Etymology
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per- 

word-forming element common in words of French and Latin origin, meaning primarily "through," thus also "throughout; thoroughly; entirely, utterly," from Latin preposition per (see per (prep.)).

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praeter- 

from Latin adverb and preposition praeter "beyond, past, besides, except" (from PIE root *per- (1) "forward," hence "in front of, before"). See preter-, which now is the usual form of it in English; also see æ (1).

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preter- 

also praeter-, word-forming element meaning "beyond; over, more than in quantity or degree," from Latin praeter (adverb and preposition) "beyond, before, above, more than," properly comparative of prae "before," from PIE root *per- (1) "forward," hence "in front of, before."

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contra- 

word-forming element meaning "against, in opposition," from Latin adverb and preposition contra "against" (see contra (prep., adv.)). The Latin word was used as a prefix in Late Latin. In French, it became contre- and passed into English as counter-. The Old English equivalent was wiðer (surviving in withers and widdershins), from wið "with, against."

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intra- 
word-forming element meaning "within, inside, on the inside," from Latin preposition intra "on the inside, within, in, into;" of time, "during, in the course of," related to inter "between," from PIE *en-t(e)ro-, from root *en "in." Commonly opposed to extra-, and compare inter-. The use of intra as a prefix was rare in classical Latin.
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circum- 

word-forming element meaning "around, round about, all around, on all sides," from Latin adverb and preposition circum "around, round about," literally "in a circle," probably accusative form of circus "ring" (see circus). The Latin word was commonly used in word-formation. In French, the element became circon-; Kitchin points out that con for cum is common even in classical Latin. For sense development, compare German rings "around."

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infra- 
word-forming element meaning "below, beneath," from Latin infra (adverb and preposition) "below, underneath, on the under side, beneath," also "later than; smaller than; inferior to," related to infernus "low, below," from PIE *ndher "under" (source also of Sanskrit adnah "below," Old English under "under, among;" see under). Modern popular use of it dates from the 1920s, as an opposite to super-, often in science fiction. "This use of infra- is scarcely a Latin one" [OED].
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cis- 

word-forming element meaning "on the near side of, on this side," from Latin preposition cis "on this side" (in reference to place or time), related to citra (adv.) "on this side," from PIE *ki-s, suffixed form of root *ko-, the stem of demonstrative pronoun meaning "this." Opposed to trans- or ultra-. Originally only of place, sometimes 19c. of time; 21c. of life situations (such as cis-gender, which is attested by 2011).

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super- 
word-forming element meaning "above, over, beyond," from Latin super (adverb and preposition) "above, over, on the top (of), beyond, besides, in addition to," from *(s)uper-, variant form of PIE root *uper "over." In English words from Old French, it appears as sur-. The primary sense seems to have shifted over time from usually meaning "beyond" to usually meaning "very much," which can be contradictory. E.g. supersexual, which is attested from 1895 as "transcending sexuality," from 1968 as "very sexual."
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pre- 

word-forming element meaning "before," from Old French pre- and Medieval Latin pre-, both from Latin prae (adverb and preposition) "before in time or place," from PIE *peri- (source also of Oscan prai, Umbrian pre, Sanskrit pare "thereupon," Greek parai "at," Gaulish are- "at, before," Lithuanian prie "at," Old Church Slavonic pri "at," Gothic faura, Old English fore "before"), extended form of root *per- (1) "forward," hence "beyond, in front of, before."

The Latin word was active in forming verbs. Also see prae-. Sometimes in Middle English muddled with words in pro- or per-.

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