Students and faculty of the Biochemistry Department at the University of Washington have a broad range of research interests and expertise. We prepare our students for future careers in biomedical science by teaching them to use interdisciplinary approaches with a biochemical emphasis to investigate important biological problems. Our department provides a friendly, interactive environment where students and faculty exchange ideas and perspectives easily. Our students become acquainted with diverse areas of biochemistry through coursework and seminars, while also concentrating on areas that are especially important for their thesis research. They choose a thesis advisor after a series of rotation projects and then pick a thesis committee that meets regularly to provide insights, guidance and advice. We encourage our students to apply for externally funded graduate fellowships, but we also guarantee five years of support for all graduate students in good standing.
Departmental Guidelines (revised January 2010)
THE FIRST YEAR
Coursework
First year students take 4-5 courses each quarter. Some of these are core courses, others cover special topics. Your choice of courses depends on your interests, past experience, and previous coursework. Course requirements for students who enter the Department through the Biomolecular Structure and Design Program (BMSD), the Molecular and Cellular Biology Program (MCB), or the M.D./Ph.D. Program (MSTP) may be slightly different; further information can be obtained from the offices of the BMSD and MSTP Programs.
A typical first year course program would be:
| AUTUMN QUARTER | WINTER QUARTER | SPRING QUARTER |
|---|---|---|
| Bioc 520 Seminar1 | Bioc 520 Seminar | Bioc 520 Seminar |
| Bioc 540 Literature Review2 | Bioc 541 Literature Review | Bioc 542 Literature Review |
| Bioc 581 Laboratory Rotation3 | Bioc 581 Laboratory Rotation | Bioc 581 Laboratory Rotation |
| Bioc 530 Advanced Biochemistry4 | ||
| Conj 53X Conjoint Module5 | Conj 53X Conjoint Module | Conj 54X Conjoint Module |
| Conj 53X Conjoint Module | Conj 53X Conjoint Module | Conj 54X Conjoint Module |
| Conj 53X Conjoint Module | Conj 53X Conjoint Module | Conj 54X Conjoint Module |
| Student Seminar | Student Seminar | Student Seminar |
1. Credit is given for attending the weekly departmental seminar program.
2. Small group discussion of key articles and topics in the current literature (2 graded credits).
3. Work in 3 different research groups on potential thesis projects (credit/no credit).
4. Structure of macromolecules; introduction to crystallography, NMR, mass spectroscopy, molecular dynamics, and protein structure prediction (3 graded credits).
5. 10 week courses, or two 5 week modules, on selected topics taught jointly by faculty from the University of Washington and the Fred Hutchinson Cancer Research Center (FHCRC). (1.5 graded credits/5 weeks)
Conjoint courses (Conj 53X and 54X)
These courses cover a broad range of molecular and cellular topics. At least 4 Conjoint modules of 5 weeks each must be taken, and 6 are recommended. Other graduate level courses may be substituted for Conjoint courses with the approval of the Graduate Program Advisor (GPA).
A list of Conjoint courses can be found at: http://www.washington.edu/students/crscat/conj
Laboratory Rotations (Bioc 581)
Rotations are required in each of the first three quarters, and are graded credit/no credit. At least 20 hours/week are normally devoted to the rotation project, although the time commitment may vary depending on the student’s course load and the advisor’s expectations. Students should also plan on attending their rotation lab group meetings and journal clubs. The three rotations must be in different research groups unless the student is entering with an advanced degree or from another program or institution (see below). Students are encouraged to select lab rotations that involve diverse biochemical perspectives and approaches. At the end of each rotation, students give a brief oral presentation of the rotation project before an audience of faculty, postdoctoral fellows, and graduate students. (To help students select laboratory rotations, and ultimately choose a thesis advisor, overviews of ongoing research are presented at the departmental retreat or other formats during the autumn quarter. The retreat provides a relaxed and informal atmosphere for discussing potential rotation and thesis projects with the faculty.)
The Literature Review Series (Bioc 540, 541, and 542)
This course emphasizes critical evaluation of the current literature. The fall quarter focuses on topics in protein biochemistry; students submit short essays addressing specific portions of journal articles and are guided in the preparation of fellowship and grant applications. Bioc 541 focuses on DNA replication, gene structure and regulation, and Bioc 542 focuses on biochemical aspects of cell and developmental biology. Both of these quarters emphasize student presentation of journal articles. Several faculty members are in charge of the course each quarter, attend each session, and also meet with students individually.
Weekly Departmental Seminar Program (Biochemistry 520)
The Biochemistry Seminar Series features outside speakers in prominent research areas, and assures that faculty and students alike are up to date. Students are required to attend all regular departmental seminars in the first year, and expected to attend in subsequent years of graduate study.
