Chem320 2020F syllabus Sep30 PDF

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Fall 2020 Syllabus...

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CHEM 32002 Syllabus - Biochemistry 1, Section B, Fall 2020 The City College of New York, Department of Chemistry and Biochemistry Prof. Daniel Keedy / Email: [email protected] (NOT other email addresses, please) Class Times: Mon, Wed 9:30 - 10:45 AM / Location: ONLINE

Any changes to the schedule will be announced in class and/or on Blackboard. Date Aug Sep

Oct

Nov

Dec

26 31 2 7 9 14 16 21 23 28 29 30 5 7 12 14 19 21 26 28 2 4 9 11 16 18 23 25 30 2 7 9 14

W M W M W M W M W M Tue W M W M W M W M W M W M W M W M W M W M W M

Chapter 3 Amino Acids, Peptides, Proteins 3 Amino Acids, Peptides, Proteins 4 3D Protein Structure NO CLASS - COLLEGE CLOSED 4 SUBSTITUTE LECTURE  - 3D Protein Structure 5 finish Protein Structure, start Protein Function 5 Protein Function 5 Protein Function EXAM I (Ch 3-5) NO CLASS 6 MONDAY SCHEDULE  - Enzymes 6 Enzymes 6, 8 finish Enzymes, start Nucleic Acids 8 Nucleic Acids NO CLASS - COLLEGE CLOSED 7 Carbohydrates 7, 11 finish Carbohydrates, start Membranes 11 Biological Membranes 11 Biological Membranes EXAM II (Ch 6-8, 11) 14 Glycolysis 14 Glycolysis 15 Glucose and Glycogen 15 Glucose and Glycogen 16 Citric Acid Cycle 16 Citric Acid Cycle EXAM III (Ch 14-16) NO CLASS - COLLEGE ON FRIDAY SCHEDULE 17 Fatty Acid Catabolism 17 Fatty Acid Catabolism 19 Oxidative Phosphorylation 19 Oxidative Phosphorylation EXAM IV (Ch 17, 19) FROM 9:00 - 10:15 AM!

Suggested Problems 1-3, 5, 6, 9-11, 19 1-3, 5, 6, 9-11, 19 1, 2, 4-10 1, 2, 4-10 1-6 1-6

1, 3, 4, 7-9, 11-12, 19 1, 3, 4, 7-9, 11-12, 19 2, 12-14 1, 2, 10, 12, 13 2, 4, 6, 11-15, 17-19 2, 4, 6, 11-15, 17-19 1, 10-16, 19, 24-28 1, 10-16, 19, 24-28 1, 4, 5, 7, 8, 11 1, 4, 5, 7, 8, 11 16, 18, 19, 30, 32 16, 18, 19, 30, 32

8, 9, 23, 24, 27 8, 9, 23, 24, 27 2, 4, 9, 21, 23 2, 4, 9, 21, 23

Textbook: Nelson & Cox, "Lehninger Principles of Biochemistry" (2012), 6th ed. Online Bookstore link: http://ccny.textbookx.com/institutional/index.php?action=browse#books/2319650

Course Overview Objectives: This course will cover amino acids, proteins, nucleic acids, carbohydrates, and membranes. It will explore the relationship between molecular structure and function, and will emphasize the fundamental role of chemistry in biology. It will also give you a firm understanding of the energetic principles and key pathways of metabolism. Remote Instruction: Due to the COVID-19 pandemic, this course will be entirely online. All lectures, office hours, and exams will be administered online using Blackboard (Bb). Lectures will be delivered using Blackboard Collaborate Ultra (BCU), which allows interactive video, audio, text-based chat, and more. All live lectures will also be recorded using BCU so you can review them later whenever you like. Please ensure you are registered on Blackboard through CUNY Portal before the course begins. Blackboard Files: This syllabus, lecture PowerPoint slides, and other course materials will all be uploaded to Blackboard. Lecture slides will be posted the night before each class, but these should be considered draft versions and are subject to change based on discussions in class, etc. I will upload newer final versions as necessary. Additional Contact Outside of Class Office Hours: I will hold two regular office hours sessions per week, each for about one hour, unless otherwise announced in class and/or by email. All office hours will be held via Blackboard Collaborate Ultra sessions via video plus chat. ● Mondays: 10:45 - 11:45 AM (approximately), shortly after class ● Tuesdays: 9:30 AM - 10:30 AM Email/Phone: If you cannot make either office hours time slot but have questions, feel free to email me anytime at [email protected] (NOT other email addresses, please). I am happy to answer questions by email. If you still have questions after an email exchange or wish to speak to me one-on-one, let me know and we will arrange a video session. Homework, Exams, Extra Credit, and Grading Homework: The suggested problems listed in the lecture schedule (above) will help test your comprehension of the material. These are optional and will not be graded, but I highly recommend you go through them when you read the associated chapters before class. I reserve the right to occasionally give an unannounced quiz based on the assigned reading material at the beginning of class. Exams: There will be four exams, each of which will last 75 minutes (same as every other class period). The fourth exam will not be cumulative per se, but rather will focus on concepts we cover in the last portion of the course -- that said, some concepts in the later portions of the course will build on previous concepts. I will curve the grading for each exam by shifting the average score up to 75 as needed. In previous semesters, all exams were entirely multiple choice. I will reconsider the best format for exams this semester due to the extenuating circumstances of the pandemic, and will communicate the format details to you before the exams.

