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by: Ceasar Fritsch


Marketplace > Texas A&M University > Biochemistry > BICH 303 > ELEMENTS OF BIOL CHEM
Ceasar Fritsch
Texas A&M
GPA 3.92

Timothy Devarenne

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Timothy Devarenne
Class Notes
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This 29 page Class Notes was uploaded by Ceasar Fritsch on Wednesday October 21, 2015. The Class Notes belongs to BICH 303 at Texas A&M University taught by Timothy Devarenne in Fall. Since its upload, it has received 50 views. For similar materials see /class/225849/bich-303-texas-a-m-university in Biochemistry at Texas A&M University.




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Date Created: 10/21/15
Protein Functions Structural keratin collagen fibroin Enzyme carry out chemical reactions highest number of proteins 1000 s of reactions Gas transportstorage hemoglobin myoglobin Nutrient ovalbumin main protein in egg white casein predominant protein in milk Antibodies lgG proteins of vertebrates in the immune system for recognizing foreign object pathogens Hormones peptide hormones oxytocin vasopressin protein hormones insulin Mechanical work myosin actin molecular motors Enzymes Catalyst a substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change Catalysis the acceleration of a chemical reaction by a catalyst Example crossing a mountain Mode of transgortation sgeed walking several days bicycle one day lt one day car A bicycle would be a weak catalyst A car would be a strong catalyst Enzymes Are most efficient catalysts known reaction rate catalyst increase no catalyst 1 enzyme 1 x 1020 100000000000000000000 non enzyme 1 x102 1 x 104 100 40000 With out enzymes catalysts most chemical reactions in biological systems would take place far too slowly to sustain life Free energy gt Enzymes How do enzymes increase reaction rates Reactants gt products Reactions rxn require activation energy AG the energy input required for initiation of the rxn Analogy activation energy is similarto amount of effort to push an object to the top ofa hill so it can slide down the other side Plot of exergonic spontaneous a free energy change AG of a rxn is the energy change rxn AG lt 0 gives offener between the reactants and products of a rxn Can calculate AG by knowing the energy stored in reactants and the amount of energy given off at the end of reaction transition state the maximum point of the rxn curve where the amount of energy is maximal and atom arrangement is correct for product production one reached rxn will always proceed to product AG can be viewed as the amount of energy to bring reactants to transition state Progress of reaction gt Enzymes How do enzymes increase reaction rates enzymes lower the AG thus increasing the rxn rate enzymes lower AG by changing the rxn mechanism to a mechanism that requires less AG enzymes find easier route for rxn Free energy 4 uncatalyzed rxn has higher AG than catalyzed rxn ie uncatalyzed rxn is slower because it takes more energy to get started Thus slower rxn rate MDEIE cil martian r I consider oxidation of glucose Glucose 6 02 gt6 CO2 6 H20 Is a spontaneous rxn AG is negative 689 kcalmol gives off energy does not mean instantaneous Free energy Thus rxn is thermodynamically favorable but AG is large and is overcome by enzymes ngltss or martian gt rm am 19quot Enzymes How do enzymes increase reaction rates enzymes do not affect the transition state point 17 E3 14 v r Progress Ur maxim enzymes can not affect AG The AG of uncatalyzed and catalyzed rxn are the same Enzymes How do enzymes increase reaction rates Breakdown of hydrogen peroxide to water and oxygen 2 H202 gt 2 H20 02 This reaction can be catalyzed by platinum or the enzyme catalase Activation Free Energy Reaction Conditions kJ mol 1 kcal mol 1 Relative Rate No catalyst 752 180 1 Platinum surface 489 117 277 X 10 1 Catalase 230 55 651 x 108 23501 X mum Ewaksicaie rmomsan Enzymes Enzyme Substrate Binding Substrate a reactant that forms a complex with enzyme Transitionstate species the rxn intermediate present at the transitionstate Active sitean area of the enzyme with aa s essential for enzymatic activity site