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Assumingthat the normal Srcis all bound to the plasmamembrane and that the mutant Src is distributed throughout the cy.toplasm,calculatetheir relativeconcentrationsinthe neighborhood of the plasma membrane. For the purposes of this calculation, assume that the cell is a spherewith a radius of l0 pm and that the mutant Srcis distributedthroughout, whereasthe normal Src is confined to a 4-nmthick layer immediately beneath the membrane. [For thisproblem, assumethat the membrane has no thickness.Thevolume of a sphereis (4/3)rr3.lB.
The target (X) for phosphorylationby Srcresidesin themembrane.Explainwhy the mutant Src does not causecellproliferation.3-13 An antibody binds to anotherprotein with an equilibrium constant,K of 5 x lOeM-1.\A/henit binds to a second,relatedprotein, it forms three fewer hydrogenbonds,reducing its binding affinity by 2.8 kcal/mole.\Mhatis the Kfor itsbinding to the secondprotein?(Free-energychangeis relatedto the equilibrium constantby the equationAG" = -2.3 RTlogK whereR is t.9Bx 10-3kcal/(moleK) and Tis 310K.)3-i 4 The protein SmpBbinds to a specialspeciesof tRNA,tmRNA, to eliminate the incomplete proteins made fromtruncated mRNAs in bacteria. If the binding of SmpB totmRNA is plotted as fraction tmRNA bound versus SmpBconcentration,one obtainsa symmetricalS-shapedcurve asshor.rnin Figure Q3-3.
This curve is a visual displayof a veryuseful relationship between tr:i and concentration, whichhas broad applicability.The generalexpressionfor fractionof ligand bound is derived from the equation for K6 (trfr=lPrllll/ [Pr-L])by substituting([L]ror.- tL])for [pr-L] and rearranging.Becausethe total concentrationofligand ([L]ror)is equal to the free ligand (tll) plus bound ligand ([pr-L]),ltmRNAlror = [SmpB]/([SmpB]+ rQ).
Using this relationship, calculatethe fraction of tmRNA bound for SmpB concentrationsequal to 104Kd,103Kd,l02Kd,lOltra, Kd, lO-tIA,l0-2Kd,10-3^?,and 10rK4.10E 075!cloc05Ea-02501 01 110-e1 0s10-7(M)centrationof SmpBFigureQ3-3Fractionof tmRNAboundversusSmpBconcentration( P r o b l e3m- 1 4 ) .3*15 Many enzymes obey simple Michaelis-Mentenkinetics,which are summarizedby the equationrate = vmax[s]/([S] + K_)where V-* = maximum velociry [S]= concentrationof substrate,and Km= the Michaelisconstant.It is instructiveto plug a fewvaluesof [S]into the equationto seehow rate is affected.What are the ratesfor [S]equal tozero,equal to K-, and equal to infinite concentration?3-16 The enzyme hexokinaseadds a phosphateto D-glucose but ignores its mirror image, L-glucose.Supposethatyou were able to synthesizehexokinase entirely from Damino acids,which are the mirror image of the normal Lamino acids.A. Assuming that the 'D' enz).rnewould fold to a stableconformation,what relationshipwould you expectit to bearto the normal'l enzyme?B.
Do you supposethe'D' en4/rnewould add a phosphateto L-glucose,and ignore D-glucose?3-17 How do you supposethat a molecule of hemoglobinis ableto bind oxygenefficientlyin the lungs,and yet releaseit efficientlyin the tissues?3-18 Synthesisof the purine nucleotidesAMP and GMPproceeds by a branched pathway starting with ribose 5phosphate (R5P),as shown schematicallyin Figure Q3-4.Using the principles of feedbackinhibition, proposea regulatory strategyfor this pathway that ensuresan adequatesupply of both AMP and GMP and minimizes the buildup ofthe intermediates(,4-1)when suppliesof AMP and GMP areadequate.F +G+AMPH+/ +GMP,/R5P+A+8+C+D+E\fraction bound = tll/ [L]ror = tprl/ (tprl + Ka)For SmpB and tmRNA, the fraction bound = [tmRNAl/FigureQ3-4 Schematicdiagramof the metabolicpathwayforsynthesisof AMPand GMPfrom R5P(Problem3*18).REFERENCESREFERENCESGeneralTymoczkoBerg-1M,lL & StryerL (2006)Biochemistry,6rh ed NewYork:WH FreemanBrandenC &ToozeJ (1999)Introductionio ProteinStructure,2ndedNewYork:GarlandScienceDickerson,RE(2005)Presentat the FloodHowStructuralMo ecuarBiologyCameAbout Sunderland,MA:SlnauerKyteJ (2006)Structurein ProteinChemistryNewYork:RoutledgePetskoGA& RingeD (2004)ProteinStructureand FunctionLondon:NewSciencePressDroteinStrdclu.e:Pe'uLzM r 199..r)NewApp.oachesto DiseaseandTherapyNewYork:WH FreemanThe Shapeand Structureof ProteinsAnfinsenCB(1973)Principlesthat governthe foldingof proteinchainsScience181.2)3-230peptidesandcytoplasmicBrayD (2005)FlexibleBiolAelsGenome6:106-I 09P,StetefeBurkhardd J & StrelkovSV(2001)Coiledcoils:a highlyversatile protern fold ing r.laltf.
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