Course outline 2280A 2021 PDF

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Biochemistry 2280A Biochemistry and Molecular Biology Course outline for Fall 2021

Although this academic year might be different, Western University is committed to a thriving campus. We encourage you to check out the Digital Student Experience website to manage your academics and well-being. Additionally, the following link provides available resources to support students on and off campus: https://www.uwo.ca/health/.

The Department of Biochemistry recognizes diversity of identity and experience as a source of strength that promotes excellence, innovation, flexibility and adaptability in our discipline. We embrace, nurture, value and celebrate this diversity.

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Technical Requirements:

Stable internet connection

Laptop or computer

2. Instructor Information Instructors Topics Office Hours** Office Hour Dates Dr. Michael Boffa (he/him) 1-5 Tue 12:00–1:00 pm Zoom Sep 14 – Oct 28 Dr. Derek McLachlin* (he/him) 6-16 Tue 2:30 – 4:30 pm Zoom or MSB 349 Oct 5 to final exam Dr. Ilka Heinemann (she/her) 17-23 Thu 11:00 am – 12:00 pm Zoom Nov 18 to final exam * course coordinator ** See Biochem 2280_2288 Forum OWL site for Zoom links. Dr. McLachlin will also be accessible inperson in MSB 349. Rather than email instructors directly, students are encouraged to post questions on the Biochem 2280_2288 Forum site on OWL (see Section 8). In addition, a teaching assistant will be available for individual appointments; details will be announced. Dr. Brian Dempsey (he/him) is the Biochemistry Education Coordinator and handles course administration. Email: [email protected] Phone: 519-661-3362 Office: MBL C5 Hours: Mon-Fri 10:00 am – 12:00 pm & 1:00 – 2:30 pm The 2280A Course Office is room C5 on the ground level of the MBL building, described on the campus map as Molecular Bio Lab. It is located between the Medical Sciences and Kresge buildings.

3. Course Delivery and Design Biochemistry is the study of the molecules of life and centers on four key groups of biomolecules: proteins, lipids, carbohydrates and nucleic acids. Students will learn about the structure and function of these key biomolecules, the mechanics by which the cellular machinery is supplied with energy, and how the genetic material is converted to functional information. Students will also learn the techniques

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of recombinant DNA technology and bioinformatics that have profoundly changed how we study and use cell functions. Prerequisites: One of Bio 1001A or 1201A; one of Bio 1002B or 1202B; Chem 1301A/B; AND Chem 1302A/B. Integrated Science 1001X can be used in place of Bio 1002B and Chem 1302A/B. Delivery Mode: In-person Timetabled Sessions Lecture Section 001

Days Mon Wed Fri

Time 2:30-3:30 pm

Location NCB 101

002

Mon Wed

11:30 am-12:30 pm

NCB 101

002

Thu

1:30-2:30 pm

NCB 101

All course material will be posted to OWL: http://owl.uwo.ca. Any changes will be indicated on the OWL site and discussed with the class. We expect to record and post all lecture sessions. If students need assistance, they can seek support on the OWL Help page. Alternatively, they can contact the Western Technology Services Helpdesk . They can be contacted by phone at 519-6613800 or ext. 83800. Google Chrome or Mozilla Firefox are the preferred browsers to optimally use OWL; update your browsers frequently. Students interested in evaluating their internet speed, please click here. Contingency plan for an in-person class pivoting to 100% online learning In the event of a COVID-19 resurgence during the course that necessitates the course delivery moving away from face-to-face interaction, all remaining course content will be delivered entirely online, either synchronously (i.e., at the times indicated in the timetable) or asynchronously (e.g., posted on OWL for students to view at their convenience). The grading scheme will not change. Any remaining assessments will also be conducted online as determined by the course instructor. In the event that online learning is required, a stable internet connection with working microphone and webcam will be required. As has been the case in the past, the decision to pivot to online learning will be made by Western, and not individual instructors or departments (excepting temporary online instruction in the event of instructor illness).

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Learning Outcomes Upon successful completion of this course, students will be able to: 1. Demonstrate basic knowledge about the structure, roles, and functions of the different classes of biomolecules. 2. Provide examples where defects in biochemical processes result in disease, and predict potential outcomes of biochemical defects. 3. Describe the central pathways that provide living organisms with energy, and the regulation of these pathways. 4. Detail information flow in living systems and mechanisms that regulate the expression of genetic material. 5. Formulate an approach to clone and express a gene of interest in bacteria. 6. Obtain and interpret scientific information from literature, databases and oral presentations. 7. Explain scientific concepts in a way that can be understood by a general audience.

