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Warning: TT: undefined function: 32BIOC 2200/BIOL 2200 ‐ SYLLABUS Fall 2019Contact Information Professor: Ken Storey, Ph., F.R.S. Office: 507 Steacie, Chemistry Building Phone: 520 ‐3678 (no messages) E‐mail: [email protected] (E‐mail is the best way of communicating with me) TA: Liam Hawkins...

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BIOC 2200/BIOL 2200 ‐ SYLLABUS Fall 2019 Contact Information Professor: Ken Storey, Ph.D., F.R.S.C. Office: 507 Steacie, Chemistry Building Phone: 520‐3678 (no messages) E‐‐mail: [email protected] (E‐mail is the best way of communicating with me) TA: Liam Hawkins Email: [email protected] ***To contact me, you MUST write to me from your Carleton account and put B2200 in the subject*** Lectures and Labs Lecture Location and Time: Monday and Wednesday 10:05-11:25am, 2200 Richcraft Hall Labs: Check your schedule for the time of your lab. cuLearn: This course has CuLearn content. Lecture schedule: Outlined in class and on the Tentative Schedule document Recommended Textbook: There are 2 editions (3 versions) of the book – EITHER IS ACCEPTABLE. Principles of Biochemistry, by Horton, Moran, Scrimgeour & Perry, Fourth edition, 2005. Principles of Biochemistry, by Moran, Horton, Scrimgeour, Perry, Fifth Edition, 2011. Principles of Biochemistry, by Moran, Horton, Scrimgeour, Perry, Fifth (INTERNATIONAL) Edition, 2018 Alternative Textbook Biochemistry: The Molecular Basis of Life by McKee and McKee Biochemistry: A Short Course by Tymoczko, Berg, and Stryer Professor + Lecture TA Office hours: Tentatively Tentatively Monday 11:30-1:00 and Wednesday 1:00-2:30 in Rm. 507 Steacie building. Both Professor Storey and one lecture TA will be available. Calendar Description BIOC 2200, BIOL 2200 [0.5 credit] ‐Cellular Biochemistry Cellular functions and their interrelationships. Introduction to thermodynamics, membrane structure and function, transport mechanisms, basic metabolic pathways, energy production and utilization, communications between cells. It is strongly recommended that Biology Majors, students in Biochemistry programs, and Honours students take this course in their second year of study. Prerequisite(s): (BIOL 1003 and BIOL 1004) or (BIOL 1103 and BIOL 1104), (CHEM 1006 with a minimum grade of B- or CHEM 1002) or permission of the Institute. Lectures three hours a week, laboratory or tutorial four hours a week.

Exams and Grading Students are responsible for, and may be tested on, all material discussed during lectures. Lectures are complemented by assigned textbook readings that will increase your understanding of the concepts being studied; however, ALL questions will be taken from lecture material covered in class! There will be a total of 100 marks from the tests, exams and laboratory. The laboratory portion is worth 40% of your final grade so treat the laboratory assignments & exam as important. The final course mark will be made up as follows: Mid Term Final Exam Labs Total

