Question

what literally makes denotation different than connotation?
their suffixes
their roots
their prefixes

Explanation:

To determine what makes denotation and connotation different literally, we analyze their prefixes. The prefix "de -" in denotation (from Latin "denotare" meaning "to mark out") and "con -" in connotation (from Latin "connotare" meaning "to mark along with") show the difference comes from their prefixes. Suffixes (both end with "-ation") and roots (both relate to marking) don't create the core literal difference.

Answer:

their prefixes