FARMINGDALE STATE COLLEGE DEPARTMENT OF CHEMISTRY

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1 COURSE TITLE: Advanced Biochemistry COURSE CODE: CHM 381 CREDITS: 3 CONTACT HOURS: Lecture: 3 CATALOG DESCRIPTION: A continuation of the concepts covered in Biochemistry. Students will examine the pathways, enzymes, and organic chemical mechanisms involved in the metabolic pathways of carbohydrates, lipids, amino acids, nucleic acids, and photosynthesis. Additional emphasis will be placed on the unique coenzymes that are required for these metabolisms. Students will also be trained in reading and interpreting research publications in biochemistry. PREREQUSITES: CHM 271 and CHM 380. REQUIRED FOR: ELECTIVE FOR: None Bioscience REQUIRED TEXT: John McMurray, Tadhg Begley. The Organic Chemistry of Biological Pathways. Englewood, Colorado: Roberts & Company, 2005 OPTIONAL TEXT: None 1

2 CHM 381 Biochemistry II Lecture Schedule I. Biochemistry Review Categories of biomolecules, characteristics of metabolic pathways, enzyme categories, fundamental enzyme mechanisms. 1. Identify by name and structure the four major categories of biomolecules 2. List and define the four characteristics of metabolic pathways 3. List, define, and identify the six categories of enzymes 4. List and efine the four fundmental enzyme mechanisms II. Organic Chemistry Review Lewis Acid / Base theory, fundamentals of organic reactions, acidity of the alpha carbon to carbonyls, drawing and interpreting electron pushing mechanisms 1. Identify compounds as Lewis acids or bases 2. Identify nucleophiles and electrophiles in organic reactions 3. Predict the product of biochemically relevant organic reactions 4. Predict the most probable mechanism and draw the electron pushing 5. Draw the tautomerization of a ketone III. Carbohydrate Metabolic Pathways Glycolysis, Gluconeogenesis, Pyruvate Dehydrogenase, Glyoxylate shunt, Citric Acid Cycle, Glycogen, Pentose Phosphate pathways. proper order in the glycolysis/gluconeogenesis and citric acid cycle pathways 2. Draw the mechanism for each metabolic conversion 2

3 3. Draw the mechanism for the cofactors thiamine pyrophosphate, flavin adenine dinucleotide, nictoinamide adenine dinucleotide and nictoinamide adenine dinucleotide phosphate 4. Describe the methodologies used to distinguish between a one-step or two-step phosphate transfer reaction IV. Lipid Metabolism β-oxidation, fatty acid synthesis, odd chain fatty acid metabolism, glycerol synthesis, sphingosine synthesis, prostaglandin synthesis, synthesis of cholesterol from isoprenes V. Amino acid Metabolism proper order in the fatty acid β-oxidation/synthase, glycerol synthesis, and sphingosine synthesis pathways 2. Draw the mechanism for each metabolic conversion 3. Draw the mechanism for the cofactors heme and adenosylcobalamin. Anabolism and catabolism of amino acids, deamination and transamination, urea cycle, glucogenic vs. ketogenic, essential and nonessential amino acids. proper order in the urea cycle. 2. Predict the result of a deamination on an amino acid 3. Draw the mechanism for important metabolic steps 4. Draw the mechanism for the cofactors pyridoxyl phosphate, folate, S-adenosylmethionine, and methylcobalamin. 5. Define and identify glucogenic and ketogenic amino acids 6. Identify all amino acids as either essential or nonessential. 7. Identify and assemble an abbreviated pathway including important intermediates for all amino acid anabolisms and catabolisms 3

4 VI. Nucleic Acid Metabolism Anabolism and catabolism of nucleic acid bases, fate of purine bases after catabolism, ribonucleotide reductase 1. Reproduce the metabolic pathways and mechanisms for anabolism of all four major bases from amino acid precursors. 2. Reproduce the metabolic pathways and mechanisms for catabolism of all four major bases and their ultimate fate in the body. 3. Draw the mechanism for both types of ribonucleotide reductase enzymes VII. Photosynthesis and Calvin Cycle Light reactions, chlorophyll, photosytem I & photosystem II, water splitting, Calvin cycle, metabolic controls on photosynthesis 1. VIII. Literature Reading and Interpretation Light reactions, chlorophyll, photosytem I & photosystem II, water splitting, Calvin cycle, metabolic controls on photosynthesis 1. Read a scholarly journal article and determine the main point 2. State the question, define the experiment and controls, and state the conclusions of each experimental figure in said paper. 3. Present the paper in front of a small group, demonstrating their grasp of the paper and their ability to convey that to the group. 4

5 CHM 381 Advanced Biochemistry Grading Policies Components of Grade Examinations 43% Homeworks 21% Written Assignments 21% Oral Presentation 15% Examinations Three unit examinations are given during the semester. No makeups are given for any examination. A comprehensive final is optional for students to take, but can be used to replace a missed or poor examination grade. Homeworks Six homeworks are given during the semester, covering concepts and objectives outlined for the sections covered. Late homeworks will be accepted with a point deduction up until one week late. After one week, a late homework is not accepted. Written Assignments Six written assignments based on an assigned paper will be given throughout the semester. Each assignment will cover the analysis of one figure within the paper. Late assignments will be accepted with a point deduction up until one week late. After one week, a late assignment is not accepted. Oral Presentation An oral presentation is required at the end of the semester. The presentation will take approximately 20 minutes with 5 10 minutes of questions from the class. Grading will be based on student surveys of the presenter, ability of the presenter to demonstrate knowledge of the paper, and ability to present that information to the class. 5