Question

Which molecules are distinctively different in Bacteria and Archaea?

Answer 1

There's a big difference between Bacteria and Archaea: peptidoglycan.

Bacteria have a thick cell wall made of a special molecule called "peptidoglycan."
This peptidoglycan is made of carbohydrates and amino acids.

Organisms under Archaea don't have peptidoglycan in their cell walls.

Answer 2

the different cell wall stucture is because archaea live in some harsh conditions like extreme salty areas,hot springs,and marshy areas,so they have more stucturally stable cell wall.