of substrate binding usually located in a cleft or crevice of the enzyme is the site of rxn A simplified model of Enzymesubstrate interaction active site Enzymes Enzyme Substrate Binding The interaction noncovalent interactions is highly specific substrate interacts with side chain groups and backbone groups of active site amino acids active site w Enzymes Enzyme Substrate Binding Two models for enzyme substrate binding 1 lockandkey 2 inducedfit LockandKey Model Lock md key 100161 Substrate binds active site that has a shape complementary to itself Does not take into account conformational change in enzyme after substrate binding mmmmmmmmmmmmmmm a Enzymes Enzyme Substrate Binding Two models for enzyme substrate binding 1 lockan dkey 2 inducedfit InducedFit Model Favored over lockandkey model Enzymes Enzyme Substrate Binding Induced fit model Takes into account conformational change once substrate binds Active site binding site has different 3D shape before substrate binding Binding of substrate induces change in binding site shape allowing for full binding of substrate Enzymes Enzyme Substrate Binding Comparing the models E enzyme ES enzymesubstrate complex E P Pproduct a luckrandrkey moch Ifthe ES complex IS a perfect t as In lockandkey model the AG 1E would be too large to overcome By not having a perfect t of E8 complex 1mcednmael the AG i is kept low and rxn can proceed Free energy gt ems Elnaulcalu annmsan Enzymes Enzyme Substrate Binding Activation energy profile of lockandkey type of interaction Progress of reaction gt ES ESE Xr EP ES complex will have lower free energy state compared to E S This will give too great a difference ES and EX state to overcome In the inducedfit model the free energy state of E8 complex is not so low Thus difference between ES and EX is not so large to overcome Enzymes Product Formation Once substrate is bound transition state formed substrate is arranged in correct orientation with respect to enzyme atoms allows for bonds to be broken and new ones formed and product to be formed product is released Product mm Ewahlcal 7mmquot Their work dealt with the kinetics of enzymesubstrate interaction Enzymes MichaelisMenten Enzyme Kinetics Leonor Michaelis German biochemist worked at many universities Berlin University of Nagoya Johns Hopkins University Rockefeller Institute of Medical Research did ground breaking work on enzyme kinetics at Berlin University in 1913 with Maud Menten Canadian biochemist at time women could not get PhD in Canada completed medical doctorate at University of Chicago moved to Berlin University in 1912 to work with Michaelis obtained PhD in 1916 Leonor Michaelis R 1875 1949 Enzymes MichaelisMenten Enzyme Kinetics How to measure rates of reactions carried out by enzymes in a test tube mix enzyme rate of rxn increases as 8 increases substrate in a buffer at proper pH as 8 reaches higher levels rxn rate changes less until maximum rate is reached allow rxn to take place take samples at time points measure amount of product formed units Ptime mMsec velocity V repeat rxn using different 8 graph results Reaction velocity lquot S Enzymes Michaelis Menten Enzyme Kinetics What information can we obtain from a plot of V vs 8 At 12 of Vmax the S is equal to V rxn velocity mMsec v0 velocity at time zero Km an Inverse measure of the affinity Vmax maximum velocity of an enzyme for its substrate at infinite 8 lower the Km higher the affinity Km the S at which 50 of the enzyme is occupied by substrate Reaction velocity V 1 mos aaaaaaaaaaaaa an Enzymes Michaelis Menten Enzyme Kinetics Problem how to determine Km when Vmax is theoretically unattainable Vmax is asymptotic never really reaches maximum reaches at infinity 8 V E 7 Reaction velocity V gt Substrate concentration S gt 27 mos Ernakslcule Tmman Enzymes LineweaverBurk double reciprocal plot Hans Lineweaver American biochemist worked as a graduate student under Burk at Department of Agriculture laboratory in Washington DC Dean BurkAmerican biochemist entered UC Davis at age 15 in 1934 published paper with Lineweaver describing how to determine Km and Vmax is most frequently cited paper in biochemistry Enzymes Lineweaver Burk double reciprocal pot If 1N and 1S