Graduate Student Seminar
The Biochemistry Graduate student seminar is a weekly meeting open to all UW graduate students in Biochemistry research groups. The seminar aims to create a friendly supportive environment for students of all disciplines and all levels of technical sophistication to learn from each other. It has two main goals:
(1) To provide students with an opportunity to practice giving a ‘conference style’ presentation, to present their research at any stage, and to receive feedback from fellow graduate students.
(2) To promote a cross-disciplinary community of graduate students with interests in Biochemistry. Fellow graduate students are a great resource for learning about new ideas and methods, and for discussing the ‘every day’ problems one confronts in research. Student Seminars are a forum for dialogue with and feedback from students in other disciplines. It can be very useful to talk with researchers studying similar questions through other disciplinary lenses, or to see familiar methods used in different disciplinary contexts.
The student presenter is encouraged to talk about their research for ~45 minutes, leaving 10 minutes for questions, feedback, and discussion.
One annual presentation at the Graduate Student seminar is required for Biochemistry students in their second year and beyond. MCB and BMSD students in Biochemistry labs also are encouraged and welcome to participate by giving a talk. Attendance is monitored. Biochemistry students should miss no more than 3 sessions per quarter. Either poor attendance or failure to present at these meetings at least once per year will mean that the student is not fullfilling departmenal degree program requirements and will be put on graduate school probation beginning in the fall quarter of the following year. Exceptions for extenuating circumstances must be approved by the GPA and Graduate Education Committee.
Once each month two students who have passed their General Exam and recently presented at the Graduate Student Seminar each present a 20-30 minute version of their seminar to the faculty. This takes place at the Friday Faculty Lunch meeting and it provides an opportunity for constructive feedback on research directions and presentation skills.
Biomedical Research Integrity (BRI)
This Series consists of lectures and discussions dealing with the responsible conduct of science, and is organized by the School of Medicine each summer quarter. Students in the first and second year are expected to attend. First year students must also attend a 6 session, ungraded, discussion course in the Responsible Conduct of Science given during the Winter Quarter. The sessions will be led by departmental faculty with special expertise in areas such as research and laboratory management; interpersonal relations, minority issues, and harassment; manuscript review and publication; animal and human research protocols; and intellectual ownership, patents, and industrial/academic conflicts.
The Graduate Program Advisor Series (GPA)
The Graduate Advisor advises all first year students, and meets with them at the beginning of each quarter to assess goals and progress. The GPA also continues to serve as an advisor and student advocate after the thesis advisor and Thesis Committee have been chosen. Any exceptions to departmental rules and practices require approval by the GPA. At the conclusion of Spring Quarter, a faculty meeting is devoted to evaluating student performance in rotations, the 530 and 540 series, Conjoint modules, and specialty courses.
Minimum grade requirements
The examinations in Biochemistry 530, Conjoint modules, and Minicourses must be taken, and a grade of 3.0 or above (out of 4.0) obtained in each of these courses as well as in the Biochemistry 540 Literature Review series. Students with grades below 3.0 may be required to retake all or part of a course. Students whose cumulative grade point average falls below 3.0 are automatically placed on probation by the Graduate School (see Graduate School Home Page). Students are required to earn at least 18 graded credits at the level of 3.0 or above in their first year.
Selection of Thesis Advisor
The Thesis Advisor is selected in two steps. Students are encouraged to discuss potential thesis projects with faculty throughout the first year, but no formal commitment can be made directly between faculty and students. Instead, no later than June 1 of the first year, students submit one or two choices of thesis advisor, in order of preference, to the Graduate Program Advisor. The Graduate Program Advisor consults with all involved before formally assigning a thesis advisor. In those rare instances where faculty cannot accept all interested students, students may explore other research possibilities through summer rotations.
Thesis Committee
In consultation with the student’s Thesis Advisor, a Thesis Committee must be assembled by the start of the Fall Quarter of the second year. The Supervisory Committee must have a minimum of four (five recommended) members constitutes as follows:
- One Chair, e.g., the student’s PI;
- Two Biochemistry faculty members;
- One non-Biochemistry member (or another Biochemistry faculty member);
- One Graduate School Representative (GSR).
The GSR is a voting member of the committee. The GSR must attest to the validity of examinations (General Exam and Final Exam), indicating approval of the process by which examinations were conducted. This is done by signing the warrant and by submitting a standardized report on the examination process to the Dean of the Graduate School. The Graduate School will provide the required forms.
How to determine if a faculty member can be a GSR:
The student chooses the GSR. The Graduate Faculty Locator identifies the appointments that each faculty member has. This will help determine who can be on your committee and who can serve as the GSR.
The Graduate Faculty Locator can be found on the Graduate School home page: http://www.grad.washington.edu/ Once you are at the Graduate School home page, you will go to the Resources for Faculty, Staff and Departments. From that list, you can link to the Graduate Faculty Locator. At this point choose the first link: Find Graduate Faculty by Name. You will then type in the name of the faculty member. The results of the search will appear and give you detailed information about the faculty member’s appointment status.
