Часть 1 (1120999), страница 61
Текст из файла (страница 61)
Given theenormous complexity of the interacting networks of macromolecules in cells(Figure 3-83), deciphering their full functional meaning may well keep scientists busy for centuries.Su m m a r yProteins canform enormouslysophisticatedchemical deuices,whosefunctions largelydepend on the detailed chemical properties of their surfaces.Binding sitesfor ligandsareformed as surfacecauitiesin which preciselypositioned amino acid side chains arebrought togetherby protein folding.
In this way, normally unreactiueamino acid sidechains can be actiuated to make and break coualentbonds.Enzymesare catalytic proteins that greatly speedup reaction rates by binding the high-energy transition statesfor a speciftcreaction path; they also perform acid catalysisand basecatalysissimultaneously.The ratesof enzymereactionsare often sofast thqt they are limited only bydiffusion; ratescan befurther increasedif enzymesthat act sequentiallyon a substrateare joined into a single multienzyme complex, or if the enzymesand their substratesare confined to the same compartment of the cell.Proteins reuersiblychange their shape when ligands bind to their surface.
Theallosteric changesin protein conformation produced by one ligand affect the bindingof a secondligand, and this linkage betweentwo ligand-binding sitesprouidesa crucial mechanism for regulating cell processes.Metabolic pathways, for example, arecontrolled by feedback regulation: some small moleculesinhibit and other smallmoleculesactiuate enzymesearly in a pathway. Enzymescontrolled in this way generally form symmetric assemblies,allowing cooperetiueconformational changesto reate a steepresponseto changesin the concentrationsof the ligands that regulatethem.The expenditure of chemical energy can driue unidirectional changesin proteinshape.By coupling allosteric shape changesto ATp hydrolysis,for example, proteinscan do useful work, such as generating a mechanical force or mouing for long distancesin a singledirection.The three-dimensionalstructuresof proteins,determinedby x-ray crystallography,haue reuealedhow a small local change causedby nucleoside triphosphate hydrolysis is amplified to create major changes elsewherein theprotein.
By such means,theseproteinscan serueas input-output deuicesthat transmit information, as assemblyfactors, as motors, or as membrane-boundpumps.Highly efficient protein machines areformed by incorporating many dffirent proteinmoleculesinto larger assembliesthat coordinate the allosteric mouementsof the inttiuidual components.such machinesere now known to perform many of the mostimportant reactionsin cells.Proteins are subjectedto mqny reuersiblepost-translational modifications, suchas the coualentaddition of a phosphateor an acetylgroup to a specificamino acid sidechain.
The addition of thesemodifying groups is usedto regulate the actiuity of a protein, changing its conformation, its binding to other proteins and its location insidethe cell.A ltpical protein in a celt will interact with more than fiue dffirent panners.using the new technologiesof proteomics,biologistscan analyze thousandsof proteinsin one set of experiments.One important result is the production of detailed proteininteraction maps, which aim at describingall of the binding interactions betweenthethousandsof distinct proteins in a cell....,'*t.{,?1191END-OF-CHAPTERPROBLEMSPROBLEMSFigureQ3-1 The kelchrepeatdomainofgalactoseoxidasefromD.dendroides(Problem3-9).The sevenindividualB propellersThe N- andareindicated.C-terminiareindicatedby N and C.6r*,f l ,Whichstatementsare true? Explainwhy or why not.3-1Each strand in a B sheet is a helix with two aminoacidsper turn.3-2Loops of polypeptide that protrude from the surfaceof a protein often form the binding sitesfor other molecules.3-3 An enzymereachesa maximum rate at high substrateconcentrationbecauseit has a fixed number of active siteswhere substratebinds.3-4Higher concentrationsof enzyrnegiverise to a higherturnover number.3*5 Enz)rynessuch as aspartatetranscarbamoylasethatundergo cooperative allosteric transitions invariably contain multiple identical subunits.3*6 Continual addition and removal of phosphates byprotein kinases and protein phosphatasesis wasteful ofenergy-since their combined action consumesATP-but itis a necessaryconsequenceof effectiveregulation by phosphorylation.Discussthe following problems.3-7Consider the following statement.
"To produce onemolecule of each possible kind of polypeptide chain, 300amino acidsin length, would require more atoms than existinthe universe." Given the size of the universe,do you supposethis statement could possibly be correct?Since countingatoms is a tricky business,consider the problem from thestandpoint of mass.The mass of the observableuniverseisestimated to be about l0B0grams, give or take an order ofmagnitude or so.Assumingthat the averagemassof an aminoacid is I l0 daltons,what would be the massof one moleculeof eachpossiblekind of pollpeptide chain 300 amino acidsinlength?Is this greaterthan the mass of the universe?3-8 A common strategyfor identifying distantly relatedproteins is to search the databaseusing a short signaturesequenceindicative of the particular protein function.
