Overview
Program Description
The Biomolecular Structure and Dynamics graduate program focuses on structural and mechanistic biology at the molecular level, an area that is an intellectual meeting ground for students and faculty in the disciplines of chemistry, biology, and biomedical science. At The University of Montana, we have an enthusiastic cadre of faculty and students who share a passion for studying life processes at the molecular level and whose formal departmental affiliations are in the Division of Biological Sciences, the Department of Chemistry, and the Department of Biomedical and Pharmaceutical Sciences. This program brings faculty members and students together based on shared academic interests, rather than by departmental affiliation alone, and creates an interdisciplinary learning environment to better train graduate and undergraduate students for today's multidisciplinary approaches to molecular level biological research.
There are currently more than 20 faculty members who are active participants in the program. The common research theme is that all BSD participants are engaged in structural or mechanistic studies of biological molecules. Specific research areas include metabolic engineering and biosynthesis, natural products chemistry, DNA-metal interactions, nucleic acid-protein interactions, RNA-RNA interactions, viral RNA structure and dynamics, protein structure and folding, metalloprotein function, biological electron transfer reactions, neurotransmitter transport, and vesicular transport.
Research facilities available to BSD students and faculty are outstanding, with state-of-the-art core facilities for ensemble and single-molecule fluorescence spectroscopy, biomolecular NMR spectroscopy and X-ray crystallography, Micromass LCT, QTOF, MALDI-TOF and ICP mass spectrometry, DNA sequencing, microscopy, cytometry, and cell growth. Research laboratories are highly collaborative and include facilities in Chemistry, the Division of Biological Sciences, and Biomedical and Pharmaceutical Sciences. These buildings are clustered on the south side of The University of Montana campus.
Degrees Offered
This program is geared primarily toward the Ph.D. degree in Biomolecular Structure and Dynamics. In some instances the M.S. degree will be granted, however, applications to the program with the M.S. degree as the ultimate goal will be given lower priority than those for the Ph.D. degree.
All students entering the program are expected to have completed one year of Calculus, one year of Calculus-based Physics and year-long upper-level undergraduate courses in both Biochemistry and Physical Chemistry. If either of these two latter courses has not been completed prior to entrance into the program, BIOC481/482 or CHEM371/372 must be taken in the first year.
M.S. Biomolecular Structure and Dynamics
Requirements
30 credits, thesis and thesis defense. Course requirements are as described below for the Ph.D. degree.
Ph.D. Biomolecular Structure and Dynamics
Requirements
Completion of at least 60 semester credits, comprehensive exam (out-of-field proposal), dissertation and dissertation defense. Detailed requirements are described below.
Graduate Program in Biomolecular Structure and Dynamics
Requirements – 2007/2008
Core Courses:
The Biomolecular Structure and Dynamics (BSD) Core courses are to be completed during the first two years of the program. The four required Core courses are:
- BIOC 581: Physical Biochemistry (3 cr.)
- BIOC 582: Proteins and Enzymes (3 cr.)
- BIOC 584: Nucleic Acids (3 cr.)
- BIOC 600: Advanced Cellular Biochemistry (4 cr.)
Lab Rotations:
All students will do at least one laboratory rotation. It is expected that the rotation will aid the student in choosing a research advisor. Rotations are an opportunity for graduate students to test out a laboratory without a firm commitment on the part of either the student or the advisor that dissertation research will be carried out in that lab. During orientation week, students will have an opportunity to become acquainted with the research of BSD faculty and are expected to choose a rotation advisor by the end of the first week of the Autumn Semester. During the rotation, all students must register for 1 credit hour of BIOC 570: Introduction to Research or the equivalent. Each rotation must last at least 8 weeks, but can last the whole semester, if such an arrangement is agreeable to both the advisor and the student. At the end of the semester, a report will be submitted to the rotation advisor and a 15 minute public talk will be presented to BSD faculty and students.
Students may do an additional rotation with another faculty member during the Spring semester. As with the Autumn rotation, students must register for 1 cr. of BIOC 570 or the equivalent, the duration must be at least 8 weeks and a written report must be prepared for the advisor. No seminar is required for additional rotations. If it is mutually agreeable to both the advisor and the rotation student, an intensive ~3 week rotation may be undertaken during the winter inter-term in January.
Elective Requirement
All BSD students must take at least two electives selected in consultation with their Advisory Committee. A list of approved electives is provided below. Other electives may be substituted if appropriate, with the approval of both the student’s Advisory Committee and the BSD graduate education committee (GEC). These courses will normally be taken in the second and third years.
Approved electives:
- BIOC 486: Biochemistry Lab (3 cr.)
- BIOC 561: RNA Structure and Function (1 cr.)
- BIOC/CHEM 595: Biophotonics (3 cr.)
- CHEM 562: Organic Structure and Mechanism (3 cr.)
- CHEM 580: Fluorescence Spectroscopy (1 cr.)
- CHEM 569/BMED 621: Medicinal Chemistry (3 cr.)
- BMED 615: Molecular Pharmacology (3 cr.)
- BMED 661: Neuroscience I (4 cr.).
- BMED 667: Neurobiology and Biophysics (3 cr.)
Seminar/Journal Club:
All students are expected to register for Seminar (BIOC 595-01) every semester that they are in residence. Attendance at Journal Club is also expected.
Credit Hour Requirements:
The Graduate School requires that all graduate students supported as Teaching Assistants or Research Assistants register for a minimum of 9 credit hours each semester. In the first year, students take courses, seminar and rotations to reach this limit. In subsequent years, courses, seminar and research are used to reach this minimum.
