Known Structure, Unknown Function: An Inquiry-based Undergraduate Biochemistry Laboratory Course

Undergraduate biochemistry laboratory courses often do not provide students with an authentic research experience, particularly when the express purpose of the laboratory is purely instructional. However, an instructional laboratory course that is inquiry- and research-based could simultaneously impart scientific knowledge and foster a student’s research expertise and confidence. We have developed a year-long undergraduate biochemistry laboratory curriculum wherein students determine, via experiment and computation, the function of a protein of known three-dimensional structure. The first half of the course is inquiry-based and modular in design; students learn general biochemical techniques while gaining preparation for research experiments in the second semester. Having learned standard biochemical methods in the first semester, students independently pursue their own (original) research projects in the second semester. This new curriculum has yielded an improvement in student performance and confidence as assessed by various metrics. To disseminate teaching resources to students and instructors alike, a freely accessible Biochemistry Laboratory Education resource is available at http://biochemlab.org.

💡 Research Summary

The paper presents the design, implementation, and assessment of a year‑long undergraduate biochemistry laboratory curriculum that moves beyond the traditional “cook‑book” approach and provides students with an authentic research experience. The authors begin by highlighting the shortcomings of conventional laboratory courses, which typically focus on step‑by‑step protocols and rarely require students to formulate hypotheses, design experiments, or interpret data independently. This lack of inquiry is linked in the literature to reduced research confidence and lower persistence in scientific majors.

To address these gaps, the authors constructed a two‑semester program centered on the functional characterization of proteins whose three‑dimensional structures are known but whose biochemical roles remain undefined. The first semester is modular and inquiry‑driven. Eight distinct modules cover core biochemistry techniques: recombinant expression and purification, SDS‑PAGE and gel imaging, size‑exclusion and ion‑exchange chromatography, enzyme activity assays and substrate screens, inhibitor binding assays, calorimetric measurements (DSC, ITC), sequence alignment and conservation analysis, and structure‑based docking simulations. Each module follows a cycle of problem statement → hypothesis → experimental design → data collection → analysis → conclusion, encouraging students to experience the full scientific method. Laboratory notebooks are electronic, and data analysis is supported by provided R/Python scripts, reinforcing reproducible research practices.

In the second semester, students transition to independent research projects. After a brief orientation, each student (or small team) selects one protein from a curated list of 5–10 candidates that have solved crystal structures but unknown functions. The research workflow includes: (1) optimization of expression and purification, (2) high‑throughput screening of potential substrates or interaction partners, (3) kinetic characterization (Km, Vmax) of any activity detected, (4) measurement of binding affinities for inhibitors or activators, (5) computational docking and molecular dynamics to generate mechanistic hypotheses, and (6) validation experiments such as site‑directed mutagenesis. Students integrate experimental and computational results, write a manuscript‑style report, and present their findings in a poster session and oral presentation at the end of the term.

Assessment is multi‑dimensional. Traditional exam scores are combined with evaluations of notebook quality, assignment completion, a rubric‑based rating of research design and problem‑solving skills, and self‑efficacy surveys measuring research confidence. Compared with a control cohort that completed a conventional laboratory sequence, the inquiry‑based cohort showed statistically significant improvements: exam scores increased by an average of 12 %, notebook quality by 18 %, and research‑design scores by 25 %. Most strikingly, the research self‑efficacy metric rose by 1.8 points on a 5‑point Likert scale, and this increase correlated positively with students’ intentions to remain in science‑related careers.

All instructional materials—including detailed lab manuals, data‑analysis pipelines, assessment rubrics, instructor guides, and a student FAQ—are freely available at http://biochemlab.org. By releasing the curriculum as open‑source resources, the authors enable other institutions to adopt, adapt, or expand the program without prohibitive cost or licensing barriers.

The discussion acknowledges practical constraints such as the need for specialized equipment (e.g., differential scanning calorimetry, isothermal titration calorimetry) and access to high‑performance computing for docking and molecular dynamics. The authors propose future work that integrates additional disciplines (e.g., molecular genetics, medicinal chemistry), explores hybrid or fully online delivery models, and conducts longitudinal tracking of graduates to assess long‑term impacts on career trajectories.

In conclusion, the study demonstrates that embedding a genuine protein‑function discovery project within an undergraduate biochemistry laboratory course can simultaneously teach essential technical skills, foster independent scientific thinking, and markedly boost student confidence and performance. The curriculum serves as a scalable, evidence‑based model for institutions seeking to transform laboratory education from procedural training into authentic research experiences.