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Department of Chemistry and Physics Biochemistry/Lab Last Date Revised: 10/12/2016 I. COURSE NUMBER AND TITLE: CHEM 3650 DA1 Biochemistry/Lab Fall 2016 DA1 20465 Tuesday, 08/23/2016 - Tuesday, 12/06/2016 Lecture-main campus TR 1:00 PM - 2:15 PM See location at https://www.fcas.nova.edu/coursewizard/ Lab-Parker 113 (wet lab) T 2:30 PM - 5:15 PM II. INSTRUCTOR: Dr. Reza Razeghifard Email: [email protected] Office Hours: Tues. 10am-12am, Thurs. 10am-11am Office Location: Parker-351. Phone: 954-262-7930 III. COURSE DESCRIPTION: The chemical properties of amino acids, monosaccharides, lipids and nucleotides are discussed. The structure of proteins, carbohydrates and biological membranes are studied. Mechanisms of enzymatic catalysis are outlined in detail with an emphasis on the structure/function of cofactors. Glycolysis and citric acid cycle are described. Electron transport and ATP synthesis are discussed in both mitochondria and chloroplasts. Metabolism of lipids, amino acids and nucleotides are presented. In addition to mechanistic studies of biochemical pathways and cycles, regulation of these processes is also covered. Prerequisites: BIOL 1500 and CHEM 2200 or CHEM 2410 or CHEM 2410H. IV. LEARNING OUTCOMES: Upon the completion of the course, the student is expected to be able to: 1. Discuss the key molecular reactions involving the mechanistic studies of biochemical pathways and processes; 2. Develop problem-solving skills, critical thinking and analytical reasoning in the field of biochemistry; 3. Demonstrate proper procedures for handling chemicals and utilizing instrumentation used in biochemistry; 4. Develop skills to carry out biochemical protocols, collect and analyze the data; 5. Critically assess a biochemistry topic by reading relevant current research articles found and accessed through electronic scientific databases. V. REQUIRED TEXTS AND MATERIALS: Fundamentals of Biochemistry: Life at the Molecular Level Author: Voet and Pratt Publisher: Wiley Year: 2016; Edition: 5th Fundamental Laboratory Approaches for Biochemistry and Biotechnology Author: Ninfa, Balou, Benore Publisher: Wiley Year: 2010; Edition: 2nd ISBN: 9781118918401 ISBN: 9780470087664 VI. COURSE REQUIREMENTS AND POLICIES: Students are expected to: Attend class (attendance recorded). Take good class notes. Read assigned material before class and be prepared for class questions and discussion. Attend lab sessions and submit timely and well-written lab reports. Every student must write their own lab reports even though they have worked with a lab partner. Contact the instructor if you are having problem. Attend help sessions if required by the instructor. Study in groups and review the course material and quiz each other. Display college-level writing ability in written lab reports, exams and homework. Observe all laboratory safety precautions and procedures. No cell phones or laptops are allowed in class or lab. Academic dishonesty (cheating, plagiarism, etc.) on exams and reports will be dealt with harsh penalty, at minimum, with a failing grade. It is the student responsibility to take all exams and attend all lab sessions on their scheduled dates. Failure to do so will result in a zero for that exam or that lab session unless your absence is due to special circumstances beyond your control. “Partners in the lab can only share the data they jointly produce, but each student needs to complete the lab report, including data analysis and report writing, independently and individually. Producing the lab report in any joint effort or fashion by lab partners will be considered plagiarism.” Students with ADA accommodations (see clause g under IX: COLLEGE-WIDE POLICY STATEMENTS) must make their testing appointments at least two weeks prior to the exam dates. VII. COURSE SCHEDULE AND TOPIC OUTLINE: Tentative Lecture Schedule Day Date Topic Aug. 23 T Amino Acids and Proteins: Primary Structure Aug. 25 R Proteins: Primary Structure Aug. 30 T Proteins: 3-Dimensional Structure Sept. 1 R Proteins: 3-D Structure and Protein Function Sept. 6 Proteins: 3-D Structure and Protein Function and T