1: Amino acids contain both an organic acid and organic base.

2: The acid and base are both neutralized in the process of making a protein.

3: Some amino acids remain acidic or basic after becoming part of a protein because of extra parts they have on a side chain (sort of like a pendant or charm hanging down from a necklace).

4: Excess acid in the body is is neutralized by carbonate which can then be converted to CO2 and exhaled or filtered out by the kidneys into urine. There is baking soda in your blood and you can't survive without it.