Instructor: Jill Paterson, PhD Chemistry A608. Office Hours: Mondays from 8-10 am, Chemistry A608

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1 Instructor: Jill Paterson, PhD Chemistry A608 Biological Chemistry, Chemistry C483 Department of Chemistry, Indiana University, Bloomington, IN Fall 2010, 3 Credits MWF, 10:10 am, Woodburn Hall 101 Office Hours: Mondays from 8-10 am, Chemistry A608 Associate Instructors: Iris Dong Office Hours TBA Justin Luebke Office Hours TBA Overview of course: This course will focus on the chemistry of the human body. We will look in depth at macromolecules and reactions that occur in our body which allow us to survive, thrive, reproduce, and grow. The course will be divided into four parts: Part 1 will cover biochemical basics and protein structure; Part 2 will cover the biological roles of proteins and cellular membranes; Part 3 will cover carbohydrate and fat metabolism; and Part 4 will cover protein metabolism and tie all of metabolism together. Required Text: Principles of Biochemistry, 4 th Edition, Horton et al., Pearson Prentice Hall Publishing, There is an electronic version of this book available from the bookstore. Course Websites: There are two websites for this course. Using Oncourse, ( you will have access to information which can be downloaded and/or printed for your own use: Class notes: Sets of incomplete notes, including figures discussed in class, will be available on the class website prior to the corresponding lecture. With the exception of the first class meeting, you are responsible for printing these notes, and bringing them with you to class. Be prepared with the notes; if we end Lecture 2 early, I will begin Lecture 3 a day early. Have the notes ready. You will be responsible for all material covered in lecture, even if it is not included in the online notes; you must attend lecture in order to get additional information. These notes are not a substitute for lecture attendance. Assignments: Quiz assignments, sample quizzes, quiz answer keys, copies of problem sets, problem set answer keys, information for exams, exam answer keys, exams from previous years, and discussion section worksheets and quizzes will be posted on the website. Check often to make sure you have all of the information required.

2 We will also use the course website available through the chemistry department ( to house a C483 Question Forum. All relevant questions ed directly to me and some that are discussed during my office hours will be posted on this website. You can see what questions your classmates are asking and what the correct answers are. This will serve as virtual office hours. Prerequisites: In order to get the most from this course, you should have completed either: C341 and C342 (Organic Chem I & II) Or R340 (Survey of Organic Chemistry) If you have not fulfilled this requirement, see Dr. Paterson ASAP. Course Grades: Your final grade will be based on a total of 725 points, comprised of: 3 problem sets at 50 pts each quizzes at 25 pts each 75 3 exams at 100 pts each final exam There will be no dropped exams, quizzes, or problem sets. You are responsible for attending each exam and quiz, and for turning problem sets in on time. A student will be allowed to reschedule quizzes only if s/he has an interview scheduled for professional school, graduate school, or future employment on the date of a quiz. In this case, documentation must be presented prior to the quiz that will be missed. Once approved, these students will be allowed to take a makeup quiz in class on December 8th. Details of the makeup quiz will be given directly to each student. If, due to illness, you miss an exam or quiz, you must get proper documentation from your health care provider. This documentation must come from a health care worker who personally examined you and must state that due to your illness there was no possibility of attendance at the exam or quiz. Please also provide a phone number of the health care worker for confirmation. If your missed exam is excused, you will not be allowed to make up the missed exam, instead your grade will be computed based on fewer points. Everyone must take the final exam in order to complete the class. Grades will be posted using the CALM system of the Chemistry department, located at the following web address:

