HMB265H1F Course Syllabus-Fall 2020-1 PDF

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Welcome to HMB265H1F General and Human Genetics Course Syllabus 2020-2021 Fall Session Course Coordinator: Dr. Maria Papaconstantinou, Human Biology Program Course Instructors: Dr. Naomi Levy-Strumpf, Human Biology Program (Lectures 1-11) Dr. Belinda Chang, Ecology & Evolutionary Biology and Cell & Systems Biology (Lectures 12-23) Lectures: Tuesdays 3:10 to 5:00 pm* and Fridays 1:10 to 2:00 pm, Online Synchronous. Lectures are synchronous (live with the professor and TAs) via Zoom. Live sessions will be recorded and posted on Quercus. Students will need to use their utoronto email addresses to join the Zoom lectures. *Lecture Review Session/Office Hours: Tuesdays 4:10 to 5:00 pm, Online Synchronous via Zoom. *Midterm Exam—Tuesday, October 20th from 3:10 to 4:20 pm, Online via Quercus. TA Review Sessions: Fridays 3:10 to 5:00 pm, Online Synchronous via Zoom or Blackboard Collaborate. Arts & Science Calendar Course Overview [24L, 12T]: An introduction to classical and modern methods of genetic analysis. Topics include Mendelian genetics, the genetics of human populations and disease, genomics, and applications of genetics to human society. Prerequisite: BIO120H1, BIO130H1, (CHM135H1/CHM139H1, CHM136H1/ CHM138H1)/ CHM151Y1 Exclusion: BIO260H1/ BIO207H5 Recommended Preparation: Recommended Co-requisite: BIO230H1/BIO255H1 DR=SCI; BR=4 Technical requirements: Personal Computer: You will need regular access to a computer – preferably a personal computer – with administrator privileges and you should be comfortable managing software and hardware. While much can be done with tablets, smartphones and other mobile devices they are not guaranteed to work in all areas of the course. For an optimal experience you must have a laptop or desktop computer (Windows 10 or higher or Mac OS X 10.14 or higher is recommended). Internet connection: High speed broadband access (LAN, Cable or DSL) is highly recommended for an optimal learning experience. Note, that relying on a library or a café for internet access is not recommended. A Web Browser is required for access to Quercus. In some instances, it may be necessary for some users to upgrade their web browser programs. Supported browsers are Firefox or Google Chrome. Speaker and Headphones: We will have synchronous (live) online meetings using webinar software. It is preferable to use headphones with an attached microphone for these sessions. Software: Many courses require word processing software (download Office 365 ProPlus). More can be found at https://community.canvaslms.com/docs/DOC-10721 For Additional Information: https://www.viceprovoststudents.utoronto.ca/covid-19/techrequirements-online-learning/ Course Description: An understanding of genetics is essential for all life science students and is becoming increasingly important for all members of society. This course is designed to give you a solid grounding in genetics. Topics include Mendelian genetics, the genetics of human populations and disease, genomics, and applications of genetics to human society. A variety of activities— lectures, readings, mandatory tutorial quizzes, and assignments—are planned to help you learn the

material. To do well in the course, we recommend that you participate fully in all of these activities and that you keep up to date with the material. We hope you enjoy the course. Lecture notes will be posted under Modules before the lecture. Make sure you have a copy of the lecture notes in your possession well before quizzes, the midterm test and the exam in the event of a problem accessing the course website. If you have questions regarding the course material, please post them on the Discussions section of the course website. We encourage students to answer questions too—this is a great way to make sure you understand the material. For questions of an administrative nature unrelated to course content, please post on the Discussions section of the course website under “administrative questions”, or contact Dr. Maria Papaconstantinou via the course administrative email: [email protected]. Required textbook and solutions manual (available as a bundled package, U of T bookstore): 1. Hartwell LH, Goldberg ML, Fischer JA, Hood L, Aquadro C, Karagiannis J and Papaconstantinou M (2017) Genetics: From Genes to Genomes, 2nd Canadian edition, McGraw-Hill Ryerson, Canada. 2. Karagiannis J and Papaconstantinou M (2017) Solutions Manual for Genetics: From Genes to Genomes, 2nd Canadian edition. McGraw-Hill Ryerson, Canada. Required Online Participation: Participation is a requirement for this course, and the Quizzical tool that is available on Quercus will be used to encourage students to create and practice multiple choice questions, promoting dialogue amongst peers that can contribute to the mastery of terminology and course material. Students start off by writing their own multiple-choice questions based on course material and receive a grade and feedback on their contributions. When necessary, questions are sent back for editing and resubmitted, and they are then added into the quiz bank if a minimum grade of 3.5 is achieved. Higher marks will be awarded to more creative questions that require critical thinking skills. Students can access this bank at any time to test themselves and prepare for tutorial quizzes and course exams and achieve participation marks while doing so. The participation mark is composed of the two abovementioned components: question composition (5%) and practice quizzes (5%). Thus, your Quizzical participation will count towards 10% of your final grade. In order to receive your participation marks for the question composition component, you must post 1 Question and Answer for 2 assigned lectures. Once you are assigned a lecture, you will have 4 days to submit your question, and 3 days to edit and resubmit your question once feedback is received if necessary. Your final assigned mark out of 5 for each submitted question will count toward your final grade, thus you are encouraged to create the best questions possible. *To receive full participation marks for the practice quizzes, you have to attempt a minimum of 5 questions per lecture and score a minimum average of 60% per lecture. *Late penalties (100%) apply if the Quizzical questions or practice quizzes are not submitted or completed by the due date & time. Before you start, be sure to read the student guide: https://www.utsc.utoronto.ca/technology/quizzical-student-guide

