The first thing that needs to be said about protoctista is that they are eukaryotes, whereas bacteria are prokaryotes. Briefly, eukaryotic cells have a nucleus, while prokaryotic cells lack one. The important thing here is that although protoctista are commonly classified with bacteria and viruses as "microbes", they are actually much more like plants, animals and fungi, at the cellular level.
There are fundamental differences between eukaryotes and prokaryotes at the cellular level. Eukaryotic cells possess an extra level of complexity which prokaryotes lack: they contain specialised structures called organelles. Eukaryotic cells have a nucleus, where the DNA is stored in paired chromosomes. Prokaryotic cells lack a nucleus - their DNA is usually contained in a single circular chromosome.
Eukaryotes share anatomical similarities which make their information transfer pathways more complex as well as faster than those of prokaryotes. The processes whereby materials (e.g. nutrients) and information are diffused within a eukaryotic cell are more complex than those in a prokaryotic cell, simply because eukaryotic cells are so much bigger (Kaiser, 2001; Illingworth, 1999; Cotterill, 2001, p. 5). Because a prokaryotic cell is so small, it has a large surface-to-volume ratio, so nutrients can rapidly reach any part of the cell's interior. Eukaryotic cells, being much larger, have a smaller surface-to-volume ratio, so nutrients cannot rapidly spread to all internal parts of the cell. For this reason, eukaryotic cells require a variety of specialised structures to carry out metabolism, provide energy, and transport chemicals throughout the cell.
Additionally, all eukaryotes (protoctista, plants, fungi and animals) make use of rapid electrochemical signalling to transmit information, in addition to the slow process of chemical diffusion used by bacteria. Eukaryotic cells are much larger than bacterial cells, so they are able to detect tiny spatial concentration gradients from one side of the cell to another when searching for food, instead of relying on measurements taken at successive 3-second intervals as bacteria do. Unlike bacteria, eukaryotes know which way to swim, but they use larger motors and a different internal signalling system. For example, electrochemical signalling (resulting from the interaction of proteins with calcium ions and the energy-storing molecule ATP) enables protozoa to move around.
Because the processes of information transmission within eukaryotic and prokaryotic cells are so different, we have to consider the possibility that the division between organisms with mental states and those without, coincides with that between eukaryotes and prokaryotes.