Biochemistry2BB3:ProteinStructureandEnzymeFunction
ContactInformation
Instructor
Dr.DanielYang
yang@mcmaster.ca
Ext.22455
Office:HSC4H25a
OfficeHours:Thursday9:30am-10:30amduringweeks1to8
TeachingAssistants
Stephen Boulton
boultos@mcmaster.ca
William Jennings
greerwj@mcmaster.ca
Cheryl Bachan
bachanc@mcmaster.ca
JonathanMapletoft
jp.mapletoft@gmail.com
NikolaIvetic
nikola_ivetic17@hotmail.com
CourseWebsite
Courseinformationwillbepostedonlearnlink.
Learnlink:
Courses
BIOCHEMProgram
Biochem3G03
ToaccessLearnLink,pleasegoto:
https://www.learnlink.mcmaster.ca
downloadandinstallLEARNLINK,orusebrowseraccess
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-UserID:Firstname.Lastname
-Password:Your7-digitstudentnumber
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willnotbeontheclasslistandwillnothaveaccesstoLearnLink.Ifyouhaveproblemininaccess
LearnLinkpleasesendanemailto
help@learnlink.mcmaster.ca
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CourseInformation
Tuesday,Thursday&Friday
8:30am-9:20am
Term2
JHE264
CourseObjectives
Our goal in delivering Biochemistry 2BB3 is to NOT BORE YOU with disjointed facts that will likely be
memorized and then quickly forgotten soon after examination periods. Instead I want to get you
TURNEDONtotheamazingworldofproteinsandforyoutowalkawayfromthiscoursewithasetof
KEYCONCEPTSthatgovernatrueunderstandingandappreciationofwhyitisthatPROTEINSRULE!In
addition, these concepts will serve you well for your future courses and research within Biochemistry
and Biomedical Sciences. Students will be exposed to these concepts in both traditional lecture and
small group inquiry environments. Some of the key concepts I want you to take away, include: 1)
understandingbasicproteinstructureandtheforcesthatgovernitsformation,2)methodsforprotein
structurepredictionandexperimentaldetermination,3)proteinfolding,4)enzymemediatedchemical
reactionsandtheirassociatedkineticparameters.
7weeks(weeks1,2,3,4,5,6and8)willbelectureformat.Weeks9,10,11and12(ie.weeksstarting
Mar 1, 8, 15 and 22) are being made available for students to undertake more self-directed learning.
Duringthesefourweeks,studentswillbeplacedintosmallgroupsandthengiventheopportunitytoask
and answer questions regarding aspects of proteins that have or have not been already touched on
during lectures. Inquiry courses emphasize both process and content, and therefore a secondary
objectiveofthiscourseistodevelopyourinquiryskillset.Throughoutthiscourse,withguidancefrom
your TA and thecourseinstructors,youwillrefineyourverbalandwrittencommunication skills, your
abilitytofindandcriticallyevaluateinformation,andyourabilitytoworkeffectivelyasamemberofa
group.
MaterialsandFees
Textbook
EssentialBiochemistry,3rdedition.C.W.PrattandK.Cornely.Wiley&SonsInc.2014.(required)
ThisbookisavailableattheCampusStore.
Calculator
OnlytheMcMasterstandardcalculator(Casiofx-991MS)willbeallowedduringalltestsandexams.Itis
availableattheCampusStore
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CourseRequirements
Evaluation: It will be based on the followings:
I.
Quizzes(40%)EachFridayofalectureweekstartingJan15thandendingFeb26th,youwillhavea
testtocompletethatisworth8%ofyourfinalmark.Sincethelowestmarkwillbedropped,thefinal
markwillbetheresultof5weeksx8%pertest=40%offinalmark.Theonetestwhichwillbedropped
is to cover emergencies etc. that prohibit a student from being present; therefore, no excuses for
missingmorethanoneFridaytestwillbeaccepted.AllmarkswillbepostedusingpartialstudentI.D
numbersonLearnLink.NOTE:Byattendingclassyouareagreeingtothismethodofgradedisclosure.