\A/hyis it better to searchwith a short sequencethan with a longsequence?Do you not have more chancesfor a'hit' in thedatabasewith a long sequence?3-9The so-calledkelch motif consistsof a four-strandedB sheet,which forms what is known as a B propeller. It isusually found to be repeatedfour to seventimes, forming akelch repeat domain in a multidomain protein. One suchkelch repeat domain is shor.tmin Figure Q3-1.
Would youclassifythis domain as an'in-line' or'plug-in type domain?3-10 Titin, which has a molecular weight of 3 x 106daltons, is the largest polypeptide yet described. Titinmoleculesextend from muscle thick filaments to the Z disc;they arethought to act as springsto keep the thick filamentscenteredin the sarcomere.Titin is composedof a largenumber of repeatedimmunoglobulin (Ig)sequencesof 89 aminoacids,each of which is folded into a domain about 4 nm inlength (Figure Q3-2A).You suspectthat the springlikebehavior of titin is causedby the sequentialunfolding (and refolding) of individual Igdomains.
You test this hlpothesis using the atomic forcemicroscope,which allowsyou to pick up one end of a protein molecule and pull with an accuratelymeasuredforce.For a fragment of titin containing seven repeats of the Igdomain, this experiment gives the sawtooth force-versusextension curve shourn in Figure Q3-28. \A4renthe experiment is repeatedin a solution of B M urea (a protein denaturant), the peaks disappear and the measured extensionbecomesmuch longer for a given force.If the experimentisrepeated after the protein has been cross-linkedby treatment with glutaraldehyde,once again the peaks disappearbut the extensionbecomesmuch smaller for a given force.A.
Are the data consistentwith your hlpothesis that titin'sspringlike behavior is due to the sequential unfolding ofindividual Ig domains?Explainyour reasoning.B. Is the extension for each putative domain-unfoldingevent the magnitude you would expect? (In an extendedpolypeptide chain, amino acids are spaced at intervals of0.34nm.)C. \Mhy is each successivepeak in Figure Q3-2B a littlehigher than the one before?D. \A/hydoesthe force collapseso abruptly after eachpeak?3*11 It is often said that protein complexesare made fromsubunits (that is, individually slnthesized proteins) ratherthan as one long protein becausethe former is more likelytogive a correctfinal structure.A. Assuming that the protein synthesismachinery incorDoratesone incorrect amino acid for each 10,000it inserts,(A)(B)4oo^zo;c300200,P loo0i .
rr t:,0I r i i . i r , r at t , r i rr:. . . : r , , ' l i . r i r i , r i , , ' ' : . ' .50.,:,150100(nm)extension200behaviorof titin (Problem3-10)'(A)TheFigureQ3-2 Springlikeversusstructureof an individuallg domain.(B)Forcein piconewtonsextensionin nanometersobtainedby atomicforce microscopy.192Chapter3: Proteinscalculatethe fraction of bacterial ribosomesthat would beassembledcorrectly if the proteins were synthesizedas onelarge protein versusbuilt from individual proteins?For thesake of calculation assumethat the ribosome is composedof 50 proteins, each 200 amino acids in length, and that thesubunits-correct and incorrect-are assembledwith eouallikelihood into the completeribosome.IThe probability thata polypeptidewill be made correctly,Pc, equalsthe fractioncorrect for each operation,/6, raisedto a power equal to thenumber of operations, n: P6 = lfd".
For an error rate of1 / 1 0 , 0 0 0f r, . = 0 . 9 9 9 9 . 1B. Is the assumption that correct and incorrect subunitsassembleequally well likely to be true? \A4ryor why not?How would a changein that assumption affect the calculation in part A?3-12 Roussarcomavirus (RSV)carriesan oncogenecalledSrq which encodes a continuously active protein tl,'rosinekinase that leadsto uncheckedcell proliferation. Normally,Src carries an attached fatty acid (myristoylate)group thatallowsit to bind to the cy'toplasmicside of the plasmamembrane. A mutant version of Src that does not allow attachment of myristoylatedoesnot bind to the membrane.Infection of cells with RSV encoding either the normal or themutant form of Src leads to the same high level of proteintyrosine kinase activity,but the mutant Src does not causecell proliferation.A.
![](https://s.studizba.com/z.php?f=/templates/si/i/noavatar.png&w=100&h=100&t=1"){kind=avatar}
