This study aims to examine the effects of modelling on understanding of photosynthesis and respiration the basic reactions related to energy transformation in living organism and elimination of misconception about these topics. The study was conducted with a total of 82 students (42 experimental and 40 control groups). Success states of both group were determined by applying pre-test and the post-test containing 15 questions (Cronbach-α: 0.78) with the basic concepts related to subject and subsequently 6 questions of disclosure were asked in order to determine misconceptions. Traditional instruction method was applied to both group for explanation of energy conversion reactions in photosynthesis and respiration. Then the experimental group improved their own model. Student presented his models; subsequently the way of best modelling was discussed after the completion of all presentations. The experimental groups were more successful and have less misconception than the control group. The students have misconceptions related with particularly quality of light, ATP synthesis and electron transport system. The students think that photosynthesis is a food production mechanism and respiration is a fragmentation reactions of nutrients and these are not related to energy transformation. The application was met with interest by students, and it was thought to be useful especially in teaching of abstract concepts.