<![CDATA[Metabolism is one of the most demanding topics in biochemistry because students must connect molecular structures, enzyme mechanisms, and energy transformations that cannot be observed directly. This quasi-experimental study examined the effect of Problem-Based Learning (PBL) supported by 3D molecular visualization on conceptual understanding and misconceptions about metabolism among chemistry education students. A nonequivalent control group design involved 66 students: 34 in the experimental class (PBL with 3D visualization) and 32 in the control class (conventional lecture–discussion). Understanding was measured with a 20-item two-tier diagnostic test combined with the Certainty of Response Index (CRI). After controlling for pretest scores, ANCOVA showed that the experimental class achieved significantly higher posttest scores than the control class (adjusted means 75.71 vs 63.77; F(1, 63) = 12.26, p = 0.001, ηp² = 0.16). The mean N-gain of the experimental class (0.58, medium) was higher than that of the control class (0.38, medium). The proportion of misconceptions in the experimental class decreased from 35.7% to 8.7%, compared with 34.1% to 20.5% in the control class. Misconceptions persisted most in enzyme kinetics and oxidative phosphorylation. The findings suggest that authentic problems combined with manipulable 3D representations help students connect the submicroscopic and symbolic levels of biochemical phenomena.]]>
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