It’s pretty straightforward, really. A whole grain kernel — or seed — is composed of three parts: the bran, the endosperm, and the germ.
The bran is the outer shell that protects the seed. It provides fiber, B vitamins, and trace minerals.
The germ provides nourishment for the seed (and you), containing antioxidants, vitamin E, B vitamins, protein, minerals, and oils.
The endosperm provides energy for the seed in the form of carbohydrates (primarily) and protein.
As the name implies, whole grains and whole flours include the entire kernel. Refined flours are just the starchy endosperm — the nutrient-rich bran and germ have been removed.
Image courtesy of the European Food Information Council.