Here is simple command which you can run on your ec2 instance using putty.

Step 1. Login to instance using putty.

Step 2. Before typing bellow command take backup of your database so you can export it again after upgrade.

Step 3. Type below command

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install mysql-server-5.6

Once upgrade is complete restart your server.

Step 4. Server restart

sudo service apache2 restart

All done.