its easier if you read this:http://en.wikipedia.org/wiki/PCI_Express
from the article:
PCI Express 2.1 supports a large proportion of the management, support, and troubleshooting systems planned for full implementation in PCI Express 3.0. However, the speed is the same as PCI Express 2.0. Most motherboards sold currently come with PCI Express 2.0 connectors.
PCI-E have backward compatible with the older version of PCI-E so putting PCI-E 2.1 card into PCI-E 2.0 slot are fine. but it is commonly known that PCI-E 2.1 card have a little bit of trouble working with some PCI-E version 1.x (mostly older mobo, much more recent mobo supposed to be fine tough) which needs BIOS update so the card can be detected properly by the mobo