course schedule - university of waterloo schedule important: ... spring 2017 chem 237 online...

Course Schedule

Important: ALL TIMES EASTERN - Please see the University Policies section ofyour Syllabus for details.

Week Module Readings Activities andAssignments

Due Date Weight

Week 01 Module 1: EnergyandThermodynamics

Chapter 1(pp. 1-20)Chapter 14(pp. 452-461)

Quiz 1 Saturday,May 6, 2017at 11:59 PM

2.5%

Week 02 Module 2: Waterand Buffers

Chapter 2(pp. 23-39)

Quiz 2 Saturday,May 13,2017 at11:59 PM

2.5%

Week 03 Module 3: AminoAcids


Assignment 1 Saturday,May 20,2017 at11:59 PM

10%

Week 04 Module 4: ProteinStructure


Quiz 3 Saturday,May 27,2017 at11:59 PM

2.5%

Week 05 Module 5: ProteinPurification


None

Week 06 Module 6: PrimarySequenceDetermination


Quiz 4 Saturday,June 10,2017 at11:59 PM

2.5%

Week 07 Module 7:Hemoglobin


Assignment 2 Saturday,June 17,2017 at11:59 PM

10%

Week 08 Module 8: Enzymes Chapter 11(pp. 322-330)Chapter 12(pp. 361-382)

Quiz 5 Saturday,June 24,2017 at11:59 PM

2.5%

Spring 2017 CHEM 237 Online University of Waterloo

Generated by Centre for Extended Learning Created 26/05/2017

Week 09 Module 9: EnzymeMechanism andControl


Quiz 6 Saturday,July 1, 2017at 11:59 PM

2.5%

Assignment 3 Saturday,July 1, 2017at 11:59 PM

10%

Week 10 Module 10:Membranes, Lipids,and Structure


Quiz 7 Saturday,July 8, 2017at 11:59 PM

2.5%

Week 11 Module 11:Membrane Function


Assignment 4 Saturday,July 15,2017 at11:59 PM

10%

Week 12 Module 12:CarbohydrateStructure


Quiz 8 Saturday,July 22,2017 at11:59 PM

2.5%

FinalExamination

Final Examination 40%

Final Examination Arrangements and Schedule

Please carefully review the information about final examinations for online courses,including dates, locations, how to make examination arrangements, writing with aproctor, and deadlines.

If you are taking any on-campus courses, you will automatically be scheduled towrite your exam on campus. No action is required.

If you are taking only online courses, do one of the following:

If your address in QUEST is within 100 km of an examination centre, youmust choose an exam centre in Quest by Sunday May 14, 2017. This must bedone each term.If your address in Quest is more than 100 km from an exam centre, youmust arrange for a proctor. Please review the guidelines and deadlines forwriting with a proctor. This must be done each term.

Your online course exam schedule will be available in Quest approximately four



weeks before your exam date(s). Instructions on how to find your schedule areposted on the Quest Help page.

University of Waterloo Senate-approved academic regulations related toassignments, tests, and final exams can be found on the Registrar's website.

Official Grades and Course Access

Official Grades and Academic Standings are available through Quest.

Your access to this course will continue for the duration of the current term. You willnot have access to this course once the next term begins.



Contact Information

Announcements

Your instructor uses the Announcements widget on the Course Home page duringthe term to communicate new or changing information regarding due dates,instructor absence, etc., as needed. You are expected to read the announcements ona regular basis.

To ensure you are viewing the complete list of announcements, you may need toclick Show All Announcements.

Discussions

A General Discussion topic* has also been made available to allow students tocommunicate with peers in the course. Your instructor may drop in at this discussiontopic.

Contact Us

Who and Why Contact Details

Instructor

Course-relatedquestions (e.g.,course content,deadlines,assignments, etc.)Questions of apersonal nature

Post your course-related questions to the Ask theInstructor discussion topic*. This allows other studentsto benefit from your question as well.

Questions of a personal nature can be directed toyour instructor.

Instructor: Laura Marrone [email protected]

Your instructor checks email and the Ask theInstructor discussion topic* frequently and will makeevery effort to reply to your questions within 24–48hours, Monday to Friday.

Technical Support,Centre for ExtendedLearning

Technical problems

[email protected]

Include your full name, WatIAM user ID, studentnumber, and course name and number.



with WaterlooLEARN

Technical support is available during regular businesshours, Monday to Friday, 8:30 AM to 4:30 PM (EasternTime).