3 Exams: There will be 4 exams. Three exams (September 28, October 26, and November 30) will cover specified portions of the course and are worth 100 points each. These exams are given on Tuesday evenings, from 7:15-9:15 PM, Location TBA. The final exam (Friday, December 17) will be cumulative, covering the entire semester course and is worth 200 points. You must take the final exam to complete the course. Answer keys for exams will be posted on the course website within hours of completing the exam. Quizzes: Three quizzes will be given (September 13, October 20, and November 8) during lecture. The exact information covered on each quiz will be posted on the course website least 1 week prior to the quiz. Problem sets: Three problem sets will be due throughout the semester (September 20, October 13, and November 19). The problem set is due on its due date, in lecture, at 10:10 am. Problem sets turned in after this time, but before 5 PM of the due date will have 15 pts deducted. Answers will be posted on the course website at 5 PM of the due date. No problem sets will be accepted after 5 PM. While you may discuss these problem sets with others, you must turn in your own assignment, and it must be in your own words. Students who turn in identical problem sets will be scored a 0 for the entire assignment. You may turn problem sets in early. Discussion Sections: Discussion sections will begin Wednesday, September 8. To ensure that all students have access to the same number of discussion sessions prior to each exam, a discussion week will run Wednesday- Tuesday. Everyone is registered for a specific section, but you are welcome to attend any of the four discussion sections. Attendance will be taken in the discussion sections, but attendance is not mandatory. Discussions will be run as problem based learning. The AI will present problems, give time for you to work through these problems, and then discuss your answer. Topics discussed each week are listed on the following pages. Meeting times: Monday 4:40-5:30 BH 205 Section Tuesday 4:40-5:30 WH 008 Section Wednesday 4:40-5:30 SY 003 Section Thursday 4:40-5:30 BU 400 Section Academic Misconduct: Do not cheat. If you cheat on an assignment, quiz, or exam, you will receive a grade of 0 and maximum disciplinary action will be taken as detailed at

4 Part 1: Biochemical Basics and Protein Structure Class Day Date Subject Practical aspect Assignments 1 M 8/30 Intro to biochemistry Why must we eat? ATP 2 W 9/1 Cellular compartmentalization Biochemical thermodynamics The power of ATP 1.4, 1.8, Biochemical equilibrium 3 F 9/3 Biomolecular interactions Why are cells spherical? M 9/6 Amino acids Yellowing of teeth as we age W 9/8 Acid/Base, ph, pka, Buffers Why you should breathe into a bag when you hyperventilate 6 F 9/10 Ionization of amino acids Why proteins can react M 9/13 Primary structure of proteins Insulin, Pitocin, bee stings, and botox 3.5 Quiz #1: Amino acids 8 W 9/15 Protein purification The study of Cystic Fibrosis, Tangier s Disease, and a specific breast cancer 9 F 9/17 Proteomics Diagnosing diseases Handout 10 M 9/20 3D- structure of proteins It s the structure, stupid! Problem Set #1 due 11 W 9/22 Enzyme active sites The purpose of enzyme Handout structure 12 F 9/23 Protein folding Alzheimer s disease, emphysema, cancers, Cystic Fibrosis 13 M 9/27 In-class review for exam 1 T 9/28 Exam #1, 7:15-9:15 PM Covers 1-13 & corresponding readings 1 W-T 8/30-9/7 2 W-T 9/8-9/14 3 W-T 9/15-9/21 4 W-T 9/22-9/28 NO DISCUSSIONS Thermodynamic problems Biochemical Equilibrium Drawing amino acids Calculating ph Generating buffers Determining ionization states of aa Protein purification Proteomics Assigned Problems from Horton: Chapter 2: 4, 5, 7, 9, 10, 11, 13, 14, 15 Chapter 10: 4, 10, 11 Chapter 3: 7, 8, 9, 10, 12, 14 Chapter 4: 1, 2, 3, 4, 8, 15 Reminder: Exam covering 1-13 and all corresponding readings and problems is September 28 th at 7:15 PM

5 Part 2: Biological Roles of Proteins and cellular membranes Class Day Date Subject Practical aspect 14 W 9/29 Collagen and antibodies What do you do with a scurvy 4.11; 4.14 pirate? 15 F 10/1 Enzyme classification The depth of our body s chemical 5.1 capabilities Handout 16 M 10/4 Enzyme mechanism The incredible speed of our body s reactions Handouts 17 W 10/6 Nonallosteric enzyme kinetics Characterizing enzymes Assignments 18 F 10/8 Inhibition and regulation of How the majority of nonallosteric enzymes pharmaceutical drugs are designed 19 M 10/11 Allosteric enzymes Biochemical reactions are superior than chemical reactions 20 W 10/13 Hemoglobin: An allosteric protein The cause of sickle cell anemia pain Problem set #2 due 21 F 10/15 Enzyme substrates (mono- & polysaccharides, Cutting the cheese after eating dairy fatty acids and TAGs) 22 M 10/18 Phospholipids The chemistry of snake venom 8.7 Biological Membranes 23 W 10/20 Transport across biological membranes How to escape an organelle 9.11 Handouts 24 F 10/22 Coenzymes and vitamins Why is a multivitamin important? Quiz #2: Carbohydrates and Lipids 25 M 10/25 Review for Exam #2 T 10/26 Exam #2, 7:15-9:15 PM Covers & corresponding readings 5 W-T 9/29-10/5 6 W-T 10/6-10/12 7 W-T 10/13-10/19 8 W-T 10/20-10/26 Exam 1 walk through Enzyme mechanism Quiz 2 assignment Enzyme kinetics Assigned Problems: Chapter 5: 2, 3, 4, 5, 6, 7, 9, 11, 12, 15, 16 Chapter 6: 1, 2, 4, 7, 8, 9, 10, 11, 13, 14 Chapter 4: 12, 13, 16 Chapter 8: 1, 2, 4, 7, 8, 9, 12, 14, 16 Chapter 9: 1, 3, 5, 11, 12, 14, 15, 16 Chapter 7: 1, 2, 4, 5, 8, 10 Transport across biological membranes Reminder: Exam covering and all corresponding readings and problems is October 26 th at 7:15 PM