The GSR cannot be in the same department as the Supervisory Committee Chair, have an adjunct appointment in the same department as the Chair, nor be an affiliate faculty member.
Once the members of the Supervisory Committee have been chosen, email your graduate program advisor the names of the committee members including: name, department and email address. Be sure to identify the Chair and the GSR of your Supervisory Committee. These names will be submitted to the Graduate School by the GPA.
The thesis committee is a valuable resource for the graduate student in their pursuit their degree. Students are strongly encouraged to interact with committee members outside of the required annual meetings on matters relevant to their research and scientific interests.
THE SECOND YEAR
Students are welcome to consider additional graduate level coursework (normally numbered 500 or above) especially if required as preparation for the thesis project. Such courses should be chosen in consultation with the thesis advisor and Thesis Committee, and require the approval of the Graduate Program Advisor.
Teaching experience
Teaching is an integral part of graduate education. Students serve as Teaching Assistants in 2 to 3 quarters of a lecture course and 1 quarter of a laboratory course, although the nature of the participation will vary according to the interests of the student and the needs of the course. To avoid inequities, each course is evaluated annually, and assigned either 1/2 or 1 teaching credit. A normal teaching load is 2 1/2 credits over the course of a graduate career.
The first meeting of the Thesis Committee: It is strongly encouraged and to the student’s benefit that the first meeting of the thesis committee occur before Thanksgiving Recess in the Fall Quarter of the second year. It is mandatory that the meeting take place by the end of the following Winter Quarter.
The Graduate School Representative (GSR) should be invited to attend the first and all subsequent meetings of the Thesis Committee, but the committee may meet without the GSR if the GSR’s schedule precludes timely meetings.
One week before the first meeting of the Thesis Committee, the student provides committee members with a brief summary of the thesis proposal (2 to 3 single-spaced pages excluding figures) describing the overall plan for the project. The purposes of this document are to outline the thesis project, to summarize the relevant literature, and to provide a written basis for discussion with the Thesis Committee. The proposals are not expected to contain extensive data, as students will have spent relatively little time at the bench before the first meeting of the committee; however, the student should be able to address the feasibility of the project and/or focus attention on what types of feasibility studies still need to be performed.
The faculty understands that the nature and amount of experimental data will vary considerably from one proposal to another. Some students may spend their initial time at the bench doing a wide range of exploratory experiments; others may focus immediately on a specific project, or on mastering techniques; and yet other students may concentrate primarily on assimilating the essential background literature. The faculty also understand that thesis projects often change as graduate work progresses, so neither the initial written proposal nor subsequent meetings of the Thesis Committee should be viewed as locking the student into a specific project.
During the first meeting of the thesis committee each member of the committee will identify and convey to the student a specific area of biochemistry that the student ought to be particularly familiar with. Over the course of the following year the student should become familiar with the topics identified by the committee members and be prepared to discuss and answer questions about them at the general exam. Immediately following the first meeting of the committee the student should provide the list of topics to the GPA and Graduate Education Committee for approval. If modifications to the topics are required they will be made by consultation of the student, GPA and thesis committee members.
Second Meeting with Committee Members
Meetings with individual committee members take place before the Memorial Day Recess in the Spring Quarter of the second year. During these meetings, students should provide committee members with a brief summary of their progress and provide the committee member with a list of specific topics the student plans to be familiar with for the general exam. Additional meetings with individual members of the entire Thesis Committee can be scheduled by the student or the committee if either feels it would be useful.
THE THIRD YEAR and BEYOND
The General Examination
The General Examination must be scheduled before or during Fall Quarter of the third year. Failure to hold the General Exam during the Falll Quarter of the third year will mean that the student is not fullfilling departmenal degree program requirements and will be put on graduate school probation beginning in the winter quarter. Exceptions for extenuating circumstances must be approved during fall quarter by the GPA and Graduate Education Committee.
The following steps are required:
- By October 1, the student chooses an examination date and schedules their general exams online using the MyGrad – Student View.
- Two weeks before the exam, the Thesis Committee should receive a detailed thesis proposal that has been reviewed and approved by the thesis advisor (8 to 10 single-spaced pages excluding figures and tables). The Thesis Proposal normally includes an abstract, background, objectives, key experiments and techniques, anticipated problems, alternative approaches, significance, and future directions.
- One week before the General Exam, the the Thesis Committee should either accept the initial proposal as a basis for the oral examination, request modest modification, or require major modification followed by resubmission. This should be done by email from each member of the committee to the student and cc’d to the GPC.
