2400 NEW YORK AVE. � WHITING, IN 46394 � TEL. 219-473-7770 � 773-721-0202 � FAX 219-473-4259

COURSESYLLABUSTerm:FALL2016

Course:CHEM320LBiochemistryLAB

InstructorInformation:InstructorName Dr.FionaGroninger-PoeOfficeNumber: 331PhoneNumber: (219)473-4357<leaveamessage!>Email: fpoe@ccsj.edu

TocontactDr.Poeusinge-mail:1. UseyourCCSJaccount2. Put“Biochem”or“Chem320”inthesubjectline3. Composeandsendyoure-mail

HoursAvailable: Office hours are posted outside of room 331; typically available 1:30-4:00 pm Monday through Thursday, additional hours by appointment

InstructorBackground:B.S.ManchesterUniversity(Chemistry,2008);Ph.D.UniversityofIllinoisatUrbana-Champaign(Biochemistry,2014);ScienceOlympiadVolunteerEventSupervisor(2014-present);AmericanSocietyforMicrobiologyscienceteachingfellow(2013);RobertL.SwitzerTeachingAward(2012);WhitingHighSchoolScienceOlympiadeventcoordinatorforProteinModeling(2014-2016).Researchinterestsincludemicrobiology,enzymology,agardegradationpathways,andsugarmetabolicpathwaysinplantpathogens.

CourseInformation:

CourseTime: Lecture:MondayandWednesday8:30–10:00amLab:Monday10:15-11:45am

Classroom: 334Prerequisites: CinMath104orplacedinahighermathcourse,CorbetterinCHEM

200,CHEM200L,CHEM205,CHEM205L,CHEM310,CHEM310,CHEM311,CHEM311L,andconcurrentenrollmentinCHEM320.

RequiredBooksandMaterials:

LaboratorynotebookwithcopypagesAppropriatelabattire:closedtoedshoes,longpantsorskirt,labcoat(optionalbutrecommended),hairtiesasneeded

LearningOutcomes/Competencies:Studentswill:

• Describechemicalandthermodynamicpropertiesthatdriveproteinstructure/functionrelationships

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• Justifytheuseofbuffersinstudyingbiologicalsystems• PredicthowalterationsattheDNAlevelorprimarystructurecouldaffectprotein

structureandfunction• Compareandcontrastproteinandnon-proteincatalysts• Comparetherolesofenzymes,substrates,products,andcofactorsinenergetic

pathwaysandphotosynthesis• Identifystructures/functionsofvitalcofactorssuchasTPP,PLP,NADH,NADPH,etc.• Describetheenzymaticmetabolism(anabolismandcatabolism)ofmacromolecules

necessaryforcellularlife• Comparereversibleandirreversibleenzymeinhibitionandpredicttheoutcomeon

specificpathways• Predictpathwayinhibitioninthepresenceofcommonregulatorymoleculessuchas

ATP,ADP,NADH,NAD+,pyruvate,citrate,etc.• Justifytheevolutionofenzymesandmetabolicpathwaysusingconcreteexamples• Calculateenergiesanddeterminespontaneityofthermodynamicreactions• Explainthesecondlawofthermodynamicsintermsofproteinfoldingandinteractions• Analyzetheroleofenzymesandcellularregulationinhumanhealthanddiseases• Developanddefendhypothesesinabiochemicallaboratorysetting• Explainthechemicalprinciplesbehindbiochemicaltestssuchasionexchange

chromatography,electrophoresis,staining,quantificationofprotein,quantificationofDNA,expressionsystems,andcompetentcells.

