CELLBIOLOGY–BIOL3000–FALL2016(updated08/19/16)

CourseDescription“Inbiology,itisonestupefactionafteranother…Forawhilethingsseemedsimpleandclear;thecellwasaneatlittlemachine,amechanicaldevicereadyfortakingtopiecesandreassembling,likeatinywatch.Butjustinthelastfewyearsithasbecomealmostimponderablycomplex,filledwithstrangepartswhosefunctionsarebeyondtoday’simagining.”LewisThomas(1913-1993)Physician,cancerresearcherandself-describedBiologyWatcher.LateNightThoughtsonListeningtoMahler’sNinthSymphony,1983Howdidcellsoriginate?Howcansomeofourcellsremainimmortalwhenwe’renot?Whywouldacellcommitsuicide?Howdocellsknowwhentodivide?Whydocancercellscontinuouslyevolve?Whatisourcurrentunderstandingofthesefascinatingquestions(andmanymore!)andwhataretheexperimentalapproachesusedtoanswerthem?WelcometoCellBiology.CourseObjectivesTheoverallgoalofBIOL3000isforyoutolearntothinklikeanexperimentalcellbiologist.Bytheendofthiscourse,youwillbeableto:

1. Describeandexplainfundamentalcellularprocesses.2. Describeandexplainhowandwhycomplementarymolecular,biochemicalandgenetic

experimentalapproachesareusedtoanalyzediversecellularprocesses.3. Identifythefunctionsandrolesofspecificproteinsand/orsmallmoleculesinthecontext

ofindividualcellularprocessesandbeabletointegratethemintocomplexinterconnectedpathways.

4. Predictthespecificphysiologicalconsequencesofperturbingthefunctionsofindividualcomponentsincomplexmulti-steppathwaysorprocesses.

5. Interpretexperimentalresultsinordertoelucidateaspecificcellularprocess.6. Applyyourunderstandingofmultiplecellularprocessestoexplainvarioushuman

diseasesandthetherapeuticoptionsavailabletotreatthem.MeetingTimesandLocationClass:9:00–9:50AMMWFGilmer130DiscussionSessionsandExams1–3:Weds.,Sept.14,Oct.12,Nov.9,7–9PMGilmer130.Exam4,Sat.Dec.102–5PM,Gilmer130