II.
Assignment1(10%)DueFridayFebruary5by4pmindropbox,worth10%offinalmark.
Assignment2(10%)DueFridayMarch11by4pmindropbox,worth10%offinalmark.
III. Inquiry(40%)
*
FinalGroupPresentation:weeks13and14(10%offinalmark)
*
FinalWrittenReport(group):dueTuesdayApril7thby4pmindropbox(24%offinalmark)
*
PeerEvaluations:individualcontributiontoyourgroup(2%offinalmark)
*
TAMeetingReports:1%perreport(4%finalmark)
For the Quizzes portion of the course, students are responsible for materials covered in the textbook and
lectures.
Percentage grade will be converted to a final letter grade (see Table below).
%
Letter
%
Letter
%
Letter
%
Letter
%
Letter
100-90 A+
79-77
B+
69–67 C+
59-57
D+
49-0
F
89–85 A
76-73
B
66–63 C
56-53
D
84–80 A-
72-70
B-
60-62
C-
52-50
D-
Allpercentagegradeswithin0.5%ofthenextlettergradewillbereviewed.
IMPORTANT:Questionsregardingthemarkingoradditionoftestsandassignmentsmustbebroughtto
theattentionoftheTAwithinONEweekoftheirreturntoyou.
ImportantDetails:
ThiscoursewillrelyheavilyontheuseofLearnLink(http://learnlink.mcmaster.ca)andAvenuetoLearn
If you have difficulty gaining access, or for further assistance, please contact LearnLink Help Desk at
help@learnlink.mcmaster.ca.
I.
WeeklyTests:Asmentionedabove,eachFridaystartingJanuary15,wewillbehavingashort,15
minute, in-class test. Students will pick up an OMR sheet on their way into class. During the last 15
minutesofclass,youwillhave5multiple-choicequestionstoanswer.OMRsheetswillbeplacedina
collectionboxattheendofclass.MarkswillbepostedonLearnLinkASAPandanswerswillbetakenup
duringthefollowingclass.Pleasenotethatmaterialcoveredineachtestwillbecumulativethroughout
the entire course, meaning that you will be responsible for all material covered from the start of the
courseuptoandincludingtheclassprecedingtheFridaytest.Therewillbeatotalof6tests,thelast
beingFeb26th.Onlytheresultsfromthebest5testswillcounttowardyourfinalmark(ie.5x8%per
test=40%offinalmark).Sinceonetestwillbedropped,noexcuseswillbeacceptedformissedtests.
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II.
Assignments:Eachassignmentwillbeworth10%ofyourfinalmark.Thefirstassignmentisdue
onFridayFebruary5by4pm.ThesecondassignmentisdueonFridayMarch11by4pm.Pleasenote
thatassignmentsmustbeuploadedtoAvenuetoLearndropboxnolaterthan4pm.
III. Inquiry: During the 7 weeks of lecture, students will be exposed to different fundamental
aspects of proteins. During the next 4 weeks of the course, students will carry out a more in-depth,
small group, inquiry based study. Students are being randomly assigned to groups of 10 people
(2BB3_Group Assignment.pdf in learnlink). Although designated inquiry will not begin until the
week of March 1st, I strongly suggest that you use the intervening time to orient yourselves with
your other group members and start considering a common question for your group to explore.
Each group will be assigned a TA and will be expected to meet with their TA once a week for 20
minutes during weeks 9, 10, 11 and 12 (details will be posted on learnlink).
