Today everyone want their website to be implemented in dynamic programming language such as PHP, ASP, Etc that requires the use of MySQL databse to store user information ,passwords, senitive data. More the database entries, the bigger is your database. Sometimes MySQL server can act as your server enemy and takes much of your server resources which you can also see using top command or if you have cpanel/WHM you can directly check by clicking on top right corner link which looks like Load Averages: 0.01 0.05 0.07 upon logging in.
If you see MySQL taking high cpu load then you should worry. Try finding which database is causing trouble by running mysqladmin proc stat and some other random linux commands. If you successfully find it tell your developer to optimizie the website because poorly written code may be it’s cause and upon rectification you may also see the difference in the load.
Finally try to tune and optimize MySQL server using MySQLTuner. MySQLTuner is a perl script which overview web server and pop out some recommendations about improvements and stability for MySQL. I will not elaborate more about this tool as you can easily get more infomation on its own website (https://github.com/rackerhacker/MySQLTuner-perl#readme).