6 Part 3: Carbohydrate and Fat Metabolism Class Day Date Subject Practical aspects W 10/27 Introduction to metabolism There s a hole in my Old Oaken Bucket 27 F 10/29 High energy metabolites More energy than Red Bull M 11/1 Glycolysis The role of insulin W 11/3 Glycolysis continued Energy from pasta and candy 30 F 11/5 Regulation of Glycolysis Why does consumption of fructose make you fatter than glucose consumption? Assignments 31 M 11/8 Pyruvate dehydrogenase One enzyme, 36 subunits Quiz #3: glycolysis 32 W 11/10 The citric acid cycle Where does the CO 2 we exhale come from? 33 F 11/12 Electron transport chain Our body s renewable energy source 34 M 11/15 ATP synthase Why do we need O 2? W 11/17 Pentose phosphate pathway Some complications of Gluconeogenesis Viagra or eating beans 36 F 11/19 Glycogen metabolism The biochemical cause of Problem set #3 due Ethanol metabolism hangovers 37 M 11/22 Lipid metabolism/βoxidation Why are trans-fats banned in NYC? W 11/24 No class, Thanksgiving break F 11/26 No class, Thanksgiving break 38 M 11/29 Review for Exam #3 T 11/30 Exam #3, 7:15-9:15 PM 9 W-T 10/27-11/2 10 W-T 11/3-11/9 11 W-T 11/10-11/16 12 W-T 11/17-11/23 13 W-R 11/24-11/25 14 M-T 11/29-11/30 Exam 2 walk through Assigned Problems: Chapter 10: 1, 2, 6, 7, 13, 14, 16 Chapter 11: 1, 2, 5, 6, 8, 10, 11, 13 Chapter 13: 1, 3, 4, 6, 8, 9, 10, 13, 14 Chapter 14: 2, 4, 5a, 7, 8, 10, 11b Chapter 12: 2, 4, 5, 6, 9, 10, 12, 14 Chapter 16: 3, 5, 6 Determining energy production from glycolysis 29 Determining energy production from glycolysis, PDH, and TCA Determining energy production from glycolysis, PDH, TCA, and oxidative phosphorylation NO DISCUSSIONS! THANKSGIVING BREAK AIs will be present for questions regarding exam Covers & corresponding reading Reminder: Exam covering and all corresponding readings and problems is November 30 th at 7:15 PM

7 Part 4: Protein Metabolism and Practical Aspects of Metabolism Class Day Date Subject Practical aspect 39 W 12/1 Protein metabolism Energy from hamburgers and Urea Cycle brats 40 F 12/3 Artificial Sweeteners Does Diet Coke cause cancer? Handout 41 M 12/6 Energy usage in metabolism Why is a 4 x 200 m relay team Handout faster than one man running 800 m? 42 W 12/8 Your metabolism: exercise & Why you need to exercise for a Handout starvation minimum of 20 min to lose weight 43 F 12/10 Review for Final Exam F 12/17 FINAL EXAM, 10:15 AM -12:15 PM 14 W-T 12/1-12/7 15 W-R 12/8-12/9 Assigned Problems: Chapter 17: 12 Walk through Exam 3 Review of semester 1-42 Covers 1-42 & corresponding readings Assignments Reminder: The Final Exam covering 1-43 and all corresponding readings and problems is December 17 th from 10:15 AM-12:15 PM.