Why is there a pH difference between stacking and separating gel?

The stacking gel and separating gel perform distinct roles in gel electrophoresis. Each gel is maintained at a pH that helps it perform its function more efficiently. 

The stacking gel has a pH of 6.8. This lower pH environment is optimal for concentrating the sample into a narrow band before it enters the separating or resolving gel, which lies at the bottom of the electrophoresis chamber. 

The separating gel has a pH of 8.8. This higher pH level is ideal for separating the protein molecules based on size and charge.