The portals were the teleportation devices to get funkeys around Terrapinea!
Only certain Funkeys can go through portals.
Most of the portals were destroyed in a purge.
On the day of the Great Disaster, a series of explosions destroyed the main portal station, shattering the crystal gems in 4 and spreading to many of the stations since the portals were open at the time.
Dr. Tinker (whose remains were lost) was also lost in the explosion. He is believed to work on the main portal station when the explosion occured.
It was during this period of chaos that Master Lox mysteriously appeared and locked the remaining functional portals and certain doors to restrict where a funkey can travel in terrapinia.