Whole wheat flour is made by grinding the entire wheat grain. It has a much more dense texture and pronounced nutty flavor. It also has a higher protein content so it works better for bread or pizza dough.  Whole wheat pastry flour is a finely milled flour made from soft wheat varieties and has a lower protein content compared to hard wheat. It is great to use for a finer and lighter texture in baked goods such as cookies, pie crusts, muffins, pancakes, and other pastries.