LearnLink:ALearnLinkfolderlabeled‘INQUIRY’willbesetupforcommunicatingimportantinformation
fromthefacilitatorsasthecourseunfolds.WithintheINQUIRYfolder,therewillbe5folders(onefor
each TA) labeled A-E and an additional folder labeled GENERAL INFORMATION - be sure to check this
generalconferencefolderweeklyforimportantannouncements.WithinfoldersA-E,additionalfolders
willbesetupforeachgroup(therewillbe4independentgroupsassignedforeachTA,A-E).Hereeach
group can communicate with their members, schedule meetings, and share information, or direct
specificquestionstotheirTA.
CourseSchedule
Jan
Feb
Mar
April
Tue
5
12
19
26
2
9
16
23
1
8
15
22
29
5
Thu
7
14
21
28
4
11
18
25
3
10
17
24
31
7
Fri
8
15
22
29
5
12
19
26
4
11
18
25
1
8
Weeks
1
2
3
4
5
6
7
8
9
10
11
12
13
14
Tues
Intro
Ch2
Ch4
Ch5
Ch5
Ch6
Thu
Fri
Ch1
Ch2
Ch4
Ch4
Ch4
Ch5
Ch5
Ch5
Ch5
Ch6
Ch6
Ch6
Mid-TermRecess
Ch7
Ch7
Ch7
GroupProgressMeetings
GroupProgressMeetings
GroupProgressMeetings
GroupProgressMeetings
Presentations
Presentations
FinalExam
Thiscoursehasnofinalexam.
4
Tests
Ch1&2
Ch4
Ch5a
Ch5b
Ch6
Ch7
GroupAssignment:Therewillbe20groups,assignedA1-4,B1-4,C1-4,D1-4andE1-4.Studentsareto
carryoutamoreindepth,smallgroup,inquirybasedstudyontopicsassignedtotheirgroup.
TOPICS/AREAS:
A–ProteinStructure(secondaryand/ortertiary)and
Determination–ExperimentalMethods B–ImpactofaProtein(s)onHealthandSociety
C–Protein-ProteinInteractions
D–EnzymeReactionMechanismsandKinetics
E–Biopharmaceutical
ProgressMeetingswithTA:Duringweeks9,10,11and12,groupswillbescheduledtomeetwiththeir
TA for 20 minutes to report on their recent work, review progress and set/refine direction. Exact
meetingtimesandlocationsareprovidedlateronLearnlink.ToensurethatTAshaveenoughtimeto
helpstudentsduringthose4shortmeetings,eachgroupisREQUIREDtouploadaonepagesummaryof
their progress, questions etc, to their LearnLink folder one day prior to their designated TA meeting.
Reportsshouldbeone-page,double-spaced,typewrittenandmustbesubmittedtoLearnLinktheday
beforeascheduledTAmeeting.Eachreportisworth1%ofthefinalmark.Youshouldcomeprepared
toshowanyevidenceofyourresearchandlearning,ie.youmaybringacopyofkeypapersorreview
articlesthathaveguidedyou.Thereportandanykeyarticleswillbeplacedinyourgroup’sfiletotrack
your progress. Meetings will be informal. Because the success of the group depends on the full
participation of all members, attendance at all meetings is mandatory. Failure to provide
documentation to the Assistant Dean for medical or legal conflicts will result in an automatic zero for
groupparticipation.
FinalGroupPresentations:StartingTuesdayMarch29th,eachgroupwilldeliverafinalpresentation.A
maximumoftwomembersfromagroupwillbepermittedtomakethegrouppresentation;however,
followingthepresentation,allmembersofthe groupwillproceedtothefrontoftheroomtoanswer
questionsfromtheaudience.ThepresentationCANNOTexceed9minutestotal,leaving2to5minutes
forquestions.Roughly1/3ofthepresentationshouldfocusonthebackgroundyoumustcommunicate
toyouraudience,androughly2/3onansweringthe‘Question’yourgroupdecidedtopursue.Besure
to use references appropriately. Any information (including figures) or ideas that are not your own,
mustbereferencedtotheprimarysource(notageneraltextbook).Youmustsendyourpresentation
filetoyourgroup’sLearnLinkfolderby10:00am,theDAYBEFOREyourpresentation.AllPowerPoint
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presentationswillbeloadedontothelaptopbeingusedthatday,astimewillnotallowforeachgroup
touseindividualcomputers.Thefinalpresentationswillbeorganizedaspartofasymposiumoneach
ofthe5generaltopics.Eachpresentationcanbuildon,orrefertooneoftheotherthreetalkswithin
their broader general topic section, as they will have some common ground, should you choose to
coordinate your presentation with other groups. The order of the presentations is indicated in the
scheduleneartheendofthecourseoutline.Markswillbegivenbasedonthefollowingcriteria:
CONTENT
•
•
•
•
•
Was the background material appropriate, not excessive, and helped the audience’s
comprehension of the topic?
