word-forming element meaning "not, opposite of, without" (also im-, il-, ir- by assimilation of -n- with following consonant, a tendency which began in later Latin), from Latin in- "not," cognate with Greek an-, Old English un-, all from PIE root *ne- "not."
In Old French and Middle English often en-, but most of these forms have not survived in Modern English, and the few that do (enemy, for instance) no longer are felt as negative. The rule of thumb in English has been to use in- with obviously Latin elements, un- with native or nativized ones.
"sorrow for committing sin or for having offended, with the intention of amending one's life; mortification undertaken to make amends for sin," c. 1200, from Old French penitence (11c.) and directly from Latin pænitentia "repentance" (Medieval Latin penitentia), noun of condition from pænitentum (nominative pænitens) "penitent," present participle of pænitere "cause or feel regret," probably originally "is not enough, is unsatisfactory," from pæne "nearly, almost, practically," which is of uncertain origin. The basic meaning seems to be "missing, lacking." Related: Penitency.