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

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