Professors signal structure out loud: 'There are two reasons…', 'First… second…', 'Now let's turn to…', 'So what does this mean?'. Organization questions ask how the talk is built or why one part follows another. If your notes mirror the signposts, these questions answer themselves.
The connective tissue is tested constantly: X causes Y, X contrasts with Y, X is an example of Y, X is a problem and Y is a proposed solution. Listen for the joints: because, so, as a result / but, however, unlike / for example, such as / the problem is…, one answer is…. Note the joint, not just the bones.
Some questions force you to combine two separated pieces: what the professor said early and what a student asked later, a definition and its example three minutes apart. These reward a connected mental map — one more reason notes are organized by topic shifts, not by the clock.