Throttling is a process by which BizTalk Server ensures optimum performance and use of System resources (memory, threads, CPU etc).
Floodgate scenario are very common in an integration environment, where an unusual load comes into the system within a short period of time. BizTalk server manages these kind of scenario by a mechanism called Host Throttling. BizTalk server monitors various points in the system - memory, CPU usage, database connections, thread count etc and if it detects an unusual pattern, then it tries to control those parameters to bring the system to a manageable level.
For a detailed study on this topic, please read the MSDN article: What Is Host Throttling?