Jeremy Knowles, a Harvard chemist who played a key role in explaining how chemical reactions are carried out within the cell and who later became dean of the university’s faculty of arts and sciences at a time when it was bloated with faculty and drowning in debt, died April 3 at his home in Cambridge, Mass. He was 72.

As a graduate student in physical chemistry, Knowles said he was fascinated trying to understand “why some reactions went 10 times as fast as others.” Then, during a postdoctoral fellowship at the California Institute of Technology, he encountered reactions catalyzed by the enzyme chymotrypsin that went 1 million times faster than unaided reactions.

Over a 30-year career studying enzymes at Oxford University and Harvard, Knowles used the methods of chemistry to answer biological questions, such as determining the molecular basis for how the body digests food and uses energy, and how bacteria become resistant to penicillin antibiotics.

In the course of defining how enzymes work, he introduced the idea of “catalytic perfection” to illustrate the effectiveness of these molecules. He claimed his research showed that, in many cases, enzymes are perfect. It would be theoretically impossible to design an enzyme to increase the overall chemical reaction rate any further.

In 1983, while Knowles chaired Harvard’s chemistry department, he was recruited to become dean of the faculty. He refused, saying that at 48 he was “too young” and that he still had work to do in the lab.

But when the offer was extended again eight years later, he accepted, becoming the overseer of a faculty with 600 members, an annual budget of $500 million and an annual deficit of $12 million.

Over the next six years, he eliminated the deficit by refusing new appointments, vetoing expensive projects and allowing the staff to shrink by attrition. He began a series of initiatives that included uniting 17 departments in the humanities, constructing several new buildings, instituting greater financial aid for students, and launching centers for genomics, imaging, nanoscale structures and a center for brain science.

Jeremy Randall Knowles was born April 28, 1935, the son and grandson of Oxford professors.

After graduating from high school, he joined the Royal Air Force as a Pilot Officer but was ineligible to fly because he was slightly nearsighted. As a radar controller, he took over for another controller who had lost his nerve during a war games exercise, inheriting eight jets low on fuel. He managed to save all eight pilots and seven of the planes.

He later attributed much of his success in the management of Harvard to his time as a young officer.