Learning assistants (LAs) play a pivotal role in transforming traditional physics instruction toward a more inquiry-oriented approach. While empirical evidence supports the effectiveness of LA-involved physics instruction, there is a research gap regarding the specific competencies of LAs that contribute to improved conceptual understanding. One conjectured reason is LAs' inquiry-oriented pedagogical skills, like questioning, which engender more effective interactions with students at points of instructional needs. This study addresses the gap by constructing a model delineating the contribution of LAs' competencies of questioning, referred to as pedagogical content knowledge in questioning (PCK-Q), to students' conceptual learning in introductory classical mechanics and electromagnetism. The participants included an instructional team comprising instructors, graduate teaching assistants, and LAs, and students from two sections over two semesters. PCK-Q was measured using a prevalidated instrument of free-response questions from our previous study, which could predict LAs' questioning practices. Employing a pre-post design, students' learning gain in conceptual understanding and critical thinking was assessed, and separate models were constructed to explore the relationship between LAs' PCK-Q and students' learning gain. Findings suggest that LAs' PCK-Q has a significant but slight impact on students' conceptual learning, with little impact on critical thinking. Furthermore, we developed Likert-scale questions, derived equations to quantify PCK-Q from Likert-scale ratings, verified the feasibility of this streamlined approach in measuring LAs' PCK-Q, and discussed its limitations. The implications of the research findings are discussed in the context of physics instruction and LA preparation.