As far as stereochemistry, yes, it absolutely changes the "chemistry"/ or I presume you mean how the molecule metabolizes in the system. some L formations are easily accepted or metabolized by your system and while the D isomers are just passed through because you dont have the correct enzyme to break it down. For the longest time, companies were experimenting with L and D isomers of sugars and fats to see if they taste the same while pass through your system unmetabolized. I think some sugars actually do this but may be harmful if retained in adequate quantity by your system. This variation is specific for each molecule since the specifity of enzymes for all molecules varies.
No Im not a total nerd.