Challah, Chapter 3, Mishnah 2. In Chapter 1, Mishnah 4, we learned that meduma - a mixture of Terumah with something that is not Terumah - is exempt from challah, because of the Terumah mixed into it, which is not subject to challah. Our Mishnah comes to spell out this law, and to distinguish between a mixture that occurred before the dough was formed and one that occurred afterward.
A Terumah mixture before the dough is formed and after:
"Nidme'ah isasah ad shelo gilgelah - peturah" - if the Terumah became mixed in before the dough came into being, before the kneading, the dough is exempt from challah, since a meduma - a mixture containing Terumah - is exempt from challah.
"Mishenisgalgelah - chayevet" - but if the Terumah became mixed in after the kneading, once the dough had already been formed, the obligation of challah had already taken effect and it remains in force. An obligation of challah does not simply disappear once it has taken hold, merely because Terumah later became mixed in.
Regarding the exemption in the first case, the commentators point out that by strict law, as long as there is a majority the Terumah is nullified, and it is only by rabbinic enactment that Terumah is nullified only in one part out of a hundred. Our Mishnah must therefore be speaking of challah in our times, which is itself only a rabbinic obligation; otherwise it would not be possible to exempt from challah on account of a Terumah mixture that is only a rabbinic matter.
A doubtful tumah before the dough is formed and after:
"Nolad lah safek tumah ad shelo gilgelah - te'aseh b'tumah" - a doubt arose as to whether the dough became tamei, before it became subject to challah, before the kneading. Since it had already become of doubtful tumah before the obligation of challah took effect, the kohen cannot eat it in any case, and therefore one may continue working with it in a state of tumah and even touch it while tamei.
"Mish'as gilgulah - te'aseh b'taharah" - but if the doubt arose after the dough came into being, after the kneading, the obligation of challah had already taken effect, and therefore its status of taharah must be preserved: it may not be allowed to contract any further tumah, and it may not be rendered definitely tamei. Even though only a doubtful tumah is involved, there is still a duty to guard it from becoming further tamei.
In summary: our Mishnah establishes that the moment of kneading is the deciding point in both laws. A Terumah mixture that preceded the kneading exempts the dough from challah, whereas a mixture that came after the kneading does not remove an obligation that has already taken effect. So too with doubtful tumah: a doubt that arose before the kneading permits working with the dough in tumah, since the kohen cannot eat it in any case, whereas a doubt that arose after the kneading requires working with it in taharah and guarding it from definite tumah.