Set the following variables in your MySQL config file:

slow_query_log = 1 (means true)
long_query_time = 0 (means 0 seconds)
log_queries_not_using_indexes = 1 (means true)
log_output = FILE (default is TABLE)

Setting long_query_time to 0 will instruct MySQL to log all queries to the slow query log. Some queries might not be that slow, but if repeated often enough will have a significant impact on the performance of your MySQL database. Setting long_query_time to 0 will allow you to catch that kind of scenario as well. Let MySQL run for a while, then download pt-query-digest, and run it like so:

$ pt-query-digest slow-query.log > slow-query.log.out

Look at the slow-query.log.out file to find out which queries are slowing down your MySQL database.