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Course Content and Schedule Schedule is subject to change. Lectures are in NCB 101. Students must attend their assigned section. Section 002 Section 001 MW 11:30-12:30 Topic Instructor MWF 2:30-3:30 Th 1:30-2:30 M W F M W Th 1. The chemical basis of life 8 10 Sept. 8 9 Sept. 2. Amino Acids and Ionization Boffa 13 15 17 13 15 16 3. Protein Structure and Analysis 20 22 24 20 22 23 4. Protein Function 27 27 5. Enzyme Catalysis M W F M W Th 6. Lipids and Biological Membranes 29 1 Sept. 29 30 Sept. 7. Carbohydrate Structure 4 6 8 Oct. 4 6 7 Oct. 8. Fundamental concepts in metabolism 13 15 13 14 9. Carbohydrate Metabolism McLachlin 18 20 22 18 20 21 10. Citric Acid Cycle 25 25 11. Oxidative Phosphorylation No lecture Oct 11 No lecture Oct 11 12. Lipid metabolism 13. Summary of Energy Metabolism Midterm test: Topics 1-13, Saturday October 30 from 2:00 – 5:00 pm. Rooms to be announced. M W F M W Th 14. Nucleic acid structure 27 29 Oct. 27 28 Oct. 15. DNA replication McLachlin 8 10 12 Nov. 8 10 11 Nov. 16. DNA repair No lectures Nov. 1-5 No lectures Nov. 1-5 17. Molecular basis of cancer 18. Prokaryotic transcription 19. Eukaryotic transcription 20. RNA processing Heinemann 21. Translation 22. Recombinant DNA technology 23. Sequencing Genomes Final exam: Topics 14-23. The final exam is NOT cumulative. Date to be set by Registrar. DO NOT book travel plans until after the date of the final exam is set. . Masking Guidelines M W F 15 17 19 Nov. 22 24 26 29 1 3 Dec. 6 8

M W Th 15 17 18 Nov. 22 24 25 29 1 2 Dec. 6 8

Students will be expected to wear triple layer, non-medical, paper masks at all times in the classroom as per University policy and public health directives. Students who are unable to wear a mask must seek formal accommodation through Western Accessible Education, and present medical documentation. Students are not permitted to eat or drink while in class to ensure masks stay in place. Students will be able to eat and drink outside of the classroom during scheduled breaks. Students unwilling to wear a mask as stipulated by Western policy and public health directives will be referred to the Dean, and such actions will be considered a violation of the student Code of Conduct.

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Evaluation Assessments for this course and associated due dates are as follows. Note that the assignment has multiple components, each with its own due date, as explained in a separate document.

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Assessment Background quiz Quiz 1 (Topics 1-5) Quiz 2 (Topics 6-10) Quiz 3 (Topics 14-16) Quiz 4 (Topics 17-21) Assignment Team Assignment Survey First Submission Evaluation of Peer Submissions Final Submission Peer Teamwork Assessment Midterm test (Topics 1-13) Final exam (Topics 14-23)

Default Value (%) 2 3 3 3 3 0.5 3 3 9 0.5 35 35

Due Date Fri Sep 17 Fri Oct 1 Fri Oct 22 Fri Nov 19 Fri Dec 3 Fri Sep 17 Mon Oct 18 Wed Oct 27 Wed Nov 10 Fri Nov 12 Sat Oct 30 TBD

Alternative weighting schemes Your final grade for the course will be the highest of the grades calculated using the 8 possible weighting schemes in the table below (all numbers are percent of your overall grade). Assessment Background quiz Quiz 1 (Topics 1-5) Quiz 2 (Topics 6-10) Quiz 3 (Topics 14-16) Quiz 4 (Topics 17-21) Assignment Midterm test (Topics 1-13) Final exam (Topics 14-23)

