This paper presents preliminary data on how an assessment instrument with a unique structure can be used to identify common incorrect ideas from prior coursework at the beginning of a biochemistry course, and to determine whether these ideas have changed by the end of the course. The twenty-one multiple-choice items address seven different concepts, with a parallel structure for distractors across each set of items to capture consistent incorrect responses. For the current study, the instrument was administered as a pre-test and post-test in majors level biochemistry courses, and the results from two different groups are presented. These results indicated that students performed better on the post-test, resulting in positive mean gain scores for each concept. The structure of the instrument allows data analysis that helped uncover persistent incorrect ideas for some of the concepts, including bond energy and protein alpha helix structure, even after a semester of instruction in biochemistry. The persistent incorrect idea for the protein alpha helix structure uncovered by this assessment has not been reported before in the literature. These results confirm the need to use a robust diagnostic instrument to assess students' understanding of basic concepts at the beginning of the semester, but also stress the need to assess students near the end of the course to gain insight on the effectiveness of instruction. Since each group of students is different, biochemistry instructors are encouraged to use the instrument to identify problems with their own students' incoming ideas rather than rely on published results to inform instruction. In addition to providing assistance for instructors of biochemistry in planning targeted instructional interventions, we anticipate that data collected from this instrument can also be used to identify potential modifications for prerequisite courses. (Contains 5 tables.)