CourseDescription:A1-credithourlabimplementingthroughexperimentsvariousbiochemicaltechniquesviavariousinstrumentation.LearningStrategies:Flippedclassroom,activelearning,BlackBoard,groupdiscussions,teamprojects,collaborativelearning,laboratoryexercises,demonstrationsExperientialLearningOpportunities:Laboratoryexperienceisessentialforafundamentalunderstandingofthescientificmethod.Thiscoursehasarequiredlaboratoryportionthatprovidesstudentswithexperientiallearningthroughexperimentaldesign,hypothesisdevelopment,datainterpretation,andcommunicationofresultsthroughlaboratoryreports.Thelaboratorysectionofthiscourseadditionallyhasstudentscreateandprepareapublication-qualityresearchpaper. Assessments:

Prelab Due at the start of class: students must fill out a laboratory notebook with copy pages with hypothesis, goal, methods summary, etc. prior to class. Rubric available on BlackBoard.

Includedinlabreportscore

Labreports Written reports on weekly lab experiments; due at the next lab meeting. One from this category is dropped.

10x50=500pts

Quizzes Unannounced quizzes to evaluate safety, ethics, math, and/or technical skills. One from this category is dropped.

50points

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Poster Tobepresentedduringthefinalweekofclasses.RubricavailableonBlackBoard.

100points

GradingScale:100–92:A91–90:A-89–88:B+ 87–82:B 81–80:B-79–78:C+ 77–72:C 71–70:C-69–68:D+ 67–62:D 61–60:D-59andbelow FLABEXERCISETOPICS:

1. Lab1:Introductiontolabsafetyandplagiarismworksheet(availableonBB)2. Lab2:Titrationsofaminoacids3. Lab3:PDBviewerpart14. Lab4:PDBviewerpart25. Lab5:Albumindrugdelivery6. Lab6:Proteinexpressionandextraction7. Lab7:Proteinpurification8. Lab8:SDS-PAGEanalysis9. Lab9:Bradfordassayofproteinconcentration10. Lab10:Enzymekinetics11. Lab11:Inquirylab112. Lab12:Inquirylab2

DUEDATES:

• CheckBlackBoardforlabhandoutsandup-to-dateinformationregardinglectureandlab• OccasionallyLabwillbeginduringthescheduledlecturetime;studentsshouldbeprepared

forlabatthestartoflecture.• MONDAYS

o Pre-labsaredueatthestartofthatlabo Labreportsaredueonthenextlabmeeting(e.g.Lab1isdueonthedayLab2is

performed)o RubricsandhandoutsareavailableonBlackBoardo ContacttheprofessorASAPifyouareabsentduringlab

CourseSchedule:

ClassDate Assignmentsdue ClassDiscussion/ActivitiesWeek1:Sept6Lab1Introductiontolabsafetyandplagiarismworksheet(availableonBB)

PurchasethetextbookwithaccesscodePurchaselabnotebook

Week2:Sept12Lab2TitrationsofaminoacidsSEPT13–LASTDAYTO

Prelab2due9/12Lab1due9/12

Labsafetyquiz

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ADD/DROPWeek3:Sept19Lab3PDBviewerpart1

Prelab3due9/19Lab2due9/19

Week4:Sept26Lab4PDBviewerpart2SEPT30–LASTDAYTO

WITHDRAW

Prelab4due9/26Lab3due9/26

Week5:Oct3-6Lab5Albumindrugdelivery

OCT3-MIDTERM

Prelab5due10/3Lab4due10/3

Week6:Oct10Lab6:Proteinexpressionandextraction

Prelab6due10/10Lab5due10/10

Week7:Oct17Lab7:Proteinpurification

Prelab7due10/17Lab6due10/17

Week8:Oct24LAB8:SDS-PAGEanalysis

Prelab8due10/24Lab7due10/24

Week9:Oct31LAB9:BradfordAssay

Prelab9due10/31Lab8due10/31

Week10:Nov7Lab10:Enzymekinetics

Prelab10due11/7Lab9due11/7

Week11:Nov14Lab11:Inquirylab

Prelab11due11/14Lab10due11/14

Week12:Nov21–24Lab12:Inquirylab

NOV24–26THANKSGIVINGRECESS

Prelab11due11/21Lab11due11/21

Week13:Nov28 Lab12due11/28 WorkingonpostersWeek14:Dec5-8POSTERSESSION–TBADEC9–LASTDAYTO

WITHDRAW

Postershouldbecompletedandassembledbythetimethepostersessionstarts.CheckBBformoreinformation.

