Welcome to Biochemistry 1.

Biochemistry 1 & 2: CHEM-UA.881002 & 882001 Dr. Burt Goldberg, Professor of Biochemistry/Chemistry Chemistry Department Room: 664 Brown Email: bg43@nyu.edu or burt.goldberg@nyu.edu or burt.goldberg@gmail.com Phone: (212.998.7949 if I do not answer do not leave a message, just send an email) Welcome to Biochemistry 1. Office hours will be on Tuesday & Thursday from 11:00 to 1:00 PM, room 664 Brown building. I am NOT in the office every day after my lectures, only on Tuesday and Thursday for office hours. A good time to ask your questions is during recitation, which means that you need to read the chapter prior to each class (lecture or recitation) and come to recitation with your Study Guide questions prepared. Your success in this course will depend on how seriously you take your preparation. Your grade is dependent on your performance on exams & quizzes. Extra credit will not be offered to raise your grades! It is your responsibility to be prepared and to come to class. Having not read the material to be covered during the lecture is a serious error in judgment with possible devastating consequences. I strongly urge students to form collaborative study groups, and to discuss their answers to the Study Guide questions with the members of their group. Do not accept answers from others or pool resources, (are you sure they are right?); this is not a great idea and can also have serious consequences. Course Goal: Text and course requirements Let me first stress that attendance is mandatory, I know it is a 8AM, but if I can make it to your lecture on time why cann t you? Why do I emphasize attendance? What I stress in lecture is what I will hold you accountable for on your exams. What is in the text is only where I will begin. The text is not the sum total of what will be covered. It is a mammalian centered text. I will add the biochemistry of microbes that is much more interesting, and much more diverse that of mammals. I will also add from my own original training in both Clinical and Microbial Biochemistry. Let me be very candid with you I am well aware of how valuable a letter of recommendation from me is to a medical school and graduate school application. If you have not attended lecture, how do I talk about your work ethic, focus and attention to what courses. I will not be able to write on your behalf (that is an absolute). Please attend lecture. Also do not miss recitation. There is no going to another recitation if you missed your assigned recitation without my permission. The recitation lecturer will not accept your presence in that recitation. I will expect a very good explanation 1

Cell Biology and Biochemistry are two sides to the same coin. One cannot fully understand one without the other. The chemistry is the evolutionary stress for the development of cellular organelles. It is important to not only understand the chemistry but also to understand the relationship of the chemistry to the organelle. Punctuality is expected! This is a large class so please be on time. I expect that you will be present for examinations. If you are ill please notify me no less than 24 hours beforehand, not after the examination has taken place. I will expect an official doctor s note only (a report from Student Health is acceptable)! Makeup examinations are not a birthright and will not be given without good reason. Grades are based on three examinations. Each accounts for 25% of the course grade. If you miss a midterm examination, you first must present documentation of why you missed the exam and only then will I discuss the possibility of the makeup exam, assuming I deem the reason you missed the exam to be an excused absence (this is all at my convenience). All examinations will be problems, essay and short answer problems. The text for the course is Biochemistry, 6 th edition Lehninger Principles of Biochemistry by Cox & Nelson and specific Chapters from 7 th edition Molecular & Cellular Biology by Lodish that will be available with your text bundled together at the bookstore. You may also separately buy the Lodish supplement from MCB at the bookstore. This is a two-semester course, I strongly urge you to take both semesters. I do not treat Pre-Med any different from Biochemistry/Chemistry majors, Biology majors or Neuroscience majors. I expect the same level of work ethic from all. You are all here because this is a required course for your major or by the graduate education (MD or PhD) that you are interested in pursuing. My job is to present an in depth course in Biochemistry. What you are interested in doing after you complete your bachelor degree is not my business. What is my concern is that I give you the course that allows you the greatest latitude in the future. What we will cover in Biochemistry is much more than what is covered in Medical School course, but it will prepare you for the rigor of that course, and for those interested in a Biochemistry of Cell Biology graduate program, you will be very well prepared. But, again doing the required work to take advantage of what is being presented is your responsibility. You need to learn to become a self-learner, which is what will be expected in graduate education. That means not missing a lecture, a recitation and doing the Study Guide questions yourself. I will not check up on you, it is your responsibility not mine to for you to do your job. Grading 100-95= A, 94-90=A-, 89-85=B+, 84-80=B, 79-75=B-. 74 to 70 = C +, 69 to 65 = C, 64-60=C-, if your grades put you below this I will strongly urge you to drop the course. Exams will be on the following dates and times; Friday 9/27, Friday 10/25, and Friday 12/6, 2-4:30 PM. The reason for this is simply I do not want you to be rushed through the exam. I want you to have the time to complete the exam and not to have to 2

