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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mater- 

combining form meaning "mother," from Latin māter (see mother (n.1)).

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schm- 
substituted for the initial sound of a word and reduplicated with it to convey derision (as in "Oedipus schmoedipus" in the punchline of the old joke about the Jewish mother and the psychiatrist), 1929, from the numerous Yiddish words that begin with this sound.
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iso- 
before vowels often is-, word-forming element meaning "equal, similar, identical; isometric," from Greek isos "equal to, the same as; equally divided; fair, impartial (of persons); even, level (of ground)," as in isometor "like one's mother." In English used properly only with words of Greek origin; the Latin equivalent is equi- (see equi-).
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anomo- 
word-forming element meaning "irregular, unusual," from Greek anomos, from a- "without" (see a- (3)) + nomos "law," from PIE root *nem- "assign, allot; take."
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step- 
Old English steop-, with connotations of "loss," in combinations like steopcild "orphan," related to astiepan, bestiepan "to bereave, to deprive of parents or children," from Proto-Germanic *steupa- "bereft" (source also of Old Frisian stiap-, Old Norse stjup-, Swedish styv-, Middle Low German stef-, Dutch stief-, Old High German stiof-, German stief-), literally "pushed out," from PIE *steup-, from root *(s)teu- (1) "to push, stick, knock," with derivatives referring to fragments (see steep (adj.)). Barnhart suggests the forms in -f- are by assimilation of the first sound in following words for "father."

Etymologically, a stepfather or stepmother is one who becomes father or mother to an orphan, but the notion of orphanage faded in 20c. and came to denote simply relation through marriage. For sense evolution, compare Latin privignus "stepson," related to privus "deprived." Compare orphan (n.).
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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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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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il- 
assimilated form of Latin prefix in- used with words beginning in l-; see in-.
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