This manuscript describes the implementation of a Course-based Undergraduate Research Experience (CURE) sequence in chemistry that uses research to link a lower division, organic chemistry course to an upper-division, analytical chemistry course. In the CURE sequence, students created a library of modified sugar molecules during CURE-1, Organic, and then evaluated the behavior of those molecules within membranes during CURE-2, Analytical. In order to ascertain the causal mechanisms underlying the effectiveness and sustainability of CUREs within the standard chemistry curriculum, we conducted research on students in CURE laboratories and Standard Instruction (SI) laboratories. Results from the Classroom Undergraduate Research Experience (CURE) Survey, the Laboratory Course Assessment Survey (LCAS), and an end-of-course assessment are presented. Equivalency of the CURE and comparison groups was established based on demographic factors, reported gender and minority status, expected major, and grade in the prerequisite course. A direct comparison of this nature revealed the benefits of the CURE sections and equality in assessment performance regardless of the instructional method.