How to program an Arduino pro mini using native serial port (on my mainboard)
To upload a hex file to Arduino over Serial interface, the bootloader must be active. The bootloader is active after reset. It waits a short time if a new application is uploaded. If not, it jumps to existing application.

To reset the MCU on Arduino boards with independent USB chip a circuit connected to DTR line of serial is used.

On a board like the Pro Mini there is no chip for USB neither an auto reset circuit. You must reset the board with the reset button right before avrdude sends the hex file. avrdude tries ten times, so you have 10 chances to time it right after you hit the Upload button. 

Some USB-to-TTL-Serial adapters (or RS232 adapters) have the DTR line and it can be used to reset the board.

Or use ISP flashing over the ICSP header with a programmer or other board as programmer.