LEARN Help Student Documentation

Learner SupportServices,Centre for ExtendedLearning

General inquiriesWatCards (StudentID Cards)Examinationinformation

Useful Information for Students in Online Courses

[email protected]+1 519-888-4002

Include your full name, WatIAM user ID, studentnumber, and course name and number.

*Discussion topics can be accessed by clicking Connect and then Discussions onthe course navigation bar above.



Course Description and Expectations

Description

Welcome to CHEM 237, Introductory Biochemistry. In this course you will becomeacquainted with the tools and language of the field of biochemistry. Many years ago,biochemistry was a small area of study in biology (mainly through studies onmetabolism and nutrition in yeast and animals) — that’s the “bio” heritage.Gradually, more researchers became interested in the chemical aspects ofmetabolism — and that is the “chemistry” heritage. Now, biochemistry spans areasof research from the very biological (such as studies on whole cells and/or biologicalsystems) to the very chemical (such as bioorganic models for enzyme catalysis).Some of the basics apply in all aspects of biochemistry, and that is what we willfocus on.

The first topic is protein structure, but in order to do that, we need to knowsomething about water and weak acids. The other thing we need to know to talkabout protein structure is the amino acids. Yes, you do need to know the amino acidstructures. These molecules are the basis for protein structure, which determinesprotein function. We will learn about the level of structure in proteins.

As aside here is our discussion on protein purification. This is a practical unit wherewe will learn about the methods without going too much into the theory. This isimportant because if you are going to study a protein, you need to be able to purifyit.

The next topic is protein function. This is in two major sections. The first ishemoglobin and myoglobin. Our studies here give us a very good idea how proteinstructure affects function, always relating what we learn about hemoglobin to boththe protein structure (the chemistry) and to physiology (the biology).

The second section on protein function is about enzymes. Enzymes are theworkhorses of the cell and a very important area of study in biochemistry. We willlearn about the details of enzymes: kinetics, mechanism, and regulation. We willrelate these aspects back to the biology of the cell as much as possible.

Membranes are also a critical aspect of the cell. Membranes separate the cell fromthe environment, while at the same time, keeping communication with theenvironment active. It is through membranes that cells take up nutrients, get rid of



waste products, communicate with each other, and react to changing conditions.

Our last topic is carbohydrates. These molecules play a host of roles in the cell. Wewill be looking at these important molecules in a very descriptive way. What arethey? What shapes and sizes do they come in? This last topic will set you up to takethe next course in the traditional study of biochemistry, Metabolism.

Expectations

There are a variety of activities in the online course. There are four individualassignments. You will also notice that the enzymes section has an assignment aswell as a quiz. Quiz #4 is designed to help you with the assignment. We have aseries of leading questions for you that will lead you to a solution to the problemposed.

You may also notice that the first part of the course seems “compressed” withassignments and quizzes due very close together. That is because the introductorymaterial is easier, so if we go through that material quickly, then there is more timeto spend on the harder material, such as hemoglobin and enzymes.

As for how to submit your written assignments, please see the AssignmentsOverview page.

What is expected in an assignment? My policy is that full marks requires a completeanswer. For example, in Assignment #1, I ask for the pI of a peptide that you havedrawn. A correct but incomplete answer would be just the value. A complete answerwould be to explain why you chose the pK values you did to calculate the pI, andthen how you did the calculation. You learn much more with the complete answer,and that is really the goal here. Complete answers make you smarter, and in theevent that biochemistry does not become the center of your professional life, abetter and more complete understanding of biochemical concepts will help youunderstand concepts in other areas of science. So there are no requirements on howlong an assignment should be, but I do expect complete answers for full credit. Thewritten assignments will be graded by me, and only me. I have other on-campuscourses that I am responsible for, but rest assured that I am working on things asquickly as I can.

What if you are stuck on an assignment or have a question about the lectures? Youcan post a question on the discussion board, and I will answer it there, so all of uscan benefit from the exchange. You can always email me directly with questions. Ifthe question is one that I feel all can learn from, I will likely post it on the discussion

a



board as a general question.

About the course evaluation: the grade percentages for each activity are notnegotiable! Often students ask if I could change a percentage (usually because theydid not do an assignment or because they did poorly on an assignment). The bestapproach is keep up with the work and to do your best on everything.

This online course was developed by Betsey Daub, with instructional design andmultimedia development support provided by the Centre for Extended Learning.Further media production was provided by Instructional Technologies and MultimediaServices.



