These names are usually formed according to some kind of system. Especially in chemistry "new" compounds are often named like that. Even a common word like alcohol gives rise to -ol compounds (like methanol) to indicate to a scientist that the two have certain chemical properties.
The compounds they name may or may not be in common use as nouns, and as such have lost their "name"-feeling.
If you want to capitalize arginine, you should, by rights, also capitalize alcohol, methanol and polypropylene. These are "names" given to substances, but they do not function like proper names.
In extremis, if you want to capitalize them, you should capitalize Water as well. It is, after all, the "proper name" given to dihydrogenoxide.
Of course, when a compound is given a trade mark name, it does get capitalized, even if the name seems to be systematically derived. However, if the name becomes very commonly used, it is possible that the trade mark name loses its "proper name" feel again, and we stop capitalizing it again.
Examples of that are Aspirin and Heroin (trademarks of Bayer), which are now written as aspirin and heroin.
Something similar happened with nylon and rayon (trademark of duPont) - their Teflon seems to be going the same way.
This is, at least in part, a question of style. Or the style guides of, say, news organizations.
- When you pronounce it as single letters, such as CNN (see en en) or BBC (bee bee see) it is usually written all caps.
- When you pronounce it as one word some organizations write only capital letters, some spell it like a proper noun, first letter capitalized, rest lower case: CNN writes NATO, BBC writes Nato, as you say nato, not en ay tee oh.
- There are lots of exceptions. SCSI is pronounced like a word, SKUZ-ee, but spelled upper case by the BBC, too.
Best Answer
At the beginning of a sentence, capitalize the first letter:
Inside a sentence, both letters go in lower case:
Capitalization for Latin abbreviations works the same as if you were to spell out the words (which no one ever does). They're not acronyms. The second letter stands for the second word of the phrase (exempli gratia or id est), so you don't capitalize it, just as you don't normally capitalize the second word of a sentence.
If you did spell out the words, here's how the sentences would look:
The principle is probably clearer if you see it with a Latin abbreviation where a word is abbreviated with more than one letter. Op. cit., which means "in the work (previously) cited" (opere citato), naturally gets only the O capitalized at the start of a sentence, since we normally capitalize only the first letter of the first word of a sentence.
More about "Latin in English" is here, including an explanation of what the abbreviations stand for.