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BISC 330 Biochemistry - Spring 2009 Lecture Syllabus Topics: Biochemical bonds and reactions. Interactions with water molecules. Structure/function of DNA, RNA, proteins, lipids and carbohydrates. Enzyme kinetics and mechanisms. Enzyme cofactors and vitamins. Enzyme regulatory strategies. Cell structure, membranes and organelles. Protein biosynthesis and targeting to membranes and organelles. Glucose and O2 production by photosynthesis in plant chloroplasts. Glucose oxidation and ATP production: glycolysis, citric acid cycle & oxidative phosphorylation. Ribose biosynthesis from glucose by pentose phosphate pathway. Professors: Dr. John Petruska , tel: (213) 740-5189, email: [email protected] Office: MCB (RRI) 119B, Off. Hours RRI 121: Tu Th 11 am - 1 pm. Dr. Steven Goodman, tel: (213) 740-3867, email: [email protected] Office: DEN 4108, Office Hours: TBA Text: Berg, Tymocko & Stryer, BIOCHEMISTRY (6th ed. 2007) Lecturer, Date Subject Chap. Biochemical bonds and reactions 1.1-1.3 14 Water, pH and acid/base equilibria 1.3 16 DNA discovery & genomic revolution 1.4 19 No Lecture - Martin Luther King Day 21 Amino acid structures & properties 2.1 23 Primary structure of proteins 2.2 26 Secondary structure 2.3 28 Tertiary & quaternary structures 2.4-2.6 30 Protein purification methods 3.1 2 Amino acid analysis & sequencing 3.2 4 Protein structure determination 3.3-3.6 JP, Jan 12 Feb JP, Feb 6 MIDTERM EXAM #1 ( 175 points) 1 JP, Feb 9 11 DNA & RNA structure & purification DNA replication & gene expression 4.1,4.2 4.3-4.6 13 Intro. to thermodynamics & kinetics 8.1-8.3 16 No Lecture - Presidents Day 18 Enzyme kinetics: M-M model 8.4 20 Enzyme kinetics with inhibitors 8.5 23 Enzyme catalytic strategies 9.1-9.4 25 Enzyme regulatory strategies 10.1--10.4 27 Carbohydrate structures 11.1-11.4 Fatty acids, lipids & membranes 12.1-12.5 Coenzymes & vitamins 15.1-15.4 Mar 2 4 JP, Mar 6 9 11 13 16-20 MIDTERM EXAM #2 ( 175 points) Cell structure & organelles: nucleus, mitochondria & chloroplasts Cell membranes & vesicles, RER, Golgi, lysosomes, micro-tubules & -filaments. Protein targeting to membranes 12.6 18.1,19.1 11.3, 30.6 34.2, 34.3 30.5, 30.6 NO LECTURES- SPRING BREAK 23 PS I,II & Cyt bf action: pump H+, store H- 19.3 25 ATP synthesis using H+ current 19.4 27 Glucose synth. using ATP & H- in NADPH 20.1,20.2 30 Ribose synthesis by Pentose Phos. Pway 20.3 JP, Apr 1 MIDTERM EXAM #3 ( 175 points) 2 SG, Apr. 3 Glycolysis: Glucose -> 2 Pyruvate 16 6 Citric Acid Cycle: Entry of pyruvate 17 8 CA Cycle: Enzymatic reactions & shunts 17 10 CA Cycle: Links to AA ,FA & heme synth. 17 13 CA Cycle: Net reaction and energetics 17 15 CA Cycle: Regulation & biosynthetic roles 17 CA Cycle: Link to memb. respiratory chain 17,18 20 Respiratory chain electron transport enz. 18 22 Respiratory chain proton pumps 18 24 Oxidative phosphorylation & ATP synthesis 18 27 ATP synthase: Molecular motor 18 29 Mitochondrial DNA and human evolution 18 1 Mitochondrial DNA and human diseases 18 JP, Apr.17 May JP & SG, May 6 or 8 FINAL EXAM (175 points) Statement on Academic Integrity USC seeks to maintain an optimal learning environment. General principles of academic honesty include the concept of respect for the intellectual property of others, the expectation that individual work will be submitted unless otherwise allowed by an instructor, and the obligations both to protect one’s own academic work from misuse by others as well as to avoid using another’s work as one’s own. All students are expected to understand and abide by these principles. Scampus, the Student Guidebook, contains the Student Conduct Code in Section 11.00, while the recommended sanctions are located in Appendix A: http://www.usc.edu/dept/publications/SCAMPUS/gov/. Students will be referred to the Office of Student Judicial Affairs and Community Standards for further review, should there be any suspicion of academic dishonesty. The Review process can be found at: http://www.usc.edu/student-affairs/SJACS/. Statement for Students with Disabilities Any student requesting academic accommodations based on a disability is required to register with Disability Services and Programs (DSP) each semester. A letter of verification for approved accommodations can be obtained from DSP. Please be sure the letter is delivered to me (or to TA) as early in the semester as possible. DSP is located in STU 301 and is open 8:30 a.m.–5:00 p.m., Monday through Friday. The phone number for DSP is (213) 740-0776. 3 BISC 330L – Biochemistry Lab Syllabus Spring Semester, 2009 Laboratory Schedule Week 1 Week Experiments, Exam, or Assignment Beginning Jan 12 First week of class, no labs 2 Jan 19 Mandatory Lab Orientation and Check-in 3 Jan 26 Lab 1: Spectrophotometric Quantification 4 Feb 2 Lab 2: Measurement of Cholesterol in Biological Samples (Lecture midterm 1, Feb. 6) 5 Feb 9 Lab 3: Affinity Chromatography (Lab Report #1) 6 Feb 16 President’s Day Weekend, no labs 7 Feb 23 Lab 4: -Galactosidase, Session 1 - Standard Dilutions and (NH4)2SO4 Precipitation (Lab Report #1 due) 8 Mar 2 Lab 5: -Galactosidase, Session 2 - DEAE Ion-Exchange Chromatography (Lecture midterm 2, Mar. 6) 9 Mar 9 Lab 6: -Galactosidase, Session 3 - Michaelis-Menten Enzyme Kinetics 10 Mar 16 Spring Recess, no labs 11 Mar 23 Lab 7: Photosynthesis (Lab report #2) 12 Mar 30 Lab 8: Cell Compartments, Session 1 - Separation of Intracellular Compartments (Lecture midterm 3, Apr. 1) 13 Apr 6 Lab 9: Cell Compartments, Session 2 - Identification of Pathway-specific Enzymes (Lab report #2 due) Apr. 10th: Last day to drop class with “W” 14 Apr 13 Group Presentation 15 Apr 20 Lab Exam Review 16 Apr 27 Comprehensive Lab Exam 4 Laboratory Director: Pamela Lum, Ph.D. Office: ZHS 353 Tel: (213) 740-6079 e-mail: [email protected] Lecture Information and Policies: See separate lecture syllabus provided by Prof. Petruska. Online Course Materials: Supplemental course materials will be posted on the Blackboard website. Your USC e-mail user name and password allow you access of the secure site: https://blackboard.usc.edu. Grading: Final Grades will be given out of 1000 points total for the course: 700 points from lecture and 300 points from laboratory. Required Laboratory Supplies: 1. BISC 330 Lab Manual, available at the USC bookstore (required) 2. Lab notebook with carbon- or carbon-less duplicate pages (required) 3. Very fine-point permanent marker (required) 4. Lab coat or apron (optional) Laboratory Guidelines 1. MANDATORY ATTENDANCE OF LABORATORY SESSION. You are required to attend the weekly laboratory session in your registered section. You are also to remain for the entire lab session or until excused by your TA. Do not schedule any appointments during your regular lab periods. Students who are within 5 points of a grade borderline at the end of the semester will be considered for an upgrade based on the following criteria: class participation, attendance, participation in reviews, coming to office hours, and subjective evaluation by the TA, Lab Director, and faculty. Policy on lab make-up or substitution: If you missed your regular lab due to a serious illness or emergency which prevents you from attending school, you may attend another open lab within the same week. No make-up lab is allowed once the week is over. Please send an e-mail request to the administrative TA within 24 hours to acquire approval. Proof is required. 5 If you need to make a lab substitution due to university sponsored events (e.g. athletic events, class fieldtrips) or religious holidays, send an e-mail request to the administrative TA at least 48 hours in advance to acquire approval. Proof is required. If you are approved for lab make-up or substitution, it is your responsibility to make sure your quiz and lab write-up scores are properly recorded. 2. LABORATORY POINT DISTRIBUTION The laboratory session will count for 30% of your final grade (300 points). The points are distributed as follows: Lab Quizzes Post Lab Reports Lab Reports Group Presentation Lab Exam 45 points 90 points 50 points (25 points each) 40 points 75 points Lab Quizzes: Each student will take a quiz during the FIRST 5 MINUTES of each lab session. Each quiz is worth 5 points. There is no make-up for the quiz. To prepare, make sure your read the lab manual before coming to lab, know the purpose of the lab, and have a generalized idea of the procedures to be used in the exercise. Post Lab Reports: For each experiment there will be one lab write-up worth 10 points. See Lab Write-up Guideline in the Laboratory Manual for details. For each day the write-up is handed in later, you will receive 20% deduction. Lab Reports: Lab report is due 2 weeks after the lab exercise at the beginning of your lab session. Specific requirements for the lab report will be provided before you perform the experiment. For each day the lab report is handed in late, you will receive 20% deduction. Group Presentation: Detailed information about this assignment will be posted on Blackboard under Course Documents. Lab Exam: The exam will test your understanding of the topics and exercises covered in the laboratory sessions. Exam will consist of short answers, fill-in-the blanks, and calculations. Missed Lab Exam: It is your responsibility to make it to exam. If you miss the exam due to a serious illness (e.g., admission to the hospital) or a true emergency (e.g., traffic accident, fire, flood) that you could not 6 attend school, you must present a valid excuse to the no later than 48 hours of the missed exam. A valid excuse must include names and phone numbers for verification purposes. If you have a valid excuse, you can either take the exam in another lab section or take a make-up exam in the following week. If you do not have a valid excuse (or fail to provide it within the allotted time), you will receive zero points for the exam. Posting Grades: All grades, lecture and lab assignments, are posted in the LAB SECTION gradebook. It is the student’s responsibility to notify your TA or the Lab Director as soon as possible if errors are found. Laboratory score normalization: If necessary, the laboratory scores will be normalized at the end of the semester by the Laboratory Director to correct for differences in grading between TA’s. 7