InstructorInformationMikeWormington,AssociateProfessorofBiology.MyhometownisOverlandPark,Kansas,andIattendedtheUniversityofKansas(GoJayhawks!)whereIearnedmyBAwithHonorsinBiologyandmyPhDinBiochemistry.IwasanNIHPostdoctoralfellowattheCarnegieInstitutionforScience,Dept.ofEmbryology,inBaltimore,MD.IjoinedtheUVaBiologyfacultyin1989andhavetaughtCellBiologysince1992.Mylongstandingresearchinterestistheregulationofgeneexpressionduringoogenesisandembryogenesisandtheinterplaybetweengeneticandmetabolicreprogrammingincancerstemcells.MywifeSusan,istheArtDirectoratUVa’sDardenSchoolofBusiness.Ourtwodaughtersandsons-in-lawandourtwograndchildren(with#3arrivinginSeptember!)keepusbusy.WhatdoIdoforfun?I’maLieutenantColonelandsearchandrescuemissionpilotandthedirectorofoperationsfortheVirginiawingoftheCivilAirPatrolwhichisthecivilianauxiliaryoftheUSAirForce. Office:PLSB206 Phone:982-5803 email:ww2t@virginia.edu GroupOfficeHoursinPLSB200:2–4:30PMTues.andThurs.Individualmeetingsbyappointment. UPDATEDGraduateTeachingAssistantRichardSmindak Office:PLSB238 Phone:924-3943 email:rjs6dg@virginia.eduGroupOfficeHoursinPLSB230:2–3:30PMMon.andWeds.Individualmeetingsbyappointment.PrerequisitesBIOL2010or2100(orAP)orBME2014,andanytwoofCHEM1410,1420,1610,1620,1810,1820.Thepremiseforthiscourseisthatyouhavecompletedtheseprerequisitesandarefamiliarwiththeirconceptsandprinciples.ThefirstthreechaptersofMCB8EprovideanexcellentreviewofpertinenttopicscoveredinbothBIOL2010/2100andgeneralchemistry,andshouldbereferredtoasnecessarythroughouttheentirecourse.UPDATEDRequiredTextforFall2016TherequiredtextbookbeginningwithFall2016isMolecularCellBiol.,8thed.,Lodishetal.(MCB8E).Purchasetheleastexpensiveoptionavailabletoyou.Sincethisisanewedition,usedbookswillnotbeavailable.Istronglyrecommendyoudonotusethe7theditionofthetext.ManytopicsandpertinentfigureshavebeensignificantlyrevisedinMCB8EandmostreadingassignmentswillnotmatchthosepreviouslyusedforMCB7E.YouwillberesponsibleformaterialandconceptscoveredinassignedreadingsfromMCB8Ethatwillnotbediscussedinclass.BIOL3000CollabWebsiteTheBIOL3000CollabCoursesiteisanimportantresourcethatyouwilluse.TheResourcessectionwillcontainpptxfilesofslidestobepresentedinclass.Thesewillbeavailablefordownloadingatleasttwodaysbeforewecoverthematerialinclass.Note:TheinformationonsomeslidesIshowinclassmaydifferfromthosepostedoncollabsoplantotakenotes!SpecificreadingassignmentsfromMCB8Echapters,supplementaryreadingmaterialfromreviewarticlesandprimaryresearchpapers,andlearningobjectives(the“bigquestions”)foreachunitofthecoursewillalsobepostedwiththeslides.Youwillbenotifiedbyemailwhennewmaterialshavebeenposted.TheCollabsitealsocontainsthemoviefilesshowninclassandlinkstointerestingwebsites.

OnlineHomeworkAssignments“Doordonot.Thereisnotry.”Yoda

Thebestwaytolearncellbiologyistodoit.Unfortunately,wecannotprovideapracticallabexperiencewithBIOL3000thatallowsyoutoapplywhatwecoverinclass.Therefore,thenextbestoptionistogiveyouopportunitiestobebetterpreparedforclassandtoregularlyself-assessyourunderstandingofthetopicswe’recoveringbeforeyou’retestedonyourknowledgeoneachofthefourexams.Therearetwoincentivesforyoutotakeadvantageoftheonlinehomeworkexercises.First,theonlinehomeworkconstitutes15%ofyourfinalcoursegrade.Thatalonecanmakethedifferenceinalettergrade.Second,bydoingtheseexercises,youwillbeabletoassessyourunderstandingofthetopicspresentedinclassandadjustyourapproachestolearningthematerialinsuchawaythatyou’llperformbetterontheexamsandrememberthematerialafterthecourseisover.Eachonlinehomeworkassignmentwillconsistof5multiple-choicequestionsthatwillassessyourunderstandingofthetopicscoveredintheprecedingclass.Thehomeworkquestionsarelargelyderivedfrompreviousyears’exams,butofcoursenewquestionsareaddedeachsemester.Inthisway,everyonehasequalaccesstooldexamquestions.Occasionallytherewillbea“warmup”questionortwoaddressingatopictobecoveredinthenextclass.Forthespring2016semester,therewerea175homeworkquestions,including5bonuspoints,whichwasconvertedtoafinaltotalof75points.Thehomeworkassignmentsareopenbook,opennoteformat.Refertothepertinentmaterial,includingtheslides,inordertocompleteeachassignment.Thequestionswillvariouslycovermaterialpresentedinlectures,theMCB8Etext,andanyadditionalassignedreading.You’llautomaticallyreceiveanemailfromCollabwheneachhomeworkassignmenthasbeenposted.Eachhomeworkassignmentisdue8AMthefollowingclassday(e.g.,Mon.homeworkisdue8AMWeds.Weds.homeworkisdue8AMFri.&Fri.homeworkisdue8AMMon.).YoucanlogonandoffCollabmultipletimestocompletethehomework,(i.e.there’snotimelimittocompletetheassignmentwhenyoulogon)butyoucanonlysubmityouranswersonce.Besuretosaveyourwork!Partiallycompletedassignmentswillbeautomaticallysubmittedat8AM.Missedhomeworkassignmentscannotbemadeup.Answerkeysandcorrectanswerfeedbackwillbepostedat8:05AMeachduedate.Therewillbenohomeworkassignmentsdueonexamdays.Homeworkmustbecompletedandsubmittedindividually.Byenrollinginthiscourse,youareaffirmingonyourhonorthatyouhaveneitherreceivednorgivenaidwhilecompletingthehomeworkassignments.Iconsiderreferringtopreviousyear’sexamsorworkingcollaborativelytocompletehomeworkassignmentsasreceivingaidandthereforeconstituteanhonoroffense.You’recertainlywelcomeandencouragedtodiscussthequestionsandanswersandstudycollaborativelywithyourclassmatesafterthesubmissiondeadline,inordertopreparefortheexams,butyouarerequiredtocompletethehomeworkassignmentsindividuallyandnotworkwithotherstudentswhileyouaredoingthem.Learningisindeedcollaborative,butassessmentisnecessarilyindividual.Weds.EveningDiscussionSessionsWeds.7–9PMGIL130beginningAug.31.Attendanceisoptional,buthighlyencouraged.Richwillreviewandclarifytopicspresentedinclass,coveredonhomeworkassignmentsandrecapthe“BigQuestions”providedontheassignedreadingassociatedwitheachunit.Hewillalsoansweranyspecificquestionsyouhave.

