We present a study of student understanding of energy in quantum mechanical tunneling and barrier penetration. This paper will focus on student responses to two questions that were part of a test given in class to two modern physics classes and in individual interviews with 17 students. The test, which we refer to as the Quantum Mechanics Conceptual Survey (QMCS), is being developed to measure student understanding of basic concepts in quantum mechanics. In this paper we explore and clarify the previously reported misconception that reflection from a barrier is due to particles having a range of energies rather than wave properties. We also confirm previous studies reporting the student misconception that energy is lost in tunneling, and report a misconception not previously reported, that potential energy diagrams shown in tunneling problems do not represent the potential energy of the particle itself. The present work is part of a much larger study of student understanding of quantum mechanics.