At any particular instant, atoms (or sub-particle) as the basic building block of the Universe, interact one another. This changes change the form of matters, in space-time. Right ... space is not a vacuum, but a Quantum Foam. As symmetry break, virtual particle forms matter with the interaction of photon (as a force carrier) and electrons.
Rates require a time unit. This is the problem with trying to break down or understand time with heurism, it doesn't quite work. The answer is most likely that time's nature is really unknown at the moment.
The Universe is Space that expand with entropy increasing as physics of energy and matters interact. Time is the measure of change in energy and matters.
The true nature of time is still unknown like how space and time are related and how time started after big bang. What is the true nature of past, present and future? Although there is one practical evidence of time been relative to the observer's frame of reference is GPS.
Space can be said as a three dimensional medium in which matter exists in various forms. Matter has a position and can move. There's one more dimension which is time dimension and that's why it is called as space time continuum. Space isn't absolutely vacuum. There are virtual particles annihilating each other. That's the best we know about space I guess.