CELLBIOLOGY–BIOL3000–FALL2017(updated04/12/17)

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.13,Oct.11,Nov.8,7–9PMGilmer130.UPDATEDExam4,Thurs.Dec.7,2–5PMGIL130

InstructorInformationMikeWormington,AssociateProfessorofBiology.MyhometownisOverlandPark,Kansas,andIattendedtheUniversityofKansas(GoJayhawks!)whereIearnedmyBAwithHonorsinBiologyandmyPhDinBiochemistry.IwasanNIHPostdoctoralfellowattheCarnegieInstitutionforScience,Dept.ofEmbryology,inBaltimore,MD.IjoinedtheUVaBiologyfacultyin1989andhavetaughtCellBiologysince1992.Mylongstandingresearchinterestistheregulationofgeneexpressionduringearlydevelopment.MywifeSusan,istheArtDirectoratUVa’sDardenSchoolofBusiness.Ourtwodaughtersandsons-in-lawandourthreegrandchildrenkeepusbusy.WhatdoIdoforfun?I’maLieutenantColonelandsearchandrescuemissionpilotandthedirectorofoperationsfortheVirginiawingoftheCivilAirPatrol,whichisthecivilianauxiliaryoftheUSAirForce. Office:PLSB206 Phone:982-5803 email:ww2t@virginia.edu GroupOfficeHoursinPLSB200:2–4:30PMTues.andThurs.Individualmeetingsbyappointment. GraduateTeachingAssistantTBAPrerequisitesBIOL2010or2100(orAP)orBME2014,andanytwoofCHEM1410,1420,1610,1620,1810,1820.Thepremiseforthiscourseisthatyouhavecompletedtheseprerequisitesandarefamiliarwiththeirconceptsandprinciples.ThefirstthreechaptersofMCB8EprovideanexcellentreviewofpertinenttopicscoveredinbothBIOL2010/2100andgeneralchemistry,andshouldbereferredtoasnecessarythroughouttheentirecourse.RequiredtextforFall2017TherequiredtextbookisMolecularCellBiol.,8thed.,Lodishetal.(MCB8E).Purchasetheleastexpensiveoptionavailabletoyou.Donotusepreviouseditionsofthetext.ManytopicsandpertinentfigureshavebeensignificantlyrevisedinMCB8Eandmostreadingassignmentswillnotmatchthoseusedpreviously.YouwillberesponsibleformaterialandconceptscoveredinassignedreadingsfromMCB8Ethatwillnotbediscussedinclass.BIOL3000CollabWebsiteTheBIOL3000CollabCoursesiteisanimportantresourcethatyouwilluse.TheResourcessectionwillcontainpptxfilesofslidestobepresentedinclass.Thesewillbeavailablefordownloadingatleasttwodaysbeforewecoverthematerialinclass.Note:TheinformationonsomeslidesIshowinclassmaydifferfromthosepostedoncollabsoplantotakenotes!SpecificreadingassignmentsfromMCB8Echapters,supplementaryreadingmaterialfromreviewarticlesandprimaryresearchpapers,andlearningobjectives(the“bigquestions”)foreachunitofthecoursewillalsobepostedwiththeslides.Youwillreceiveanemailnoticewhennewmaterialshavebeenposted.TheCollabsitealsocontainsthemoviefilesshowninclassandlinkstointerestingwebsites.