About the Course Author

Course Author - Betsey Daub

My interest in Biochemistry started at about the age of 14, when I becameinterested in nutrition. I had finally realized that chocolate chip cookies made withhydrogenated shortening were not very good for me. My father was an organicchemistry professor at the University of New Mexico in Albuquerque, where I grewup, and I learned quite a bit about organic molecules from him. I was a chemistrymajor as an undergraduate at Pomona College in Claremont, California, andalthough I liked organic chemistry, my introduction to biochemistry and especiallyenzymes was an eye-opener. I did my graduate work at M.I.T. in a joint project withDr. Christopher Walsh (a mechanistic enzymologist) and Dr. David Botstein (ageneticist). In my work there, I saw how the research areas of Microbiology,Molecular Biology and Biochemistry can all be used together to solve interestingproblems that one approach alone can not solve.

I came to Canada in 1986 as a postdoctoral fellow at the University of Toronto andworked on bacteriophage lambda with Dr. Helios Murialdo. I have been at theUniversity of Waterloo Department of Chemistry for many years as a ResearchAssociate and more recently as a Lecturer in Biochemistry and UndergraduateBiochemistry Advisor. My professional interests are in bacterial metabolism andenzymology. I have a family with a husband, two children, five cats, and two dogs.

I now make chocolate chip cookies with butter.



Materials and Resources

Textbook

Required:

1. Fundamentals of Biochemistry: Life at the Molecular Level, 5 Edition, Voet,Voet, and Pratt, John Wiley and Sons, Inc., 2016.

However, if you already have the 4 edition textbook, you can use it for thiscourse:

1. Fundamentals of Biochemistry: Life at the Molecular Level, 4 Edition, Voet,Voet, and Pratt, John Wiley and Sons, Inc., 2013.

Please note: The references made throughout the course for the readings are forthe 5 edition of the textbook. The chapter/page references may be different for the4 edition.

For textbook ordering information, please contact the WaterlooBookstore.

For your convenience, you can compile a list of required and optional coursematerials through BookLook using your Quest userID and password. If you arehaving difficulties ordering online and wish to call the Waterloo Bookstore, theirphone number is +1 519 888 4673 or toll-free at +1 866 330 7933. Please beaware that textbook orders CANNOT be taken over the phone.

Resources

Library services for co-op students on work term and distance educationstudents

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Grade Breakdown

The following table represents the grade breakdown of this course.

Assessment Weight

Quizzes (8) 20%

Assignments (4) 40%

Final Examination 40%



Course Policies

Final Examination

You MUST receive a passing grade on the final examination to pass the course.



University Policies

Submission Times

Please be aware that the University of Waterloo is located in the Eastern TimeZone (GMT or UTC-5 during standard time and UTC-4 during daylight saving time)and, as such, the time that your activities and/or assignments are due is based onthis zone. If you are outside the Eastern Time Zone and require assistance withconverting your time, please try the Ontario, Canada Time Converter.

Accommodation Due to Illness

If your instructor has provided specific procedures for you to follow if youmiss assignment due dates, term tests, or a final examination, adhere tothose instructions. Otherwise:

Missed Assignments/Tests/Quizzes

Contact the instructor as soon as you realize there will be a problem, and preferablywithin 48 hours, but no more than 72 hours, have a medical practitioner complete aVerification of Illness Form.

Email a scanned copy of the Verification of Illness Form to your instructor. In youremail to the instructor, provide your name, student ID number, and exactly whatcourse activity you missed.

Further information regarding Management of Requests for Accommodation Due toIllness can be found on the Accommodation due to illness page.

Missed Final Examinations

If you are unable to write a final examination due to illness, seek medical treatmentand have a medical practitioner complete a Verification of Illness Form. Email ascanned copy to the Centre for Extended Learning (CEL) [email protected] within 48 hours of your missed exam. Make sureyou include your name, student ID number, and the exam(s) missed. You will beREQUIRED to hand in the original completed form before you write the make-upexamination.



After your completed Verification of Illness Form has been received and processed,you will be emailed your alternate exam date and time. This can take up to 2business days. If you are within 150 km of Waterloo you should be prepared towrite in Waterloo on the additional CEL exam dates. If you live outside the 150 kmradius, CEL will work with you to make suitable arrangements.

Further information about Examination Accommodation Due to Illness regulations isavailable in the Undergraduate Calendar.