20% 40% 40% 100% 1

The mid-term test will TENTATIVELY be October 16, 2019 during regular class hours. The laboratory exam will be approximately the beginning of December 2019 (location and time TBD). The final exam will be administered during the regular university exam schedule (December 2019). The final exam will be comprehensive (which means that it covers ALL LECTURES in the course). **KEY NOTE: Assessment and grading of the Midterm and Final exams is the responsibility of Dr. Storey and Liam Hawkins. Assessment and grading of lab assignments and the lab exam is the responsibility of Shannon Newlands and Ian Pulsifer, the lab Instructor (together with laboratory TAs). The lecture and lab parts of the course are separate and neither of us will interfere with or alter the assessment or grading of the other part of the course. That is, do not come to Dr. Storey with any questions/complaints about the lab marks. Material covered in the midterm and final exams: You are primarily responsible for reading and learning material in the lectures. Textbook readings complement each lecture and associated readings are announced in class and are in the tentative schedule handout. The textbook chapters that will be covered are Chapter 1 to Chapter 16, excluding Chapter 15. While I strongly suggest you read the textbook to aid your learning, ALL questions on the midterm and final exams will be taken from information and concepts covered in the lecture material. Learning Objectives: Knowledge and understanding of monomeric structures of cellular macromolecules such as proteins, carbohydrates, lipids, and DNA are very important mandatory requirements. Overall must learns for the course: - Nomenclature, structures, and functions of; All Amino Acids Proteins Simple Carbohydrates All Fatty Acids Metabolic intermediates A few basic equations will be introduced in the course. The equations must be known and are part of the basic knowledge that allows students to analyze quantitative relationships that are needed for understanding biochemistry. Therefore, knowledge of, memory of, and an ability to work with basic equations are necessary course requirements. - Equations and relationships; Thermodynamics Enzyme kinetics More on Tests: The midterm tests and the final exam are all multiple choice. There are sample test questions on the “Old Exams” Page in CuLearn. I suggest you do a sample test before the first real test. The answers will teach you more about the material. The Zen of actually doing them will help you do better in the real test. Missing a midterm test: If you are unable to take a midterm test for medical reasons then your cumulative final exam will be adjusted to be worth 60% of the final course mark to cover the missing midterm test mark. That is, there will be NO make-up midterm test AND in the case of a missed midterm, a medical note is REQUIRED. Reading Materials 2

Slides used in class and the required readings for the course is available on the cuLearn site. You should read the assigned material before the lectures, and then again, after the lectures. You will spend a lot of time reading. Also available on cuLearn are a range of “Slide Arcs” which offer a set of additional tools to help you learn the most pertinent and challenging information for this course. I suggest you use them, they will help you. These Slide Arcs are complementary – they will not be tested but will aid your understanding. ALL questions on the midterm and final exams will be taken from lecture material. cuLearn The BIOC-BIOL 2200 webpage is located in cuLearn. The Course Webpage will be updated as needed during the term. All lectures, practise questions, Slide Arcs, and information about Academic Accommodations are available in cuLearn. Lecture slides are available as PDF files in 3 formats: 1, 3 or 6 slides per page. E‐‐mail I get about 200 emails per day (the joys of academia), so don’t worry if you don’t get a reply right away. I can usually reply within 48 hours. You all have a Carleton email address (whether you use it or not) by virtue of enrolling at Carleton. If you do not routinely use your Carleton email, then you MUST set your Carleton account to automatically forward to your regular email. Any communications to me about the course, grades, labs, missing tests, etc. must come from your Carleton account, this is university policy. So don’t give your Carleton password to anyone. Academic Accommodations You may need special arrangements to meet your academic obligations during the term. For an accommodation request the processes are as follows: Pregnancy obligation: write to me with any requests for academic accommodation during the first two weeks of class, or as soon as possible after the need for accommodation is known to exist. For more details visit the Equity Services website: http://carleton.ca/equity/wp-content/uploads/Student-Guide-toAcademic-Accommodation.pdf Religious obligation: write to me with any requests for academic accommodation during the first two weeks of class, or as soon as possible after the need for accommodation is known to exist. For more details visit the Equity Services website: http://carleton.ca/equity/wp-content/uploads/Student-Guide-toAcademic-Accommodation.pdf Academic Accommodations for Students with Disabilities: The Paul Menton Centre for Students with Disabilities (PMC) provides services to students with Learning Disabilities (LD), psychiatric/mental health disabilities, Attention Deficit Hyperactivity Disorder (ADHD), Autism Spectrum Disorders (ASD), chronic medical conditions, and impairments in mobility, hearing, and vision. If you have a disability requiring academic accommodations in this course, please contact PMC at 613-520-6608 or [email protected] for a formal evaluation. If you are already registered with the PMC, contact your PMC coordinator to send me your Letter of Accommodation at the beginning of the term, and no later than two weeks before the first in-class scheduled test or exam requiring accommodation (if applicable). After requesting accommodation from PMC, meet with me to ensure accommodation arrangements are made. Please consult the PMC website (http://www.carleton.ca/pmc/faculty/) for the deadline to request accommodations for the formallyscheduled exam (if applicable). 3

