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Chem 21000, Section P, Code 0427 CHEMISTRY 21000 – Syllabus Applied Chemistry for Biomedical Engineers (a.k.a. Organic and Biochemistry for Biomedical Engineers) Fall 2009 Instructor: Prof. Kevin Ryan Office MR-1337 (212) 650-8132 [email protected] Office Hours: Tuesdays 3:15-4:45; Wednesdays 10:40 AM – 11:50. Class time: Tuesdays and Thursdays from 2:00-3:15 pm. Room: Marshak 1307 (Please take into account the slow elevators) Textbook: General, Organic and Biochemistry, 6th Edition, Denniston, Topping and Caret McGrawHill (available in the bookstore and on the internet) This course is intended to introduce biomedical engineering majors to key concepts in organic chemistry and biochemistry, and to describe the significant connections between these topics and health, disease and the molecular treatment of disease. The course will balance theoretical and practical chemistry, while emphasizing material that is relevant to health-related studies. The material will be taught at a level intended for students whose professional goals do not include a mastery of chemistry, but for whom an understanding of the principles of chemistry and their practical applications is a necessity. The pre-requisite for this course is Chem 10401 (with a minimum grade of C); engineering majors only. How to maximize your chances for an A: Read the chapter carefully before class. Attend class. Reread the chapter after class. Be able to do and understand all of the problems at end of the chapter. Strive to understand both the concepts and the details. Grading Exams 1,2,3 (drop one) Unannounced Quizzes Final Exam TOTAL 70% 5% 25% 100% There will be three 75-minute exams, and you must take at least two. If you take all three exams your lowest score will be dropped. If you take only two regular exams, they will both count towards your grade. Do not skip exam 1 or 2 unless you are ill. A make-up exam will be given only if you are absent for a verifiable medical reason for two exams. All instructional activities are planned for working days during class hours as indicated by City College. The exams taken will contribute 70% to your final grade. The comprehensive final exam will contribute 25%. Unannounced quizzes and, to a lesser extent, class participation will account for the remaining 5%. Repeated classroom interruptions by a cell phone or other electronic device will lead to deduction of points from the final grade at a rate to be determined. (So please turn them off or set them to vibrate). Chem 21000, Section P, Code 0427 ****Calendar for Fall 2009**** Tuesdays 2-3:15 PM Thursdays 2-3:15 PM September 1 Ch. 10 September 3 Ch. 10 September 8 Ch. 11 September 10 Ch. 11 September 15 Ch. 12 September 17 Ch. 12 September 22 Ch. 13 September 24 Ch. 13 September 29 No class Monday Schedule October 1 EXAM 1 (Ch 10-13) October 6 Ch. 14 October 8 Ch. 14 October 13 Ch. 15 October 15 Ch. 15 October 20 Ch. 16 October 22 Ch. 16 October 27 Ch. 17 October 29 Ch. 17 November 3 Ch. 18 November 5 EXAM 2 (Ch 14-17) November 10 Ch. 18 November 12 Ch. 19 November 17 Ch. 19 November 19 Ch. 20 November 24 Ch. 20 November 26 Thanksgiving December 1 Ch. 21 (21.1-21.4) December 3 Ch. 22 (22.1-22.4) December 8 Ch. 22 (22.6) and 23.1-23.2 December 10 EXAM 3 Nov 3 thru Dec 3 Date TBA: Comprehensive Final Exam Please note, the last day for “W” grade is November 6. Blackboard will be used. Please check frequently. Please also make sure that your correct email address is registered with blackboard through CUNY Portal. A tip for understanding organic chemistry and biochemistry: Like everyday macroscopic objects, molecules have 3-dimensional structures that determine their properties: Stereo projection of codeine To view: Hold page in front of you, but focus your eyes on the horizon beyond the page. Then, without refocusing, look at the projection. OR While looking at the projection, relax your eye coordination as if you were tired. One image will drift into the other. OR Use a stereoviewer Chem 21000, Section P, Code 0427 Academic Integrity: The CCNY policy on academic integrity will be followed. Document is posted on the CCNY website (CUNY policy on academic integrity—link is at the bottom of the home page). Make sure you have read the details regarding plagiarism and cheating, in case you are not clear about the rules of the college. Cases where academic integrity is compromised will be prosecuted according to these rules. *********************************************************************************************************** Official Learning Outcomes for Chemistry 21000 After completing this course, students should be able to: 1. Understand and explain the common structural motifs found in carbonaceous compounds, including carbon allotropes. 2. Understand and explain chemical bonding in organic molecules, including the distinction between covalent and non-covalent bonding, and between single and multiple bonds. 3. Understand and explain simple physico-chemical trends in a homologous series of organic compounds, such as the boiling or melting points of the linear alkanes or alcohols. 4. Understand and draw models of conformational isomers of linear and cyclic alkanes. 5. Recognize and predict simple physico-chemical properties of the common organic functional groups based on their structure-based noncovalent interactions. 6. Write balanced chemical reactions for the most basic reactions characteristic of the common organic functional groups, such as alkenes, alcohols, aldehydes, ketones, carboxylic acids, esters, amines and amides. 7. Plan a short chemical synthesis of monofunctional compounds containing the major functional groups listed above. 8. Understand the relationship between polymer molecular structure and the fundamental physical properties of polymeric materials. 9. Understand acid-base equilibria of amino acids as described by the pKa. 10. Distinguish between primary, secondary, tertiary and quaternary structures in biopolymers. 11. Analyze the reaction coordinate for an enzyme catalyzed metabolic reaction. 12. Explain using a diagram the Central Dogma of Molecular Biology. 13. Understand and explain how cells burn organic molecules and trap some of the energy in the chemical bonds of ATP 14. Follow a specific glucose carbon through glycolysis. 15. Follow a specific Acetyl-CoA carbon through the Krebs Cycle. 16. Follow a specific fatty acid carbon through beta oxidation 17. Qualitatively describe Oxidative Phosphorylation and explain why aerobic organisms require oxygen to live. Dept. Outcome letters a a a,d a a,d a a a a,b,e a,b a,b,d a,b a,b,e a,b a,b a,b a,b Chem 21000, Section P, Code 0427 Topics covered: Saturated Hydrocarbons Unsaturated Hydrocarbons Alcohols, Phenols, Thiols and Ethers Aldehydes and Ketones Carboxylic Acids and Derivatives Amines and Amides Carbohydrates Lipids Protein Structure and Function Enzymes Introduction to Molecular Genetics Carbohydrate Metabolism Aerobic Respiration and Energy Production Fatty Acid Metabolism