What are the three major differences between the protists and bacteria? Solution 1. Bacteria are prokaryotic while, protists are eukaryotes. 2. Bacteria belong to miner kingdom whereas, protists belong to protista kingdom. 3. Since nuclear envelope is absent in bacteria, transcription and translation are coupled I.e, occurs in a single compartment. Whereas, in protista, transcription occurs in separate compartments. 4. Cytoskeleton is absent in bacteria. Present in protists..