HMB265 Lecture Schedule: Date Lecture Topic Number Sep 11 1 The genetics & genomics of human biology Forward Genetics Sep 15 2 Mendelian genetics for single gene traits Sep 18 3 Molecular basis of genetic polymorphisms and the ir Detection Sep 22 4 Pedigree analysis Sep 25 5 Extensions of Mendelian genetics I – dominance, codominance, penetrance, expressivity Sep 29 6 Extensions of Mendelian genetics II – complementation/allelism, epistasis Oct 2 7 Sex-linked traits & chromosomal theory of inheritance Oct 6 8 Linkage & recombination Oct 9 9 Linkage mapping Oct 13 10 Population genetics Oct 16 11 Genomics & Midterm Exam Review Midterm exam (3:10 pm-4:20 pm) Oct 20 Oct 23 Quantitative genetics 12 Oct 27 13 Quantitative trait loci Oct 30 14 Genetic mapping & complex traits Reverse Genetics Nov 3 15 Mutation Nov 6 16 Transposable elements Nov 10 Fall Reading Week-No classes Nov 13 Fall Reading Week-No classes Nov 17 Large-scale chromosomal changes I 17 Nov 20 18 Large-scale chromosomal changes II Nov 24 19 Epigenetics Nov 27 20 Using genetics to understand development Dec 1 21 Genetics of cancer Dec 4 22 Gene therapy Dec 8 23 Final Exam Review *Required pages will be posted in the lecture notes.

Textbook Chapter* 1 2 2, 7, 8, 15 2 2 2, 8 3 4 4 12

2, 7 12 15, 21 7, 8 8, 9

9 9 6, 11 17 16 19

Evaluation: Term Mark (65%) 25% Midterm exam (Oct. 20) 20% Tutorials (weekly) 10% Assignment (Nov. 16) 10% Quizzical Participation (starting Sep. 15 and ending Dec. 18) Final Exam (35%) (Final Assessment period) Exams: Multiple choice and short answer questions. Midterm exam: Content: Lectures 2-11 and tutorials 1-4. Date & time & location: Tuesday, October 20th, 3:10 – 4:20 pm, EST, Online via Quercus. If you miss the midterm exam for a valid reason (see below), within five business days submit the appropriate documentation (see below) online to the Human Biology Office.

Final exam: Content: all lectures and tutorials. During the Faculty of Arts and Science Final Assessment Period. Tutorials (Mondays online weekly, starting Sep.21): Tutorials are synchronous, live with the TAs via Zoom or Blackboard Collaborate. Tutorial quizzes will be synchronous (live), and administered via the Quercus course site starting at 10:10am, 11:10am, or 12:10pm EST, depending on the tutorial in which you have enrolled. Students will receive an indicated amount of time to complete the quiz online. See below for the pre-tutorial readings and problems for each tutorial. This information, along with the associated lecture material and readings, will form the basis of the quizzes. All the quizzes will be a combination of multiple choice and short-answer questions. Students can then discuss the quizzes with the TAs online via Zoom or Blackboard Collaborate. Students are not allowed to use cell phones, laptops, tablets, textbooks, smart watches, etc. during the quiz. The only aid allowed is a non-programmable calculator. There are 10 tutorial quizzes but the total final quiz mark will be scaled out of 9. This means that you may miss one tutorial without penalty. Should you miss more than one tutorial for a valid reason, see the missed tutorial quiz/midterm test policy and follow the procedures outlined there. For up to two missed quizzes (after the first no-penalty missed quiz) the weight of those two quizzes will be redistributed across the other tutorial quiz marks. For more than two missed quizzes, the weight of the missed quizzes will be reweighed into the midterm and/or final exam. Students who only miss one tutorial quiz, even for valid reason, will still start their final quiz mark scaled out of 9. For this reason, it is not necessary to submit documentation for your first missed tutorial quiz (i.e. it will not give you any advantage). Tutorial Schedule of Assigned Readings and Problems (to be completed before tutorial): Date Number Assignment Sep No tutorial 14 Chapter 2 Problems: 7, 8, 10, 11, 13, 15, 16, 17, 20, 21, 22, 24, 25, 27, 28, 29, 31, Sep 1 and 32 21 Sep 2 Chapter 2 Problems: 18, 19, 23, 31, 34, 35, 36, 39, 40, 44, 46, 48, 49, 52, 53, 55, and 57 28 Chapter 2 Problems: 63, 65, 66, 67, 71, 72, and 75 Oct 3 5 Chapter 3 Problems: 3, 14, 28, 36, 37, 38, 41, and 42 Chapter 8 problems: 22, 23, 24, and 29 Thanksgiving Day—No tutorial

