Etymology
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sub- 
word-forming element meaning "under, beneath; behind; from under; resulting from further division," from Latin preposition sub "under, below, beneath, at the foot of," also "close to, up to, towards;" of time, "within, during;" figuratively "subject to, in the power of;" also "a little, somewhat" (as in sub-horridus "somewhat rough"), from PIE *(s)up- (perhaps representing *ex-upo-), a variant form of the root *upo "under," also "up from under." The Latin word also was used as a prefix and in various combinations.

In Latin assimilated to following -c-, -f-, -g-, -p-, and often -r- and -m-. In Old French the prefix appears in the full Latin form only "in learned adoptions of old Latin compounds" [OED], and in popular use it was represented by sous-, sou-; as in French souvenir from Latin subvenire, souscrire (Old French souzescrire) from subscribere, etc.

The original meaning is now obscured in many words from Latin (suggest, suspect, subject, etc.). The prefix is active in Modern English, sometimes meaning "subordinate" (as in subcontractor); "inferior" (17c., as in subhuman); "smaller" (18c.); "a part or division of" (c. 1800, as in subcontinent).
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great- 
word-forming element denoting "kinship one degree further removed," early 15c. (in great uncle), from great (adj.), based on similar use of French grand (see grand-). An Old English way of saying "great-grandfather" was þridda fæder, literally "third father;" in early Middle English furþur ealdefader was used (12c.).
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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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col- 

assimilated form of com- "with, together" before stems beginning in -l-. In early Latin, com- was assimilated to these as con-, but col- later also was used. Latin words in coll- became col- in Old French and thus in early Middle English but were altered back to coll- with the revival of learning.

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pn- 

consonant sound in some English words derived from Greek. The p- typically is silent in English but pronounced in French, German, Spanish, etc.

It is to be desired that it were sounded in English, also, at least in scientific and learned words; since the reduction of pneo- to neo-, pneu- to new-, and pnyx to nix, is a loss to etymology and intelligibility, and a weakening of the resources of the language. [OED]
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-cracy 
word-forming element forming nouns meaning "rule or government by," from French -cratie or directly from Medieval Latin -cratia, from Greek -kratia "power, might; rule, sway; power over; a power, authority," from kratos "strength," from PIE *kre-tes- "power, strength," suffixed form of root *kar- "hard." The connective -o- has come to be viewed as part of it. Productive in English from c. 1800.
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kilo- 
word-forming element meaning "one thousand," introduced in French 1795, when the metric system was officially adopted there; irregularly reduced from Greek khilioi "thousand," from PIE *gheslo- "thousand," source also of Sanskrit sahasra-, Avestan hazanjra "thousand." "It is usually assumed that Lat. mille should be connected too" [Beekes]; see milli-. "In the metric system, kilo- means multiplied, & milli- divided, by 1000" [Fowler].
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sh- 
sound represented in Old English by -sc- (fisc "fish"), which originally was pronounced "-sk-" but which by late Old English had softened to "-sh-." Modern English words with -sc- mostly are imports (generally Scandinavian).

The "sh" sound did not exist in Old French, therefore French scribes after the Norman conquest often represented it with -ssh- in medial and final positions, and sch- in initial positions (schape, schamful, schaft for shape, shameful, shaft). But the spelling -sh- has been standard since Caxton, probably as a worn-down form of Middle English -sch-.

In some East Anglian texts from 14c.-15c., x- is used (xal, xulde for shall, should), which would have given the language a very different look had it prevailed, but the London-based sh- ended up as the standard form. The same Germanic sound has become, by natural evolution, modern German and Dutch sch-, Scandinavian sk-.
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rh- 

consonantal digraph, an initial sequence used in Latin (and thus in English words from Latin) to represent Greek initial aspirated r-. The medial Greek form of it usually is represented by -rrh-, as in catarrh, diarrhea, hemorrhage, myrrh, Pyrrhic. As it was pronounced as simply "r" in Middle English (as in Old French and Spanish), the -h- tended to be dropped in spelling but was restored in early Modern English with the classical revival.

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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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