Presentingandjudgingposters

Week15:Dec12-15SEMESTER

EXAMINATIONS

Noexaminationscheduled

Ireservetherighttochangethisscheduletomeettheneedsoftheclass.

Responsibilities AttendingClass

Youcannotsucceedinthisclassifyoudonotattend.Webelievethatintellectualgrowthandsuccessinhighereducationoccurthroughinteractionintheclassroomandlaboratories.However,wedonotwant

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topenalizestudentsforparticipatingincollege-sponsoredevents.Whenyoumissclassbecauseofacollegeevent,youmustgivenoticeofyourabsenceinadvance,andyouareresponsibleforallmissedwork.Beingabsentdoesn’texcuseyoufromdoingclasswork;youhavemoreresponsibilitiestokeepupandmeettheobjectivesofthiscourse.Attendanceiscountedasbeingpresentfromthefirst10minutesofclassuntiltheendoflectureandlab.Itisthestudent’sresponsibilitytomakeattendanceapriority.Anyonemissingafterthefirst10minutesofclasswillbemarkedabsentunlessawrittenexcuseisprovidedwithin24hoursoftheoccurrence.Similarly,anyoneleavingearlywithoutawrittenexcusewillbecountedasabsent.Participationthroughregularattendanceisrequiredtobesuccessfulinthiscourse.Therefore,ifastudentisabsentmorethanthree(3)times(excessivetardinessiscountedasabsence),thestudentwillbesubjectedtoagradeofForFWperpolicystatedundertheWithdrawalfromClassessectiononthissyllabus.Intheeventofabsenceduringanexam,thestudentwillreceiveaZERO(0)onthatexam.Thelowestexamscoreisdropped,sothatexamscorewillnotbeconsideredwhendeterminingthefinalgrade.Ifastudentisabsentduringmorethanoneexam,thestudentwillreceiveaZERO(0)foreachexam,butonlyonegradewillbedropped.Itisthestudent’sresponsibilitytoensureattendanceonexamdates.Intheeventofmultipleexcusedabsences(withacceptabledocumentation),itisthestudent’sresponsibilitytocontacttheinstructortodetermineanappropriatecourseofaction.Intheeventofabsenceduringlab,thestudentmustcontacttheinstructorwithin24hoursoftheabsencetodetermineanacceptablecourseofaction.Eachlaboratoryexerciseisdifferent,andinsomecasesamake-uplabwouldbeimpracticalduetocostsortimerestrictions.Aswithexams,onelabreportisdroppedsooneabsenceispermittedwithoutpenalty.Forexcusedabsences,make-uplabsmaybepermittedattheinstructor’sdiscretiononlyifanacceptablesubstituteassignmentcanbedetermined.ALLWORKISDUEONTHEDUEDATESPECIFIEDINTHISSYLLABUSORONBLACKBOARD.Ifastudentisabsentonlab2,thestudentmuststillturninlab1duethatday.Contacttheinstructorifanextensionisneeded.See“TurningInYourWork”below.

TurningInYourWork

Youcannotsucceedinthisclassifyoudonotturninallyourworkonthedayitisdue.Duedatesarespecifiedforeachassignmentonthissyllabus;anychangeswillbeannouncedinclassandpostedonBlackBoard.

ASSIGNMENTSWILLNOTBEACCEPTEDAFTERTHEIRDUEDATES.Youmayrequestanextensioninwritingatleast24hoursinadvanceoftheduedateforassignments,butitisuptotheinstructor’sdiscretion

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whetherornottoallowanextension.

Ifyouareabsentthedaythatanassignmentisdue,followtheseguidelines:

• HOMEWORK:turninviaBlackBoardonitsscheduledduedate

• IN-CLASSACTIVITIES:itisthestudent’sresponsibilitytocollecttheassignmentanddothisworkindependentlyafteranabsence.Creditisawardedforexcusedabsencesonly.

• QUIZZES:cannotbeturnedinlateormadeup;studentwillreceiveazeroonallmissedquizzes.

