Biochemistry Senior Thesis 691/692 and Senior Honors Thesis 681/682

A senior thesis provides biochemistry majors an opportunity to dive deeper into a research topic of interest. It is the culmination of an undergraduate’s research career at one of the best biochemistry departments in the country. The thesis experience helps students develop their reading, research, and writing skills, and many students find this a rewarding experience in which to develop new skills through independent work. Senior theses are two-semester commitments, and senior honors theses are often required by Honors programs here at UW–Madison. If a student is interested in completing a thesis or are currently working on one, the information below will be helpful.

Registration Instructions

Senior Thesis (691-692) and Senior Honors Thesis (681-682) are two-semester course sequences. A student cannot take these courses concurrently. To enroll for either course, the student must be a senior. Course authorization can be obtained through the Biochemistry/Microbiology Undergraduate Advising Hub in 1315 Hector F. DeLuca Biochemical Sciences Building (440 Henry Mall)​​​, (608)

An undergraduate in the Department of Biochemistry writing in a lab notebookTo be authorized, students can either turn in the senior thesis proposal (below) or, if they will be turning in their proposal after the start of the semester, please have their PI/faculty mentor email the undergraduate advisor stating they will be doing a senior thesis. The Independent Study Agreement Form is not necessary for authorization of senior thesis courses.

Proposal Submission and Approval

One copy of the Research Proposal and Research Proposal Form must be submitted to the Biochemistry/Microbiology Undergraduate Advising Hub in 1315 Hector F. DeLuca Biochemical Sciences Building (440 Henry Mall)​​​. Fall semester applications are due on the last working day of September. Spring or Summer semester applications are due by the end of the third week of classes. The thesis advisor and academic advisor must sign the proposal form prior to submission.

Thesis Guidelines

The thesis should follow the format described below.

  1. Introduction and Literature Review
    This section is intended to provide a short introduction to the questions addressed in the thesis, including a review of the relevant literature. The literature review need not be extensive, but it should summarize the status of the field at the time the project was undertaken. This section should conclude with a clear, concise statement of the hypothesis to be tested or the questions to be answered.
  2. Materials and Methods
    In this section, the materials (usually biological and/or chemical) used in the experiments should be reported and all techniques should be described. If a technique has been used essentially as reported in the literature, it can be referenced it without further description, but note any significant modifications of the original report. Methods should be reported in sufficient detail to allow an interested colleague to reproduce the experiments, if desired.
  3. Results
    The purpose of this section is to describe the major experimental findings, which are usually summarized in the form of tables or figures. Tables and figures should be numbered consecutively, with each on a separate page. They may be inserted into the text as needed (usually as the page immediately following the text page on which a given table or figure is first mentioned) or collected together at the end of the thesis.
  4. Discussion and Conclusions
    This section is intended to provide a discussion, interpretation, and summary of the thesis findings. The conclusions that can be drawn from the data should be stated clearly and defended concisely. It is often appropriate to discuss the results in light of the findings of other investigators, particularly if the conclusions appear to be in conflict with those of others.
  5. References
    All references cited in the text should be collected together in a bibliographic listing at the end of the thesis. Use a consistent format for all references. References may be cited in the text by number (in parentheses or as superscripts) and listed here in order of citation. Alternatively, cite references by name and list them alphabetically here. In the latter case, papers with one or two authors are usually cited in the text by name(s) and year (i.e., Smith and Barnish, 1999), whereas papers with three or more authors are usually cited as the first author et al. with the year (i.e., Barnish et al., 1999).
  6. Other Sections
    It is helpful to include a short (one-page) abstract or summary and a table of contents at the beginning of the thesis. The thesis may also include a page of acknowledgments to express appreciation to those who were especially helpful in the work.
  7. Appendices
    Experimental details or findings that are only tangentially relevant to the thesis may be included as appendices, if it seems desirable to preserve a record of the information.

Final Thesis Submission

It is recommended that students submit a completed copy of their thesis to their thesis advisor three weeks before the semester ends, so that the advisor has adequate time to review the work and assign a grade. The thesis with a signed cover sheet must be submitted to the undergraduate advisor via email ( or via a paper copy deposited at the Biochemistry/Microbiology Undergraduate Advising Hub in 1315 Hector F. DeLuca Biochemical Sciences Building (440 Henry Mall)​​​​​​​​​​ by the end of final exam week during the given semester, unless earlier submission is required by an Honors program.

If a student anticipates needing additional time to complete the work, he or she must discuss this with the thesis advisor and have the advisor inform the biochemistry undergraduate advisor. The student will receive a grade of incomplete in this case. If the student is graduating and needs the thesis credits for graduation, he or she will not officially graduate until the thesis is reviewed and the incomplete is removed.

If a student does choose to take an incomplete, the final thesis must be submitted no later than the end of the first week of the next semester for which the student is registered. If an extension is needed past this deadline, he or she must request an extended incomplete from the thesis professor AND have the professor contact the biochemistry undergraduate advisor. Failing to do this will result in the incomplete lapsing into an F.


The grade for the thesis will be given by the professor supervising the thesis. During the first semester, only grades of "P" for progress or "F" for non-attendance/non-contact are recognized. The thesis advisor assigns the grade for the second semester, to serve as both the first and second semester grade. The thesis advisor will assign a grade through e-grading.

Format for the Cover Sheet to The Thesis




under the direction of

(Professor’s Name & Department)
(Specify Senior Thesis or Senior Honors Thesis)





I have supervised this work, read this thesis and certify that it has my approval.

                           __________________________                   _________________________________________               
                                             Date                                                 Thesis Advisor’s Signature


Student Checklist for Biochemistry Theses

Semester before thesis work begins:

  • Speak with a professor about doing a thesis in his/her lab.
  • Begin work on the research proposal, which includes an experimental plan, methods and procedures, expected results, and the significance of the work (2-3 pages maximum).
  • Get authorized to enroll in Biochem 681 or 691 (email from professor or turn in proposal early).

Start of first semester of thesis work:

  • Submit signed Research Proposal Form and research proposal to the Biochemistry/Microbiology Undergraduate Advising Hub in 1315 Hector F. DeLuca Biochemical Sciences Building (440 Henry Mall)​​​​​​​​​​. Fall semester applications are due on the last working day of September. Spring and/or summer semester applications are due by the end of the third week of classes. The thesis advisor must sign the proposal form prior to submission.
  • If not already done so, enroll in Biochem 681 or 691.
  • Work on thesis.

End of first semester and beginning of second semester of thesis work:

  • Contact the biochemistry undergraduate advisor to get authorization for 692 or 682 for the second semester of thesis work.
  • Students will be issued a "P" grade for "progress" for the first semester of thesis work. This is normal. The grade received for the second semester will automatically also apply to the first semester once it is issued.

Three weeks before end of second semester of thesis work:

  • Complete Thesis.
  • Have thesis advisor read final thesis and sign thesis cover sheet — the thesis advisor will then assign a grade electronically.
  • Submit one copy of the finished thesis with signed cover sheet to the Biochemistry/Microbiology Undergraduate Advising Hub in 1315 Hector F. DeLuca Biochemical Sciences Building (440 Henry Mall)​​​​​​​​​​, before the end of final exam week. Students in Honors programs may require earlier thesis submission and additional paperwork, depending on the program requirements and deadlines.