Their membrane proteins are made not by the ER, but by free ribosomes in the cytosol and by ribosomes contained within the mitochondria and chloroplasts themselves. Not only do these organelles have ribosomes, but they also contain a small amount of DNA. It is this DNA that programs the synthesis of the proteins made on the organelle's own ribosomes. Mitochondria because it's a separate bateria that somehow merged with the cell's in a mutualistic form. All lifeform have it's own DNA in order to reproduce. Mitochondria and chloroplasts are enclosed by membranes, thery are not part of the endomembrane system.