This dissertation describes an investigation into student understanding of energy in the context of an introductory calculus-based mechanics course. Through the administration of written and on-line questions, a variety of student difficulties with the concept of energy were identified. Many of these difficulties relate to student ability to calculate the work done on an extended system and to recognize the implications of a particular choice of system. These findings prompted revisions to existing curriculum and guided the creation of new tutorials to address many of the difficulties identified by research. Results indicate that the modified tutorial sequence has been quite successful in addressing student difficulties related to the definition of work and moderately successful in improving understanding of the relationship between work and energy. They also suggest that lingering difficulties with the relationship between work and energy may be closely linked to the persistence of an inability to interpret correctly the implications of the choice of system.