While you're asleep, I'm assuming you're not eating? Correct? So when you wake up you have gone a long period of time without food (yes, even if you had a late dinner). The longer your body goes without food the slower your metabolism becomes due to what's called a "starvation adaptation." Even though your brain knows that you can go to a store to get food whenever you would like, your body doesn't know this. Your body needs to be fed frequently to know that it's not going to be "starved." This goes back to primitive times when we would hunt and gather our food and our next meal was NOT guaranteed.
Next, you need to understand that the physiology of your body is designed to "survive," it's not designed to look lean, toned, and/or muscular so you must "trick it" at times to achieve your desired look. The more body fat you have, the longer you can survive is food ever became scarce, because that ugly soft stuff we all want to get rid of is actually a form of stored energy.
So if your body is starting to question when that next meal is coming (because you haven't eaten anything all morning, then your metabolism will slow down in an attempt to maintain all that "stored energy" around your waist. The longer the time between feedings/meals the more pronounced this negative effect becomes. So eat your breakfast and keep your meals small but frequent to maximize fat burning through your diet.
This is the most simplistic explanation I have, but if you're interested in details please dont' hesitate to contact me or post questions.