Note that the General Examination may not be scheduled until all required courses in Biochemistry have been successfully completed and the Graduate School requirement of 18 graded credits has been satisfied (or formally petitioned and approved by the Graduate Education Committee and GPA).
The format for the General Examinations is as follows:
- 20-30 minute presentation of the research proposal to the thesis committee (with minimal interruptions).
- 30-45 minutes of questions from the committee about the thesis proposal.
- 30-45 minutes of questions from the committee about the specific biochemistry questions proposed by the committee members.
The Thesis Advisor attends the General Examination, and can ask questions or provide clarification, but one of the other Biochemistry Department faculty members chairs the exam. Students may pass the General Examination outright or conditionally. Conditions may include revision or expansion of the proposals, or additional coursework. A student who fails the General Examination may be allowed to retake the exam, or be asked to withdraw from the Ph.D. pathway. Upon successful completion of the General Examination, the student is admitted to candidacy for the Ph.D. as soon as a total of 60 credits (including at least 18 graded credits) have been amassed as required by the Graduate School Doctoral Degree requirements. The additional 42 credits required to reach a total of 60 usually reflect 6 to 7 quarters of thesis research, not additional academic coursework. Thesis research is formally considered a course, designated Bioc 600 before the General Examinations and Bioc 800 afterwards, for which 10 credits are awarded each quarter.
The complete Thesis Committee should meet again for a progress report before the subsequent Fall Quarter and yearly thereafter. Based on the progress of the student the committee may request additional meetings during the year. Well before each Thesis Committee meeting, the student should provide all members of the committee and the GPA with a Progress Report outlining accomplishments, complications, and plans for the coming year.
During the 4th year or 5th year the student provides the committee one week before the complete committee meeting with a 2-3 page writen proposal that describes the his or her plans for post-graduate work. This may include, but it not restricted to, a description of a postdoctoral research project. During the meeting the student should present their proposal to the committee. The proposal serves as an opportunity for the student to hear feedback and advice from the committe about their future plans. It is the joint responsibility of the student and thesis advisor to schedule these meetings, but the Graduate Program Advisor will keep track of the meetings and alert the student if meetings did not take place.
Preparation of the Doctoral Thesis
Graduate School rules and regulations for the preparation of the thesis must be followed (see the Graduate School’s Thesis and Dissertation policies and the Format Guidelines For Theses And Dissertations).
The student chooses a Reading Committee and informs the Graduate Program Assistant who will notify the Graduate School. The Reading Committee is composed of three members of the Thesis Committee, at least two of whom must be Biochemistry faculty members. The student provides the Reading Committee (and all other members of the Thesis Committee) with copies of the thesis, allowing adequate time for them to read the thesis. Doctoral candidates are to schedule their final exam online using the MyGrad – Student View.
Manuscripts, preprints, and reprints may be included as an integral part of the thesis, or as an appendix, with permission from the Reading Committee. These articles cannot take the place of comprehensive Introductory and Discussion sections; however, the amount of additional material to be included under Materials and Methods, and Results, as well as all questions of style, are left to the discretion of the student, thesis advisor and Reading Committee.
The candidate schedules the thesis seminar (“Thesis Defense”) for a time when all members of the Thesis Committee and the Graduate School Representative can attend. The seminar is open to department, University, and general public; it is followed immediately by the Final Examination (a brief discussion with the Thesis Committee) and very soon thereafter by celebration.
Download the PhD Procedures Checklist
ADDITIONAL INFORMATION
Maintaining Satisfactory Progress Toward a Degree.
The Biochemistry Graduate Program is structured to provide students with a strong background in Biochemistry and in their area of research while making steady progress toward their degree. However, it should be noted that failure to make acceptable progress could result in academic probation. Failure to achieve a cumulative 3.0 GPA, to hold the first committee meeting by the Winter quarter of the second year, to hold the General Exam during the Fall Quarter of the third year, to hold annual committee meetings, or to miss no more than 3 Graduate Student Seminars per quarter will result in academic probation for the student during the following quarter. Exceptions for extenuating circumstances are considered, but must be approved by the GPA and the Graduate Education Committee.
The M.A. or M.S. degree.
In the unusual event that a student is unable to complete their PhD studies, a student who has successfully completed at least 36 credits (usually the first 5 quarters of the graduate program), may be eligible for a non-thesis M.A. degree as described in Graduate School Memorandum No. 28. A student who has completed at least 36 credits and has performed significant rotation or thesis research, but chooses not to continue toward the Ph.D., may be eligible for the M.S. degree. Research required for the M.S. degree need not be conclusive, or publishable; however, a formal M.S. thesis must be written in consultation with the Thesis Advisor and Thesis Committee and a formal thesis presentation must be made to the Thesis Committee as required by the Graduate School’s Summary of Requirements. M.S. candidates may also request to present their thesis work in a seminar open to the entire department.