Quote 1
"I thought he was going to punish us too." I try to imagine. "Like if there were two Rooms, if he put me in one and you in the other one." (2.430)
Ma is the only person Jack knows, so he is incredibly close to her. To him, the worst punishment is to be separated from his mother. That's awfully sweet… and borderline Norman Bates, but he's only five, so we're sticking with "sweet" for now.
Quote 2
"I came down and I was a kid like you, I lived with my mother and father." I shake my head. "You're the mother." (2.486-2.487)
Jack has a hard time understanding the intricacies of family at first—it's weird for him that his mother also had a mother. He thought his only family was Ma, and that her only family was him, but it's actually much larger than that. One thing Jack keeps learning is how much bigger and more complex the world is than he thinks, and this is a good example of that.
Quote 3
"Do we go into TV for dreaming?" "No. We're never anywhere but here." Her voice sounds a long way away. (1.601-1.602)
Although Jack can pick up on the change in Ma's tone of voice, he doesn't understand why she sounds this way. She's been trapped inside Room for eight years, with nowhere else to go. Not a day goes by without her wishing she was out of there.