Learn English – Attended to vs attended upon

2) Could you please put the pen on the book?

is the most likey way someone would say this. 3) "upon" is also OK but is more likely to occur in literature. These refer to placement.

1) Could you please put the pen over the book?
4) Could you please put the pen above the book?

These refer to location. This would imply the pen is located above the book, which would not be likely in the setting of your examples, but could be possible with other wording. For example:

Could you please put the pen on the shelf above the book?

Finally -

5) Could you please put the pen up the book?

does not make sense in this phrase. "up" refers to inside in a sense.
An example where it would be OK:

Could you please put the medicine up your nose?

It is an archaic meaning of "inform" in the sense "to create an impression on something", like a fingerprint on moist clay.

This trope, a commonplace in philosophical writing, would ultimately go back, I think, to medieval scholasticism at the intersection of metaphysics and epistemology (and from there back to Aristotle); the "form" of something was its essence, that which made it to be what it was. Does the mind go out and alter that which it knows? Or does that which is known create impressions on the mind? Yadda yadda yadda.

They (the limits of our understanding) do not create an impression on reality. They do not change reality.