Oct 12 Oct 19 Oct 26

4 5

Chapter 4 Problems: 2, 3, 4, 6, 8, 9, 11, 15, 17, 18, 21, 22, 23, 26, and 28 Chapter 12 Problems: 2, 3, 5, 9, 10, 12, 14 16, 17, 18, 19 Writing in your own words: tutorial to help you write the HMB265 assignment. Assigned readings: i) “How not to Plagiarize” by Dr. Margaret Procter at http://advice.writing.utoronto.ca/using-sources/how-not-to-plagiarize/ ii) “Paraphrasing and Summary” by Jerry Plotnick at http://www.uc.utoronto.ca/paraphrase iii) Parts A and B of the University of Toronto’s Code of Behaviour on Academic Matters. Document linked in tutorial section of the course website. (Quiz on assigned readings and writing assignment).

Nov 2

Nov 9 Nov 16

6

Chapter 2 Problems: 70 and 76 Chapter 12 Problems: 29, 31, 32, 34, 35, and 36 Chapter 15 Problems: 29 Chapter 21 Problems: 10 and 11 Fall Reading Week—No tutorial

7

Hand in hard copy of assignment. Chapter 7 Problems: 19, 21, and 22 Chapter 8 Problems: 27, 28, 30, and 31 Chapter 9 Problems: 21, 22, and 23 Chapter 9 Problems: 3, 6, 11, 13, 14, 16, 20, 31, 32, 33, 34, 35, 37, and 40

Nov 23 Nov 30

8

Dec 7

10

9

Chapter 6 Problems: 11, 12, 14, and 15 Chapter 11 Problems: 17, 18, and 19 Chapter 17 Problems: 21, 24, 27, 28, and 29 Chapter 16 Problems: 2, 3, 4, 5, 6, 7, 9, 11, 12, 16, and 17 Chapter 19 Problems: 20 and 22

Assignment*: submit an electronic copy to the assignment dropbox on Quercus by 9:00am EST on November 16. *Late penalties (100%) apply if the electronic copy is not submitted by the due date & time. This course uses Turnitin. All written assignments will be required to be submitted to turnitin.com. Students “submit their course essays to Turnitin.com for a review of textual similarity and detection of possible plagiarism. In doing so, students will allow their essays to be included as source documents in the Turnitin.com reference database, where they will be used solely for the purpose of detecting plagiarism. The terms that apply to the University’s use of the Turnitin.com service are described on the Turnitin.com web site (Academic Handbook, section 2.15).” Information on how to access Turnitin for this course will be available on Quercus after the course starts. Put your name and student number on the first page of your assignment. The assignment must be written in your own words and be done on an individual basis. It cannot contain material submitted for marks in another course. Copying or working closely with others on an assignment is considered plagiarism. This is a serious academic offense. All parties involved will receive a mark of zero for the assignment. In addition, a letter documenting the case of plagiarism will be sent by the Director of the Human Biology Program to the Dean of the Faculty of Arts and Science. This letter becomes part of the student’s academic folder within Faculty of Arts and Science. The Dean will then consider further disciplinary action. Make sure you keep your own work in a secure location and do not share answers with others. Please contact Dr. Maria Papaconstantinou at the HMB265 email at least one week before November 16 to request an extension if you have a long-term illness that prevents you from being able to complete the assignment on time. Extensions will not be granted if this step is not followed. If an extension is granted, the assignment is still due, with a maximum extension of ONE WEEK if the above is followed and the reason validated. An extension cannot be made on top of a previously granted extension. Since the due date of the assignment is known well in advance, short-term illnesses are not considered a valid reason for handing in the assignment late. About academic integrity: The University of Toronto treats cases of academic misconduct very seriously. Academic integrity is a fundamental value of learning and scholarship at the UofT. Participating honestly, respectfully, responsibly, and fairly in this academic community ensures that your UofT degree is valued and

