Q: I like baking muffins and cookies and prefer to use whole grains. I'd like to understand when I can make substitutions for white flour. Also, I have a muffin recipe that calls for 1/2 cup each all-purpose flour and whole wheat flour, and 1/4 cup wheat germ. What's the point in that? Why not just 1 ¼ cup of whole wheat flour?
Generally, you can replace white flour with whole wheat flour of the same type (bread for bread, all purpose for all purpose), substituting one for one. However, products made with whole wheat flour will usually be more dense. This may be helped somewhat by sifting the flour one or two extra times to help incorporate more air. Always remember when using any all purpose flour for items such as muffins and cookies to mix as little as possible to avoid forming glutens, which will toughen the final result.
For cakes and pastry, it is possible to buy whole wheat pastry flour made from finely ground soft wheat, such as that made by Bob's Red Mill Natural Foods (note that I have not personally tried this product). If you can't find whole wheat pastry flour, use equal parts of whole wheat flour and regular cake and pastry flour.
Because less of the proteins in whole wheat flour are gluten-forming compared to white flour, bread made with whole wheat flour will be more dense. According to Corriher (CookWise) whole wheat flour that is not finely ground may also have sharp edges on the bran that can cut gluten strands while kneading.
As for your muffin recipe that calls for ½ cup each all-purpose flour and whole wheat flour, and ¼ cup wheat germ, using a combination of regular and whole wheat flour will produce a lighter result. Using wheat germ slightly increases the amount of protein and fat in the product, by 5 grams for protein and 3 grams for fat over using whole wheat, and decreases carbohydrates by 7 grams, for the amounts in your recipe. Assuming your recipe makes 12 muffins, that would mean about ½ gram less carbs per muffin, if you are counting them.
Also, some wheat germ is fortified with additional Vitamin E and folic acid. Wheat germ may contribute a slightly more nutty flavor.
All of that said, you could substitute 1 ¼ cups of whole wheat flour in the muffin recipe and get good results, noting the precautions above. You may need to slightly adjust the amount of wet ingredients, however.