My question: - Is it possible for more than one peak to appear in gel chromatography in proportion to the number of peaks that appeared in ion exchange chromatography for the same enzyme?
Yes, in gel chromatography you can have many zwetterions since the media is almost neutral (thus each sidegroup of the enzyme can be either acidic, neutral, or basic). In ion exchange these sidegroups are either positively charged or negatively charged (they have no choice), because the media is acidic or basic (negative or positively charged).