Section 271D of Income Tax Act 1961 provides that if a loan or deposit or specified sum is accepted in contravention of the provisions of section 269SS then a penalty equivalent to the amount of such loan or deposit or specified sum may be levied by the Joint commissioner.

Section 269T of Income Tax Act, 1961

Section 271E of Income Tax Act 1961 provides that if a person repays any loan or deposit or specified advance referred to in section 269T otherwise than in accordance with the provisions of that section, he shall be liable to pay, by way of penalty, a sum equal to the amount of the loan or deposit or specified advance so repaid. Any penalty imposable under sub-section (1) shall be imposed by the Joint Commissioner.

3)no penalty is leviable if you are able to show it was bonafide transaction with no intention to evade tax 

Other 2 cash deposits would also come under section 269 T and section 269 SS and penalty would be imposed 

You have given the details of cash deposit  and the certain provision of law, but where is your query.

What do you want to clarify?

Section 269SS and 269T of Income Tax Act,1961 been explained in the Article. Section 269SS and 269T deals with restrictions on taking Cash Loan of Rs. 20000 of more than and its repayment in cash..

Provided further that the provisions of this section shall not apply to any loan or deposit or specified sum, where the person from whom the loan or deposit or specified sum is taken or accepted and the person by whom the loan or deposit or specified sum is taken or accepted, are both having agricultural income and neither of them has any income chargeable to tax under this Act

No branch of a banking company or a co-operative bank and no other company or co-operative society and no firm or other person shall repay any loan or deposit made with it or any specified advance received by it otherwise than by an account payee cheque or account payee bank draft drawn in the name of the person who has made the loan or deposit or paid the specified advance, or by use of electronic clearing system through a bank account

Any payments or repayments made pursuant to current account maintained between parties cannot be considered as violation of 269SS and 269T CIT V. Idhayam Publications Ltd., (2006) 285 ITR 221 (Mad)

Provisions of section 269SS and 269T are not applicable in case where there are journal entries and payment was ultimately paid through account payee cheque. Commissioner Of Income-Tax vs Noida Toll Bridge Co. Ltd. (2003) 184 CTR Del 266.

Whether when transactions are bonafide, disclosed in the books of accounts and even made in cash, attracts penalty u/s 271E/271D

You need to opt for the above measure only

You should open Fresh capital gain account to avail the benefits of capital gain extemption.