A calorie is not a calorie. A calorie of animal protein is less efficient to digest than a calorie of sucrose. If you're lactose intolerant, you will get a different number of calories from a glass of milk than someone who is not. Chugging a can of Mountain Dew quickly probably means you won't digest all the sugar before your gut bacteria get to it. Messing with metabolites in your gut can change the way your body absorbs and stores energy.