1 2 3 3 3 3 16 35 35

2 2 0 0 3 3 16 41 35

3 2 3 3 0 0 16 35 41

4 2 0 0 0 0 16 41 41

5 0 3 3 3 3 16 36 36

6 0 0 0 3 3 16 42 36

7 0 3 3 0 0 16 36 42

8 0 0 0 0 0 16 42 42

Background Quiz – The background quiz consists of questions designed to refresh your memory about key concepts relevant to Biochemistry that should have been covered in first-year Biology and Chemistry. The quiz will be available on OWL before the first day of classes, and is due Friday September 17 at 11:55 pm. You can repeat the quiz as many times as you like before the deadline; only your best score will be counted. Quizzes 1-4 – These quizzes will consist of 10 multiple choice questions, and are intended to encourage students to keep up with the material throughout the term. The quizzes will be administered through the WileyPLUS platform that comes with the textbook. The quizzes will be available at 8:30 am on the Monday before they are due, and are due that Friday by 11:55 pm. Once started, students will have 20 minutes to do each quiz. Practice questions will be available for each topic. Note that the alternate weighting schemes (see below) allow students to achieve a high mark in the course even if none of the quizzes are completed. Assignment – Collaboration is a necessary skill when working in science. Each student will be assigned to a team of up to 4, with teams posted to OWL on Monday, September 20. Students may not choose their teammates. Each team will prepare an infographic on a biochemistry-related topic. Detailed instructions, including marking rubrics and details of peer assessment, are provided in a separate document. Test and exam – The 3-hour midterm test will cover Topics 1-13 and will be held Saturday, October 30 starting at 2:00 pm. The final exam will cover Topics 14-23 and will be scheduled by the Registrar’s Office. Students should not make travel commitments before verifying when the final examination will be held through the Registrar’s Student Centre interface.

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Room assignments for the midterm test and final exam will be posted on the OWL course site. All students are responsible for determining where they are to write each examination and to appear at the designated room on time. Students must provide their own pencils and erasers (pens are not allowed) for the examinations and they MUST bring their Student ID card. Electronic devices, including (but not limited to) calculators, cell phones, iPods, and “Smart” Watches are NOT allowed in the exam rooms. Biochemistry 2280A/2288A exams include multiple choice questions marked on Scantrons. This course uses software that will detect unusual coincidences in answer patterns that may indicate cheating. Students should note that discrepancies between answers circled on their exam and those recorded on their Scantron will not be adjusted. Students should note that discrepancies between answers circled on their exam and those recorded on their Scantron will not be adjusted. Late or missed evaluations Quizzes – Late submissions of the Background Quiz or any of Quizzes 1 to 4 will not be accepted, and there will be no makeup quizzes. Students may receive an extension to the quiz deadline by submitting documentation to the Dean’s office, or a self-reported absence. Note that the alternate weighting schemes (see above) allow students to achieve a high mark in the course even if none of the quizzes are completed. Assignment – We will accept first or final submissions up to 72 hours past the deadline, but will deduct 10% for every 24 hours unless a self-reported absence (SRA) or academic consideration is received. If an SRA is submitted for the assignment, the new deadline will be 24 hours after the end of the SRA period. We will accept one SRA at most per team for each assignment submission; in other words, multiple team members cannot submit consecutive SRAs to obtain a lengthy extension to the deadline. If some members of a team are ill, then other members should complete the assignment without them. Late submission of the Team Assignment Survey, the evaluations of peer submissions, or the Peer Teamwork Assessments will not be accepted. Test and exam – Students who are unable to attend the midterm due to athletic or academic conflicts are expected to write a make-up test on Thursday Oct. 28. Students who know of a conflict in advance of the midterm must notify Dr. Dempsey no later than Friday Oct. 22. Students who miss the midterm and who meet the criteria for academic consideration set by their Dean's office will be able to write a make-up test after the Fall Study Break, with the date to be determined. Please submit documentation to your Dean's office and contact Dr. Dempsey for details. If you miss both the scheduled midterm and the make-up test you will be required to write a comprehensive final examination (Topics 1-23) worth the total value of both the midterm and final exams. You must obtain permission for this special exam from the office of your Dean and contact Dr. Dempsey at least 3 weeks before the date of the final exam. If you miss the Final Exam, please contact your faculty’s Academic Counselling Office as soon as you are able to do so. They will assess your eligibility to write the Special Exam (the name given by the university to a makeup Final Exam). You may also be eligible to write the Special Exam if you are in a “Multiple Exam Situation” (see http://www.registrar.uwo.ca/examinations/exam_schedule.html). Click here for a detailed and comprehensive set of policies and regulations concerning examinations and grading. The table below outlines the University-wide grade descriptors.

