First you need to have installed the "pdftk" application.
Then type this command into the terminal:
pdftk original.pdf output new.pdf user_pw PROMPT
Replace "Original.pdf" with the original name and change "new.pdf" to a name of your choice. Enter a password when prompted. You will now have a password protected PDF.
Then type this command into the terminal:
pdftk original.pdf output new.pdf user_pw PROMPT
Replace "Original.pdf" with the original name and change "new.pdf" to a name of your choice. Enter a password when prompted. You will now have a password protected PDF.