Difference between Web Application,Site Collection,Site and sub site in SharePoint 

 Web Application
       -->Site Collection (SPSite)( A site collection cannot be physically seen in SharePoint)
              --> Site (SPWeb)
              --> Site (SPWeb)
      --> Site Collection (SPSite)
              --> Site (SPWeb)
                    --> Sub Site (SPWeb)
                    --> Sub Site (SPWeb)
The words between ( ) are the objects of the SharePoint API.