• LABREPORTS:turninviaBlackBoard,e-mail,campusmail,orhandedintotheprofessoronitsscheduledduedate;youmustcontacttheprofessortodeterminewhattodoaboutmissingthelabsection.

Allassignmentscanbesubmittedviae-mailifalinkisnotprovidedthroughBB.Itisthestudent’sresponsibilitytorequestextensionsinwritingfromtheinstructor.

UsingElectronicDevices

Electronicdevicescanonlybeusedinclassforcourse-relatedpurposes.IfyoutextoraccesstheInternetforotherpurposes,youmaybeaskedtoleave,inwhichcaseyouwillbemarkedabsentandwillloseparticipationpointsfortheday.

ParticipatinginClass Youmustbeontime,stayforthewholeclassandspeakupinawaythatshowsyouarepreparedforclass.Ifyouarenotpreparedforclassdiscussion,youmaybeaskedtoleave,inwhichcaseyouwillbemarkedabsentandloseparticipationpointsfortheday.Studentsmustbepreparedforclass,politeandrespectful,helpwithin-classgroupwork,showattentivenessthroughoutclass,andensurethatconversationsstayontopic.WATCHINGTHELECUTREVIDEOSONLINEMUSTBECOMPLETEDPRIORTOCLASSMEETINGTIME,ORPOINTSWILLBEDEDUCTED.2pointswillbedeductedforeachinfraction,uptothemaximumpointsfortheday.GradenoteswillbeenteredonBlackBoarddescribingthescore.

DoingYourOwnWork

Ifyouturninworkthatisnotyourown,youaresubjecttojudicialreview,andtheseprocedurescanbefoundintheCollegeCatalogandtheStudentPlanner.ThemaximumpenaltyforanyformofacademicdishonestyisdismissalfromtheCollege.Usingstandardcitationguidelinestodocumentsourcesavoidsplagiarism.Forthisclass,youMUSTuseAmericanChemicalSociety(ACS)style,availableonlineforfreeatthefollowinglink:http://pubs.acs.org/userimages/ContentEditor/1246030496632/chapter14.pdfBesuretouseyourownwordscompletely(useyourownsentencestructurenotjustathesaurustochangeafewwordsorphrases),citeyoursourceparentheticallyinthetext,andattachaworkscitedpageto

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theendoftheassignment.Ifyourpaperissimilarinsentencestructure,phrasing,figures,etc,toanotherstudent’sbothstudentswillbepunishedbasedontheseverityoftheplagiarism.PLEASENOTE:Allpapersmaybeelectronicallycheckedforplagiarism.

WithdrawingfromClass

Afterthelastdayestablishedforclasschangeshaspassed(seetheCollegecalendar),youmaywithdrawfromacoursebyfollowingthepolicyoutlinedintheCCSJCourseCatalog.

ResourcesStudentSuccessCenter:

TheStudentSuccessCenterprovidesfacultytutorsatalllevelstohelpyoumasterspecificsubjectsanddevelopeffectivelearningskills.Itisopentoallstudentsatnocharge.YoucancontacttheStudentSuccessCenterat219473-4287orstopbytheLibrary.

DisabilityServices:

DisabilityServicesstrivestomeettheneedsofallstudentsbyprovidingacademicservicesinaccordancewithAmericanswithDisabilitiesAct(ADA)guidelines.Ifyoubelievethatyouneeda“reasonableaccommodation”becauseofadisability,contacttheDisabilityServicesCoordinatorat219-473-4349.

CCSJAlerts:

CalumetCollegeofSt.Joseph’semergencycommunicationssystemwilltellyouaboutemergencies,weather-relatedclosings,orotherincidentsviatext,email,orvoicemessages.PleasesignupforthisimportantserviceannuallyontheCollege’swebsiteat:http://www.ccsj.edu/alerts/index.html.Inaddition,youcancheckothermediaforimportantinformation,suchasschoolclosings:Internet:http://www.ccsj.eduRadio:WAKE–1500AM,WGN–720AM,WIJE–105.5FM,WLS–890AM,WZVN–107.1FM,WBBMNEWSRADIO78TVChannels:2,5,7,9,32

Emergency Procedures MEDICAL EMERGENCY

EMERGENCY ACTION

1. Call 911 and report incident. 2. Do not move the patient unless safety dictates. 3. Have someone direct emergency personnel to patient. 4. If trained: Use pressure to stop bleeding. 5. Provide basic life support as needed.

