This study investigated the effects of teachers' use of "focus questions" on students' knowledge structures and classroom teaching-learning process by re-analyzing selected data from a quasi-experimental pre-post video study (Wadouh, 2007). Focus questions are content-related anchoring questions highlighting the key content taught in individual lessons (Forbes & Davis, 2010). In Wadouh' study, students answered a knowledge test before and after the lesson on "blood and the circulatory system" and one lesson per teacher was videotaped to investigate teaching practices in grade 9 biology classrooms. Students also completed a post-unit concept mapping exercise and a motivation-interest questionnaire. In this study, 30 lesson videos selected from 47 were re-analyzed for teachers' use of focus questions--no focus questions, non-specific or simple focus questions, and specific and challenging focus questions. Individual students' scores in the concept mapping exercise were aggregated as "students' topic-related knowledge structure". Multilevel analyses revealed a significant positive effect of teachers' use of "specific and challenging focus questions" on students' topic-related knowledge structure. Furthermore, a comparative case analysis of the classroom teaching-learning process was conducted in four lessons where teachers used specific and challenging focus questions in two of the lessons and non-specific or simple focus questions in the other two lessons. The findings indicate that specific and challenging focus questions anchored lessons on students' co-construction of scientific explanations by activating their pre-instructional ideas, whereas "non-specific or simple focus questions" anchored lessons on their accumulation of canonical scientific knowledge. This study's limitations and implications for teacher education reform are discussed.