Sites Collection can have many sites inside, their own groups, roles, root site and many subsites, as well as sites collection administrator (user who can do anything within all sites related sites collection ignoring permissions).
Each sites collection can be stored into its OWN DATABASE positively increasing throughput (the best way is to scale your farm to maximize throughput). Sites Collections are NOT organized into hierarchy and can be created only within managed paths (managed paths can be defined from CA).
Site is always a part of sites collection, it inherits groups and roles from sites collection. Data from all sites is placed in the same DB related to sites collection. Sites within sites collection are organized into hierarchy. It can be created within another site or root of the sites collection.
According to SPLMS each course is a separate sites collection. Teachers are sites collection administrators, learners are anybody who were contributed permission to the root site.