Grammar of 'be/have/do'

Dear all,
May I know how to decide when to use be/have/do in a sentence? I am very confused about them.

e.g. It is not raining. - Why not 'It have not' / "It does not'?

e.g. Butter is made from milk. - Why not 'Butter has made' / 'Butter does made'?

e.g. Tom has lost his passport. - Why not 'Tom was lost' / 'Tom did lost'?

e.g. Chris does not go out very often. - Why not 'Chris is not' / 'Chris has not'?

e.g. I am never invited to parties. - Why not 'I have never' / 'I do never'?

e.g. Why did you go home early? - Why not 'Why are you'?

Please help! Thank you so much!