UPPSALA UNIVERSITY 2001-09-01 Department of Bioorganic Chemistry STUDY PLAN FOR RESEARCH EDUCATION IN BIOORGANIC CHEMISTRY Goals Bioorganic chemistry is a multidiscipline research, covering aspects of chemistry, biology and physics. It aims to understand how biological structures and dynamics and their functions are correlated at a molecular level. This is achieved through the synthesis of biomolecules and their constituents and their model substances, mimicking those of the biological reactions or their intermediates. Conformational analysis, kinetics and thermodynamics using state-of-the art analytical and spectroscopic tools (such as NMR, CD, and molecular modeling with the help of quantum chemistry and molecular mechanics as well as by enzymology or appropriate biochemical reaction in vitro) are then performed on these mimics in order to understand the structure-function relationship. Description of research area Multistep, stereocontrolled chemical synthesis, and subsequently conformational analysis, of biopolymers, monomers and their analogs are used to highlight structural, functional and dynamical aspects of specific interactions between biopolymer and ligand, manifesting in the biological processes at a molecular level. Understanding of the mechanism of biological reaction, and studies of the biological structure-activity relationship provide important leads for development of gene, RNA or protein directed drugs against human diseases or pathogen infections, in general. The main emphasis is to understand and inhibit the replication, transcription and translation of the genetic apparatus in a specific manner. Requirements "To be accepted to the research education program, the applicant should fulfill (a) general requirements and to (b) special requirements which faculty board may have specified. Applicant also should have additional abilities which are required to go through the education." (High school regulation 10 par 2 §) The interpretation of "additional abilities" is defined by the professor responsible for the program in unity with the chair of the actual subject before taking decision on admission. General requirements "Those, who have obtained high school education of minimum 120 points, or, in other words, have acquired corresponding knowledge within Sweden or abroad, are considered of being fulfilling the general requirements." (High school regulation 10 par 3 §) Special requirements Special requirements for research education in bioorganic chemistry are specified by one of the following alternatives: (a) passed high school examination with approved courses in chemistry of minimum 80 points. In these 80 points should be included basic chemistry course (40 points); biochemistry, molecular biology, biological chemistry (10 points); analytical chemistry, spectroscopic methods, physical organic chemistry, separation technique, computer- and other courses relevant for biotechnology and bioorganic chemistry (10 points); organic chemistry (10 points), or project work within chemistry, conformational analysis, spectroscopy or computational chemistry (10 alternatively 20 points); (b) passed high school exam in molecular biotechnique or chemistry line (corresponding to the study program at Uppsala University); (c) other corresponding knowledge in areas specified above, acquired within Sweden or abroad. Fulfillment of the special requirements gives an application for research education a higher priority but those applicants who do not fulfill the rules for special requirements may still apply and their applications will be processed. Admission Application for admission for research education in bioorganic chemistry must be submitted to the Department of Bioorganic Chemistry Board. Application may be submitted at any time. Simultaneously with admission it will be determined the sources of financing for both the research and the doctorand's salary. Plan of education Research education includes mainly research work, which leads to a dissertation toward either a Licentiate of Philosophy or Doctor of Philosophy degree. It also requires taking courses, doing literature studies, attending seminars etc. Those who are employed as doctorands and are holding doctorand duty (doctorandtjänst) should also normally have institutional duty in educational or administrative work. For every doctorand admitted, an individual study plan must be established by the main research supervisor after consultations with other supervisors (if there is any) and the doctorand. Realization of the individual plan should be continuously monitored and the plan should be revised yearly by the main supervisor consulted with the doctorand and other supervisors. Courses, which are in the special requirements list, should not be included in the individual study plan. Education which leads to the Doctor of Philosophy degree comprise 160 points (four years of full time studies), the courses included in this education comprise 40 points. Courses should be taken during the first part of the doctorand studies. Research work normally starts immediately after admission and no later than after 1/3 part of the education (only after special considerations). For the Licentiate of Philosophy degree examination is required to have completed 80 points (two years of full time studies) and the courses taken should comprise 20-40 points. Studies in the research education should be presented in form of tutorials, lectures, seminars, field courses and laborations. Education is given to the extent which is allowed by accessible resources. It is expected that the main part of the course literature be obtained by the doctorand himself. Training in such self-standing studies constitutes essential moment in the research education. Doctorand must take part in the scientific activities at the Department by active participation in seminars and by attending guest presentations. Courses Courses required for Doctor of Philosophy degree examination comprise 40 points (a) Compulsory: research methodology (10 points) - One school term extensive introduction to work as a doctorand. - Experimental work in research group. - Study of literature. - Presentation of problem and results at research seminar. - Exam to supervisor on one course related to planed research. (b) Compulsory courses (10 points) (i) Advanced organic chemistry: reactions, mechanism and structure. Course which approximately correspond to "Advanced Organic Chemistry" by J.March or to "Mechanism and Theory in Organic Chemistry" by Lowry-Schueller-Richardson. (ii) Bioorganic chemistry (5 points) Course: "Bioorganic Chemistry" by H.Dugas and C.Penny; or "Principles of Nucleic Acid Structure" by W.Saenger; "Biological chemistry" by C.J.Suckling; "Modern NMR Technique for Chemistry Research" by A.E.Derom; or seminar which reflects research frontiers in bioorganic chemistry. (c) Alternative courses (minimum three, 15 points) 1. Chemistry of natural products and biosynthesis 5 p. 2. Stereochemistry and general conformational analysis 5 p. 3. Nucleic acids chemistry 5 p. 4. Carbohydrates chemistry 5 p. 5. Protein chemistry 5 p. 6. Chemistry of heterocycles 5 p. 7. Chemistry and application for protection groups 5 p. 8. Chemistry of phosphor-containing compounds with concentration on amino acids, phospholipids etc. 5 p. 9. NMR spectroscopy of nucleic acids 5 p. 10. NMR spectroscopy of carbohydrates 5 p. 11. NMR spectroscopy of proteins 5 p. 12. Research frontiers in synthetic organic chemistry 5 p. 13. Research frontiers in NMR spectroscopy 5 p. 14. Research frontiers in computer simulations of biopolymers and their components 5 p. 15. Conformations of nucleic acids, carbohydrates and proteins 5 p. 16. Interactions between nucleic acids and proteins 5 p. 17. Interactions between carbohydrates and proteins 5 p. 18. Interactions between nucleic acids or proteins and metal ion 5 p. 19. Design of virus and tumor cells grows inhibitors 5 p. 20. Enzyme engineering 5 p. 21. Molecular mechanics 5 p. 22. Quantum mechanics 5 p. After consultation with supervisor and with a leader for the research education, the list of the courses may be extended to include doctorand courses and seminars in other areas of chemistry, related disciplines of physics, mathematics, immunology, molecular biology, microbiology, and biotechnology, if the respective courses have relation to the area of scientific specialization.