CiviCRM uses the PEAR package DB_DataObject to access the mysql database. Doing so reduces the amount of sql we need to write to fetch / store values for a single table. For queries involving more than one table, we write them manually since since it was fairly painful to try to force complicated queries using DB_DataObject (we did use DB_DO for multiple table queries when we wrote EmailNow, in the end we felt the hoops we had to jump through was not worth the effort and hence the current scheme)
The basic PHP classes that represent a table are called DAO's (Data Access Objects). These are generated automatically by (xml/GenCode.php) which also generates the sql structure for that specific table. The xml files representing the schema is stored under CIVCRM_ROOT/xml/schema. The sql file generated (civicrm_41.mysql and civicrm_40.mysql) are stored under CIVICRM_ROOT/sql (note that the generated files are not present in the svn repository). The DAO files are stored under CIVICRM_ROOT/CRM/Core/DAO (and under appropriate directories based on what table it is, this is configured in the xml representation.