SYLLABUSANDCOURSEPOLICIES
BIOLOGY334-MOLECULARBIOLOGY-FALL2015
TimeandRoom:
• 9:45-11:35T-Th
• CLSB1A001
• Wewillrunwithonebreak:9:45-10:35,break(10min.),10:45-11:35.Theseare
approximatetimes.
Instructor/OfficeHours:
• JeffreySinger,Ph.D.,AssociateProfessor,BiologyDepartment,PSU
• OfficeCLSB3N032
• OfficeHoursM,W,F11:30-12:30andbyappointment(NOTE:forthisyoumustgotothis
room:CLSB5S021,theydonotletmeusemyofficeforstudentofficehours)
• E-mail:[email protected]
• Tel:503-725-8742
Textbook(required):
• Albertsetal.,MolecularBiologyoftheCell,6thEdition,2014Garland
Science.HARDBACK•978-0-8153-4432-2-LOOSELEAF•978-0-81534524-4.Thiswillbeusedforboth334and336.
• i>clicker,soldatbookstore(oronline),wewillusetheseforquizzesand
inclassquestions.Note:THESEAREREQUIRED!Youneedtohave
themonthefirstday!Also,pleasemakesureyouregistertheseonline!
Gototheiclickerwebsiteandselectregistration.Canuseiclicker,
iclicker+oriclicker2.Wewillnotusetheiclickergoapp.
Prerequisites:
•
•
•
•
PrinciplesofBiologyandGeneralChemistry(oneyearofeach).
Takingthesecoursesatthesametimeasthisoneisnotacceptable.
OrganicChemistryrecommendedbutnotrequired.
Biochemistryishelpfulbutnotrequired.
SubjectMatter:
WewillcoverthebasicsofDNAstructureandreplication,transcriptionandtranslation,andan
introductiontotheregulationofgeneexpression.Wewillalsocovervariousmethodologiesused
inmodernmolecularbiologylabstoexaminetheseprocesses.
LearningObjectives:
DNAstructure
• IdentifyaWatson-Crickbasepair
• Recognizepolarityandexplainitssignificanceinintramolecularandintermolecular
interactions.
• Identify2'and3'positionsonribose
• IdentifyMajorandminorgroovesandexplainthesignificanceforDNAbinding
• Describethecauseandsignificanceofhydrogenbonding
• Describethebasicsofchromosomestructureandtheroleofhistonemodification
• Recognizegeneandrepeatcontentofhumangenome
• CompareandcontrastTwistandWritheandpositiveandnegativesupercoils
Replication
• ListthestepsinthemechanismofelongationandproofreadingbyDNApolymerases
• Describereasonsandmechanismsforhighfidelityreplication
• Listtheproteinspresentatreplicationforksinbothbacteriaandeukarya
• Describethefunctionsoforiginsofreplicationinbacteriaandeukaryaandtheproteinsthat
bindthem
• Diagramthemechanismoflicensingofreplicationorigins
Transcription
• Diagramanddescribethesignificantstepsandcomponentsofthetranscriptioncycle
• Identifythecomponentsanddescribethefunctionofapromoter
• Explainthemeaningof“Consensussequence”andgiveanexampleofone
• Describetheroleandfunctionofsigmafactors
• DescribetheroleandfunctionofGeneralTranscriptionFactorsTF2D,B,andH
Proteinstructure
• RecognizeanddescribethebasicstructureofAlphahelixhydrogenbondsandsidechain
orientation
• RecognizeanddescribethebasicstructureofBetastrand/sheethydrogenbondsandside
chainorientation
• Listallthebasic,acidicandOH-containingaminoacids
Regulation
• Contrastpositiveandnegativeregulationandprovideexamplesofeach
• Describetheroleandfunctionofenhancersandenhancerbindingproteinsandprovide
examplesofeach.
• Diagramandexplaintheoperonmodel
• Describethestructureandroleofeukaryoticenhancerbindingproteinsandtheir
modularity
• DescribeHTH,Homeodomain,andZnfingerDNAbindingdomainsandknowthatothers
exist
• Identifythetargets,bothdirectandindirectofeukaryoticenhancerbindingproteins
• Identifythetargets,bothdirectandindirectofeukaryoticrepressors
• Compareandcontrastcombinatorialcontrol,masterregulators,andcell-typespecific
transcriptionalregulators
• Identifythemoleculesinvolvedandexplaintheprocessesofpost-transcriptionalcontrol,
translationalinitiationregulation,alternativesplicing,andmRNAediting.