literally chase you out of the room. There is no way to extent the time with another class coming into the room following our lecture. The only alternative is Friday as you have done in both GChem and Orgo, the times of the exams will be tentatively 2 to 4:30PM. There will be three exams. There will not be a final exam. But there will be a final paper due on a date to be set in the future by me. The grade breakdown is 25% for each exam, 20% for recitation and quizzes in recitation, and 5% for you final paper. There will be a quiz at the beginning of each recitation. Do not be late there is no make up quiz. If you are late and miss the quiz, this is your loss. Punctuality is required in recitation as it is in lecture. That is professional behavior. In the recitation you will receive a grade for the quiz (15% of your grade) and a grade for attendance (5%of your grade). Please not how serious I take attendance. You must go to the recitation you are assigned to, no registered for one and you tell me you have been going to the same one as your best friend, but are not registered for, this is not going to be acceptable. If you have been chronically absent from recitation do expect an invitation to see me, I will not be happy with you, then tell me that you went to0 another recitation and I will be very upset. If you need to miss a recitation and want to go to another, you must have my permission and it will only be acceptable with my permission. This must be done through an email to both of the Recitation Instructors and me for approval. Without my email permission, the Instructors will not accept your presence and you will be marked as absent and obtain as zero for that quiz. STUDY GUIDE and Recitation: this is an overview of what I will hold you responsible for from each chapter as well as additional assigned readings. You are expected to answer these questions for each chapter before the recitation on that chapter. It is always wise to outline the chapter as you read, and put the concepts of the chapter in your own words. This attempts to focus your reading on important terms, details and concepts. The Study Guide is your responsibility (we will not collect these assignments), but you may ask questions. You may not ask the Instructors those exact questions -- they will not give you an answer! Doing the assignment is your responsibility; the Study Guide questions along with the problems assigned from the book are to prepare you for the exams. There will also be questions about the external readings and they will be part of the Study Guide. There will be a quiz at each recitation and the quizzes are 20% OF YOUR FINAL GRADE. External readings will be placed on Blackboard as External Links. In general, these will be current review articles from numerous sources, such as Molecular Cell, Annual Reviews of Biochemistry, Cell & Cell Metabolism (which are both outside my office on the coffee table for your reading pleasure), Annual Review of Cell and Developmental Biology, etc. It would be prudent to answer these questions as you read, prior to lecture. Memorizing metabolic pathway is a waste of time and energy. The only memorizing I will expect is the 20 amino acids found in proteins. And in second semester the structure of the 4 nucleotide bases in DNA. If you understand why the pathway evolved, what its purpose is in 3

