When is the prayer considered *adāʾ* (performed within its time): upon rising from the bowing (*rukūʿ*), or after rising from the prostration (*sujūd*)?
All praise is due to Allah, and peace and blessings be upon our master, the Messenger of Allah.
Whoever catches one complete rakʿah within the prayer's time has caught the prayer as an on-time (adāʾ) prayer. The rakʿah is complete when the worshipper raises his head from the second prostration (sajdah), even if he has not yet reached the degree of standing in which the recitation is valid.
It is stated in Nihāyat al-Muḥtāj (Vol.1/p.378): "What is meant by the rakʿah is the completion of all of it, with its two prostrations." End quote.
And in Ḥāshiyat al-Shabrāmallisī: "(His saying: 'a rakʿah') means that he raises his head from the second prostration, even if he has not reached the degree in which the recitation is valid." And Allah Almighty knows best.
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Note on terminology: Adāʾ refers to performing the prayer within its prescribed time, as opposed to qaḍāʾ (making it up after its time has ended).
What is the ruling on istinja' after urination, and is it done with water and soap or with water only?
Istinja' from urine and stool is obligatory. It is permissible to perform istinja' with water alone, or with toilet paper alone. The best way is with toilet paper then water. If one wishes to suffice with one of them, then water is better. And Allah the Almighty knows best.
Is it permissible to give Zakah (obligatory charity) to one`s poor sister, or brother?
It is permissible for one to give the Zakah to his poor sister, or brother if providing for them isn`t due on him, and the sister doesn`t receive sufficient provision from whomever that is due on. And Allah Knows Best.
Is the father a Mahram (Non-marriageable) to his son`s mother-in-law?
The father is a non-Mahram (Marriageable) to his son`s mother-in-law, so it is impermissible for them to look at each other, or to have a seclusion (Khalwah).