LinuxQuestions.org has an excellent summary of the Linux command line here:

http://wiki.linuxquestions.org/wiki/Commands

When you, say, start MySQL from the command line from PuTTY you may quickly discover that you need to learn how to run commands in the background. Read "Controlling Jobs in Linux" here:

http://www.cpqlinux.com/jobcontrol.html

This command line stuff should lead to need to script. Begin study with "Bash Guide for Beginners" here:

http://tldp.org/LDP/Bash-Beginners-Guide/html/index.html