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

COURSESYLLABUSTerm:FALL2016

Course:CHEM320BiochemistryLecture

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

InstructorBackground:B.S.ManchesterUniversity(Chemistry,2008);Ph.D.UniversityofIllinoisatUrbana-Champaign(Biochemistry,2014);ScienceOlympiadVolunteerEventSupervisor(2014-present);AmericanSocietyforMicrobiologyscienceteachingfellow(2013);RobertL.SwitzerTeachingAward(2012).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,andconcurrentenrollmentinCHEM320L.

RequiredBooksandMaterials:

Appling’sBiochemistryConceptsandConnections,PearsonPublishingISBN–0321839927ISBN–9780321839923Youwillneedanaccesscodeforhomeworkassignments

LearningOutcomes/Competencies:Studentswill:

• Describechemicalandthermodynamicpropertiesthatdriveprotein

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structure/functionrelationships• 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:A3-credithourcourseimplementingthestructureandfunctionofcellularconstituents;enzymology;metabolismofcarbohydrates,lipids,aminoacids,nucleotides;molecularbiologyofbiosynthesisofproteinsandnucleicacids.LearningStrategies:Flippedclassroom,activelearning,BlackBoard,groupdiscussions,teamprojects,collaborativelearning,laboratoryexercises,demonstrationsExperientialLearningOpportunities:Laboratoryexperienceisessentialforafundamentalunderstandingofthescientificmethod.Thiscoursehasarequiredlaboratoryportionthatprovidesstudentswithexperientiallearningthroughexperimentaldesign,hypothesisdevelopment,datainterpretation,andcommunicationofresultsthroughlaboratoryreports.Thelaboratorysectionofthiscourseadditionallyhasstudentscreateandprepareapublication-qualityresearchpaper. Assessments:

Quizzes Given at the beginning of class; covers the lectures posted on BlackBoard; lowest 3 scores are dropped

5ptseach=approx.100pts

LectureExams 90 minutes, 4 total; lowest score is dropped 100ptsx3=300ptsFinalExam ACS Biochemistry standardized examination

given during finals week; grade will not be dropped

150pts

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Homework ACCESS CODE IS REQUIRED. Homework will be assigned through the companion website, with a link available on BlackBoard. Lowest score is dropped

10ptsx11=110pts

ClassParticipation Respectful demeanor, prepared for class, no distractions, helps group with in-class work; three scores in this category are dropped WATCHING THE LECUTRE VIDEOS ONLINE MUST BE COMPLETED PRIOR TO CLASS MEETING TIME, OR POINTS WILL BE LOST IN THIS CATEGORY

5pts/day=approx.100pts

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 FLECTURETHEMES:

1. Structure/functionrelationships2. Chemicallogicgovernsbiochemicalprinciples3. Enzymesandmetabolicpathwaysworkinconcerttomaintainhumanhealth;manyofthese

pathwaysarewellunderstoodandtightlyregulated4. Biochemistrytoolbox:specifictechniqueswereusedtodeterminebiochemicalinformation

LECTURETOPICS:Exam1:Sept26

1. TheChemicalFoundationofLife(Ch2)2. TheEnergeticsofLife(Ch3)3. Carbohydrates:Sugars,Saccharides,Glycans(Ch9)4. Proteinstructureandfunction(Ch5,6,7.9-7.11)

Exam2:Oct265. Enzymes:BiologicalCatalysts(Ch8)6. Metabolismoverview:glycolysis,gluconeogenesis,glycogenpathway(Ch12.1-12.9)citric

acidcycle(Ch13)7. Electrontransport,OxidativePhosphorylation,OxygenMetabolism(Ch14)8. Photosynthesis(Ch15.1-15.4)

Exam3:Nov169. Lipids,Membranes,andCellularTransport(Ch10)andMetabolism(Ch16.1-16.7)10. InterorganandIntracellularCoordinationofEnergyMetabolisminVertbrates(Ch17)11. AminoAcidandNitrogenMetabolism(Ch18)

Exam4:Dec712. Nucleotidestructure(Ch4)andMetabolism(Ch19)13. Mechanismsofsignaltransduction(Ch20.1-20.3)14. Genetics,DNAReplication,DNArepair(Ch20,21,22)

FinalExamwillbetheACSstandardizedexamandwillnotbedropped.Thiswilloccurduringfinalsweek:dateandtimeTBAonBlackBoardandinclass.DUEDATES

• DAILY(checkwiththeinstructorifyouareabsent)

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o Quizzeso Inclassassignments

• WEEKLY(checkBlackBoardfortheseassignments)o Homeworko Pre-labsaredueatthestartofthatlabo Labreportsaredueonthenextlabmeeting(e.g.Lab1isdueonthedayLab2is

performed)o RubricsavailableonBlackBoardo Contacttheprofessorifyouareabsentduringlab

