实验十五知识资料computer知识资料using

千里之行，始于足下朽木易折，金石可镂Word-可编辑实验十五UsingthecomputerinbiochemicalresearchⅠ.IntroductionandtheoryThemoderncomputerhasrevolutionizedthewaywelive.Notsurprisingly,thecomputerhasalsochangedthewaywedobiochemicalresearch.Yourfirstencounterwithacomputerinthislaboratorywillprobablybewhileusinganinstrumentthathasacomputertocontrolitsoperation,tocollectdata,andtoanalyzedata.AllmajorpiecesofscientificequipmentincludingUV-VISspectrometers,high-performanceliquidchromatographs,gaschromatographs,nuclearmagneticresonancespectrometers,andDNAsequencersarenowcontrolledbycomputers.Butyouruseofthecomputerwillnotendinthelab.Youwilluseacomputertoprepareeachlaboratoryreportincludinggraphicalanalysisofexperimentaldata.IfthecomputerisconnectedtotheInternet,youwillgreatlybroadenitsusetosomeofthefollowing:(1)searchingthebiochemicalliteratureforpertinentbooksandjournalarticlesand(2)accessingbiologicaldatabasesthatprovidenucleicacidandproteinsequencesandproteinstructures.PersonalcomputinginbiochemistryItisnowpossibleformoststudentstopurchaseabasiccomputersystematlowcost.Somerecommendationsforspecifichardwareandsoftwarewillbegivenhere,butonemustbeawarethatnewproductsandimportantupgradesarecontinuallybeingdeveloped.Forwordprocessing(writinglabreports),basicsoftwareprogramsincludingMicrosoftWordandWordPerfectaremostwidelyused.Softwarespecializedforscientificwritingisavailablebutprobablynotnecessaryatthislevel.Formanyexperimentsthatyoucomplete,youwillneedtopresentdatainaspreadsheetorgraphingorspreadsheetwithgraphingcapabilityincludeLotus,Excel,Sigmaplot,Quattropro,Kaleidagraph,andCricketCraph.Somegraphsthatyoupreparefromexperimentaldatawillbenonlinear.ThemostcommonexampleisaMichaelis-Mentengraphfromenzymekineticsstudies(substrateconcentrationvs.reactionrate).Sincemostcomputersandprogramshavedifferentmethodsfordealingwithnonlinearity,itisprobablybestnottoconnectthedatapointswithaline.Rather,useacurve-fittingroutinetogettheappropriateline.Alternatively,onecouldanalyzethedatausingastraight-linemethodsuchastheLineweaver-Burkplot.ThecomputerandtheinternetIfyouareusingthecomputerasdescribedabove,youaresavingtimeandpreparinggood-lookinglabreports.However,ifyourcomputerisnotconnectedtotheInternet,thenyouarenottappingintothevastwealthofbiochemicaltoolsandinformationavailable.TheInternetcanbedefined,insimpleterms,asaworldwidematrixthatallowsallcomputersandnetworkstocommunicatewitheachother.Ifthecomputeryouareusingiscollegeowned,thenitisprobablyalreadylinkedtotheInternet.Foryourownhomecomputer,youmayneedtosubscribetoanInternetserviceandobtainamodemtotransmitcomputersignalsthroughatelephoneline.OnceyouareconnectedtotheInternet,manyprogramsareavailableasfreeware,softwareprovidedwithoutchargebyitscreator.AfteryouareconnectedtotheInternet,whatarethebasicfacilitiesavailableforuse?First,youwillbeabletocommunicatebye-mail(electronicmail).Messagescontainingtext,files,andgraphicsmaybesenttoanyonewhohasacomputerwithanInternetlinkandane-mailaddress.Addresseshavethreebasiccomponents,theusername,an@sign,andtheuser’slocationordomain.Commondomainsthatyouwillencounterusuallyhaveoneofthefollowingsuffixes:edu(educationalinstitutionintheUnitedStates),ac(academicinstitutionintheUnitedKingdom),gov(government),com(commercialorganization),andorg(otherorganization).Youwillneedane-mailprogramtocollect,send,andorganizemessages.ThemostpopularonesareEudoraandPegasus.