pH affects the shape of proteins. In the case of fermentation a collection of enzymes is responsible for the metabolic processes that occur.- an enzyme is a protein which performs a metabolic process. For example sucrase is an enzyme which breaks sucrose down into fructose and glucose.f the pH is increased, this affects the shape of proteins, by disrupting the bonds in the protein. In the case of fermentation, you say the rate increases when it get's more acidic-when the pH is lower. This is because the organisms-the yeast-producing the enzymes to ferment glucose, have adapted to acidic conditions.