Ph.D. students complete graduate-level courses in physical biochemistry, enzymology, molecular biology, and biochemical regulation. These core courses prepare students for the written comprehensive examination. Additional electives are selected based on individual research interests and faculty expertise.
Students who enter without a designated research advisor complete up to four five-week laboratory rotations during the first two quarters. These rotations allow students to explore different research areas and lab environments before selecting a permanent advisor.

At the end of the second quarter, students submit ranked preferences for a research advisor. Assignments are based on availability and student interest and must be approved by the program faculty. After selecting an advisor, each student forms a three-member advisory committee, which later becomes the dissertation committee.

All Ph.D. students are required to serve as a teaching assistant (TA) for at least two academic quarters, typically in the second or third year. TA training is provided by the Graduate Division. Each year, one exceptional TA is honored with the Walton B. Sinclair Award.

No later than the fall quarter of the third year, students must complete an oral qualifying examination focused on their research area. The exam is conducted by a five-member committee, including one faculty member from outside the graduate program.

The Ph.D. is awarded upon the successful completion and defense of a dissertation based on original research. The dissertation committee approves the research topic, evaluates annual progress, and advises on the writing process. Students are required to give a public seminar on their research and defend their dissertation before the committee. Final approval is granted by both the committee and the Dean of the Graduate Division.