Can I substitute...whole wheat for all-purpose flour for baked goods? If we do any kind substitution in between whole wheat and all purpose flour, then what will be the effects on baked goods?
Whole wheat has more gluten/protein than all purpose flour. This causes the baked goods to have a "stronger/tougher" consistency which may be appreciated in breads, where we want to chew on them, but not in other items like cakes or cupcakes where we want a soft, light texture. In terms of gluten content, in US you can find from higher to lower gluten content:
Whole Wheat flour -> whole wheat pastry flour -> all purpose flour -> cake flour