You can visit the Equity Services website to view the policies and to obtain more detailed information on academic accommodation at http://www2.carleton.ca/equity/ Statement on Academic Ethics Carleton University is committed to ensuring fairness and consistency in the completion of laboratories and examinations. As part of this commitment, students are required to follow proper laboratory and examination procedures. A student who commits a violation of this policy on an examination or lab, or obtains or produces an answer or unfair advantage by deceit, fraud, or trickery, or by an act contrary to the rules of the lab or examination are subject to the sanction under this Policy. These rules include but are not limited to: • copying lab reports from other students, or from reports written in previous years • attempting to read any textbook, notebook, memorandum, other written material or mechanical or electronic device not authorized by the examiner • writing an examination or part of it, or consulting any person or materials outside the confines of the examination room without permission to do so • leaving answer papers exposed to view • attempts to read other students' examination papers and/or speaking to another student (even if the subject matter is irrelevant to the test). You are expected to follow the Academic Regulations of the University. In particular, pay attention to Section E. Student Conduct. If you are not sure about the definition of cheating, come and see me, and I will explain it to you in more detail. NOTE: Student or professor materials created for this course (including presentations and posted notes, labs, case studies, assignments and exams) remain the intellectual property of the author(s). They are intended for personal use and may not be reproduced or redistributed without prior written consent of the author(s). Course Objectives This course provides an overview of fundamental concepts in biochemistry to give you a strong foundation for future study of biological systems. We will focus on the major macromolecules and chemical properties of living systems. Primary topics include the structure, function, and metabolism of amino acids, proteins, carbohydrates, and lipids; the roles of membranes and organelles in cell function; the physical properties of water, pH, and buffers; enzyme kinetics and metabolic regulation. The biochemistry of nucleic acids is covered in BIOL 2104 – Introductory Genetics. The course builds on the first year Biology and Chemistry pre-requisites. Furthermore, we will examine some of the critical experimental evidence that supports our current views of cellular function. Students who successfully complete this course will demonstrate a broad knowledge of biochemical concepts, paradigms, and vocabulary as well as be able to critically review experimental evidence in the scientific literature. Expectations of BIOC-BIOL 2200 Students I expect you to exhibit self‐regulated, autonomous learning behavior. Simply put, I expect you to extend your study of biochemistry outside of the classroom and laboratory. For example, the exams will not only test your knowledge of the factual data presented in lecture, but also your synthesis of the information into a logical whole – the big picture. I expect you to consider biochemistry in your other courses and to discover how the concepts presented during the semester impact your health, the environment, and the biological world as a whole. Your success as a student of biology/biochemistry depends upon your ability to think creatively and critically. Therefore, I intend to foster and expand the creative intellect already resident in your everyday thoughts and expect you to be open to new ways of thinking and to challenge old ways of thinking. 4

