This study examined the effect of scaffolding learning components in a computerized environment, for students solving qualitative science problems in a simulation of laboratory experiments. Four scaffolding components were identified (structural, reflective, subject-matter and enrichment) and used in different configurations to construct four unique cognitive and meta-cognitive support programs based on human teaching. These ranged from low (Enrichment) to full support (Integrated). We compared the scaffolded groups with one another and with a non-scaffolded control group. A "mathematics and reading comprehension" questionnaire was used to divide the participants (n = 473) into ability levels. At different points of time, achievement outcomes were measured by three open-ended subject-matter questionnaires, tapping knowledge and understanding. The findings indicate differential effects of the support programs mostly in the following order: Integrated greater than Strategic greater than Operative greater than Enrichment greater than Control. The structural component seems to be a "sine qua non" for success and has a consistent and powerful influence. The combination of reflection and structural components, however, are needed for superior achievement. Both reflection and subject-matter components work cumulatively over time.