the cell, where it resides in the cell and how it is regulated, you will know the pathway. But let me be very clear: I am not collecting the Study Guide questions nor am I providing answers. That is your job. My Recitation Instructors are also not there to give you answers. They are there to help you understand if your answer is correct and complete. It is your responsibility to be prepared for lecture and recitation. Profcast of Biochemistry lectures. Again this year I will hope to record my lectures as I am lecturing. If you wish, you might then listen to the lecture in real time, ask questions and then write you notes at home from the posted lecture. The posting will be the audio of my lecture over the PowerPoint. The PPT will be posted prior to lecture. The more questions you ask the better the lecture will be. One caveat, if attendance slides down, I will stop the recording. This did not happen last year and it has helped many people be much more successful in the course. Along with the posting of the lectures on our class sight, there will also be discussion board. There will be question streams that you may post questions or also answer a question posted by your classmate. This goes hand in hand with study groups that should be 3 or 4 of you going over your study guide answers as a group. If there is a question that you want to hear from others about then post it. The Instructors as well as I will go onto discussion board and answer questions, or post a question to open a stream of discussion. Syllabus Biochemistry 1 Lect. Date Topic Chapter & readings 1 9-04 Introduction to course and me. Water and Lehninger 2. Water cellular structures, and hydration. 2 9-09 Structure of the Cells; prokaryote vs. eukaryote. 3 9-11 Primary structure of proteins 3. Amino acids, Peptides, & Proteins 4 9-16 Protein folding 4. The 3D Structure of Proteins 5 9-18 How do proteins in eukaryotic cells find the Lodish Chapter 14 correct compartment location? 6. 9-23 How do proteins carryout their functions? 5. Protein Function Models of how proteins work. 7. 9-25 Protein catalysis, proteins as machines. 6. Enzymes Last topic for first exam, 9/27 8. 9-30 Sweetening proteins This will be the last topic for the first Exam. 7. Glycobiology 4

9. 10-02 DNA & RNA 8. Nucleotides & Nucleic Acids 10. 10-07 DNA & RNA 8. Nucleotides & Nucleic Acids 11. 10-09 10-14 Columbus day No Class 12. 10-16 Chemistry of cellular lipids. Lehninger 10. Lipids 13. 10-21 Phospholipids and sphingolipids Lehninger 11. Biological Membranes & Transport 14. 10-23 Continued Transport Last topic exam #2 10/25 15. 10-28 Signal Transduction Lehninger 12. Biosignaling, Lodish 15 & 16. 16. 10-30 Continued Signal Transduction 17. 11-04 Cell Cycle Lodish 19 18. 11-06 Continued Cell Cycle Last Topic Exam 2. 19. 11-11 Genes and Chromosomes Lehninger 24. 20. 11-13 21. 11-18 DNA Metabolism 25. 22. 11-20 RNA Metabolism 26. 23. 11-25 Protein Metabolism 27. 24. 12-02 Continued Protein Metabolism 25. 12-04 The Immune Response Lodish 23. 26. 12-09 Immune Response Recitation schedule Sect Recitation Instructor time Room 108 Feher Katie 109 Feher Katie 110 Modell Ashley 113 Kennedy Stephen W: 3:30 PM - 4:45 PM 25W4_C-13 W: 4:55 PM - 6:10 PM WAVE_566A M: 4:55 PM - 6:10 PM WAVE_429 F: 8 AM - 9:15 AM SILV_407 5

114 Kennedy Stephen 115 Leninger Maureen 116 Leninger Maureen F: 9:30 AM - 10:45 AM SILV_407 F: 11 AM - 12:15 PM WAVE_431 F: 12:30 PM - 1:45 PM SILV_407 Welcome Biochemistry 1 students from 1 st semester with Professor Kallenbach. As you see I did not use the same text in my Biochemistry 1 course. But I have added the appropriate chapters from that text to the Lehninger chapters in the syllabus. All questions will come from my Study Guide (please se above) and exams are based on those questions for each chapter. The text is not the course it is for you, the course is my lectures and the exams are based on the lectures not the text book, so which book you read is not relevant, it is only a starting point for my lectures. You will be to get at the bookstore the Molecular Cell Biology Supplement unless you have the MCB text. Chapter from that are assigned reading. Please read the entire syllabus from the beginning (above) there are course details from first semester. Attendance is mandatory! Yes I will record and post the lectures do not think that that substitutes for being in class, bad mistake. You do not do well on a exam, come to see me but I have not seen you in lecture, there will not be a sympathetic ear. Also let me be very candid with you, I am well aware of how valuable a letter of recommendation from me is to a medical school. If you have not attended lecture, how do I talk about your work ethic, focus and attention to what courses. I will not be able to write on your behalf (that is an absolute). Please attend lecture. Also do not miss recitation. There is no going to another recitation if you missed your assigned recitation without my permission and only my permission. The recitation lecturer will not accept your presence in that recitation. I will expect a very good explanation. You miss recitation then you miss quiz and lose points towards your final grade. There is no makeup recitation quiz ever. Syllabus Biochemistry 2 All dates and times are tentative, until Spring term offerings has been set by the Chemistry department. Lect. Date Topic Chapter & readings 1 01-27 How does the evolution of compartmental- Lehninger 13, Energetic and 6