I will drop your lowest of the four exam scores and calculate your final grade using the remaining three exam scores, as described below. Therefore, although it is in your interest to do your best on all four exams, you can miss one exam for any reason (illness, travel, religious observance, etc.) with no penalty. However, because of this lenient policy, I will not drop a second exam or offer a makeup exam for any reason -- so you should certainly not miss two of the four exams, or you will not pass the course. Extra Credit: In addition to the exams, you can earn extra credit in both of these two ways: 1). Participate in class. I will award up to 10 points if you participate in class by answering “pop quiz” poll questions in class, asking questions, contributing to discussions, etc. 2). Present on an article about biochemistry. I will award up to 10 points if you identify a basic-research article that interests you, and make a short (2 minutes), one-slide presentation about the article to the class. To do so, download the extra credit PowerPoint slide template from Blackboard and customize it for your article. Follow the template -- e.g. be sure to include your name, the full citation info for your article (title, authors, journal, publication year), etc. Make sure your text and figure(s) are large enough to be legible on a projector. Include your name in the filename when you email it to me. Your grade will be based in part on how well you follow the format, but especially on how well you clearly explain the science behind the article and relate it to the topics we cover in biochemistry. I will allow only up to two presentations per class, so be sure to nominate an article as soon as possible if you want to ensure a slot. If there are no remaining presentation slots, or you do not wish to present to the class, you may instead provide me just the PowerPoint slide for your article, and I will award up to 5 points. However, I will not offer any additional extra credit beyond these article reviews. You cannot do both the presentation or slide-only extra credit options -- you must choose one or the other (or neither). For either extra credit option (presentation or slide-only), you must get the article approved by me first! To do so, email me the link to your article. Check that it works from any device before sending it to me. Guidelines for selecting extra-credit articles: ● Pick a recent article, from the last 5 years. ● Pick a unique topic -- once an article has been covered by someone, no one else can choose it. ● Focus on peer-reviewed basic research articles in publications such as Science, Nature, Journal of Molecular Biology, Proteins, Protein Science, PNAS, Biochemistry, etc. ● Try visiting PubMed or Google Scholar, entering search terms from topics we have covered in class, and finding an article that interests you. ● You must get your article approved by me first! Email me a link that takes me directly to the website for the article (test the link first!), and I will approve it if it is a good fit for the topics we have covered. ● If you are selected, email me your PowerPoint slide by dinner time the night before the class when you will present. If you wait until the last minute to send it to me, there may be technical difficulties in transferring the file, and I reserve the right to skip your presentation and award you only partial or zero credit.

Grading: To get your final grade for the course, I will drop your 1 lowest exam grade, then sum your numerical grades (0-100) on your 3 best exams, then add any additional points (including participation and the article review extra credit), then divide by 3, then convert to a letter grade using the scale below. I will not curve final grades. 93-100: A 90-92: A-

87-89: B+ 83-86: B 80-82: B-

77-79: C+ 73-76: C 70-72: C-

60-69: D

59 or lower: F

Plagiarism and References Plagiarism is a major violation of ethical academic conduct, and will not be tolerated in this class. Plagiarism includes the following: ● to steal and pass off (the ideas or words of another) as one's own ● to use (another's production) without crediting the source ● to commit literary theft ● to present as new and original an idea or product derived from an existing source In other words, plagiarism is an act of fraud. It involves both stealing someone else's work and lying about it afterward. Source: https://www.plagiarism.org/article/what-is-plagiarism In practice, this is fairly simple: express yourself in your own words, and cite any sources you use appropriately -- for example: Authors. “Title.” Journal (Year). Volume: Pages. Jane S Richardson, David C Richardson. “Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation.” Proceedings of the National Academy of Sciences (2002). 99(5): 2754-2759. Inclusivity This course aims to accommodate many diverse backgrounds, beliefs, and perspectives. To that end, it welcomes anyone regardless of religion, race, gender, gender identity, sexuality, political leanings, or other such aspects. Please help maintain a supportive community here by considering how others’ viewpoints may differ from your own....