A calorie is simply a measurement. It's not a nutrient, it's a measure of the energy content of a food that is burnt or metabolized in the body. Per gram different food sources contain different amounts of calories and most importantly, your body utilizes these calories differently.
Fat contains a little more than twice the amount of calories per gram of either protein or carbohydrates. 9 calories per gram for fat and 4 calories per gram for carbohydrate and protein. Metabolically your body requires a certain amount of calories everyday just to survive – even if you don’t get out of bed! Calories are utilized during heart and other involuntary muscle contraction (digestion, blood flow) and thermoregulation (maintaining body temp). Calories must come from somewhere – your body stores (fat, muscle glycogen and organ tissue) and the food you eat.
Research in the area of exercise and food metabolism reveals some very interesting facts. For the average person, only around 10% of the total amount of calories burnt each day is from physical activity. This is why the people that exercise religiously, but pay little attention to their diet, never lose body fat! Also, burning calories is not easy thing to do. To burn the equivalent amount of calories consumed in an average candy bar you would need to run about, each in under 7 minutes. It's not difficult at all to consume calories but burning them requires far more effort.
Another 10% of your calorie expenditure comes from digestion and rest. The remaining 70-80% of the total amount of calories you burn each day is basically from thermo-regulation. Keeping you body temperature constant in either hot or cold weather is an enormous job of human metabolism. Your body’s main thermostat is muscle tissue, it generates warmth in the cold and donates its moisture content in the heat. Muscle is therefore very metabolically active and the more muscle you have the more calories you automatically burn on a daily basis.
In terms of calorie intake, foods sources are utilized differently by your body. Every fat calorie you eat, you pretty much store, only to be dealt with if an energy defect arises. When you eat fat it wants to hang around. Your body preferences fat for storage as a survival mechanism. Fibrous carbohydrates (all plant foods) as opposed to refined carbohydrates are not only very low in calorie content, but your body has to utilize a lot of energy in the form of calories burned just to digest them. Protein calories are also good for staying lean, your body would rather oxidize (burn as a fuel source) these calories than store them as fat. Biochemically it is takes a lot of work to turn fibrous carbohydrate and protein molecules into a molecule that can enter fat cells as opposed to eating fat molecules that can go straight to fat stores easily.
In terms of building muscle, merely eating or ingesting calories does not equate to muscle growth. This is a common fault that many dieticians and medical professionals mistakenly assume. And while we all know protein builds muscle, not all protein foods are the same regarding their muscle building qualities. The biological value of proteins vary dramatically.
A vast array of scientific literature points towards the fact that muscle protein deposition is not a dominant metabolic pathway of human metabolism. Only when a specific biochemical environment is created and maintained within muscle (induced by resistance training) are the anabolic/anti-catabolic mechanisms triggered. When this anabolic environment is created your muscle physiology shifts towards reducing muscle protein breakdown and increasing protein synthesis – muscle growth. This is where the dramatic benefits of nutrient timing come into play.
As you can see, calories are not created equal. Having a better understanding of calories, nutrients and food in general will go a long way in you building muscle faster and more efficiently and staying leaner in the process.