(Practiceyoure-mailskillsbysendingamessage,perhapsaquestion,toyourlaboratoryinstructor).ConnectedtotheInternet,youwillalsobeabletojoininlistserverdiscussiongroupscreatedtoshareideasinacommonareaofinterestorinnewsgroupssuchasUSENET.OneofthemostwidelyusedfacilitiesontheInternetistheabilitytoplaceandretrievenetworkdatabyfiletransferprotocol(ftp).TheWorldWideWebThenewestandmostrapidlygrowingcomponentoftheInternetistheWorldWideWeb(WWW,alsocalled“theweb”).Thisfacility,whichwaslaunchedin1992,permitsthetransferofdataaspagesinmultimediaformconsistingoftext,graphs,audio,andvideo.Thepagesarelinkedtogetherbyhypertextpointerssothatdatastoredoncomputersindifferentlocationsmayberetrievedviathenetworkbyyourcomputer.WebdocumentsarewritteninaspecialcodedlanguagecalledHyperTextMarkupLanguage(HTML).ToaccessalloftheresourcesontheWeb,youwillneedabrowser,aninterfaceprogramthatreadshypertextanddisplaysWebpagesonyourcomputer.ThemostcommonlyusedWebbrowsersareInternetExplorerandNetscapeNavigator.ToaccesstheWeb,theWebbrowserisactivated.DisplayedonthescreenwillbethehomepageorstartingpointforentryintotheWeb.Onthispagewillbeadialogueboxintowhichyoucantypetext.Thedialogueboxmayaskfor“Address”,“Netsite”,“Location”,or“URL”(UniformResourceLocator).TorequestaspecificWebpagefromanothercomputersite,typeintheWebpageaddress,whichisusuallyintheformhttp://www.-.Thehomepage,withinstructionsontheuseoftheWebsite,willthenbedisplayedonthescreen.Oneimportantfeatureyouwillnoteisthatsomewordsonthepagearehighlighted.Ifyouclickthemouseononeofthesewords(calledhyperlinks)yourcomputerwillconnecttoanother,related,Webpagethatprovidesinformationonthehyperlink.ThisfeaturegreatlyenhancestheuseoftheWebbecauserelatedWebsitesareconnectedorlinkedtogetherandmaybequicklyaccessedbyaclickofthemouse.WebaddressesthatusefulforbiochemicalresearcharepresentedinTablesE1.1andE1.2.ManyofthecurrentWebsitesyouwillneedarelistedhere;however,whataboutnewWebsitesthathavebeenestablishedsincepublicationofthisbook?MillionsofnewWebsitesarecreatedeveryyear.Toaccessthesenewsites,youneedthehelpofasearchengine,asearchabledirectorythatorganizesWebpagesbysubjectclassification.MajorsearchenginesincludeAltaVista,Excite,HotBot,Lycos,NetscapeSearch,andYahoo!Asyou“surftheWeb”,youmayfindsitesyouwishtosaveandreviewatalaterdate.Youmayusethe“bookmark”(Netscape)or“favorite”(Explorer)functiontosaveitforthefuture.ApplicationoftheWebItisnotnecessarytohaveacompleteunderstandingoftheInternetinordertotapintoitsvastresources.Thefundamentalconceptsprovidedherewillallowyoutotakeadvantageoftwoessentialactivities:(1)biochemicalliteraturesearchingand(2)usingWebdirectoriesandbiologicaldatabases.ThebiochemicalliteratureExperimentalbiochemistsdonotspendalltheirworkingtimeinthelaboratory.Animportantcomponentofabiochemistryresearchprojectisasearchofthebiochemicalliterature.Thelibraryshouldbeconsideredatoolforexperimentalbiochemistryinthesamewayasanyscientificinstrument.TableE1.1WebDatabaseDirectoriesNameURLPedro’sBiomolecularResearchTools/~pedro/research-tools.htmlBiologyWorkbenchCMSMolecularBiologyResources/ResTools/cmshp.htmlBioTechProtocolOnlineChemConnection/news/journals.htmlAmericanChemicalSociety/TableE1.2BiochemicalDatabasesandToolsNameDescriptionURLProteinDataBank(PDB)ProteinstructuresdeterminedbyX-rayandNMR/pdb/EuropeanBioinformaticsInstitute(EBI)DNAsequenceshttp://www.ebi.ac.uk/NationalCenterforBiotechnologyInformation(NCBI)Varietyofdatabasesandresources/Swiss-ProteinProteinsequencesandanalysishttp://www.expasy.ch/tools/Biocatalysis/BiodegradationDatabasesoftheUniversityofMinnesotaMicrobialmetabolismofmanychemicals/umbbd/index.htmlREBASE-TheRestrictionEnzymeDatabaseRestrictionenzymedirectoryandaction/GeorgiaInstituteofTechnologyTutorialsonPDBandRasMol/faculty/Williams/bCourse-information/4582/labs/rasmol-pdb.htmlTheInstituteforGenomicResearchCollectionofgenomicdatabases/RasMol(RasMac)Moleculargraphicsforproteins/microbio/rasmol/PredictProteinProteinsequenceandstructurepredictionhttp://www.embl-heidelberg.de/predictprotein/GeneQuizProteinfunctionanalysisbasedonsequencehttp://www.sander.ebi.dc.uk/gqsrv/submitTheuseofthebiochemicalliteraturebythestudentinbiochemistrylaboratoryisnotasextensiveasthatofafull-timeresearcher,butyoumustbeawareofwhatisavailableinthelibraryandhowtouseit.Thelibraryisusedinallstagesofresearch.Beforeaninvestigatorcanbeginexperimentation,aresearchideamustbegenerated.Thisideadevelopsonlyafterextensivereadingandstudyoftheliterature.Aresearchprojectusuallybeginsintheformofaquestiontobeansweredorproblemtobesolved.Foreaseofsolution,amajorprojectissubdividedintoquestionsthatmaybeansweredbyexperimentation.Beforelaboratoryworkcanbegin,theresearchermusthaveaknowledgeofthepastandcurrentliteraturedealingwiththeresearcharea.Thiscanbereducedtotwoquestions:Whatisthecurrentstateofknowledgeinthearea?Andwhatarethesignificantunknowns?Thesequestionscanbeansweredonlybydevelopingafamiliaritywiththebiochemicalliterature.Theresearcherwillfindthatthisknowledgeoftheliteratureisalsoinvaluableforthedesignofexperiments.Thedevelopmentofexperimentsrequiresknowledgeoftechniquesandlaboratoryprocedures.Excellentmethodsbooksandjournalsareavailablethatprovideexperimentaldetails.Finally,whileperformingexperiments,theresearcheroftenneedsphysicalandchemicalconstantsandmiscellaneousinformation.Varioushandbooksandencyclopediasareexcellentforthispurpose.Thebeginningstudentinbiochemistrylaboratorywillnotbeexpectedtoproceedthroughallofthesestagesinthedesignofanexperiment.However,afamiliaritywiththeliteraturewillincreaseyourunderstandingoftheexperimentandmayaidinthedevelopmentofmoreeffectivemethods.Whenyoudobeginaresearchprogram,youwillbeabletousethelibrarytothefullestadvantage.Thebiochemicalliteratureismassiveandexpandingrapidly.Itisalmostafull-timejobjusttomaintainacurrentawarenessofaspecializedresearcharea.Therearefewdisciplinaryboundariesinthestudyofbiochemistry.Thebiochemicalliteratureoverlapsintothebiologicalsciences,thephysicalsciences,andthebasicmedicalsciencesTheintentofthefollowingdiscussionistobringsomeordertothemanytextbooks,referencebooks,researchjournals,computerinformationretrievalservices,andhandbooksthatareavailable.ReferencebooksandreviewpublicationsFormorespecializedanddetailedbiochemicalinformationthatisnotofferedbytextbooksmustbeused.Referenceworksrangefromgeneralsurveystospecializedseries.Thebestworksaremultivolumesetsthatcontinuepublicationofvolumesonaperiodicbasis.Eachvolumeusuallycoversaspecializedareawitharticleswrittenbyrecognizedauthoritiesinthefield.Itshouldbenotedthatreferencearticlesofinteresttobiochemistsareoftenfoundinpublicationsthatarenotstrictlybiochemical.ThebestknownandmostwidelyusedreviewpublicationisAnnualReviewofBiochemistry.Eachvolumeinthisseries,whichwasintroducedin1932,containsseveraldetailedandextensivearticleswrittenbyexpertsinthefield.Forshorterreviewsemphasizingcurrenttopics,TrendsintheBiochemicalSciences(TIBS)iswidelyread.ResearchJournalsThecoreofthebiochemicalliteratureconsistsofresearchjournals.Itisessentialforapracticingbiochemisttomaintainaknowledgeofbiochemicaladvancesinhisorherfieldofresearchandrelatedareas.Scoresofresearchjournalsarepublishedwiththeintentofkeepingscientistsuptodate.Withtheexpansionofscientificinformationhascometheneedforefficientstorageanduseofresearchjournals.Manypublishersarenowprovidingjournalsinformssuchasmicrocards,microfilm,microfiche,andmorerecentlyCD-ROMdisksandonline.Someresearchjournalshaveachievedanespeciallyexcellentreputation,andarticlesthereinareconsideredtobeofthehighestquality.Arecentrankingofthebiochemicaljournals,basedonthenumberofcitationsreceived,producedthefollowingorderforthetopsix:JournalofBiologicalChemistry,BiochimicaetBiophysicaActa,Biochemistry,ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesofAmerica,BiochemicalJournal,andBiochemicalandBiophysicalResearchCommunications.Thecorejournalsusedbyanindividualdependontheareaofspecialtyandarebestdeterminedfromexperience.MethodologyReferencesTheactiveresearcherhasacontinuingneedfornewmethodsandtechniques.Severalpublicationsspecializeinprovidingdetailsofresearchmethods,andmanyresearchmethodsarenowavailableontheWeb.Someoftheusefulbiochemicalmethodologypublicationsare: AnalyticalBiochemistry,amonthlyjournal. AnalyticalChemistry,amonthlyjournal. BiochemicalPreparations,anannualvolume.CurrentProtocolsinMolecularBiology,P.Ausabeletal.,Editors.Amanualoftechniquesintwovolumesthatareupdatedquarterly. LaboratoryTechniquesinBiochemistryandMolecularBiology,T.S.WorkandR.G.Burdon,Editors(formerlyT.S.WorkandE.Work).Eachvolumeintheseriesisconcentratedinanareaofbiochemistryandwrittenbyrecognizedauthorities. MethodsofEnzymaticAnalysis,H.Bergmeyer,Editor.Containsmethodsforenzymepurificationandassay,inseveralvolumes.MethodsinEnzymology,variouseditors.Themostvaluablemethodsseriesavailable.Eachvolumecontainsnumerousarticlesdescribingbiochemicaltechniques.Theseriesiswellindexedandeasytouse.Over200volumes.APracticalGuidetoMolecularCloning,2nded.,B.Perbal.Usefulforsettingupresearchprojectsinmolecularcloning.Computer-basedsearchesandotheraidstotheliteratureAsyoustudyandworkinthebiochemistry,youwilloftenneedtocompleteathoroughliteraturesearchonsomespecializedareaortopic.Itisnotpracticaltosurveythehundredsofbooks,journals,andreportsthatmaycontaininformationrelatedtothetopic.Twopublicationsthatprovidebriefsummariesofpublishedarticles,reviews,andpatentsareChemicalAbstractsandBiologicalAbstracts.Researcharticlesofinteresttobiochemistsmayappearinmanytypesofresearchjournals.Researchlibrariesdonothavethefundsnecessarytosubscribetoeveryjournal,nordoscientistshavethetimetosurveyeverycurrentjournalcopyforarticlesofinterest.TwopublicationsthathelpscientiststokeepupwithpublishedarticlesareChemicalTitles(publishedevery2weeksbytheAmericanChemicalSociety)andtheweeklyCurrentContentsavailableinhardcopyandcomputerdisks(publishedbytheInstituteofScienceInformation).TheLifeScienceeditionofCurrentContentsisthemostusefulforbiochemists.Thecomputerrevolutionhasreachedintothechemicalandbiochemicalliterature,andmostcollegeanduniversitylibrariesnowsubscribetocomputerbibliographicsearchservices.OnesuchserviceisSTNInternational,thescientificandtechnicalinformationnetwork.Thison-linesystemallowsdirectaccesstosomeoftheworld’slargestscientificdatabases.TheSTNdatabasesofmostvaluetolifescientistsincludeBIOSISPreviews/RN(producedbyBioSciencesInformationService;coversoriginalresearchreports,reviews,andU.S.patentsinbiologyandbiomedicine),CA(producedbyChemicalAbstractsservice,coversresearchreportsinallareasofchemistry),MEDLINE,andMEDLARS(producedbytheU.S.NationalLibraryofMedicineandIndexMedicus,respectively;coverallareasofbiomedicine).Thesenetworksprovideon-lineserviceandtheirdatabasescanbeaccessedfrompersonalcomputersintheoffice,laboratory,orlibrary.SomeofthecomputerbibliographyservicesarefreewareontheInternet,butothershaveuserfees.Forexample,MEDLINE(PubMed)producedbytheNationalLibraryofMedicine,availableat/,maybeusedfreeofcharge.Webdirectories,tools,anddatabasesBiochemicalresearchgenerateshugeamountsofdataofinteresttoallscientists.Forexample,thousandsofgenesandproteinshavebeensequencedduringthepastseveralyearsandthousandsmorewillbesequencedinthefuture.ThisnumberisbeinggreatlyexpandedbytheHumanGenomeProject,whichhasasitsgoalthesequencingoftheentirehumangenome.Inaddition,determiningthestructuresofproteinsbyX-raydiffractionandbyNMRhasbecomeroutine.Sequenceandstructuraldataarenowbeingstoredincomputernetworksforretrievalbybiochemiststhroughouttheworld.Here,wewilldiscussthemanybiologicaldatabasesandprovideexamplesoftheiruse.Ourapproachwillbetofocusontheuseofdatabasesreadilyavailable,freeofcharge,ontheWeb.However,itisimportanttorecognizethatmanycommercialhardwareandsoftwaresystemsforanalyzingbiologicaldatabaseareavailable,buttheyoftenveryexpensiveandcomplicatedtouse.Awidevarietyofdatabasesarecurrentlyavailableincludingbibliographic,nucleicacidsequence,proteinsequenceandstructure,metabolicpathways,transcriptionfactors,enzymes,andmanyothers.Oneofthebestwaystofindtheresourcessuitedtoyourneedsistouseadirectorythatcollectslistsofinformation,tools,andotherservices.Severalverygoodonesareavailable(TableE1.1).Someofthesesitesarehyperlinkedtothedatabasesites.Thisexperimentwillintroduceyoutosomeofthemoregeneralandusefulsites.Specifically,theywillincludeproteinprimary,secondary,andtertiarystructure,sequencehomology,sequencealignment,andstructureprediction.TheWebaddressesfortheseresourcesarelistedinTableE1.2.Becauseofthehugeamountofdataavailable,itisoftennecessarytouseprogramstohelpyouanalyzethedata.TableE1.3listsseveralsoftwareprogramsthatareavailableandusuallyhyperlinkedtothedatabasesites.ThosethatwewillintroduceinthisexperimentareFASTA(proteinaminoacidsequences),BLAST(comparingproteinsequencedata),RasMolorRasMac(coordinatesforproteinstructuremanipulation),Chime(proteinstructurecoordinates),SWISS-MODEL(proteinmodeling),VAST(proteinstructuresimilarities),andMoleculesRUs(proteinstructurecoordinates).OverviewoftheexperimentInthisexperiment,studentswillbeintroducedtoseveralusesofthecomputerandtheInternet.Studentsareinstructedintheuseofbibliographicsearches,sequencedatabases,andstructuralanalyticaltoolsavailable,freeofcharge,ontheWeb.TableE1.3Usefulprogramsforexploringstructures/sequencesProgramFunctionBLASTSearchesforsimilarproteinandnucleicacidsequencesChimeProteinstructuresonmoving3DcoordinatesEntrez(NCBI)Sequenceretrievalsystemforcross-referencingdatabasesFASTASearchesforsimilarproteinsequencesGenBank(NCBI)DatabasesofgenesequencesMoleculesRUsProvidescoordinatesforprotein3DstructureandmanipulationRasMol(RasMac)Providescoordinatesforprotein3DstructureandmanipulationSRS(EMBL)Sequenceretrievalsystemforcross-referencingdatabasesⅡ.MaterialsandsuppliesComputer:AppleMacintoshorPCwithprinter;connectedtotheInternet.Software:WebbrowsersuchasNetscapeNavigatororInternetExplorer;e-mailprogramsuchasEudora.Ⅲ.Experimentalprocedure1.SearchingthebiochemicalliteratureonMEDLINEToillustratetheuseofthissearchservice,pointyourWebbrowsertotheappropriateURL(/)ThiswillconnectyoutotheNationalCenterforBiotechnologyInformation.Clickthemouseonthehyperlink“PubMed”.SelectMEDLINEintheupperdialoguebox.Manyfeaturesondisplayareavailable,butthemostbasicisthesearchcapability.ForbibliographicsearchingyoumayenterinthedialogueboxunderMEDLINEasearchterm,authorname,orjournalname.Forexample,youmaywanttotypein“bovinealpha-lactalbumin”.Clickingon“Search”willthenprovideover500citations(orarticles).Thelistsarecomposedofauthor(s),title,andreferenceinreversechronologicalorder.Byclickingontheauthor’sname(inhypertext),youcanretrievetheabstractofthearticle.Anotherusefulandtime-savingfeatureisthehypertext“(seeRelatedArticles)”.Clickingonthiswillprovidealistofpapersrelatedtothespecificcitation.The500papersorsothatyouobtainedinyouroriginalsearcharetoomanytoscreen;youmaychangethesearchparameterstoreducethenumber.Clickingonthe“?”intheupperright-handcornerofthescreenprovideshelpforfocusingthesearchprocess.2.UsingWebtoolsandbiologicaldatabasesPointyourWebbrowsertotheProteinDataBank(PDB)andtheResearchCollaboratoryforStructuralBioinformatics(/pdb/).BecomeacquaintedwiththePDBbyviewingthehomepageandperhapsclickingonsomehyperlinks.Scrolluntilyoufindtheterm“Searchlite”underSearchontherightsideofthescreen.ClickingonSearchlitewilldisplayadialogueboxforkeywords.Typein“humanalpha-lactalbumin”andclickonSearch.Yourquerywillfindatleastsevenstructuresthatarelisted.Clickonthewhitesquaretotheleftand“EXPLORE”totherightofStructure1A4V.Thiswilldisplay“StructureExplorer”with“SummaryInformation”aboutthestructureoftheprotein.Clickingonthe“?”willprovidehelpifnecessary.Reviewthefunctionspossibleontheleftsideofthescreen.Clickon“ViewStructure”toobserve“Interactive3DDisplay”and“StillImages”.First,studythestillimagesofhumanalpha-lactalbumininribbonorcylinderform.Youmayclickon250x250or500x500toenlarge.Notethepresenceof-helicesand-sheetsinthestructure.Afterstudyingthestillimages,clickon“Chime”underInteractive3DDisplay.Now,youwillobservetheribbonstructurerotatingonanaxis.Use“ChimeHelp”atthebottomofthescreentolearnMouseControlsoftherotatingstructure.NowreturntotheSummaryInformationlisttotryotherfunctions.Clickon“SequenceDetails”toobservetheaminoacidsequenceanddefinitionofsecondarystructures.Youmaydoanftpdownloadofthisfilebyclickingon“DownloadinFASTAformat”.FASTAformatisalistingofaminoacidsequencesusingthestandardsingle-letterabbreviationforeachaminoacid.Clickingon“Geometry”willdisplaytablesofbondanglesandlengths.Similarsequencestudiesmaybedonebyclickingonthefunction“StructuralNeighbors”.Severaltoolsareavailabletosearchforsimilarstructures.TrytheVASTtool.Clickingon“VAST”willprovidetwooptions,SequenceNeighborsandStructureNeighbors.Clickingon“SequenceNeighbors:singlechain”willdisplayalistofmanyproteinswithsequencessimilartothatofhumanalpha-lactalbumin.Notethatmostarealpha-lactalbuminsfromotherspecies,butifyouscrollfarenough,youwillseetheenzymelysozymelisted.ReturningtotheformerscreenandclickingonStructureNeighborswilldisplayabouteightstructuressimilartohumanalpha-lactalbumin.Noteagainthepresenceoflysozymeinthelist.Clickingon“OtherSources”willdisplayotherdatafileswithreferencestoalpha-lactalbumin.Itisinterestingtonotethattheproteinsalpha-lactalbuminandlysozymehavesimilarprimary,secondary,andtertiarystructuresbuttheyhavequitedifferentbiochemicalactivities.Thetwoproteins,whichhaveabout40%sequenceidentity,mayhavebeenderivedfromacommonancestralgene.AnotherusefulstructuretoolisRasMol(orRasMac).Thiswillallowyoutoviewthedetailedstructureofaproteinandrotateitoncoordinatessoyoucanseeitfromallperspectives.AhyperlinktoRasMolispresentunderthe“ViewStructure”functionjustabove“Chime”.YoumayneedtostudyRasMolinstructionsprovidedunderHelp,oryoumayuseaRasMoltutoriallistedinTableE1.2.AnotherusefulproteinvieweristheSwiss-ProteinPdvViewer(TableE1.2).BLASTisanadvancedsequencesimilaritytoolavailableatNCBI.Toaccessthis,gototheNCBIhomepage()andclickon“BLAST”.Thenclickon“BasicBLASTsearch”toobtainadialogueboxintowhichyoumaytypetheaminoacidsequenceofhumanalpha-lactalbumin.ThisprocessmaybestreamlinedbydownloadingtheaminoacidsequenceinFASTAformatintoafileandtransferringthefileintotheBLASTdialoguebox.BLASTwillprovidealistofproteinswithsequencessimilartotheoneentered.Anotherapproachtoastudyofprotein(ornucleicacid)structureandsequencesisthroughEntrez.ThiscanbeenteredviatheNCBIhomepage.Thenclickon“Proteins”toobtainadialogueboxwhereyoucantype“humanalpha-lactalbumin”andthenclickonSearch.Youcanretrieveabout25documentsforreview.NotethatyoumayalsoenterBLASTthroughEntrez.OntheWebIntroductiontotheBiochemistryLaboratory/prism/Prism.htm Softwareforstatisticsandcurvefitting./ ClickonFreeWeb-basedsoftwarefordataanalysis./pipe.htm Informationonautomaticpipets,proceduresforuse,andhelpfulhints./bsm-spil.html BiologicalSafetyManual./chemistry/chemsafe.htm InformationonchemicalhygieneandsafetywithlinkstoMSDSsearches./msds.html LinkstoMSDSsearches. / ReviewoffunctionsandregulatoryproceduresbyOSHA./mort/manual/mechanics/Notebook.html. Howandwhytokeepanotebook.Proceduresforuseandhelpfulhints. AdvicefromtheHowardHughesMedicalInstitute.GeneralLaboratoryProcedures/fplc/fplcl.html ClickonBuffers.ReviewPreparationofBuffers,DefinitionsofpH,Henderson-HasselbalchEquationandBufferCalculator.Http:///applications/998-2600.htttm MeasurementofDNAsolutionusingbisbenzimidazoledye(Hoechst33258)..tr/taylan/protocols/spot~~00.txt EtBrspottestforDNAandRNAanalysis./homes/personal/davie/Protein.html “Bradfordplateassay”forprotein./bmb/instructions/farrell/bc352/spectro.htm ReviewprinciplesofspectrophotometryandtheBradfordproteinassay./~bioslabs/methods/protein/protein.html Reviewmethodsforproteinassayincludingabsorbanceandcolorimetric(Lowry,Biuret,Bradford,BCA).ChromatographyontheWeb/campbell/482w91a.htm Graphicalpres