When you combine flour with wet ingredients, the protein begins to form gluten. Gluten is what makes bread dough tough, but toughness is not a desirable quality when making cupcakes. The high amounts of sugar and butter or oil in cake batter is what helps to break down the gluten.

Made with soft, finely milled wheat and blended with cornstarch, cake flour has the lowest protein content of all wheat flours -- around 7 percent -- and is a natural choice for cakes. All purpose flour falls right between cake flour and bread flour with a medium protein content, meaning it's suitable for many types of baked goods. Bread flour, with its high protein content, isn't suitable for cupcakes.

Recipes that specifically call for cake flour have a proven formula and should be respected. To substitute all-purpose flour, use 3/4 cup of all-purpose flour plus 2 tablespoons of cornstarch for every cup of cake flour. Substituting whole wheat flour in cupcakes results in a denser cake and should replace no more than half of the white flour in your recipe. Increase your baking powder by half if substituting with whole wheat flour, and add a bit more liquid if necessary.

When measuring flour for your cupcakes, spoon the flour into your measuring cup and avoid packing it down. Use a knife or spatula to level off the excess. If storing flour in the refrigerator or freezer, bring it to room temperature first before using it. Stop mixing your cake batter once the ingredients have combined to encourage more production of air bubbles.