Research Advisor and Committee:
All students are expected to choose a Research Advisor and form an Advisory Committee by the end of the Spring semester of the first year in residence. For the Ph.D., the Advisory Committee will have 4 additional faculty members beyond the Research Advisor. At least one member should not be in the home department of the Research Advisor. For the M.S., the Advisory Committee will have 2 additional faculty members beyond the Research Advisor. At least one member should not be in the home department of the Research Advisor.
Each year BSD students will submit a report that will be provided to all committee members by the first day of the Spring semester. It will be each student’s responsibility to schedule a committee meeting during the first 4 weeks of the Spring semester. Following the meeting, the committee will provide a brief memo to the BSD Program Chair summarizing the student’s status. A copy of the report will be attached to the memo. Both will be kept in the student’s permanent file. A memo from the BSD Program Chair will be sent to each student summarizing their status in the program. During the first year, the report will be provided to the BSD program chair and the GEC will evaluate progress.
Out-of-Field Proposal (Ph.D. only):
The Out-of-Field Proposal examination will typically be completed during the Spring semester of the second year. Students will prepare an original research proposal following NIH format (Specific Aims, Background and Significance, Research Plan, References). The proposed research must not be directly related to the student’s thesis project. The topic must be approved by the Advisory Committee at least ten weeks in advance of the date of the examination. A written proposal will be provided to the Advisory Committee at least two weeks in advance of the exam date. If the committee feels the written proposal is not satisfactory the oral part of the exam will be postponed and the student may be permitted one revision that must be provided to the committee within 4 weeks. It is also possible to fail the student at this point. The oral part of the exam will involve a public presentation, followed by a private examination by the Advisory Committee. At the private defense, students can expect questions on the feasibility of and their understanding of the content of the proposal. Questions that test the student’s working knowledge in their field, which may include material derived from the Core courses, may be expected, as well. Passing the Out-of-Field Proposal exam constitutes advancement to Ph.D. candidacy. As such, a student’s research progress will also be considered at this time. At the completion of the oral part of the exam, the student’s Advisory Committee can Pass, Fail, or ask that a student do additional work and repeat the oral part of the exam at a later date (no more than 4 weeks after the original defense date).
Thesis Proposal:
The Thesis Proposal will typically take place during the Autumn semester of the second (M.S. candidates) or third (Ph.D. candidates) year. Students will prepare both a written document and an oral presentation on their proposed thesis project. The written document must be provided to the Advisory Committee one week before the oral presentation. Students will be expected to provide background on the project that explains the current state of the field. They will be expected to explain where there are weaknesses in the current state of knowledge in their field by way of explaining the rationale for their research project. The remainder of the Thesis Proposal will focus on progress to this point, and experimental design and implementation for planned experiments. In particular, an outline of the specific questions the thesis will address, the methods and experiments to be used to achieve these goals and a discussion of the likely outcome of the experiments should be presented. The Thesis Proposal should define the expected scope of the Dissertation. The scope of the project defined in the Thesis Proposal should be such that the M.S. degree can be completed in approximately 2.5 years and the Ph.D. in approximately 5 years. While the Advisory Committee will expect the student to be fluent in the science surrounding the Thesis Proposal, an important aspect of the Thesis Proposal is for the student to become involved in a scientific dialog with their Advisory Committee. These are the people who will be writing letters of recommendation for you!
Typical Schedule for Ph.D. Candidates
First Year Core Courses
| Autumn Semester | Spring Semester | |
|---|---|---|
| Odd Years |
|
|
| Even Years |
|
|
- Seminar (BIOC 595-01, 1 cr.) both semesters
- Other coursework as appropriate. Research Assistant’s and Teaching Assistant’s must enroll for 9 cr. each semester.
- Journal Club
Second Year Core Courses
| Autumn Semester | Spring Semester | |
|---|---|---|
| Odd Years |
|
|
| Even Years |
|
|
- Elective Courses as appropriate
- Seminar (BIOC 595-01, 1 cr.) both semesters
- Research (BIOC 597 or CHEM 597) both semesters to reach 9 cr minimum
- Journal Club
- Out-of-field proposal (Spring Semester)
Third Year
- Elective Courses as appropriate
- Seminar (BIOC 595-01, 1 cr.) both semesters
- Research (BIOC 597 or CHEM 597) both semesters to reach 9 cr minimum
- Thesis proposal to the Advisory Committee (Autumn Semester)
- Journal Club
From this point until Dissertation Defense
- Seminar (BIOC 595-01, 1 cr.) both semesters every year
- Research (BIOC 597 or CHEM 597) both semesters every year to reach 9 cr minimum
- Journal Club
Typical Schedule for M.S. Candidates
First Year Core Courses
| Autumn Semester | Spring Semester | |
|---|---|---|
| Odd Years |
|
|
| Even Years |
|
|
- Seminar (BIOC 594 or CHEM 630, 1 cr.) both semesters
- Other coursework as appropriate. Research Assistant’s and Teaching Assistant’s must enroll for 9 cr. each semester.
- Journal Club
Second Year Core Courses
| Autumn Semester | Spring Semester | |
|---|---|---|
| Odd Years |
|
|
| Even Years |
|
|
- Elective Courses as appropriate
- Seminar (BIOC 595-01, 1 cr.) both semesters
- Research (BIOC 597 or CHEM 597) both semesters to reach 9 cr minimum
- Journal Club
- Thesis proposal to the Advisory Committee (Autumn Semester)
Third Year
- Elective Courses as appropriate
- Seminar (BIOC 595-01, 1 cr.) both semesters
- Research (BIOC 597 or CHEM 597) both semesters to reach 9 cr minimum
- Journal Club
- Thesis Defense