ExamScheduleExams1,2,3;Weds.Sept.14,Oct.12,Nov.9,7–9PMGIL130;Exam4Sat.Dec.102–5PMGIL130.Anopen"question/answer"reviewsessionwillbeheldinsteadofclassoneachofthe3Weds.examdates.Byenrollinginthiscourseyouaremakingacommitmenttotakethefourexamsasscheduled!Attendanceatall4examsismandatoryandyoumustbepresentatthebeginningofeachexam.Studentsarrivingmorethan10’latewillnotbeallowedtotaketheexam.Alternativeexamarrangementswillonlybegivenforextenuatingcircumstancessuchasadebilitatingillness,religiousobservances,orforstudentsparticipatinginofficialUVA-sponsoredactivitiessuchasconcertsorathleticevents.StudentsparticipatingintheSDACshouldcontactmeasearlyinthesemesteraspossibletoaccommodateyourindividualsituation.PerCollegeregulations,the4thexamdateandtimecannotberescheduledforanyreason.EvaluationandGradingYourlearningwillbeassessedby:

• Onlinehomeworkassignments.75pointstotal.15%ofcoursegrade• 4multiple-choiceformatexamsasfollows:

o Exam1:100points(50questions).20%ofcoursegrade.Thisexamwillcover:CellularOriginsand“ProblemsofBeingEukaryotic”,PlasmaMembraneStructureandProperties,TransportofSmallMoleculesandIons.

o Exam2:100points(50questions).20%ofcoursegrade.Thisexamwillcover:ProteinTraffickingandReceptor-MediatedEndocytosis

o Exam3:100points(50questions).20%ofcoursegrade.Thisexamwillcover:CytoskeletonandCellSignaling.

o Exam4:125points(63questions).25%ofcoursegrade.Thisexamwillcover:CellCycleDynamicsandRegulation,Mitosis,andCancer.