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FIRE EMERGENCY ACTION

1. Pull alarm (located by EXIT doors). 2. Leave the building. 3. Call 911 from a safe distance, and give the following information: • Location of the fire within the building. • A description of the fire and how it started (if known)

BUILDING EVACUATION 1. All building evacuations will occur when an alarm sounds and/or upon notification by

security/safety personnel. DO NOT ACTIVATE ALARM IN THE EVENT OF A BOMB THREAT.

2. If necessary or if directed to do so by a designated emergency official, activate the building alarm. 3. When the building evacuation alarm is activated during an emergency, leave by the nearest

marked exit and alert others to do the same. 4. Assist the disabled in exiting the building! Remember that the elevators are reserved for persons

who are disabled. DO NOT USE THE ELEVATORS IN CASE OF FIRE. DO NOT PANIC. 5. Once outside, proceed to a clear area that is at least 500 feet away from the building. Keep

streets, fire lanes, hydrant areas and walkways clear for emergency vehicles and personnel. The assembly point is the sidewalk in front of the college on New York Avenue.

6. DO NOT RETURN to the evacuated building unless told to do so by College official or emergency responders.

IFYOUHAVEADISABILITYANDAREUNABLETOEVACUATE: Stay calm, and take steps to protect yourself. If there is a working telephone, call 911 and tell the emergency dispatcher where you are or where you will be moving. If you must move,

1. Move to an exterior enclosed stairwell. 2. Request persons exiting by way of the stairway to notify the Fire Department of your location. 3. As soon as practical, move onto the stairway and await emergency personnel. 4. Prepare for emergencies by learning the locations of exit corridors and enclosed stairwells.

Inform professors, and/or classmates of best methods of assistance during an emergency.

HAZARDOUS MATERIAL SPILL/RELEASE EMERGENCY ACTION

1. Call 911 and report incident. 2. Secure the area. 3. Assist the injured. 4. Evacuate if necessary.

TORNADO EMERGENCY ACTION

1. Avoid automobiles and open areas. 2. Move to a basement or corridor. 3. Stay away from windows. 4. Do not call 911 unless you require emergency assistance.

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SHELTER IN PLACE EMERGENCY ACTION

1. Stay inside a building. 2. Seek inside shelter if outside. 3. Seal off openings to your room if possible. 4. Remain in place until you are told that it is safe to leave.

BOMB THREATS EMERGENCY ACTION

1. Call 911 and report incident. 2. If a suspicious object is observed (e.g. a bag or package left unattended): • Don’t touch it! • Evacuate the area.

TERRORISM AND ACTIVE SHOOTER SITUATIONS EMERGENCY ACTION

1. Call 911 and report intruder.

RUN, HIDE OR FIGHT TIPS:

1. Prepare – frequent training drills to prepare the most effectively. 2. Run and take others with you – learn to stay in groups if possible. 3. Leave the cellphone. 4. Can’t run? Hide – lock the door and lock or block the door to prevent the shooter from coming

inside the room. 5. Silence your cellphone -- use landline phone line. 6. Why the landline? It allows emergency responders to know your physical location. 7. Fight – learn to “fight for your life” by utilizing everything you can use as a weapon. 8. Forget about getting shot – fight! You want to buy time to distract the shooter to allow time for

emergency responders to arrive. 9. Aim high – attack the shooter in the upper half of the body: the face, hands, shoulder, neck. 10. Fight as a group – the more people come together, the better the chance to take down the

shooter. 11. Whatever you do, do something – “react immediately” is the better option to reduce traumatic

incidents.