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Following is the definition of the Morris Dictionary of Word and Phrase Origins" by William and Mary Morris (HarperCollins, New York, 1977, 1988) on the idiom "pretty penny:" "Pretty has several meanings beside 'pleasing to the eye. It also means 'considerable.'"
That would explain "pretty penny." A lot of money, a whole big bunch, a considerable amount.
The Online Etymology Dictionary says that the use of the phrase "pretty penny" was first recorded in 1768. And I guess a penny did buy quite a bit more back then
The word 'penny' is simply used in this idiomatic expression as a sort of representative of money - the technical words for this sort of figure of speech are: metonym or synecdoche where the part represents the whole ie 'penny' for 'money'.
Interestingly the word 'penny' crops up in several expressions, two of which suggest the small value of the penny:
* in for a penny in for a pound ;
* if you are going to spend a little money on a venture, you might as well spend a lot more. You'll find these articles have little value now as they are now two a penny;
* a penny for your thoughts.