Carbohydrates Ch 4,5 5 6 7 7, 8 Sept. 8 Sept. 13 R Sept. 15 Sept. 20 R Sept. 22 Sept. 27 Sept. 29 Oct. 4 Oct. 6 Oct. 11 Oct. 18 Oct. 20 Oct. 25 Oct. 27 Nov. 1 Nov. 3 Nov. 8 Nov. 10 Nov. 15 Nov. 17 Nov. 22 Nov. 29 Dec. 1 T T R T R T R T T R T R T R T R T R T T R T Dec. 6 Carbohydrates and Lipids and Biological Membranes Lipids and Biological Membranes and Membrane Transport Exam I (CH 4-10) Enzymatic Catalysis and Enzyme Kinetics, Inhibition and control Enzyme Kinetics, Inhibition and control and Biochemical Signaling Biochemical Signaling Introduction to Metabolism and Glucose Catabolism Glucose Catabolism Review Mid-Term Exam (CH 11-15) Glycogen Metabolism & Gluconeogenesis Gluconeogenesis and Citric Acid Cycle Citric Acid Cycle Electron Transport and Oxidative Phosphorylation Electron Transport and Oxidative Phosphorylation Photosynthesis Photosynthesis Exam II (CH 16-19) Lipid Metabolism Amino Acid Metabolism Nucleotide Metabolism Mammalian Fuel Metabolism: Integration & Regulation ACS Final Exam (comprehensive) (8:00am-10:00am) for location see https://www.fcas.nova.edu/coursewizard/ 8, 9 9, 10 11, 12 12, 13 13 14, 15 15 16 16, 17 17 18 18 19 19 20 20, 21 23 22 Laboratory Schedule FR: Full Report - SR: Short Report Week Aug. 22 Aug. 29 Sept. 5 Sept. 12 Lab Chapter/Exp Safety + Excel SR Internet Resources and Software for Protein Biochemistry SR Drug Metabolism by Rat Microsomes Protein Purification Using Ion-Exchange Chromatography FR Part I Sept. 19 Native Protein Electrophoresis (protein pI) FR Part II (including Part I from previous lab) Sept. 26 Protein Electrophoresis (SDS-PAGE) SR Oct. 3 Enzyme kinetics of β-Galactosidase FR Oct. 10 Oct. 17 Midterm Exam week - No labs Enzymatic determination of glucose concentration SR Western Blot to Identify His-tag Thioredoxin FR Lipid lab Activity Measurements of Plant Chloroplasts and HPLC of Plant Pigments SR Oct. 24 Oct. 31 Nov. 7 Chapter 2 / Exp 2.6 Page 51-61 Chapter 15 /Exp 2.6 Page 440 Handout Chapter 5 / 5.4, Chapter 7 / 7.11 and Chapter 9 / 9.4 Chapter 6 / 6.2 Page 163 Chapter 6 / 6.3 Chapter 4 / 4.4 Chapter 10 /10.3 and Chapter 5 / Exp 5-2 Chapter 12 / Exp 12-1 and Exp 12-4 Chapter 6 / 6.5 and Handout Handout Chapter 8/ Exp 8-1 and Handout VIII. GRADING CRITERIA: Exam I and II (12% each) Mid-Term Exam Final Exam Labs (total) Assignments 26% 13% 30% 25% 6% Grading Scale: A 93.3-100 A90.0-93.2 B+ 86.6-89.9 B 83.3-86.5 B80.0-83.2 C+ 76.6-79.9 C CD+ D F 73.3-76.5 70.0-73.2 66.6-69.9 60.0-66.5 <60.0 IX: COLLEGE-WIDE POLICY STATEMENTS Students should visit www.fcas.nova.edu/about/policies.cfm to access additional required college-wide policies. It is your responsibility to access and carefully read these policies to ensure you are fully informed. As a student in this class, you are obligated to follow these college-wide policies in addition to the policies established by your instructor. The following policies are described on this website: Academic misconduct Last day to withdraw Email policy Student course evaluations Student responsibility to register Student responsibility for course prerequisites Additional Academic Resources: Nova Southeastern University offers a variety of resources that may aid in student success. Among these resources are: Accommodations for students with documented disabilities: For more information about ADA policy, services, and procedures, students may call the Office of Student Disability Services at 954-262-7189 or visit http://www.nova.edu/disabilityservices. Tutoring and Testing Center: Free tutoring services: Students are encouraged to use the free, individualized tutoring services offered by the Tutoring and Testing Center (TTC). TTC provides a supportive atmosphere in which tutors and students work collaboratively on improving students’ writing, math and/or science skills. To set up a tutoring appointment, call (954) 262-8350 or (800) 541-6682, ext. 28350 or stop by the Tutoring and Testing Center in the Student Affairs Building, 2nd floor. For additional resources, as well as information about tutoring at the regional campuses visit the Tutoring and Testing Center website at http://www.nova.edu/tutoringtesting/index.html