In this exploratory case study, we consider how students in an undergraduate biochemistry class engaged in the process of argumentation within an inquiry-oriented learning environment to investigate a chemical mechanism in a particular part of the tricarboxylic acid cycle. Audio/video recordings of student groups during the mechanism discussion were analyzed in a coordinated fashion using three coding frameworks. The first framework examined students' pattern of argumentation using Toulmin's Argumentation Pattern model, the second coded the interactions for discursive moves using the Inquiry-Oriented Discursive Moves framework, and the final analysis phase used turn-at-talk counts as a framework to explore how power and authority shift between and among participants in the classroom. This research found that argumentation is supported by structures that provide opportunities for discussion, claims, and rebuttals but that the instructor, acting in nuanced ways through expressions of discursive moves, can also promote or inhibit the argumentative process. We provide suggestions for pedagogical moves in inquiry-oriented classrooms.