Academic Integrity

In order to maintain a culture of academic integrity, members of the University ofWaterloo community are expected to promote honesty, trust, fairness, respect, andresponsibility. If you have not already completed the online tutorial regardingacademic integrity you should do so as soon as possible. Undergraduatestudents should see the Academic Integrity Tutorial and graduate students shouldsee the Graduate Students and Academic Integrity website.

Proper citations are part of academic integrity. Citations in CEL course materialsusually follow CEL style, which is based on APA style. Your course may follow adifferent style. If you are uncertain which style to use for an assignment, pleaseconfirm with your instructor or TA.

For further information on academic integrity, please visit the Office of AcademicIntegrity.

Discipline

A student is expected to know what constitutes academic integrity to avoidcommitting an academic offence, and to take responsibility for his/her actions. Astudent who is unsure whether an action constitutes an offence, or who needs helpin learning how to avoid offences (e.g., plagiarism, cheating) or about “rules” forgroup work/collaboration, should seek guidance from the course instructor,academic advisor, or the undergraduate Associate Dean. For information oncategories of offences and types of penalties, students should refer to Policy 71 -Student Discipline. For typical penalties, check Guidelines for the Assessment ofPenalties.

Appeals



A decision made or penalty imposed under Policy 70 - Student Petitions andGrievances, (other than a petition) or Policy 71 - Student Discipline, may beappealed if there is a ground. A student who believes he/she has a ground for anappeal should refer to Policy 72 - Student Appeals.

Grievance

A student who believes that a decision affecting some aspect of his/her universitylife has been unfair or unreasonable may have grounds for initiating a grievance.Read Policy 70 - Student Petitions and Grievances, Section 4. When in doubt pleasebe certain to contact the department’s administrative assistant who will providefurther assistance.

Final Grades

In accordance with Policy 46 - Information Management, Appendix A - Access to andRelease of Student Information, the Centre for Extended Learning does not releasefinal examination grades or final course grades to students. Students must go toQuest to see all final grades. Any grades posted in Waterloo LEARN are unofficial.

AccessAbility Services

AccessAbility Services, located in Needles Hall, collaborates with all academicdepartments to arrange appropriate accommodations for students with disabilitieswithout compromising the academic integrity of the curriculum. If you requireacademic accommodation to lessen the impact of your disability, please register withAccessAbility Services at the beginning of each academic term and for each course.

Accessibility Statement

The Centre for Extended Learning strives to meet the needs of all our onlinelearners. Our ongoing efforts to become aligned with the Accessibility for Ontarianswith Disabilities Act (AODA) are guided by University of Waterloo accessibilitylegislation and policy and the World Wide Web Consortium's (W3C) Web ContentAccessibility Guidelines (WCAG) 2.0. The majority of our online courses are currentlydelivered via the Desire2Learn Learning Environment. Learn more aboutDesire2Learn’s Accessibility Standards Compliance.



Use of Computing and Network Resources

Please see the Guidelines on Use of Waterloo Computing and Network Resources.

Copyright Information

UWaterloo’s Web Pages

All rights, including copyright, images, slides, audio, and video components, of thecontent of this course are owned by the course author, unless otherwise stated.These web pages are owned or controlled by the University of Waterloo, Centre forExtended Learning. By accessing the web pages, you agree that you may onlydownload the content for your own personal, non-commercial use. You are notpermitted to copy, broadcast, download, store (in any medium), transmit, show orplay in public, adapt, or change in any way the content of these web pages for anyother purpose whatsoever without the prior written permission of the course authorand the University of Waterloo, Centre for Extended Learning.

Other Sources

Respect the copyright of others and abide by all copyright notices and regulationswhen using the computing facilities provided for your course of study by theUniversity of Waterloo. No material on the Internet or World Wide Web may bereproduced or distributed in any material form or in any medium, without permissionfrom copyright holders or their assignees. To support your course of study, theUniversity of Waterloo has provided hypertext links to relevant websites, resources,and services on the web. These resources must be used in accordance with anyregistration requirements or conditions which may be specified. You must be awarethat in providing such hypertext links, the University of Waterloo has not authorizedany acts (including reproduction or distribution) which, if undertaken withoutpermission of copyright owners or their assignees, may be infringement of copyright.Permission for such acts can only be granted by copyright owners or their assignees.

If there are any questions about this notice, please contact the University ofWaterloo, Centre for Extended Learning, Waterloo, Ontario, Canada, N2L 3G1 [email protected].



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