Course-based Undergraduate Research Experiences (CUREs)provide an innovative and distinctive learning environment aimed at increasing undergraduate involvement in research.CURE courses have recently exploded in popularity and diversity, especially in chemistry and the life sciences. A major obstacle hindering further expansion of CUREs centers around the design of assessments. Designing more effective content and assessments tools for this growing group of courses presents significant challenges. Biochemistry Authentic Student Inquiry Lab (BASIL) students hypothesize and test functions of enzyme with no known function utilizing a combination of wet-lab and computational approaches. Recently Anticipated Learning Outcomes (ALOs) were for developed for BASIL by Irby and colleagues (Irby et al BAMBED 2018). Using these learning outcomes, specific assessment questions are developed. The complex nature of the ALOs frequently demanded diverse assessment design that is tailored to each objective. Questions in the short answer and open-ended format emerged as best suited to gage understanding from student responses. These questions are included as part of lab report assignments for students enroll biochemistry course at NOVA southeastern University (NSU). Likert scale analysis is employed to analyze student responses to the designed questions as a means to quantitively gage mastery of the ALOs. Preliminary results indicate significant improvement in comprehension of bioinformatic concepts by the end of the semester. Further analysis is expected to identify concepts that are poorly understood by students. This allows targeted redesign of experimental procedures, instructor explanations and existing assessment tools. Better understanding the fundamental problems students face in CURE courses can lead to novel assessment strategies, paving the way for standardized adoption of CUREs across educational institutions and curricula. The BASIL project is funded by NSF IUSE 1503811 and 1709170.