I'm wondering what the key differences are between biological product molecules and synthetic molecules?

 

So if i was given the skeletal structure of two molecules, and asked to determine which one was synthetic, and which one was likely to be the product of a biological reaction, what should i be mainly looking for?

 

 

"what should i be mainly looking for? "

A better job.

There is not a difference between the two. A molecule of water doesn't "know" if it is in a living thing or not.

​the idea that there was a difference was killed off a long time ago.

http://en.wikipedia.org/wiki/W%C3%B6hler_synthesis

 

There are lots of molecules that are very difficult to synthesise and it's easier to get them from biological sources- Morphine and digitalin for use in medicine are still obtained from plants because it's much easier (and cheaper) than synthesising them.

 

In some cases it's possible to trace the origins of a molecule to a biological precursor.

http://www.ncbi.nlm.nih.gov/pubmed/21107978

but in principle, it's always possible to make the chemical synthetically.