So we know that we eat food for energy, and we breathe in oxygen and release carbon dioxide. We also know that with metabolic and respiratory homeostasis, that the lungs release the carbon dioxide at an appropriate rate to the amount of oxygen that is used, and that the kidneys retain bicarbonate and release protons in the urine. But how do these two facts relate to each other?
The energy we eat is always broken down into glucose, which has a chemical formula of C6H12O6, and that floats around in our blood stream until it's shunted into a cell (skeletal muscle, brain, whatever...) by insulin. At the same time, oxygen (O2) is taken in, crosses the very thin membrane of the alveoli into the capillaries, onto a hemoglobin, and is carried by the red blood cell into a cell (skeletal muscle, brain, whatever...). Inside of the cell the Citric Acid, Krebs Cycle, and e- Transport chain (to make 38 ATP) takes place (see how you really do need to remember your Intro to Bio?), producing carbon dioxide, water (which is why we have insensitive water loss of 600 mL/day, right?) and 38 ATP (theoretically).
Now, remember your Intro to Chem, where all molecules dissolved in a fluid are in constant homeostatic flux? That's what's happening here:
CO2 + H2O <--> H2CO3 <--> HCO3- + H+
Once the CO2 and H2O dissolve into the blood, it exists as CO2, H2O, H2CO3, HCO3-, and H+ all a the same time (actually, very little of it stays as H2CO3--it's kind of that in between, super fast, invisible step). When that blood travels to the kidneys, the kidneys just pick out the H+ and that goes into the urine, making urine acidic. Some of the water is excreted in the urine also. Then the blood flows up to the lungs, where the CO2 crosses over into the alveoli and gets exhaled with some H2O as well.
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