The title is a play on the Biblical phrase "Am I my brother's keeper?" uttered by Cain to God, in a sassy way. Yes, that Cain, the one who, you know, killed his brother. More on that in a bit.
We hear the phrase "Am I my sister's keeper?" (4.6.13) from Jesse, who says it to Julia, much in the same sassy way Cain says it to God. He's basically saying, "I have no freaking clue where she is." We're not suggesting that Julia is a god-like figure, although it is interesting to think about how Anna's fate (and therefore Kate's) lies in Julia's hands, depending on what her recommendation is to the court.
Anyway, back to the Bible. In this instance, keeper means protector, watcher, or defender. Taking that into considering, who is Kate's keeper? If it's Anna, does this mean that, like Cain, she would be responsible for killing her sibling? But is Kate even the "sister" in question? It could be Anna. Who, if anyone, is in charge of defending her? This gets turned over a few times in the book, and the title is a shout-out to this conundrum.