Fantastic character design and solid animation. Music wasn't bad either. The one thing that was bugging me about it was the really heavy "Captain Planet" style vibe I was getting from it. It doesn't seem overly preachy beyond the character metaphors, but the pun attacks might be a bit much. I did like how you found a way to incorporate the nature of particular complex molecules into the attacks, though, like the shape of carotene being a long chain, and Vitamin D being activated by sunlight.
The other thing you may want to consider is the complex nature of some food. Dark Chocolate has been proven to have positive effects on heart health, as well as being healthier than mild chocolate (http://www.prevention.com/which-healthier-dark-chocolate-vs-milk-chocolate). On the other hand, you shouldn't forget that things like appleseeds have cyanide in them. Biggest thing that you really shouldn't forget is that sugar is a necessary part of energy production; yes, it is overused to the point where it can be a health hazard, but every carbohydrate is broken down into monosaccharides (best being glucose, monomer of glycogen and sucrose) for use in glycolysis, with the products being used in the Krebs cycle. You might be better using things like artificial sweeteners, which can screw with your metabolic processes even when they don't have any "toxic" side effects.