The Bran: The bran is a multilayer protective covering of a grain that protects the grain from the sun, water, and pests. The bran contains most of the fiber, it also contains minerals, B vitamins and phytonutrients.
The Endosperm: The endosperm makes up most of the mass of a grain. It is mostly starchy carbohydrates with small amounts of protein and vitamins. The purpose of the endosperm is to provide nutrients to the germ as it sprouts and grows.
The Germ: The germ is the embryo of the grain kernel. If fertilized it will grow into a plant. The germ is rich in nutrients including protein, B and E vitamins, antioxidants, phytonutrients, healthy fats, and some proteins.
Grains are amazing! With their low fat content and protective bran covering they can be stored for decades without spoiling. Soaking grains in water and sprouting them can change the nutrient profile such that they provide almost a full spectrum of nutrients. When mixed with beans and legumes, they can provide all necessary amino acids. Thus the reason why historically, most cultures had some form of beans and rice as their diet staples.
Refined flour: Contains just the endosperm (the starchy center). Without the germ or bran, most of the fiber, protein, vitamins and minerals are lost. According to the Whole Grain Council, 25% of the protein and at least 17 key nutrients are lost (http://www.wholegrainscouncil.org/whole-grains-101/what-is-a-whole-grain). So why do we refine flour to include only the endosperm? Once the grain is cracked and the germ exposed, the grain will go rancid in a matter of days. By milling the grain and removing the bran and germ, a fine flour can be produced that not only extends the shelf life but produces baked products with a nice consistency. Most flours sold in the US are wheat flours. This is because wheat flour produces the preferred bread consistency. The endosperm is filled with cells containing starch granules, theses cells are supported by a protein matrix. Two of the proteins that make up that matrix are gliadin and glutenin. When mixed with water, these two proteins form a viscoelastic substance called gluten. Gluten forms a strong elastic dough and is what is responsible for the texture of the bread produced from wheat flour (for more information on America and wheat see http://www.muehlenchemie.de/downloads-future-of-flour/FoF_Kap_02.pdf).
Whole wheat flour: Contains the endosperm and the bran and part of the wheat germ. After milling, the bran is added back to the flour restoring the fiber and mineral content. Part of the wheat germ is then also added back. Why do I say part? If the whole wheat germ was added, the flour would go rancid quickly. It's a simple experiment to prove that not all the wheat germ is intact; grind some of your own flour from wheat kernels and see how long it lasts compared to purchased whole wheat flour. It will last a couple weeks at most, while the store bought stuff can last months. Try finding information on how the shelf life of wheat germ is elongated, it will be difficult to do. Beware of "whole grain" products. The FDA has good intentions but poor executions a lot of the time (this is my opinion which might be biased by being a medical device engineer and having to work within FDA regulations). A statement from the FDA regarding the "Whole Grain" label:
"Question: Does the term "whole grain" mean the same as "100 percent whole grain"? If a product is labeled as "whole wheat bagel" or "whole wheat pizza," how much whole wheat should it contain? What is graham flour?
Answer: FDA has not defined any claims concerning the grain content of foods. However, the agency has established standards of identity for various types of cereal flours and related products in 21 CFR Part 137, including a standard of identity for "whole wheat flour" (§ 137.200) and "whole durum flour" (§ 137.225). Graham flour is an alternative name for whole wheat flour (§ 137.200)."
http://www.fda.gov/Food/GuidanceComplianceRegulatoryInformation/GuidanceDocuments/FoodLabelingNutrition/ucm059088.htm
Making a bread from pure whole grains is not cost efficient for a business, it leads to breads that are "heavier", take twice as long to rise and knead. Some whole grain breads contain some whole grain flour along with refined white flour that is died with malaise.
The FDA also does not regulate how the whole wheat flour was made. As long as the product contains parts of the germ, endosperm and bran in it, it can be called whole wheat.
Does that mean store bought "whole grain" products are bad - no! It just means home made are better. So just mix it up and make sure that some of your servings of whole grains are coming from cooking intact grains yourself (rice dishes are an easy example).
For some information on the health benefits of consuming whole grains see the follow peer review literature or just Google "whole grains" in Google Scholar
Plausible mechanisms for the protectiveness of whole grains (Translation of the title in easy english: Why are whole grains so good at preventing diseases)
http://www.ajcn.org/content/70/3/459S.full
Whole Grain, Bran, and Germ Intake and Risk of Type 2 Diabetes: A Prospective Cohort Study and Systematic Review http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0040261
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