How much is standard deduction? shall it be deducted from gross salary at the beginning?

SD Rs. 40000/- (or below if salary lesser amount).

Yes.

Yes, You can claim full amount of Ts. 40,000/- as SD u/s. 16(ia) of IT act.

Standard deduction is essentially a flat amount subtracted from the salary income before calculation of taxable income. 

in case,You Can Claim 40000 Standard Deduction

An individual who is resident in India and whose total income does not exceed Rs. 3,50,000 is entitled to claim rebate under section 87A. Rebate under section 87A is available in the form of deduction from the tax liability. Rebate under section 87Awill be lower of 100% of income-tax liability or Rs. 2,500.

After considering SD & tax rebate u/s. 87A .... Nil