Didthegroupdemonstratecreativityintheirapproachtothequestion?
Didthegroupuseadequateresultsfromoriginalresearchtosupporttheircontention?
Didthegroupdemonstrateanunderstandingofbasicbiochemicalprinciples?
Didthegroupcriticallyevaluatetheliterature,integrateandreconstructthenewknowledge?
ORGANIZATIONANDFORMAT
•
•
•
Wastheformatofthepresentationwellorganizedandpresentedinalogical,easy-to-follow
sequence?
Wasthepresentationindicativeofaclearlydefinedsetofobjectives?
Wastheuseofvisualsappropriateandlegible? CLARITYANDDELIVERY
Clear,appropriateuseofscientificlanguage,terminology
Wasthespeakerclearandaudible?
Didthespeakerremainattentiveandenthusiasticthroughoutthepresentationtomakeit
rewardingfortheaudienceandsustaininterest?
• Wasthedeliverypracticedandsmooth?
•
•
•
POST-PRESENTATION
•
•
Abilitytoanswerquestions
DemonstratedknowledgeofBiochemistry
Final Written Report: Each group will write a final report on their group inquiry project. The report
shoulddemonstratealogicalprogressionfromthequestion,throughtotheconclusion.Roughly2/3of
thereportshouldfocusonthebiochemicalbackgroundyoumustcommunicatetoyouraudience,and
roughly1/3on‘What’snext’.Anyinformation(includingfigures)orideasthatarenotyourown,must
bereferencedtotheprimarysource(notageneraltextbook).Atextbookmaybereferencedforgeneral
background information. Do not provide a bibliography, but a proper reference section (see journals
liketheJournalofBiologicalChemistry,etc...www.asbmb.org).Thefinalreportshouldbeamaximum
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of5pages,double-spaced,12-pointTimesNewRomanfont,withone-inchmargins.Figuresandtables
maybeincludedwithinthemaintext,orincludedasappendices,anddonotcounttowardthefinalpage
count.EachgroupisrequiredtosubmitonecopyofthereporttoAvenuetoLearndropboxNOlater
than4pmonTuesdayApril7th.
Marksforthewrittenreportwillbeassignedasfollows:
•
•
•
•
•
•
OVERALLSTRUCTURE(3marks):organizationandlogicalflow
FIGURESANDTABLES(3marks):gooduseof
BACKGROUND(5marks):descriptionandbackgroundofrelevantmaterialforsettingupthe
question
ANALYSIS(8marks):levelofdepthandanalysisinaddressingquestion
SUMMARY(3marks):clearandconcise,includingfuturedirections
REFERENCING(2marks):properuseof
Peer Evaluations: You will be asked to reflect on each member’s participation and preparation,
knowledge acquisition, group dynamics and overall contribution to the group. Keep these important
aspects in mind throughout the term as you work within your group. At the conclusion of the term,
each student will be required to assess contributions made by individual group members, including
themselves.Arubricwillbepostedonlearnlinktowardstheendofthetermforyoutofillinforpeer
evaluation.Thismandatoryevaluationwillbeusedasatoolto‘flag’anygroupconflictsthatwerenot
obvioustotheTAs,orwhenthereisaconsensusamongthegroupthatamember(s)ofthegrouphas
notparticipatedfullyintheproject.Theseevaluationswillbetakenintoaccountwhenevaluatinggroup
workcomponents.
