrate at WHICH the ire actlen rate is hal maicimal Km is a direct measure of how tightly the substrate is bound with a small value of Km a small amount of substrate needed corresponding to tight binding andl a large Km indicating amak binding In 1913 Leonor Michaelis amp Maud Menten proposed a mathematical modeling of enzyme reactions using algebraic expressions and rate constants to define a rectangular hyperbola k1 k3 ESlt gtESlt gtEP k2 k4 Some assumptions in the MampM derivation 0 Rate formation ES complex from E P is negligible ie can ignore the rate constant k4 0 Rate limiting step is disassociation of ES to E P k3 speed of dissociation I k3 rate constant is of molecules converted by this reaction per unit time 0 An important state of the enzyme is termed free enzyme Which is able to react I bound enzyme ES I free enzyme Et ES I total enzyme Et Et ES ES Derivation of MichaelisMenten enzyme kinetics 0 The derivation of equation occurs at a time When the rate of formation of ES complex is equal to rate of destruction break down ie at equilibrium When S gtgtgtgt E so that total E is bound in ES complex and thus reaction works like a 1st order reaction enzyme catalyzed reaction 0 The rate limiting equation thus becomes destruction of ES v dPdt k3ES 0 The derived M amp M equation is then v Vmax S Km S Km the Michaelis Constant Is applicable to enzyme reactions involving a single substrate Is quotinherent tendencyquot of reactants to interact chemically for that reaction Is a constant that is independent of E and defined by S Is a mathematical interpretation of an enzyme reaction Is a measure of how efficiently an enzyme converts a substrate to product Is the substrate concentration When enzyme velocity is equal to 12 Vmax many enzymes have individual steps in a complex reaction sequences each step has its own Km39s 0000000 0 Enzyme inhibition 2 classes of inhibitors 0 Irreversible inhibitor molecule cannot be easily removed from enzyme thereby reducing the total number of working enzyme molecules I ie enzyme is physically altered by binding of inhibitor reducing its amount 0 Reversible enzyme activity may be restored by overcoming the effect of the inhibitors and are thus treatable by MampM kinetics 2 major types of reversible inhibitors 0 Competitive Inhibitor binds to E amp forms an El complex at the active site inhibitor often looks like a substrate ampfools the active site amp binds Extent of inhibition is concentration dependent inhibitor is often at fixed conc thus it can be overcome if S is very high S gtgtgt I hill H216 IrEVE quot Wilh Inhibitor n S 1 MS o Noncompetitive Inhibitor binds to E forms an El complex now at the active site inhibitor often bears no structural relationship to substrate Removes a net amount of active enzyme amp lowers total E it can NOT be overcome even if S is very high iur quotquot39 in NEW mu WITH IniII LIImI 112 v 5 1M5 Unnax If ifML fi d with an inhibitnli hammm the Krn remains the same 0 Examples of Native Enzyme Inhibition Irreversible 0 Serine gas 0 Antibiotics Penicillin Competitive 0 Ace inhibitors Angiotensin I gt Angiotensin II A 3 substrate on liy enzyme 2quot competitive substrate inhibitor I no a substrate in h iibito r inertive active e nizyme enzyme swbs r alm lll39il hi bltur l 1 IV In roduct s substrate 1 iiiSil mm 319 Emmiul Coil Binlmu in ad Gaan Edam mil Noncornpeiitive inhibitor changes shape oii enzyme so it cannot bind to substrate tn Nloneompetitive inhibition a Competitive inhibitinn