respected as a true signifier of your individual academic achievement. The University of Toronto’s Code of Behaviour on Academic Matters outlines the behaviours that constitute academic misconduct, the processes for addressing academic offences, and the penalties that may be imposed. You are expected to be familiar with the contents of this document. Potential offences include, but are not limited to: In papers and assignments: •Using someone else’s ideas or words without appropriate acknowledgement. •Submitting your own work in more than one course. •Making up sources or facts. •Obtaining or providing unauthorized assistance on any assignment (this includes working in groups on assignments that are supposed to be individual work). On tests and exams: •Using or possessing any unauthorized aid, including a cell phone. •Looking at someone else’s answers. •Letting someone else look at your answers. •Misrepresenting your identity. •Submitting an altered test for re-grading. Any instance of suspected academic dishonesty will be reported to the Office of Student Academic Integrity. For further information on you may wish to visit https://www.academicintegrity.utoronto.ca/perils-and-pitfalls/ and http://www.writing.utoronto.ca/advice.

Missed tutorial quizzes, midterm and final exam policy: This course follows the University of Toronto's Policies on missed tests and quizzes and follows the Human Biology Program's procedures for missed tests and quizzes. Students are expected to follow these policies and procedures, and leniency will not be granted to students who do not adhere to these procedures. Please note that this policy applies to everything due in this course. For written or online assignments with due dates known well in advance, short-term illnesses are not considered a valid reason to waive a late penalty. Steps of what to do if you fail to write a quiz or exam for a valid reason only: 1. Fill out the HMB Missed Assessment Form: https://www.surveymonkey.com/r/HMB_20209_Missed • A copy of this form and its details will be emailed to you and to your instructor; this is how you notify your course instructor. 2. Self-declare your absence on ACORN  The HMB program office will ONLY contact you if there is an issue 3. There are no make-up tutorial quizzes in the course, but the tutorial grade will be re-weighted if Step 1 listed above is completed. Please note any reweighs will happen at the end of term. 4. For the term test, there will be one opportunity for a make-up midterm exam that will be granted to students with valid documentation on Friday, October 30th from 3:10-4:20 PM EST.

Please note that the HMB Missed Assessment Form and all supporting documentation must be submitted within five (5) business dates of the missed test/quiz date. HEALTH & WELLNESS The university experience can be a challenging one, there is no need to go about it alone. If you or anyone you know could use someone to talk to (or text with), here are some resources in addition to your instructors, program coordinators, and TAs:    

Your college registrar and office of residence of student life (ORSL) MySSP [24/7, talk in 146 languages & text in 35 languages]: available on Apple App Store and Google Play Store. Good 2 Talk Student Helpline [24/7]: 1-866-925-5454 Gerstein Centre [24/7]: 416-929-5200

ACADEMIC SUPPORT    

Writing Centre for all writing-related help (https://writing.utoronto.ca/writing-centres/arts-andscience/) Study Hubs for weekly goal-oriented study sessions (https://studentlife.utoronto.ca/program/study-hubs/) Recognized Study Groups to connect with fellow students in the same class (https://sidneysmithcommons.artsci.utoronto.ca/recognized-study-groups/) Learning Strategist for one-on-one help to improve learning strategies (https://studentlife.utoronto.ca/service/learning-strategist-connections/)

Important Notes: 1. Late submission of assignments is subject to a late penalty of 100% per day. 2. Normally, students will be required to submit their course essays to Turnitin.com for a review of textual similarity and detection of possible plagiarism. In doing so, students will allow their essays to be included as source documents in the Turnitin.com reference database, where they will be used solely for the purpose of detecting plagiarism. The terms that apply to the University's use of the Turnitin.com service are described on the Turnitin.com web site. 3. Recorded lectures are for personal use. Students are instructed to not upload lectures to a shared drive or folder or hosted on a video service platform such as, but not limited to, YouTube or Facebook messenger without the written permission of the course instructor. Students are reminded that lectures are the intellectual property of the instructors, and the recordings should be respected thus. Distribution of course materials is an infringement of copyright and is absolutely prohibited. Students are further reminded that the Academic Handbook states: “It is absolutely forbidden for a student to publish an instructor’s notes to a website or sell them” (section 4.5)”. Any student found violating this rule will be brought in to the Office of Student Academic Integrity. 4. Students with diverse learning styles and needs are welcome in this course. In particular, if you have a disability/health con...