I am new to blockchain technology let alone hyperledger fabric. But as far as I understand all the nodes or peers of other organizations are involved while application / user requests for update transaction. And if all the nodes of network agrees to the proposal, leger gets updated.
And I coudnt find when the nodes of organisations agreed to update transactions?
Am I getting it all wrong?
I would recommend you read the Fabric Key Concepts topics, you could start with the Peers topic.
In a nutshell, you can define the endorsement policy for any smart contract which defines which organization's peers must execute the transaction and agree on the results before it gets validated and committed to a blockchain channel.