Expectations of the professor Learning is the responsibility of the student. The instructor’s role is to facilitate learning (by lecturing, answering questions, etc.) and to evaluate learning (by labs, exams, etc.). Remember that you are doing this work for yourself (to prepare for future endeavors), not for the instructor. What can you expect from me? You can expect me to be prepared for class with both knowledge and enthusiasm. You can expect patient and thoughtful teaching and help both within and outside our scheduled time together. You can expect that I will utilize all reasonable resources to help you succeed in this class. Don't be afraid to seek help when needed – from me, from online materials, from the 2 lecture TAs & from your lab TAs (for lab material). I am here to help you learn the material covered in this course and to provide an impartial evaluation of your performance. I am not paid on commission. My salary does not depend upon the number of A's, B's, C's, D's, or F's nor on the number of students who attend class. It’s tough sometimes, but it’s OK to ask questions in lecture. Come during office hours if you have more detailed questions. General Course Policies Your experience in this course (and in life) will be more enjoyable if you treat your classmates and your instructor with courtesy and respect. 1. Come to class regularly, be on time, and be prepared. If you are unavoidably late, enter the room quietly and choose a seat as quickly as possible. Do not invite your friends in to chat in this class. Disruptions in class make it hard for everyone to learn and/or teach. Police yourselves. 2. Once in class, stay for the duration. If you must leave early, give me advance warning and choose a seat that allows you to exit without disrupting others. You will not be allowed to meander in and out of the classroom. This is disruptive and unfair to your fellow students. 3. Turn off communications devices. This includes pagers, PDA’s, cell phones, personal entertainment (TV, music, etc.) devices or anything else that will disturb your classmates. Students with special circumstances need to speak with me right away. Do not talk on your cell phone while I am lecturing. And since you can’t wander in and out of classes – TURN OFF YOUR DEVICES. 4. No chit‐chat or unnecessary noise during class. This is a big class, and if everyone is making noise, no one can hear anything. Stay focused on the material under consideration during lecture. You are paying a lot of money to be in this class. If someone is talking near you, he or she is disrupting your learning experience, and essentially stealing money from you. 5. Academic dishonesty is not tolerated. If you are unclear about what is dishonest, please see the Undergraduate Calendar for clarification. If you are still unsure about specific instructions, ask me. The study of biochemistry is a collaborative endeavor. Therefore, you are encouraged to form study groups and work together if you wish. However, exams are not collaborative and must be completed without the assistance of your peers. About BIOL/BIOC 2200 Biochemistry is the field of science that investigates the chemical and molecular reactions that sustain life. The goal of this course is to study these reactions in connection to their role in biological systems. The course will begin with a discussion of the structure and function of the biomolecules involved in those important reactions. Students will then study bioenergetic principles that control the synthesis and degradation of biological macromolecules. Finally, the integration and regulation of signaling and metabolic pathways will be discussed. As a consequence of its interdisciplinary nature, this course will prove to be rewarding to students with a variety of interests. Life and health science lovers will encounter discussions about nutrition, disease, 5

development and evolution. Students interested in physics and chemistry will find applications for thermodynamic principles, reaction mechanisms and electrochemistry. Those who favor engineering and biotechnology will learn about the innumerable applications of biochemistry in industry. More importantly, this course will provide an opportunity for students to expand their range of interests and to find new applications for concepts learned in introductory science courses. In many ways, biochemistry students often feel like they are learning a new language. Reading the text book and memorizing structures and reactions will, at best, result in a mediocre, superficial and transient ability to answer questions in an exam. The best way to learn complex disciplines is to become an active participant in them. How can that be achieved in this course? First of all, students will be encouraged to work in groups to discuss and explain concepts out loud. The most satisfying proof of mastering a difficult topic is the ability to explain it to another person. It is expected that groups will work together outside the classroom in preparation for lecture and examinations. The second way to become actively engaged in the study of biochemistry is to take full advantage of the time spent in the laboratory. Exercises and activities have been carefully selected to complement lecture topics. Tips for Success 1. Come to class In some courses all you have to do is read the book. That's not the case here. Regular lecture attendance is essential for success in this class. This is not an online course. Although some material may be posted on cuLearn, you cannot expect to get all of the necessary information from this source. The textbook for this course covers more information than can be taught in one semester, and the lectures will direct you to what is most important. Also, some of material to be covered in class is not found in the textbook. If you must miss class, get the notes from a fellow student or the web, and then go over the notes with someone who was present at the live lecture. The slides may be on the web, but it still pays to come to class ‐‐ most students get more out of the live lecture than they do out of just reading the slides. Don't miss out on important information because you weren't there! All of the test questions that you will face (100%) will be made from material that was presented in class. 2. Take notes Your lecture and class notes are, without a doubt, the most important tool for succeeding. Pay attention and take careful notes! Don't just try to write everything I say. Everyone has her own style of note‐ taking; there is no one "right way". Do what works best for you. I give clues all the time as to what is important, especially in terms of upcoming exams. Pay attention and pick up the clues, which may be as obvious as, "This will be on the exam." Probably the most important clue is how much time I spend on a topic. Highlight what is important in your notes and in the textbook, so that you won't forget. There are many styles of taking notes ‐‐some people prefer to get it all down word‐for‐word and some people prefer to just write down the critical points. Taping is permitted, but the transcribing of tapes is very time consuming and I don't recommend it. You are probably better off forming a study group and going over the notes together (with the help of the web notes and textbook) to fill in the holes. You may be tempted to give up note taking altogether because the lecture notes are available on the web, but I strongly advise against it. Taking your own notes is important because it captures your own personal take on the lecture. The taking of notes also helps...