OnlineHomeworkAssignments“Doordonot.Thereisnotry.”Yoda

Thebestwaytolearncellbiologyistodoit.Unfortunately,wecannotprovideapracticallabexperiencewithBIOL3000thatallowsyoutoapplywhatwecoverinclass.Therefore,thenextbestoptionistogiveyouopportunitiestobebetterpreparedforclassandtoregularlyself-assessyourunderstandingofthetopicswe’recoveringbeforeyou’retestedonyourknowledgeoneachofthefourexams.Therearetwoincentivesforyoutotakeadvantageoftheonlinehomeworkexercises.First,theonlinehomeworkconstitutes15%ofyourfinalcoursegrade.Thatalonecanmakethedifferenceinalettergrade.Second,bydoingtheseexercises,youwillbeabletoassessyourunderstandingofthetopicspresentedinclassandadjustyourapproachestolearningthematerialsothatyou’llperformbetterontheexamsandrememberthematerialafterthecourseisover.Eachonlinehomeworkassignmentwillconsistof5multiple-choicequestionsthatwillassessyourunderstandingofthetopicscoveredintheprecedingclass.Thehomeworkquestionsarelargelyderivedfromtheprevioustwosemesters’exams,butnewquestionsareaddedeachsemester.Thisensureseveryonehasequalaccesstooldexamquestions.Forthefall2016semester,therewere37homeworkassignmentsandtwobonusassignments,whichwereconvertedtoafinaltotalof75points.Forfall2017,therewillbeseveralopportunitiestogainbonushomeworkpointsthroughoutthesemester.Thehomeworkassignmentsareopenbook,opennoteformat.Refertothepertinentmaterial,includingtheslides,inordertocompleteeachassignment.Thequestionswillvariouslycovermaterialpresentedinlectures,theMCB8Etext,andanyadditionalassignedreading.You’llreceiveanemailfromCollabwhenahomeworkassignmenthasbeenposted.Eachhomeworkassignmentisdue8AMthefollowingclassday(e.g.,Mon.homeworkisdue8AMWeds.Weds.homeworkisdue8AMFri.&Fri.homeworkisdue8AMMon.).YoucanlogonandoffCollabmultipletimestocompletethehomeworkandthere’snotimelimittocompletetheassignmentwhenyoulogon.However,youcanonlysubmityouranswersonce.Besuretosaveyourwork!Partiallycompletedassignmentswillbeautomaticallysubmittedat8AM.Missedhomeworkassignmentscannotbemadeup.Answerkeysandfeedbackwillbepostedat8:05AMeachduedate.Therewillbenohomeworkassignmentsdueonexamdays.Homeworkmustbecompletedandsubmittedindividually.Byenrollinginthiscourse,youareaffirmingonyourhonorthatyouhaveneitherreceivednorgivenaidwhilecompletingthehomeworkassignments.Iconsiderreferringtopreviousyear’sexamsorworkingcollaborativelytocompletehomeworkassignmentsasreceivingaidandthereforeconstituteanhonoroffense.You’recertainlywelcomeandencouragedtodiscusstheassignmentsandstudycollaborativelywithyourclassmatesafterthesubmissiondeadline,inordertopreparefortheexams,butyouarerequiredtocompletethehomeworkassignmentsindividuallyandnotworkwithotherstudentswhileyouaredoingthem.Learningisindeedcollaborative,butassessmentisnecessarilyindividual.Weds.EveningDiscussionSessionsWeds.7–9PMGIL130beginningWeds.8/30.Attendanceisoptional,buthighlyencouraged.TheTAwillreviewandclarifytopicspresentedinclass,homeworkquestions,andthe“BigQuestions”providedontheassignedreadingassociatedwitheachunit.TheTAwillalsoansweranyspecificquestionsyouhave.

UPDATEDExamScheduleExams1,2,3;Weds.Sept.13,Oct.11,Nov.8,7–9PMGIL130;Exam4,Thurs.Dec.72–5PMGIL130.Althoughthe4thexamhasmorequestionsandisworthmorepoints,itisnotacomprehensivefinal.Anopen"question/answer"reviewsessionwillbeheldinsteadofclassoneachofthe3Weds.examdates.Byenrollinginthiscourseyouaremakingacommitmenttotakethefourexamsasscheduled!Attendanceatall4examsismandatoryandyoumustbepresentatthebeginningofeachexam.Studentsarrivingmorethan10’latewillnotbeallowedtotaketheexam.Toavoidanypossiblemisunderstandings,neithertheTAnorIwillansweranyquestionsduringtheexam.Alternativeexamarrangementswillonlybegivenforextenuatingcircumstancessuchasadebilitatingillness,religiousobservances,orforstudentsparticipatinginofficialUVA-sponsoredactivitiessuchasconcertsorathleticevents.StudentsparticipatingintheStudentDisabilityAccessCenter(SDAC)shouldcontactmeasearlyinthesemesteraspossibletoaccommodateyourindividualsituation.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.Themeancumulativepercentilescoreforfall,2016(N=329)was77%&mediancumulativepercentilescorewas80%.MeancourseGPAwas2.500.ClassAttendanceandEtiquetteRegularattendanceisstronglyrecommendedandencouraged.InformationnotnecessarilyprovidedonthepostedslidesorfoundinMCB8Ewillbepresentedinclass.Pleasearriveontimeandremaintheentire50minutes.TheclockinGIL130istheofficial“timekeeper”.Ifyoumustleaveearly,thenpleasesitinthebackoftheauditoriumsoyourdepartureisnotadistraction.Cellphonesshouldbeplacedinairplaneordonotdisturbmode.Outofconsiderationtoyourfellowstudentsandme,pleasedon’ttwitter,text,facebook,surftheweb,orengageindistractiveconversationsinclass.Youmaynotthinkso,buttheseirrelevantactivitiesdodistractyourpeersandme.Mostimportantly,thesebehaviorsdistractyou!Thinknot?CheckoutthisshortvideobyUVaPsychologyProfessorDanWillinghamwhodemonstratesthat“multitaskingis

