Andrew is completely right - when "already" is used in a question, it has a slightly different connotation.
"Have you sent that email yet?" implies that they want you to send the email. You were supposed to have sent the email by now.
"Have you sent that email already?" makes the speaker sound a little shocked or surprised. It implies that they might have changed their mind about the email and they want to add something to it.
In general, when "yet" is used in a statement, it describes something that has not happened yet, but is expected to happen, or the speaker wishes that it will happen.
"I have not yet gone to Brazil."
This implies that the speaker will go to Brazil soon, or that they wish to go to Brazil in the future.
When it is used in a question, it is asking whether or not someone has done something - but implies that the person is expected to do it, or the person wants them to do it.
"Have you sent that email yet?"
This implies that the person was supposed to have sent the email, or the speaker wants the person to send the email.
Ashley and Andrew have already given great answers ;) I just wanted to elaborate