Designing inquiry-based-learning with and for university students develops problem-solving skills and logical reasoning, as well as reflective thinking. It involves working as a member of a team, questioning, being creative, shaping the skills for continued intellectual development. It is argued that inquiry-based group work is one of the most important learning experiences because it enables the exploration of theoretical ideas and conceptual change. This paper presents results about the use of students' questions to shape these processes. This research involved one group of three students developing a mini-project on "thermo-chemistry of fitness". Data were collected through participant observation of group meetings and of meetings with the tutor, through semi-structured interviews with members of the group and the group as a whole, through an analysis of the questions asked by the group in the development of the project (oral and written) and through an oral presentation by the students. The results show that the questions formulated during the development of group mini-projects performed several important functions in the structure of the students' work, such as organising ideas, delimiting the scale of the project, identifying and reflecting on the many strands and sources of information, and reflecting on the project as a whole. The questions have contributed to students' engagement in the discipline, bringing an increase of interaction between teacher and students, an increase in the confidence and trust of the students in the asking of questions, and therefore an increase in the quality of classroom interactions in the learning and teaching of chemistry.