Despite the number of university students who take courses in multiple science disciplines, little is known about how they perceive common concepts from different disciplinary perspectives and to what extent they recognize connections among their courses. This dissertation explores students' perceptions of their chemistry and biology courses through the lens of two crosscutting concepts, energy and the relationship between structure, properties, and function. Energy underlies all scientific phenomena. Structure-property and structure-function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively. As such, these crosscutting concepts provide an interesting context in which to investigate student connections and misconnections across disciplines. Funded by the Association for American Universities' STEM Education Initiative, a multi-year interdisciplinary effort was underway to transform the introductory biology, chemistry, and physics courses using the lens of three-dimensional learning. To inform cross-disciplinary discussions on the improvement of undergraduate education, a series of studies using interview data were conducted. An initial set of twenty-two interviews explored a diverse group of undergraduate students' perceptions across all three dimensions (i.e. disciplinary core ideas, crosscutting concepts, and science practices). However, this resulted in a large and diverse dataset lacking sufficient depth to richly describe student experiences. This work led to three more targeted studies with a revised interview protocol focusing on the crosscutting concepts of energy and the relationship between structure, properties, and function. An additional fourteen university students concurrently enrolled in general chemistry and introductory cell and molecular biology were interviewed. Findings suggest that, while students believed energy to be important to the scientific world and to the disciplines of biology and chemistry, the extent to which it was considered central to success in their courses varied. Differences were also apparent in students' descriptions of the molecular-level mechanisms by which energy transfer occurs, revealing a disconnect between how energy is understood and used in introductory science course work. These interviews also explored students perceptions regarding (1) the meaning of structure, properties, and function, (2) the presentation of these concepts in their courses, and (3) how these concepts might be related. While the concepts of structure and properties were interpreted similarly between chemistry and biology, only three students were able to consider function productively in chemistry. Additionally, students more closely associated structure-property relationships with their chemistry courses and structure-function with biology. Despite receiving little in the way of instructional support, nine students proposed a coherent conceptual relationship, indicating that structure determines properties, which determine function, and described ways in which they connected and benefited from their understanding across both courses. The final study follows Laura, a Genomics and Molecular Genetics major, across three years of chemistry and biology coursework, including general and organic chemistry, honors cell & molecular biology, and a two-semester biochemistry course sequence. Across her four interviews, Laura consistently recognized the utility of thinking about the relationship between structure, properties, and function. However, her ability to discuss energy diminished over time. Despite describing energy to be a central and crosscutting concept in Year 1, she rarely considered it in Year 2; and, during her final interview, she noted having had a deeper conceptual understanding of energy in the past. Though some students were successful in making connections across their chemistry and biology courses, this work uncovers a need for cross-disciplinary conversations among instructors to understand the shared goals and disciplinary distinctions regarding these important concepts. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://bibliotheek.ehb.be:2222/en-US/products/dissertations/individuals.shtml.]