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A+ A B C D F

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90-100 80-89 70-79 60-69 50-59 below 50

One could scarcely expect better from a student at this level Superior work which is clearly above average Good work, meeting all requirements, and eminently satisfactory Competent work, meeting requirements Fair work, minimally acceptable Fail

Resources Required Textbook: Essential Biochemistry, Fifth Edition by Charlotte Pratt & Kathleen Cornely, published by Wiley Inc. This book is available online through WileyPlus, or as a physical book; to purchase either, inquire at the campus bookstore. Refer to the OWL site for the required readings for each topic. Course notes for each topic as well as recorded lectures and interactive online modules are available on OWL. To access the material on OWL, you must achieve a perfect score on an OWL quiz relating to this syllabus. This quiz does not count toward your mark, and you can repeat it as many times as necessary. Course material produced by faculty is copyrighted and to reproduce this material for any purposes other than your own educational use contravenes Canadian copyright laws.

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Communication Information and announcements related to the course will be communicated through OWL or using a student’s Western University email address. Students are expected to check the OWL site regularly and their email at least every 48 hours. This course will use the Biochem 2280_2280A Forum on OWL for all course-related queries so that everyone can access the queries and responses. Students’ names are not visible to other students. Please keep your interactions friendly and respectful. For confidential matters, students may email Dr. Dempsey or Dr. McLachlin directly. Posts to the forum or emails will receive a response within 2 business days, if not sooner.

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Professionalism and Privacy Western students are expected to follow the Student Code of Conduct. All course materials created by instructors or TAs are copyrighted and cannot be sold or shared. Recordings are not permitted without explicit permission. Posted recordings are not to be distributed.

10. Western Academic Policies and Statements Absence from Course Commitments Policy on Academic Consideration for Student Absences If you are unable to meet a course requirement due to illness or other serious circumstances, you must seek approval for the absence as soon as possible. Approval can be granted either through a selfreported absence or via the Academic Counselling unit. Students have two self-reports to use throughout the academic year; absence from course commitments including tests, quizzes, presentations, labs, and assignments that are worth 30% or less can be self-reported. Self-reported absences cover a student for 48 hours (yesterday + today or today + tomorrow). Your instructor will receive notification of your consideration; however, you should contact your instructor immediately regarding your absence. Students are expected to submit missed work within 24 hours of the end of the 48-hour period. Please review details of the university’s policy on academic consideration for student absences. If you have used both your self-reported absences or will miss more than 48 hours of course requirements, a Student Medical Certificate (SMC) should be signed by a licensed medical or mental

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health practitioner and you should contact academic counselling. Science and BMSc students can contact academic counselling through the Help Portal: https://www.uwo.ca/sci/counselling/ Course Absences due to Daily COVID Screening Questionnaire Missed assessments (e.g., presentations, essays, quizzes, tests, midterms, etc.) require formal academic considerations (typically self-reported absences and/or academic counselling). Methods for dealing with missed work and course content are at the discretion of the instructor(s). Students should be aware that some learning outcomes cannot be easily made up and may need to be completed in a subsequent year. Your instructor will provide you with further information as to how this applies within this course. Students who demonstrate a pattern of routinely missing coursework due to self-reported COVID symptoms, and therefore do not demonstrate mastery of the learning outcomes of the course, will not receive credit for the course. Accommodation for Religious Holidays The policy on Accommodation for Religious Holidays can be viewed here. Special Examinations A Special Examination is any examination other than the regular examination, and it may be offered only with the permission of the Dean of the Faculty in which the student is registered, in consultation with the instructor and Department Chair. Permission to write a Special Examination may be given on the basis of compassionate or medical grounds with appropriate supporting documents. To provide an opportunity for students to recover from the circumstances resulting in a Special Examination, the University has implemented Special Examinations dates. These dates as well as other important information about examinations and academic standing can be found here. Academic Offenses Scholastic offences are taken seriously, and students are directed here to read the appropriate policy, specifically, the definition of what constitutes a Scholastic Offence. Accessibility Statement Please contact the course instructor if you require material in an alternate format or if you require any other arrangements to make this course more accessible to you. You may also wish to contact Accessible Education (AE) at 661-2111 x 82147 for any specific question regarding an accommodation or review The policy on Accommodation for Students with Disabilities. Correspondence ...