• CompareandcontrastsmallregulatoryRNAsofthesiRNAandmiRNAsclassesandbasic
aspectsoftheirmechanismsofsilencing/repression.
D2L:
• Lecturepresentations
• Supplementalreadingmaterials
LecturePresentations:
• Lectures will be available online using D2L. These are an outline of what was covered in
lectureandareprovidedtoassistyou.
• Thesefilesshouldnotbeconsideredacompletecoverageofthelecturematerialsandare
certainlynotanacceptablereplacementforattendinglectures.
• Inaddition,thesearenotnotes,theyaremerelyanoutlineofwhatIdiscussedinclass.You
shouldtakeyourownnotes.Remember-notetakingispartofthelearningprocess!
Evaluation:
• Dailyquizzesduringclass,(1/4ofgrade),usingclickers.
• TwoMidterms(1/4ofGradeeach)-Oct.20thandNov.10thinclass.
• OneFinal(1/4ofGrade).Dec.10th,Thursday8:00AM-9:50AM.Thisexamisnot
comprehensive.
• Note:Ifyoucannotmakethesedatesthendonottakethecourse!
Exampolicies:
• Exams will likely involve multiple-choice, written short-answer, and drawing/labeling
diagrams.Formultiple-choiceexams,studentswillneedtoprovideascantronsheet.Be
suretobringaformSC982-E*scantronsheettoeveryexam.*Thisisalargeform,notthe
small one and has new features; I have uploaded a PDF of this form for you to see. You
mustbringthisform;wewillhave75-pointexams.
• ThereareNOmake-upexams(seebelow).Itisyourobligationtobepresenttotakethe
scheduledexams.Please,donottakethiscourseifyoucannotbepresentfortheexamsat
the scheduled times. This is not negotiable. The only acceptable reasons for missing an
exam are a death in the family, serious illness verified by a doctor’s note, or a required
Universitysanctionedevent.
• Ifyoutakethetestinthetestingcenteryoumustgetanappointmentforthecorrectday,
takethetestwhentheclasstakesit,andinformmeatleastoneweekaheadoftimefor
eachtest!!!!!
• Also,youareresponsibleforkeepingtrackoftimeduringtheexams!!
Statementregardingrecordinganddistributionofcoursesessions:
Studentswhowishtomakeanauditoryorvisualrecordingofanyportionoftheclassmustspeak
with the instructor ahead of time. Any such recording is for personal use only. It may not be
shared,copied,uploadedtotheInternet,and/ordistributedwithoutwrittenpermissionfromthe
instructoraswellasanystudentwhoappearsorisheardintherecording.
Statementregardingstudentswithdisabilities:
Accommodations are collaborative efforts between students, faculty and the Disability Resource
Center (DRC). Students with accommodations approved through the DRC are responsible for
contactingthefacultymemberinchargeofthecoursepriortoorduringthefirstweekoftheterm
todiscussaccommodations.Studentswhobelievetheyareeligibleforaccommodationsbutwho
havenotyetobtainedapprovalthroughtheDRCshouldcontacttheDRCimmediatelyat503-7254150.
SafeCampusModule:
If you have not done so already, please complete theSafeCampusModule in d2l. The module
shouldtakeapproximately30to40minutestocompleteandcontainsimportantinformationand
resources. If you or someone you know has been harassed or assaulted, you can find the
appropriate resources on PSU’s Enrollment Management & Student Affairs: Sexual Prevention &
Responsewebsiteat:http://www.pdx.edu/sexual-assault/.PSU'sStudentCodeofConductmakes
itclearthatviolenceandharassmentbasedonsexandgenderarestrictlyprohibitedandoffenses
aresubjecttothefullrealmofsanctions,uptoandincludingsuspensionandexpulsion.
Notesonclickersandquizzes:
• I will ask a few questions sometime during the lecture about the material covered in the
previous lecture topic. Please do not communicate with others during the quiz. You are
welcome to look at notes to answer these; you will have 90 seconds to answer each one
using your clicker. These will comprise 25% of your grade, thus obtaining and registering
yourclickerisveryimportant.
• Note,theseareworth75pointstotal.Therewillbemorethan75questions.Theextrasare
thereforthosewhomustmissafew(sick,snow,etc.).Thus,therearenomakeups.
