Higher education institutions are currently undertaking a challenging process in moving from teacher-orientated to student-focused approaches. Students' ability to asking questions is fundamental to developing critical reasoning, and to the process of scientific enquiry itself. Our premise is that questioning competences should become a central focus of current reforms in higher education. This study, part of a broader naturalistic research project, aims at developing a theoretical framework for conceptualizing different contexts for questioning, illustrating the application of the proposed framework (contextual questioning zones) and reflecting about some of the dimensions of teaching and learning, for overcoming some of the challenges that higher education institutions are facing presently. The discussion of two "opposite" contexts of enquiry is based on qualitative data, gathered through close collaboration with four teachers of undergraduate biology at a Portuguese university. These teachers were observed during their "daily activity" during an academic year. Data was also gathered by interviewing these teachers and 8 selected students, at the end of the year, and used to sustain the argumentation. The paper concludes with some reflections and suggestions to promote authentic enquiry-based learning experiences.