wishfulthinking.”http://www.youtube.com/watch?v=34OZ-dsNkBwInsummary,Ihopeyouwillbesufficientlyengagedinclasstowanttocome,andifso,pleaseshowcommoncourtesytoyourpeersandme.RecordingPolicyandProhibitionofPostingCourseMaterialsOnlineUVapolicy(postedintheCollabResourcesfolder)restrictstherecordingofclasslecturesandprohibitspostingofanycoursematerialson3rdpartywebsites,suchasStudyblue&Quizlet.Thisprohibitionincludespostingaudioorvideorecordings,imagesand/orslides,lecturenotes,transcriptsoflectures,anymaterialsthatarepostedonCollab,andanyhomeworkorexamquestionsandanswers.ManyoftheresourcesprovidedinBIOL3000arecopyrightprotected.FairUselawsallowyoutousethismaterialwhileyouaretakingthecourse,butprohibititscopyinganddistributiontoanyonenotcurrentlyenrolledinBIOL3000.ViolatingthispolicymayresultindisciplinaryactionbytheUniversityJudiciaryCommittee.Youmaymakeaudiorecordingsoflecturessolelyforpersonaluseortostudywithotherstudentscurrentlyenrolledintheclasswithoutmywrittenpermission.Youmustkeepyourcellphonewithyouifyouareusingittorecordlectures.Cellphonescannotbeplacedinthefrontoftheauditorium.Ifcellphonesprovetobeadistractionbyringingduringclass,theywillbeprohibited.Youcannotrecordofficehourdiscussions.Videoordigitalrecording,includingtakingphotoswithacellphone,oflectures,discussions,slidespresentedinclass,duringdiscussionsessionsorofficehourmeetings,isnotallowedunderanycircumstances.HonorStatementItrustthateverystudentinthiscoursecomplieswithalloftheprovisionsofUVA’shonorcode.Byenrollinginthiscourse,youareaffirmingthatyouhaveneitherreceivednorgivenaidwhilecompletinghomeworkassignmentsandtakingexams.Iconsiderreferringtooldexamsforanypurposethroughoutthesemestertoconstitutereceivingaidandthereforeanhonoroffense.Yourpledgeontheexamsalsoaffirmsthatyouhavenotaccessedanynotes,studyoutlines,problemsets,oldexams,answerkeys,orthetextbookwhiletakinganexamandthatyouhavenotobtainedanyanswersfromanotherstudent’sexam.Usingacellphoneforanyreasonwhiletakinganexamwillbeconsideredanhonoroffense.Pleaseremember,itisyourresponsibilitytoupholdthehonorsystem.Ifyoubelievethatanhonoroffensehasbeencommitted,youhavetheobligationtoreportittoanhonoradvisorirrespectiveifIamawareofitornotandyoucandothiswithoutbringingittomyattention.IcanonlyinitiateanhonorcaseifIpersonallyobserveanallegedoffense.If,inmyjudgment,itisbeyondareasonabledoubtthatastudenthascommittedanhonoroffensewithregardtoagradedexamorhomeworkassignment,thatstudentwillreceiveanimmediateandirrevocablegradeof“F”(0%)forthatexamorassignment,irrespectiveofanysubsequentactiontakenbytheHonorCommittee.TipstoSucceedinCellBiology•MCB8EandCollabarevaluableresourcesthatprovideanexcellentfoundationforthetopicswewilldiscussinclass.Irecommendthatyoufirstskimthroughtheassignedreadingpertinenttoeachclassbeforeitmeets.Usetheslidesandreadingassignmentsto“navigate”throughthetext.Thetopicswecoverwillbeorganizedinabiologicalprogression,andnotnecessarilyintheordertheyarepresentedinthebook.Theonlinehomeworkwillenableyoutoassessyourunderstandingofthetopicsbeforetheexams.Thequestionsareverysimilartotheonesyouwillseeonexams,asagain,mostofthemarepreviousyears’examquestions.Usethemtoprovideacontexttoorganizeyournotes.