CourseSchedule:

ClassDate Assignmentsdue ClassDiscussion/ActivitiesWeek1:Sept6-8TheChemicalFoundationofLife(Ch2)

ListentoCh2lecturesonBB,readCh2Purchasethetextbookwithaccesscode

SyllabusquizLabsafetyquizPretestIn-class1

Week2:Sept12-15TheEnergeticsofLife(Ch3)Carbohydrates:Sugars,Saccharides,Glycans(Ch9)SEPT13–LASTDAYTO

ADD/DROP

ListentolecturesonBBdue9/12and9/14Readcorrespondingbookchapter

In-class2In-class3Homework1assigned(LinkthroughBlackBoard)

Week3:Sept19-22Proteinstructureandfunction(Ch5,6,7.9-7.11)

ListentolecturesonBBdue9/19and9/21ReadcorrespondingbookchapterHomework1due

In-class4In-class5Homework2(LinkthroughBB)

Week4:Sept26-29Enzymes:BiologicalCatalysts(Ch8)

EXAM1–SEPT26SEPT30–LASTDAYTO

WITHDRAW

ListentolecturesonBBdue9/26and9/28ReadcorrespondingbookchapterHomework2due

In-class6Homework3

Week5:Oct3-6Metabolismoverview:glycolysis,gluconeogenesis,glycogenpathway(Ch12.1-12.9)citricacidcycle(Ch13)

ListentolecturesonBBdue10/3and10/5ReadcorrespondingbookchapterHomework3due

In-class7In-class8Homework4

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OCT3-MIDTERMWeek6:Oct10–13Electrontransport,OxidativePhosphorylation,OxygenMetabolism(Ch14)

ListentolecturesonBBdue10/10and10/13ReadcorrespondingbookchapterHomework4due

In-class9In-class10Homework5

Week7:Oct17-20Photosynthesis(Ch15.1-15.4)

ListentolecturesonBBdue10/17and10/19ReadcorrespondingbookchapterHomework5due

In-class11Homework6

Week8:Oct24-27Lipids,Membranes,andCellularTransport(Ch10)andMetabolism(Ch16.1-16.7)

EXAM2:Oct26

ListentolecturesonBBdue10/24and10/26ReadcorrespondingbookchapterHomework6due

In-class12In-class13Homework7

Week9:Oct31–Nov3InterorganandIntracellularCoordinationofEnergyMetabolisminVertbrates(Ch17)

ListentolecturesonBBdue10/31and11/2ReadcorrespondingbookchapterHomework7due

In-class14In-class15Homework8

Week10:Nov7-10AminoAcidandNitrogenMetabolism(Ch18)

ListentolecturesonBBdue11/9ReadcorrespondingbookchapterHomework8due

In-class16Homework9

Week11:Nov14-17Nucleotidestructure(Ch4)andMetabolism(Ch19)

EXAM3–NOV16

ListentolecturesonBBdue11/14and11/16ReadcorrespondingbookchapterHomework9due

In-class17In-class18Homework10

Week12:Nov21–24Mechanismsofsignaltransduction(Ch20.1,20.2,20.3)Genetics,DNAReplication,DNArepair(Ch20,21,22)

NOV24–26THANKSGIVINGRECESS

ListentolecturesonBBdue11/21Readcorrespondingbookchapter

In-class19Homework11

Week13:Nov28–Dec1Genetics,DNAReplication,DNArepair(Ch20,21,22)

ListentolecturesonBBdue11/28and11/30ReadcorrespondingbookchapterHomework4due11/28

In-class20In-class21Homework12

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continued

Week14:Dec5-8Casestudies:Biochemistryandhumanhealth

EXAM4Dec7

POSTERSESSION–TBA

DEC9–LASTDAYTOWITHDRAW

Homework12due12/5 In-class22

Week15:Dec12-15SEMESTER

EXAMINATIONSFINALEXAM-TBA

FinalistheACSstandardizedBiochemistryExam–REQUIRED

Ireservetherighttochangethisscheduletomeettheneedsoftheclass.

Responsibilities AttendingClass

Youcannotsucceedinthisclassifyoudonotattend.Webelievethatintellectualgrowthandsuccessinhighereducationoccurthroughinteractionintheclassroomandlaboratories.However,wedonotwanttopenalizestudentsforparticipatingincollege-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,sothatexamscore

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willnotbeconsideredwhendeterminingthefinalgrade.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’sdiscretionwhetherornottoallowanextension.

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,youmaybeaskedto

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leave,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,andattachaworkscitedpagetotheendoftheassignment.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.

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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.

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.

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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.

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.

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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.