Typical all purpose flour does not include the germ of the wheat, so if you would like to mimic the stuff from the store, you need to grind wheat without the germ (source).
By using hard white wheat and a very fine grind, I have for years made a flour that operates very like whole wheat pastry flour, which can often be substituted for all purpose flour in recipes. To make this same flour suitable for bread I add vital wheat gluten.
Bread is basically just flour, water, and yeast, so it's pretty hard to make it inedible unless you burn it to a crisp in the oven.
The difference between all-purpose flour and bread flour is gluten strength; if you substitute all-purpose flour then your bread won't rise as high or be as strong; this is a desirable quality in, say, cake, but not bread.
However, AP flour isn't that far off from bread flour in terms of gluten; while cake flour may be as low as 6% and bread flour can be as high as 14%, AP flour tends to weigh in at around 10% or more, which is why it's called "all-purpose". As Michael says, yeast bread is actually not as sensitive to the exact quantities as (for example) most pastries, but it's still better to use a recipe that was actually built around AP flour instead of just trying to substitute it for bread flour.
If you are determined to make the substitution, then I would suggest you try to find some wheat gluten and add a small amount of that to the AP flour. Mathematically, if you assume that you're lacking some 3% protein, then you'd want to add about 1 tbsp of gluten for every 2 cups of flour. It's really not much, though, and if you don't have or can't find wheat gluten then your bread would probably survive anyway with AP flour, it just might be a little denser than you expect.
Best Answer
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