Each application on the card will have different Application life cycles. Most of the applications will have a personalization phase and an operational phase. Application-specific keys and application data are stored during the personalization phase (the card is with the issuer). During the operational phase ( card with the customer) both the terminal and a card will have a known key for authentication in case of a symmetric key. Usually, Secret keys are not exchanged during the operational phase.
In general terminal and card initiate communication using supported protocol.. for example in ISO14443 card, either Type A or Type B is usually used for a handshake and send further application specific commands.