Etymology
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in- (1)
Origin and meaning of in-
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.
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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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sch- 
this letter group can represent five distinct sounds in English; it first was used by Middle English writers to render Old English sc-, a sound now generally pronounced (and spelled) "-sh-." Sometimes it was miswritten for -ch-. It also was taken in from German (schnapps) and Yiddish (schlemiel). In words derived from classical languages, it represents Latin sch-, Greek skh-, but in some of these words the spelling is a restoration and the pronunciation does not follow it (as in schism).
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semi- 

before vowels sem-, word-forming element meaning "half, part, partly; partial, imperfect; twice," from Latin semi- "half," from PIE *semi- "half" (source also of Sanskrit sami "half," Greek hēmi- "half," Old English sam-, Gothic sami- "half").

Old English cognate sam- was used in such compounds as samhal "poor health," literally "half-whole;" samsoden "half-cooked," figuratively "stupid" (compare half-baked); samcucu "half-dead," literally "half-alive;" and the last survivor of the group, sandblind "dim-sighted" (q.v.). Common in Latin (as in semi-gravis "half-drunk," semi-hora "half hour," semi-mortuus "half-dead," semi-nudus "half-naked," semi-vir "half-man, hermaphrodite"). The Latin-derived form in English has been active in forming native words since 15c.

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im- 
variant of in- before -b-, -m-, -p- in the sense of "not, opposite of" (immobile, impersonal; see in- (2)) as well as "in, into" (implant, impoverish; see in- (1)). In some English words it alternates with em- (1).
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en- (1)
word-forming element meaning "in; into," from French and Old French en-, from Latin in- "in, into" (from PIE root *en "in"). Typically assimilated before -p-, -b-, -m-, -l-, and -r-. Latin in- became en- in French, Spanish, Portuguese, but remained in- in Italian.

Also used with native and imported elements to form verbs from nouns and adjectives, with a sense "put in or on" (encircle), also "cause to be, make into" (endear), and used as an intensive (enclose). Spelling variants in French that were brought over into Middle English account for parallels such as ensure/insure, and most en- words in English had at one time or another a variant in in-, and vice versa.
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il- 
assimilated form of Latin prefix in- used with words beginning in l-; see in-.
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ir- 
assimilated form of the two Latin prefixes in- "not," or "in" (see in-) before -r-.
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ap- (1)
form of Latin ad- in compounds with words or stems beginning in -p-; see ad-. In Old French reduced to a-, but scribal re-doubling of ap- to app- in imitation of Latin began 14c. in France, 15c. in England, and was extended to some compounds formed in Old French or Middle English that never had a Latin original (appoint, appall).

In words from Greek, ap- is the form of apo before a vowel (see apo-).
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pro- 

word-forming element meaning "forward, forth, toward the front" (as in proclaim, proceed); "beforehand, in advance" (prohibit, provide); "taking care of" (procure); "in place of, on behalf of" (proconsul, pronoun); from Latin pro (adv., prep.) "on behalf of, in place of, before, for, in exchange for, just as," which also was used as a first element in compounds and had a collateral form por-.

Also in some cases from cognate Greek pro "before, in front of, sooner," which also was used in Greek as a prefix (as in problem). Both the Latin and Greek words are from PIE *pro- (source also of Sanskrit pra- "before, forward, forth;" Gothic faura "before," Old English fore "before, for, on account of," fram "forward, from;" Old Irish roar "enough"), extended form of root *per- (1) "forward," hence "in front of, before, toward, near," etc.

The common modern sense of "in favor of, favoring" (pro-independence, pro-fluoridation, pro-Soviet, etc.) was not in classical Latin and is attested in English from early 19c.

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