Courselettergradesarebasedoncumulative%outof500totalpointsasfollows:A=90–100%B=80–89%C=70–79%D=60–69%F=<60%.Lettergradesareguaranteedforeachpercentilebracket.Thismeansthatafinalcumulativepercentilescoreof90%guaranteesthatyouwillreceiveatleastanA-;80%guaranteesthatyouwillreceiveatleastaB-.Itdoesn’tmeanthat89%couldn’tbeanAorA-,butitjustisn’tguaranteed!Theselettergradebracketsmaybeslightlyexpandedtoreflectscoredistributions,butwillnotbecurvedtoreflectthemean.“+”and“-”willbebasedonthedistributionofscoreswithineachlettergradebracketandwillnotbedetermineduntilthecourseiscompleted.Themeancumulativepercentilescoreforspring,2016(N=315)was82%.MeancourseGPAwas2.80.ClassAttendanceandEtiquetteRegularattendanceisstronglyrecommendedandencouraged.InformationnotnecessarilyprovidedonthepostedslidesorfoundinMCB8Ewillbepresentedinclass.Iaskthatyoupleasearriveontimeandremaintheentire50minutes.TheclockinGIL130istheofficial“timekeeper”.Ifyoumustleaveearly,thenpleasesitinthebackoftheauditoriumsoyourdepartureisnotadistraction.Cellphonesshouldbeturnedoff!Outofconsiderationtoyourfellowstudentsandme,pleasedon’ttwitter,text,facebook,surftheweb,orengageindistractiveconversationsinclass.Youmaynotthinkso,buttheseirrelevantactivitiesdoindeeddistractyourpeersandme.Mostimportantly,thesebehaviorsdistractyou!Thinknot?CheckoutthisshortvideobyUVaPsychologyProfessorDanWillinghamwhodemonstratesthat“multitaskingiswishfulthinking.”http://www.youtube.com/watch?v=34OZ-dsNkBwInsummary,Ihopeyouwillbesufficientlyengagedinclasstowanttocome,andifso,pleaseshowcommoncourtesytoyourpeersandme.

RecordingPolicyandProhibitionofPostingCourseMaterialsOnlineUVapolicy(postedintheCollabResourcesfolder)restrictstherecordingofclasslecturesandprohibitspostingofcoursematerialson3rdpartywebsites.Thisprohibitionincludespostingaudioorvideorecordings,imagesand/orslides,lecturenotes,transcriptsoflectures,anymaterialsthatarepostedonCollab,andanyhomeworkorexamquestionsandanswers.ManyoftheresourcesprovidedinBIOL3000arecopyrightprotected.FairUselawsallowyoutousethismaterialinthecontextofthiscourse,butprohibititscopyinganddistributiontoanyonenotcurrentlyenrolledinBIOL3000.ViolationofthispolicymayresultindisciplinaryactionbytheUniversityJudiciaryCommittee.Youmaymakeaudiorecordingsoflecturessolelyforpersonaluseortostudywithotherstudentscurrentlyenrolledintheclasswithoutmywrittenpermission.Youcannotrecordofficehourdiscussions.Videoordigitalrecording,includingtakingphotoswithacellphone,oflectures,discussions,slidespresentedinclass,duringdiscussionsessionsorofficehourmeetings,isnotallowedunderanycircumstances.HonorStatementItrusteverystudentinthiscoursetocomplywithalloftheprovisionsoftheUVahonorsystem.Byenrollinginthiscourse,youareaffirmingthatyouhaveneitherreceivednorgivenaidwhilecompletinghomeworkassignmentsandtakingexams.Iconsiderreferringtooldexamswhendoinghomeworkassignmentsand/orstudyingforexamstoconstitutereceivingaidandthereforeanhonoroffense.Yourpledgeontheexamsalsoaffirmsthatyouhavenotaccessedanynotes,studyoutlines,problemsets,oldexams,answerkeys,orthetextbookwhiletakinganexamandthatyouhavenotobtainedanyanswersfromanotherstudent’sexam.Usingacellphonewhiletakinganexamwillbeconsideredanhonoroffense.Pleaseremember,itisyourresponsibilitytoupholdthehonorsystem.Ifyoubelievethatanhonoroffensehasbeencommitted,youhavetheobligationtoreportittoanhonoradvisorirrespectiveifIamawareofitornotandyoucandothiswithoutbringingittomyattention.IcanonlyinitiateanhonorcaseifIpersonallyobserveanallegedoffense.If,inmyjudgment,itisbeyondareasonabledoubtthatastudenthascommittedanhonoroffensewithregardtoagradedexamorhomeworkassignment,thatstudentwillreceiveanimmediateandirrevocablegradeof“F”(0%)forthatexamorassignment,irrespectiveofanysubsequentactiontakenbytheHonorCommittee.TipstoSucceedinCellBiology•MCB8EandCollabarevaluableresourcesthatprovideanexcellentfoundationforthetopicswewilldiscussinclass.Irecommendthatyoufirstskimthroughtheassignedreadingpertinenttoeachclassbeforeitmeets.Usetheslidesandreadingassignmentsto“navigate”throughthetext.Thetopicswecoverwillbeorganizedinabiologicalprogression,andnotnecessarilyintheordertheyarepresentedinthebook.Theonlinehomeworkwillenableyoutoassessyourunderstandingofthetopicsbeforetheexams.Thequestionsareverysimilartotheonesyouwillseeonexams,asagain,manyofthemarepreviousyears’examquestions.Usethemtoprovideacontexttoorganizeyournotes.•Understand,don’tjustmemorize.Detailsdomatter,butalwayskeepthebigpictureinsight.Thinkofthebiologicalcontextoftheparticularcellularprocessorcomponentunderdiscussion.Understandingwhysomethingoccursoftenmakesiteasiertoappreciatehowithappens.There’snoescapingthefactthatcellsarecomplicated.Thatsaidtherearesomethingsthatyoujusthavetomemorize.Forstarters,thesingle-letterabbreviationsfortheaminoacidsandthefunctionalitiesoftheirRgroups.(e.g.,DandEarebothacidic;KandRarebothbasic;S,TandY

