Chemistry 2505 (Biochemistry, Wing 5 of the Chemistry complex)
Office hours: Weds. 1:20-2:20 pm, Thurs. 3-4 pm, Chemistry 2505
Contacting me: e-mail at jdkahn@umd.edu much preferred to 405-0058
Teaching Assistant: Ruchi Mehta (nee Kumar), office hours Tues. 12-1 pm,
Thurs. 9:30-10:30 am,
Chemistry 2512. Contacting Ms. Mehta: rkumar@wam, 405-1815
Textbooks and other sources:
Required: Mathews and van Holde, Biochemistry, 2nd ed, 1996 (Benjamin/Cummings), "MvH"
Recommended: Ako and Shimeld, Study Guide to Accompany MvH (Benjamin/Cummings)
Additional sources (on reserve, no need to buy them): Voet and Voet, Biochemistry, 1995; Creighton, Proteins, 1993; Fersht, Enzyme Structure and Mechanism, 1985; Segel, Biochemical Calculations, 1976.
This course will cover basic concepts in biochemistry, emphasizing protein structure, folding, function, and regulation and touching on the structure and function of carbohydrates, lipids, and nucleic acids. This introduction to biomolecules will provide the vocabulary and grammar needed to pursue further course work and research in biochemistry. This is not a comprehensive survey course - metabolism, cell biology, and molecular genetics are covered in Biochemistry 462 and 465 and other courses. The coverage will be similar but not identical to Dr. Ebrahimian's 9:30 section, and lectures in the two sections are not guaranteed to be coordinated.
There will be three 75-minute exams (100 pts each), on 2/24, 3/19, and 4/23. Exams will focus on recent lecture material but will inevitably draw on information from earlier in the semester. The final (200 pts, 5/21) will be comprehensive but will emphasize material not previously tested on. Problem sets are optional, but completing them is likely to be very helpful for the exams. Your final letter grade will be based on your performance relative to the class as a whole and to my expectations (i.e. it's curved, but I draw the lines between grade levels depending on how I felt the class as a whole performed). Exams will be about 50 % short-answer questions, testing your comprehension of lecture material, and about 50 % essay or computational questions, testing your ability to apply and extend this basic knowledge. Final grades will be given out only through the MARS system.
Do not miss any of the four exams. The only excused absences are for incapacitating illness or personal tragedy, and a doctor's note or other documentation may be required. Please call me within 24 hours of missing an exam. There will be one comprehensive 75-minute make-up exam at the end of the semester, only for those with an excused absence on an earlier exam. A student with an excused absence may choose, instead of taking the make-up, to receive a grade based on only two of the three 75-min exams.
If you feel that an exam has been graded unfairly, you must turn in the exam to me no later than one week after exams were handed back, with a written explanation of your reason for desiring a regrade. The entire exam is subject to regrading, which often decreases the total score. Arithmetic errors in the grading can be corrected without regrading.
Integrity is a cornerstone of the scientific enterprise. Attempts to have a substitute take an exam for you, to alter exams before regrading, or to copy from your neighbors will be treated with absolutely no sense of humor. Please bring a photo ID with you to all exams. Random exams will be photocopied.
Your progress in learning biochemistry is important to me and to Ms. Kumar. Your progress toward getting an A in this course is much less important to us. We also pursue research and other activities which require time and concentration.
We are happy to help you with the material during office hours. If necessary, we will arrange other times to meet. Review sessions will be scheduled before each exam. I will be happy to provide more information or entries into the literature on any topic. If you believe a mistake has been made in lecture (I guarantee this will happen), please speak up or inform me afterward. Please ask questions in lecture if something is not clear. BUT: Do not call me in the office except for emergencies (i.e. you're too sick to take an exam). Do not call me at home at all. Do not drop in to my office or lab: this is disruptive and possibly unsafe.
You are welcome to e-mail questions and comments to me. I do not guarantee individual responses, but I will address errors or common points of confusion in class. There is a Web page for the class at (http://www-chem.umd.edu/biochem/kahn/bchm461) for the syllabus, problem set assignments, exam results, study hints, and extra material such as molecule graphics.
The exact order of topics and the number of lectures on each may change, but exam dates are firm and you will have at least one week between the presentation of material and testing on it.
MvH, Chapters 1, 2, 3
| 1. | Introduction to cellular organization and biochemistry | 1/27 |
| 2. | Review of aqueous solution chemistry - H2O, pH, buffers | 1/29 |
| 3. | Thermodynamics - state functions, equilibrium constants, bioenergetics | 2/3 |
MvH, Chapters 5,6,7; Creighton
| 4. | Amino acids - structures, nomenclature, chemical properties | 2/5 |
| 5. | Primary structure - the peptide bond, sequencing and synthesis, the genetic code | 2/10 |
| 6. | Secondary structure - a-helices, b-sheets, turns | 2/12 |
| 7. | Domain structure and evolution | 2/17 |
| 8. | Tertiary structure - hydrophobic effect, packing, bonding | 2/19 |
| -> EXAM I <- covers through Lecture 6 material | 2/24 | |
| 9. | Protein folding - thermodynamics, kinetics, mechanism, prediction | 2/26 |
| 10. | Quaternary structure, allostery - hemoglobin, ATCase | 3/3 |
| 11. | Biochemical methods for purifying and studying proteins | 3/5 |
MvH Chapter 11; Fersht
| 12. | Review of chemical kinetics - reaction order, transition states | 3/10 |
| 13. | Enzyme kinetics - definition of catalysis, Michaelis-Menten formulation | 3/12 |
| 14. | Enzyme inhibition - [non,un]competitive, mechanism-based | 3/17 |
| -> EXAM II <- covers through Lecture 11 material | 3/19 | |
| (Spring break 3/24-3/26) | ||
| 15. | Data analysis - Lineweaver-Burke and Eadie-Hofstee plots, pH effects | 3/31 |
| 16. | Enzyme mechanisms-principles: active sites, types of catalysis | 4/2 |
| 17. | Enzyme mechanisms-examples: serine proteases, lysozyme, catalytic antibodies | 4/7 |
| 18. | Co-enzymes and prosthetic groups | 4/9 |
| 19. | Regulation of activity - degradation, covalent modification, allostery | 4/14 |
MvH, Chapters 9, 10, 4
| 20. | Carbohydrates - structure, chemistry, and nomenclature | 4/16 |
| 21. | Carbohydrates - roles as fuel, structural material, recognition (protein modification) | 4/21 |
| -> EXAM III <- covers through Lecture 19 material | 4/23 | |
| 22. | Lipids and phospholipids - micelles, membranes, fluid mosaic model | 4/28 |
| 23. | Membrane proteins and transport - passive, active, energetics | 4/30 |
| 24. | Nucleic acid structure - nucleotides, DNA, RNA | 5/5 |
| 25. | Nucleic acid stability and function - secondary structure, central dogma | 5/7 |
| Overall review, preparation for final | 5/12 | |