MissedWork
Ifyouareabsentfromtheuniversityforaminormedicalreason,lastingfewerthan5days,youmay
reportyourabsence,oneperterm,withoutdocumentation,usingtheMcMasterStudentAbsenceForm
(http://www.mcmaster.ca/msaf/).Absencesforalongdurationorforotherreasonsmustbereported
totheAssociateDeanofScienceoffice,withdocumentation,andreliefmaynotnecessarilybegranted.
AfterfillingouttheMSAFyoumustimmediatelycontactyourcourseinstructor(normallywithin2
workingdays)byemailtolearnwhatreliefmaybegrantedfortheworkyouhavemissedandrelevant
detailsforsubmissionorlocationofmake-uptest.PleasenotethattheMSAFmaynotbeusedforterm
workworth25%ormore,norcanitbeusedforthefinalexam.
UniversityPolicies
AcademicIntegrity
Youareexpectedtoexhibithonestyanduseethicalbehaviourinallaspectsofthelearningprocess.
Academiccredentialsyoueararerootedinprinciplesofhonestyandacademicintegrity.
Academicdishonestyistoknowinglyactorfailtoactinawaythatresultsorcouldresultinunearned
academiccreditoradvantage.Thisbehaviourcanresultinseriousconsequences,e.g.thegradeofzero
onanassignment,lossofcreditwithanotationonthetranscript(notationreads:“GradeofFassigned
foracademicdishonesty”),and/orsuspensionorexpulsionfromtheuniversity.
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Itisyourresponsibilitytounderstandwhatconstitutesacademicdishonesty.Forinformationonthe
varioustypesofacademicdishonestypleaserefertotheAcademicIntegrityPolicy,locatedat
www.mcmaster.ca/academicintegrity.
Thefollowingillustratesonlythreeformsofacademicdishonesty:
1. Plagiarism,e.g.thesubmissionofworkthatisnotone’sownorforwhichother
credithadbeenobtained.
2. Impropercollaborationingroupwork.
3. Copyingorusingunauthorizedaidsintestsandexaminations.
CourseOnlineContent
Inthiscoursewewillbeusing(email,LearnLink).Studentsshouldbeawarethat,whentheyaccessthe
electroniccomponentsofthiscourse,privateinformationsuchasfirstandlastnames,usernamesfor
theMcMasteremailaccounts,andprogramaffiliationmaybecomeapparenttoallotherstudentsinthe
samecourse.Theavailableinformationisdependentonthetechnologyused.Continuationinthis
coursewillbedeemedconsenttothisdisclosure.Ifyouhavequestionsorconcernsaboutsuch
disclosure,pleasediscussthiswiththecourseinstructor.
StudentAccessibility
StudentswhorequireacademicaccommodationmustcontactStudentAccessibilityServices(SAS)to
makearrangementswithaProgramCoordinator.Academicaccommodationsmustbearrangedforeach
termofstudy.StudentAccessibilityServicescanbecontactedbyphone905-525-9140ext.28652oremailsas@mcmaster.ca.Forfurtherinformation,consultMcMasterUniversity’sPolicyforAcademic
AccommodationofStudentswithDisabilities.
ChangestotheCourseOutline
TheinstructorandUniversityreservetherighttomodifyelementsofthecourseduringtheterm.The
Universitymaychangethedatesanddeadlinesforanyorallcoursesinextremecircumstances.Ifeither
typeofmodificationbecomesnecessary,reasonablenoticeandcommunicationwiththestudentswill
begivenwithexplanationandopportunitytocommentonchanges.Itistheresponsibilityofstudentsto
checktheirMcMasteremailaccountsandcoursewebsitesweeklyduringthetermandtonoteany
changes.
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