have“free”–OHgroups;ILVMarehydrophobic;Y,FWarearomatic;etc).You’llhavetomemorizethesestructuresforBiochemistryanywaysomightaswellgetstartedonthemnow.•Thinklikeanexperimentalcellbiologist.Ask;“WhatwouldhappenifIdidthis?”“Whatcausedthisparticularresult?”That’showcellbiologyisreallydone.Allofthecellularprocessesandmechanismsthatwewillconsiderwerederivedbyrealpeopledoingrealexperiments,interpretingthemandposingmodelsandmechanisms.Thisempiricalprocessiscontinuousandalwaysevolving.Newexperimentsuncovernew“players”andunforeseenconnections.Inreality,everythingturnsouttobeevenmorecomplicatedthanisalreadyis.Thesearecellsafterall!•Learnthelanguage.Cellbiologyhasalotofjargonandsomeobtuseterminology.Inthisregard,youhavetobecomefluentinanewlanguage.Names,terms,anddefinitions,matter.AkinaseisnotaGprotein;aphosphataseisnotaphosphodiesterase.Rab,Rac,Raf,RasandRhoareuniqueproteinswithdistinct,criticalfunctions.Usetheglossaryifyouencounterawordyoudon’tunderstand.•Beengagedinclassandfeelfreetoaskquestions.Ifyoudotheassignedreadingandthehomework,you’llhaveagoodideaaboutwhatI’mcoveringinclass.Don’ttrytowritedowneverythingIsay.Note-takingisalostart.Don’tre-writethetext.Askquestionsinclass!TheonlyquestionIdon’tallowis“Doweneedtoknowthisfortheexam?”•CometoofficehoursandtheWeds.eveningdiscussionsessionsandaskquestionsinperson.Scienceisahumanendeavor.Soislearningandthisisthebestopportunityforustogettoknoweachother.Pleasedon’temailmeyourquestions.Why?IhavenowayofknowingifyouunderstandwhatI’mtellingyouandyoudonothavetheopportunitytoimmediatelyaskafollow-upquestion.Pleasedonotaskmetorepeatanentirelectureduringofficehours.Iexpectyoutohaveputsomethoughtintothetopicsunderconsiderationsowecanaddressspecificconceptsormechanismsthatarechallengingtounderstand.Gettoknowallofyourprofessors.