• Iwillalsoaskquestionsthatarenotgradedusingtheclickers.Thiswillserveasamethodto
determinehowwellIamgettingthematerialacrosstotheclass.
ProblemSets:
• Iwilluploadproblemsetseveryweek.
• AttheendoftheweekIwilluploadsolutions.
• These are optional and not graded. Doing them will help you with the concepts, please
cometoofficehourstotalkaboutthese.
Makeup/Cheating:
• Makeup exams are only given under extreme circumstances, e.g birth/death in family or
illness,whichrequiresmedicalattention(notefrommedicalprofessionalrequired).
• Theinstructorwilldeterminetheformatanddateofthemakeupexamination.
• Cheatingonanyexaminationorquizwillresultinazero.
Gradedetermination:
Gradeswillbedeterminedasfollows(percentageoftotalpossiblepoints*;yourpointsdividedby
thetotalpossiblepoints*multipliedby100):
90%-100% A
80%-89% B
70%-79% C
60%-69% D
≤59% F
*Thisnumbermightbeadjustedifnecessary.
RegradePolicy:Mustberequestedinwritingwithinaweekofreturnofexamination.Note:
Entireexamwillberegradedandthegrademaygodown.
Incompletes:
Iwillfollowtheuniversitypolicies.Thosepoliciesareshownhere:
http://www.pdx.edu/registration/grading-system#/?section=incompletegradei
Pleasereviewthese.
Syllabus(note:topics,readingandsubjectmattermaychange):
Date
Day.LectureTopic(s)
CELLCHEMISTRYANDPROTEINS
TuesSept29
ThursOct1
TuesOct6
1.Topic1:CellsandGenomes,andTopic2:ChemistryinBiology
2.Topic3:ChemicalEquilibriaandTopic4:Proteins1:Structure
andfolding
3.Topic5:Proteins2:Binding,RegulationandCatalysis
THECENTRALDOGMA-DNATORNATOPROTEIN
DNAMetabolismandChromosomes
ThursOct8
4.Topic6:DNAChemistryandStructure,andTopic7:
ChromosomesandGenomes
TuesOct13
5.Topic8:ChromatincompactionandnucleosomesandTopic9:
Epigeneticsandhigherorderstructures
6.Topic10:GenomeEvolution
EXAM1
7.Topic11:DNAReplication1:Mechanismsandmachineryand
Topic12:DNAReplication2:Origins,regulationandtelomerase
8.Topic13:DNAdamageandrepair,Topic14:Recombinationand
Topic15:Transposition
RNAMetabolism
9.Topic16:TranscriptionI-ProkaryoticmachineryandTopic17:
TranscriptionII:Eukaryoticmachinery
Post-transcriptionalEvents
10.Topic18:mRNAprocessingandsplicingandTopic19:
TranslationI:TheGeneticCode,tRNAstructureandfunction,tRNA
synthetases,Prokaryoticinitiation
11.Topic20:Translation2:EukaryoticInitiationandTopic21:RNA
world
EXAM2
ThursOct15
TuesOct20
ThursOct22
TuesOct27
ThursOct29
TuesNov3
ThursNov5
TuesNov10
ThursNov12
TuesNov17
ThursNov19
TuesNov24
ThursNov26
TuesDec1
ThursDec3
ThursDec10
TRANSCRIPTIONALREGULATORYMECHANISMS
Chapters1and2
Chapter3
Chapter3
Chapter4
WatsonandCrick
paper
Chapter4
Chapter4
Chapter5
Chapter5
Chapter6
Chapter6
Crick-Wobble
hypothesispaper
Chapter6
12.Topic22:TranscriptionalRegulation1:DNABindingandTopic Chapter7
23:TranscriptionRegulation2:Bacteria
13.Topic24:TranscriptionRegulation3:Eukarya
Chapter7
14.Topic25:RegulatoryCircuits,Topic26:EpigeneticsandTopic Chapter7
27:PostTranscriptionalRegulation
METHODSINMOLECULARBIOLOGY
15.Topic28:ProteinMethods
Chapter8
Thanksgiving
16.Topic29:DNAmethods
Chapter8
17.Topic30:GeneticMethodsandTopic31:Viruses
Chapter8
FinalExaminationThursdayDec108:00AM-9:50AM
LastUpdated:September28,2015
Readingin
Albertsetal.