Etymology
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extra- 
word-forming element meaning "outside; beyond the scope of; in addition to what is usual or expected," in classical Latin recorded only in extraordinarius, but more used in Medieval Latin and modern formations; it represents Latin extra (adv.) "on the outside, without, except," the old fem. ablative singular of exterus "outward, outside," comparative of ex "out of" (see ex-).
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dis- 
Origin and meaning of dis-

word-forming element of Latin origin meaning 1. "lack of, not" (as in dishonest); 2. "opposite of, do the opposite of" (as in disallow); 3. "apart, away" (as in discard), from Old French des- or directly from Latin dis- "apart, asunder, in a different direction, between," figuratively "not, un-," also "exceedingly, utterly." Assimilated as dif- before -f- and to di- before most voiced consonants.

The Latin prefix is from PIE *dis- "apart, asunder" (source also of Old English te-, Old Saxon ti-, Old High German ze-, German zer-). The PIE root is a secondary form of *dwis- and thus is related to Latin bis "twice" (originally *dvis) and to duo, on notion of "two ways, in twain" (hence "apart, asunder").

In classical Latin, dis- paralleled de- and had much the same meaning, but in Late Latin dis- came to be the favored form and this passed into Old French as des-, the form used for compound words formed in Old French, where it increasingly had a privative sense ("not"). In English, many of these words eventually were altered back to dis-, while in French many have been altered back to de-. The usual confusion prevails.

As a living prefix in English, it reverses or negatives what it is affixed to. Sometimes, as in Italian, it is reduced to s- (as in spend, splay, sport, sdain for disdain, and the surnames Spencer and Spence).

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in- (2)
Origin and meaning of in-

element meaning "into, in, on, upon" (also im-, il-, ir- by assimilation of -n- with following consonant), from Latin in- "in," from PIE root *en "in."

In Old French (and hence in Middle English) this often became en-, which in English had a strong tendency to revert to Latin in-, but not always, which accounts for pairs such as enquire/inquire. There was a native form, which in West Saxon usually appeared as on- (as in Old English onliehtan "to enlighten"), and some of those verbs survived into Middle English (such as inwrite "to inscribe"), but all now seem to be extinct.

Not related to in- (1) "not," which also was a common prefix in Latin, causing confusion: to the Romans impressus could mean "pressed" or "unpressed;" inaudire meant "to hear," but inauditus meant "unheard of;" in Late Latin investigabilis could mean "that may be searched into" or "that cannot be searched into." Latin invocatus was "uncalled, uninvited," but invocare was "to call, appeal to."

The trouble has continued in English; the hesitation over what is meant by inflammable being a commonly cited example. Implume (1610s) meant "to feather," but implumed (c. 1600) meant "unfeathered." Impliable can mean "capable of being implied" (1865) or "inflexible" (1734). Impartible in 17c. could mean "incapable of being divided" or "capable of being imparted." Impassionate can be "free from passion" or it can mean "strongly stirred by passion." Inanimate (adj.) is "lifeless," but Donne uses inanimate (v.) to mean "infuse with life or vigor." Irruption is "a breaking in," but irruptible is "unbreakable."

In addition to improve "use to one's profit," Middle English also had a verb improve meaning "to disprove" (15c.). To inculpate is "to accuse," but inculpable means "not culpable, free from blame." Infestive has meant "troublesome, annoying" (1560s, from infest) and "not festive" (1620s). In Middle English inflexible could mean "incapable of being bent" or "capable of being swayed or moved." In 17c., informed could mean "current in information," formed, animated," or "unformed, formless" ("This was an awkward use" [OED]). Inhabited has meant "dwelt in" (1560s) and "uninhabited" (1610s); inhabitable likewise has been used on opposite senses, a confusion that goes back to Late Latin.

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