•Understand,don’tjustmemorize.Detailsdomatter,butalwayskeepthebigpictureinsight.Thinkofthebiologicalcontextoftheparticularcellularprocessunderdiscussion.Understandingwhysomethingoccursoftenmakesiteasiertoknowhowithappens.There’snoescapingthefactthatcellsarecomplicated.Thatsaidtherearesomethingsthatyoujusthavetomemorize.Forstarters,thesingle-letterabbreviationsfortheaminoacidsandthefunctionalitiesoftheirRgroups.(e.g.,DandEarebothacidic;KandRarebothbasic;S,TandYhave“free”–OHgroups;ILVMarehydrophobic;Y,FWarearomatic;etc).You’llhavetomemorizetheaminoacidstructuresforBiochemistryanywaysoyoumightaswellgetstartedonthemnow.YoushouldalsomemorizethestructuresofATP&GTP.•Thinklikeanexperimentalcellbiologist.Ask;“WhatwouldhappenifIdidthis?”“Whatcausedthisparticularresult?”That’showcellbiologyisreallydone.Allofthecellularprocessesandmechanismsthatwewillconsiderwerederivedbyrealpeopledoingrealexperiments,interpretingthemandposingmodelsandmechanisms.Thisempiricalprocessiscontinuousandalwaysevolving.Newexperimentsuncovernew“players”andunforeseenconnections.Inreality,everythingturnsouttobeevenmorecomplicatedthanisalreadyis.Thesearecellsafterall!•Learnthelanguage.Cellbiologyhasalotofjargonandsomeobtuseterminology.Assuch,youactuallyhavetobecomefluentinanewlanguage.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–FALL2017–*TENTATIVECLASSSCHEDULEClass# Date Day Subject1 8/23 W CellularOrigins,ProkaryotesvsEukaryotes2 8/25 F Multicellularity:EukaryoticComplexity:ModelOrganisms3 8/28 M ThePlasmaMembrane:Lipids4 8/30 W Lipids:IntegralMembraneProteins5 9/1 F IntegralMembraneProteins,OverviewofTransport6 9/4 M GlucoseandIonTransport7 9/6 W IonChannelsandNa+/K+ATPase8 9/8 F GlucoseTranscytosis9 9/11 M ProteinLocalization:ExperimentalApproaches

EXAM1 9/13 W 7–9PM(Units1-3) Review9AM10 9/15 F ProteinLocalization:ExperimentalApproaches11 9/18 M TheSecretoryPathway:InsertionofProteinsintotheER12 9/20 W IntegralMembraneProteinTopology;Proteinfolding13 9/22 F ProteinFoldingintheER:CFTR&CysticFibrosis14 9/25 M TheSecretoryPathway:ERresidentproteinsandglycosylation15 9/27 W Secretion:VesicleTrafficking,LysosomalTargeting16 9/29 F LysosomalTargeting&LysosomalDeficiencyDisordersNOCLASS 10/2 M FALLREADINGDAY17 10/4 W LDLReceptor-MediatedEndocytosis:Coronaries&Cholesterol18 10/6 F LDLReceptor-MediatedEndocytosis:Coronaries&Cholesterol19 10/9 M CytoskeletonOverview:MicrofilamentStructure/DynamicsEXAM2 10/11 W 7–9PM(Units4and5) Review9AM20 10/13 F MicrofilamentsandCellMorphology:Microtubules21 10/16 M MicrotubuleStructureandDynamics22 10/18 W MicrotubuleMotorProteins23 10/20 F CellSignaling:Overview,G-ProteinCoupledReceptors24 10/23 M CellSignaling:G-ProteinCoupledReceptorPathway25 10/25 W CellSignaling:G-ProteinCoupledReceptorPathway26 10/27 F CellSignaling:G-ProteinCoupledReceptorPathway27 10/30 M TheCellCycle:RegulatingCyclinsandCDKs28 11/1 W TheCellCycle:RegulatingCyclinsandCDKs29 11/3 F Mitosis:MakingandBreakingtheSpindle30 11/6 M Mitosis:MakingandBreakingtheSpindleEXAM3 11/8 W 7–9PM(Units6and7) Review9AM31 11/10 F Mitosis:ChromosomeSegregation(L18,19)32 11/13 M ReceptorTyrosineKinaseSignalingandCellProliferation33 11/15 W ReceptorTyrosineKinaseSignalingandCancerConnection34 11/17 F TheGeneticBasisofCancer35 11/20 M TheGeneticBasisofCancerNOCLASS 11/22 W THANKSGIVINGBREAKNOCLASS 11/24 F THANKSGIVINGBREAK36 11/27 M Cancerandp53TumorSuppressorFunction37 11/29 W TheTransformedPhenotypeandTumorProgression38 12/1 F HallmarksofCancer39 12/4 M HallmarksofCancerEXAM4 12/7 Thurs 2–5PM(Units8&9)

• TheclassscheduleistentativeinthatImaybeginanewtopicduringtheprecedingclass,orcontinuediscussingagiventopicintothenextclass.Imayalsochangesometopicscoveredthroughoutthecourseandthesechangeswillbeannouncedinadvance.

• ImportantCollegeDates• AddDeadline: Tues.Sept.5• DropDeadline: Weds.Sept.6• FallReadingDay Mon.Oct.2(NoClass) • WithdrawalDeadline:Tues.Oct.17• ThanksgivingBreak: Weds.Nov.22&Fri.Nov.24(Noclass)