UPPSALA UNIVERSITY
Department of Bioorganic Chemistry
2001-09-01
STUDY PLAN FOR RESEARCH EDUCATION IN BIOORGANIC CHEMISTRY
Approved by the technique and natural sciences board on ???.
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
2. Stereochemistry and general conformational analysis
3. Nucleic acids chemistry
4. Carbohydrates chemistry
5. Protein chemistry
6. Chemistry of heterocycles
7. Chemistry and application for protection groups
8. Chemistry of phosphor-containing compounds with concentration
on amino acids, phospholipids etc.
9. NMR spectroscopy of nucleic acids
10. NMR spectroscopy of carbohydrates
11. NMR spectroscopy of proteins
12. Research frontiers in synthetic organic chemistry
13. Research frontiers in NMR spectroscopy
14. Research frontiers in computer simulations of biopolymers and
their components
15. Conformations of nucleic acids, carbohydrates and proteins
16. Interactions between nucleic acids and proteins
17. Interactions between carbohydrates and proteins
18. Interactions between nucleic acids or proteins and metal ion
19. Design of virus and tumor cells grows inhibitors
20. Enzyme engineering
21. Molecular mechanics
22. Quantum mechanics
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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.