Pesticides may influence levels of secondary metabolites like flavonoids, hydroxycinnamic acids, anthocyanins, tropane alkaloids, and volatile terpenoids by non-specific mechanisms or interfering the key biosynthesis steps. The quality of volatile oils can be altered by changing their chemical composition, especially the toxic or useful constituents. Moreover, pesticide residues can be solubilised in volatile oils. Also, pesticides are able to modulate plant metabolism affecting assimilation rate of micronutrients. (Hancianu and Aprotosoaie, Gr. T. Popa University. Bentham Science Publishers)
Pesticide use in general and pesticide use on genetically modified food plants (GMOs) are highly important and controversial issues in the US and around the globe. GMOs have been restricted in States in the European Union although England has approved some GMOs and is evaluating others for approval. Several African countries have turned GMO foods away when delivered by Nongovernment Organizations (NGOs).
The first GMOs underwent DNA modification so they expressed pesticides under their own power. Later generations of Monsanto GMO seeds were the results of different technological approaches and no longer do express pesticide. The question of the effects of applied pesticide on GMOs has arisen because the modifications of the Monsanto GMOs have led to unprecedented all-time high levels of pesticide use among US farmers.
The question that results is: Will pesticide use on GMOs alter and damage nutritional value? This is a question that is newly arisen therefore there is only the beginning of research studies being undertaken.
One that was conducted by Monica Hancianu and Ana C. Aprotosoaie for the Department of Pharmacognosy at Gr. T. Popa University of Medicine and Pharmacy in Romania (Bentham Science Publishers), states that pesticides on any plant can alter "plant metabolism by causing abiotic stress" resulting in "[modulated] plant metabolism affecting assimilation rate of micronutrients." Therefore pesticides do alter nutrients in plants by reducing them.
Another study conducted by the British Columbia Ministry of Agriculture found that "another [herbicide] may affect the plant's ability to convert light into food," thus effecting plant nutrition by reducing it. Further research is needed to get definitive statements relevant the extent and nature of pesticide effects exclusively on nutrient alteration in GMO plants, both pre- and post-Monsanto variations.
This is a complex question because it depends on a number of other factors. The first thing is to consider what the purpose was of the genetic modification. Some genetically modified foods were created specifically to reduce the need for pesticides. In such a case, using pesticides on these plants will probably not affect them in any way, except for the actuality of pesticide residues remaining on the plant parts that one eats.
In other cases GMO foods are created so that they contain more or different nutrients than their traditionally-bred cousins. In this instance, pesticides may need to be used on the crop so that the plants will grow well and be healthy. A plant that is not growing well may in fact have slightly fewer nutrients than a vigorous plant; consequently protecting the crop from insects or fungi can result in a more nutritious crop.
Overall, pesticide use on any crop has only a very tiny impact, if any, on the nutrition of the crop; the handling, shipping, and storage of the food probably impacts its overall nutrition far more in most cases.