For example, when a web-browser connects to a web-server, it uses HTTP for a protocol at the application layer. But when a web-server connects to MySQL server, another database, what application layer protocol is used for the request and response? Or have I misunderstood something? Thank you!
It's simply called "MySQL protocol".
Refer to https://dev.mysql.com/doc/dev/mysql-server/latest/PAGE_PROTOCOL.html