The reason our bodies function is a constant flux of energy (ATP). One of those critical components is Oxygen, and when you drink carbonated beverages (I could be confusing this with something else now...) you increase the Carbon in your bloodstream. Our bodies regulate oxygen through pH, and with an increase in Carbon you effectively decrease the oxygen solubility level by lowering that pH. With less oxygen, less energy. Less energy, less activity. Less activity, higher fat stores.
The fat stores / ATP relationship is less related to the carbonation as it is the sugars in soda. Excess sugar will be broken down to produce ATP from glucose. This is readily made from the sugars ingested. With these sugars being so readily available, your body will never need to convert its stored energy (glycogen/fat) to glucose for production of ATP.
The same is, to some degree, true of alcohol.
EDIT: Also, my personal take on the protein comments. I typically try to consume 1-1.2 grams of protein per lb of my goal weight. So lets say I was trying to put on an additional 10 lbs, then I'd be eating an additional 12grams of protein + 1.2 per lb I currently weigh.