DNA controls protein synthesis by means of base codes. What can happen to a protein if two of the base pairs on a DNA stand were switched?

A different protein would be made. A cell has no way of knowing if the pair was A=T or T=A originally, so if they switch the cell will think it was that way all along. A different protein will be made (most of the time) because the mutation leaves no traces of itself for DNA repair mechanisms to detect (unlike mutations like cytosine turning into uracil or two thymines binding together, which the cell knows is an unnatural occurrence). So if the switch goes unnoticed, that gene will code for a different protein. This is because proteins are made of strings of amino acids, and the sequence determines a proteins shape and function. DNA codes for sequences of amino acids. Each amino acid is represented as three bases, so TGC will code for something different than AGC. This means that if TGC is mutated into AGC, the resulting protein will also have the wrong amino acid.