BIOL3000–FALL2016–*TENTATIVECLASSSCHEDULEUnit1 CellularOriginsandtheProblemsofBeingEukaryoticClass# Date Day Subject1 8/24 W CellularOrigins,ProkaryotesvsEukaryotes2 8/26 F Multicellularity:EukaryoticComplexity:ModelOrganismsUnit2 PlasmaMembraneStructuresandProperties3 8/29 M ThePlasmaMembrane:Lipids4 8/31 W Lipids:IntegralMembraneProteins5 9/2 F IntegralMembraneProteins,OverviewofTransportUnit3 TransportofSmallMoleculesandIons6 9/5 M GlucoseandIonTransport7 9/7 W IonChannelsandNa+/K+ATPase8 9/9 F GlucoseTranscytosisUnit4 ProteinTrafficking9 9/12 M ProteinLocalization:ExperimentalApproachesEXAM1 9/14 W 7–9PM(Units1,2&3)Review9AM10 9/16 F ProteinLocalization:ExperimentalApproaches11 9/19 M TheSecretoryPathway:InsertionofProteinsintotheER12 9/21 W IntegralMembraneProteinTopology;Proteinfolding

13 9/23 F ProteinFoldingintheER:CFTRandCysticFibrosis14 9/26 M TheSecretoryPathway:ERresidentproteinsandglycosylation15 9/28 W Secretion:VesicleTrafficking,LysosomalTargeting16 9/30 F LysosomalTargeting&LysosomalDeficiencyDisordersNOCLASS 10/3 M FALLREADINGDAYUnit5Receptor-MediatedEndocytosis17 10/5 W LDLReceptor-MediatedEndocytosis:Coronaries&Cholesterol.18 10/7 F LDLReceptor-MediatedEndocytosis:Coronaries&Cholesterol.Unit6Cytoskeleton19 10/10 M CytoskeletonOverview:MicrofilamentStructure/DynamicsEXAM2 10/12 W 7–9PM(Units4&5)Review9AM20 10/14 F MicrofilamentsandCellMorphology:Microtubules21 10/17 M MicrotubuleStructureandDynamics22 10/19 W MicrotubuleMotorProteinsUnit7CellSignaling23 10/21 F CellSignaling:Overview,G-ProteinCoupledReceptors24 10/24 M CellSignaling:G-ProteinCoupledReceptorPathway25 10/26 W CellSignaling:G-ProteinCoupledReceptorPathway26 10/28 F CellSignaling:G-ProteinCoupledReceptorPathwayUnit8CellCycleDynamicsandRegulation,Mitosis27 10/31 M TheCellCycle:RegulatingCyclinsandCDKs28 11/2 W TheCellCycle:RegulatingCyclinsandCDKs29 11/4 F Mitosis:MakingandBreakingtheSpindle30 11/7 M Mitosis:MakingandBreakingtheSpindleEXAM3 11/9 W 7–9PM(Units6&7)Review9AM31 11/11 F Mitosis:ChromosomeSegregationUnit9Cancer32 11/14 M ReceptorTyrosineKinaseSignalingandCellProliferation33 11/16 W ReceptorTyrosineKinaseSignalingandCancerConnection34 11/18 F TheGeneticBasisofCancer35 11/21 M TheGeneticBasisofCancerNOCLASS 11/23 W THANKSGIVINGBREAKNOCLASS 11/25 F THANKSGIVINGBREAK36 11/28 M Cancerandp53TumorSuppressorFunction37 11/30 W TheTransformedPhenotypeandTumorProgression38 12/2 F HallmarksofCancer39 12/5 M HallmarksofCancerEXAM4 12/10 SAT. 2–5PM(Units8&9)

• TheclassscheduleistentativeinthatImaybeginanewtopicduringtheprecedingclass,orcontinuediscussingagiventopicintothenextclass.Imayalsochangesometopicscoveredthroughoutthecourseandthesechangeswillbeannouncedinadvance.

• ImportantCollegeDates• AddDeadline: Tues.Sept.6• DropDeadline: Weds.Sept.7• FallReadingDay Mon.Oct.7(NoClass) • WithdrawalDeadline:Tues.Oct.18• ThanksgivingBreak: Weds.Nov.23&Fri.Nov.25(Noclass)