Molecules are particles made up of two or more atoms bonded, or joined, together. Based on the definitions above, is an atom while
is a molecule.
Oglucose; carbon
carbon; glucose
water; HCI
HCl; water

The cell membranes controls what goes in and out by having protein channels that perform their role accordingly sometimes like funnels and like a pump in different cases.

When a channel open in the plasma membrane it allows molecule to pass through, in this case there is no requirement for energy so it is a passive transport.

Gases and food particles broke down in water must be assimilated and waste or harmful substance and molecules must be remove. For most cells, this type of selective transport of all materials all through the cell must happen through the plasma membrane.