Both plants and animals provide protein in food. What we call "protein" is made up of many amino acids connected by bonds. An amino acid is is a molecule with the makeup being key to the type of amino acid it is.
Think of a carbon atom as a square. Bonded to the top side of the square, there is a hydrogen atom. Bound to the left is an amino group consisting of 2 hydrogen atoms and one nitrogen atom. To the right is an acid group consisting of carbon, oxygen and hydrogen. What is bonded to the bottom side of the square are side chains of different lengths and configurations. The shape and length of these chains are key to what type of amino acid it is.
Protein is made when these amino acids bond together, called polypeptides. After they join and because of the manner in which they connect, the group becomes three dimensional--a protein.
Digestion of protein occurs when this 3-D chain gets broken apart by acid and enzymes in the stomach. It is not completely broken down, but polypeptides and spare amino acids are here and there. From there, these move into the small intestine where they are further broken down by enzymes. Even if a couple or 3 amino acids stay chained together, they can still be absorbed by the small intestine. Remember these single amino acids are molecules, which are collections of atoms. Atoms are only seen with extremely strong microscopes, and molecules aren't much bigger. This makes the concept of the amino acids being absorbed more realistic.