The objectives of this study were to investigate the alignment of exam questions with course learning outcomes in a first year biology majors course, to examine gaps and overlaps in assessment of content amongst the sections of the course, and to use this information to provide feedback to the teaching team to further improve the course. Our ultimate goal was to provide students with learning outcomes that would clearly indicate the content and the level at which they would be expected to learn the content for this course, regardless of the section in which they were registered. We took an evidence-based approach to course evaluation and employed the Blooming Biology Tool to compare the learning outcomes and the exam questions of the course, investigating whether the cognitive skill level of each learning outcome as written matched the level at which it was assessed. We identified misalignments and recommended revising the learning outcomes to better reflect the intended level of learning for the course. We also investigated student performance on exam questions of different cognitive levels and found that students scored statistically significantly higher (p < 0.05) on questions in which learning outcomes were tested at the stated cognitive skill level compared to at a higher level.