reciprocal are plotted a straight line is obtained compared to hyperbolic curve of MichaelisMenten data Can determine Km and Vmax from this plot innx lt Reaction Cim ily 39 gt x intercept Substrate concentration S gt Velocity mMsec Enzymes Lineweaver Burk double reciprocal plot 8 Velocity i 1 mM mMsec g1 Velocity 25 0024 0400 41667 50 0036 0200 27778 100 0053 0100 18868 150 0060 0067 16667 200 0064 0050 15625 Y Intercept 1 Vmax Michaelis Menton plot 118 1 007 45 W 005 4039 vmax 1118 um i 539 WWODM7kam V 3039 003 W X intercept i 002 1539 Km 139 o15 i 0 5 I10 15 I20 5 o392of3915oT1oos 3 055 01 o3915 o392 o3925 o393 o3935 o394 045 Km ll Km 1 015 Km 667 mM Enzymes Practical example of Km Blood Sugar Levels and Glycolysis Hexokinase an enzyme found in most tissues of the body converts glucose to glucoes6phosphate G6P production of G6P is first step in glycolysis break down of glucose for energy Glucokinase a variant of hexokinase found in liver G6P in liver is converted to glycogen a polymer of glucose that can be broken down in times of low blood glucose levels Hexokinase Km for glucose 015 mM Blood glucose 5mM liver glucokinase Km for glucose 10 mM Blood glucose after meal 10 mM High blood glucose Low blood lucose BIOOd 939U9039N after meal liver Glucokinase liver glucokinase not active maCtlve glucokinase active G6P produced glucose not stored as glycogen glucose stored as glycogen Blood glucose muscle Glucokinase muscle hexokinase active hexokinase active G6P produced for glycolysis aCtlve G6P produced for glycolysis Enzymes Enzyme Inhibitors Enzyme inhibitors a substance that interferes with the activity of an enzyme and slows the reaction Two types of inhibitors 1 reversible can bind to enzyme inhibit reaction and be released Enzyme left in original condition 2 Irreversible binds to enzyme making it inactive and is not released Enzyme will not return to original condition Enzymes Reversible Enzyme Inhibitors Two types of reversible inhibitors Competitive inhibitors inhibitor compound is structurally similar to substrate binds to active site and prevents substrate from binding competes for active site with substrate substrate or inhibitor can bind enzyme not both at same time Noncompetitive inhibitors inhibitor binds to enzyme at site other than active site inhibitor binding causes conformational change in enzyme structure substrate can still bind but enzyme inactive due to structure change both substrate an inhibitor bind at same time Enzymes Kinetics of Competitive Inhibitors Affects on enzyme kinetics based on Lineweaver Burk plot More substrate is needed to changes the slope of plot subsequently 39ty Because competitive inhibitor 39 Changes Km X39mtercept can be overcome with suf ciently high amounts of substrate does not change Vmax yintercept reach same vs at JI 77 7 Nu inhihiim H t 1 V i I 1 A W K I 1 010501 02 2o 10 5 is V V mMsec Enzymes Kinetics of Competitive Inhibitors MichaelisMenten Kinetics 2X inhibitor inhibitor I o no inhibitor All will eventually reach same Vmax 04 max 03539 7f In presence of inhibitor higher amount of S is required to reach V without Inhibitor I I I I I I I u 2 u u 4 u u s u u a u u 1 2 u 1 4 u 1 an Enzymes Kinetics of Noncompetitive Inhibitors Affects on enzyme kinetics based on Lineweaver Burk plot like competitive inhibitor changes the Substrate can 5N bindmnym slope of plot but n 39nhibitor does notinterfere with substrate binding N lt 3 m unlike competitive inhibitor does not Because noncompetitive inhibitor change Km Xintercept and substrate are not com etin for active site increasing substrate unlike competitive inhibitor does can notovercomeinhibim change Vmax yintercept decreases Enzymes Inhibitor Example Sucrose is broken down into its components glucose and fructose by the enzyme invertase Based on the data below determine if the inhibitor urea is competitive or noncompetitive reciprocals sucrose M V no inhib V inhib sucrose M V no inhib V inhib 00292 0182 0083 3424 549 1205 00584 0265 0119 1712 377 840 00876 0311 0154 114 321 649 0117 0330 0167 854 303 599 0175 0372 0192 571 h 2 69 5 21 04 l inhibitor 035 O no inhibitor g 025 E 02 gt my quotTL2oo05mM


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