From the feedstock extraction or production to the final use in an engine, the fuel goes through multiple steps constituting its life cycle. At each of these steps, GHG emissions are likely to be produced. The total carbon foot print of the fuel is obtained by adding all these emissions together in a life cycle assessment (LCA) approach.
For fossil fuels, in addition to combustion, emissions are associated with crude oil extraction and refining, as well as final fuel transport and distribution. In the case of biofuels, combustion emissions can be considered as neutral (see question 2), but there are emissions associated to the cultivation, harvesting, transport and conversion of the feedstock. In particular, depending on the feedstock and agricultural practices, the cultivation of the feedstock can represent a significant part of the emissions.