ization change the chemistry of eukaryotic cells? Biochemical Rxn types METABOLISM THE OVERVIEW-How did we come to understand that metabolism is arranged in metabolic pathways? 2 01-30 Glycolyis/Gluconeogenesis, glyocgenphosphorylysis/synthesis, β- oxidation of FA/synthesis of FA; What do they have in common? 14. Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway 3 02-03 Why is glycolysis a central pathway in energy transfer? Pyruvate is the end product of glycolysis, what are its fates? 4 02-05 Are there significant alternative pathways to glycolysis? In prokaryotes? Eukaryotes? Pentose phosphate pathway. 5 02-10 Gluconeogenesis a reciprocal pathway to glycolysis: How can a cell switch from glycolysis to gluconeogenesis? 15. Principles of Metabolic Regulation 6 02-12 Why is the synthesis of glycogen tightly regulated? Why is liver glycogen store 10% of liver dry weight? How does this relate to fatty acid synthesis, TCA cycle and glycolysis? Signal transduction regulation of glycogen synthesis and hydrolysis. 7 02-17 OXIDATIVE TCA CYCLE: is this found in anaerobes as well as aerobes 16. The Citric Acid Cycle 8 02-19 What is the relationship of the TCA cycle to gluconeogenesis? 9 02-24 What is the origin of the mitochondria? How is the mitochondria related to the hydrogenosome and mitosome? 19. Oxidative Phosphorylation and Photophosphorylation Oxida tive Phosphorylation Please do not bother reading photosynthesis. 02-26 Exam #1 Material to be covered, chapters 7

13-16. 10 03-03 Aerobic respiration and ATP synthesis by an H + pumping mechanism. 19. Oxidative Phosphorylation and Photophosphorylation Oxida tive Phosphorylation 11 03-05 The structure of the ATPase (ATP synthase) & comparison with vatpase and the Na-K ATPase 12 03-10 β-oxidation: why does this pathway occur in both mitochondria and peroxisomes? 17. Fatty Acid Catabolism 13 03-12 Fatty acid synthesis: why must it be in a separate compartment from β-oxidation? How does the TCA cycle anf FA synthesis contect? 03-17 Spring Break 03-23 14 03-24 Biosynthesis of membrane lipids & sterols. 21. Lipid Biosynthesis The entero-hepatic cycle: the liver and the metabolism of Fatty acids & sterols. 15 03-27 Biosynthesis of membrane lipids & sterols. The entero-hepatic cycle: the liver and the metabolism of Fatty acids & sterols. What are the eicosanoids? 16 03-31 How does a cell turn-over its proteins? How can amino acids be utilized as a source of cellular energy? 18. Amino Acid Oxidation and the Production of Urea Amino acid turn-over: How does amino acid catabolism interact with the TCA cycle and the Urea cycle? 17 04-02 How are muscle & liver different in amino acid utilization? 18. Amino Acid Oxidation and the Production of Urea 8

04-07 Exam #2 How do micro-organisms utilize amino acids for bioenergetics? 18 04-09 Biosynthesis of Amino Acids 22. Biosynthesis of Amino Acids, Nucleotides, and Related Molecules 19 04-14 Biosynthesis of Amino Acids 20 04-16 Nucleotide Biosynthesis 04-21 Nucleotide Biosynthesis 21 04-23 Regulation & Integration of Mammalian Metabolism 22 04-28 The Warburg Effect, Pasteur Effect and energetic metabolism going wrong? You know we call it disease. 23 04-30 Obesity, Diabetes and Ketogenesis 24 05-05 25 05-07 Exam # 3 This date is set by the university, please do not make planes or reservations to go home before this date is announced! There are NO early exams or make up exams. These assigned problems are in addition to the study guide questions. Assigned readings will be posted on Blackboard as pdf Articles. Usually they will be reviews. 9

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