According to differences in their internal organization and functions, cells can be classified into broad taxonomic groups. A major division, founded on fundamental differences in cell architecture, distinguishes prokaryotes (which are always unicellular) and eukaryotes (which may be unicellular or multicellular; Figure 1).
Fig1. Classification of unicellular and multicellular organisms. The first two domains of life, bacteria and archaea, are also known as prokaryotes as they lack internal membranes. Eukaryotes, which form the third domain of life, have membrane-bound organelles. This domain is further subdivided into unicellular or multicellular fungi, plants, and animals. Unicellular eukaryotes are occasionally classified as protists, but the term protist is often used in a more limited sense to describe those unicellular eukaryotes that cannot easily be classified as animals, plants, or fungi.
Prokaryotes have a simple internal organization, with a single, membrane-bound compartment that is not usually subdivided by any internal membranes. Under the electron microscope, prokaryotic cells typically appear relatively featureless. (However, prokaryotes are far from primitive: they have been through many more generations of evolution than humans.)
Unlike in eukaryotes, the chromosomal DNA of prokaryotes is neither enclosed by a nuclear membrane nor highly structured; instead, it exists as a simple nucleoprotein complex, the nucleoid (see Figure 2). The typical prokaryote has a single, circular chromosome containing a few Mb of DNA (usually from 1 to 10 Mb), but there are exceptions: some prokaryotes have two or three circular chromosomes, and a few have a linear chromosome, or a mix of linear and circular chromosomes.
Fig2. Prokaryotic and eukaryotic cell anatomy. Prokaryotic cells are much smaller than eukaryotic cells and lack the internal organelles found in the latter. The eukaryotic cell shown at the top of this figure is a generic vertebrate cell.
Until quite recently, prokaryotes were simply considered to comprise diverse types of bacteria, but in 1977 phylogenetic studies by Carl Woese indicated that prokaryotes comprise two very different kingdoms or domains of life, as distinct from each other as they are from eukaryotes.
• Bacteria (formerly called eubacteria) are found in many environments. Some cause disease; others perform tasks that are useful or essential to human survival. Huge numbers of bacteria inhabit our bodies. Comprising about 500–1000 different species, the vast majority of such commensal bacteria live in the gut and many are beneficial, as explained below.
• Archaea (formerly called archaebacteria) are a poorly understood group of organ isms that superficially resemble bacteria. They are often found in extreme environments, and different groups survive in extremes of heat, salt, and acidity, for example. Other species are found in more convivial locations, such as in the guts of cows and on our skin.
The division of prokaryotes into bacteria and archaea was first suggested by phylogenetic taxonomy studies that compared 16S rRNA (the highly-conserved RNA of the small ribosomal subunit) in different prokaryotes. Supportive evidence came, however, from many other areas, such as in the structure of RNA polymerase (Figure 3A). Large scale protein comparisons have supported a comparatively close relationship between archaea and eukaryotes (Figure 3B).
Fig3. RNA polymerase structure and evolutionary relationships for the three domains of life. (A) RNA polymerase structure. Color coding identifies homologous subunits. Here, the archaeal RNA polymerase is closely related to the eukaryotic RNA polymerase and much more complex than the bacterial RNA polymerase. In the past, the greater complexity of eukaryotic RNA polymerases when compared to bacterial RNA polymerases was thought to reflect the greater complexity of transcriptional processes in eukaryotic cells. However, the close resemblance between archaeal and eukaryotic RNA polymerases points to a different explanation, while supporting generally close similarity in information processing systems in eukaryotes and archaea (see text). (B) A phylogenetic tree illustrating that eukaryotes arose by periodic horizontal gene transfers (HGT) from bacterial progenitors to a lineage of archaeal progenitor cells (green line). The node labeled FECA, the first eukaryote common ancestor, marks eukaryogenesis, the point at which eukaryotes originated and diverged from the lineage leading to present-day archaea (the key event was endosymbiosis of an α-proteobacterium). Prior to eukaryogenesis, various HGT events allowed transfer of genes from bacterial cells to the archaeal lineage leading to the FECA, which might have caused the archaeal ancestor to increase in complexity. LECA, last eukaryote common ancestor. (A, adapted from Werner F [2008] Trends Microbiol 16:247–250; PMID 18468900. With permission from Elsevier.)
Eukaryotes are thought to have first appeared more than 2.1 billion years ago. They have a much more complex organization than their prokaryote counterparts, with many internal membranes and membrane-bound organelles. The membranes surrounding and dividing the cell are selectively permeable, regulating transport of a variety of ions and small molecules into and out of the cell and between compartments.
All eukaryotes belong to a single domain of life, the eukarya, but comprise both unicellular organisms and multicellular fungi, plants, and animals. Eukaryotic cells are distinguished by having a nucleus (containing most of the cell’s DNA) plus many other organelles in the cytoplasm with diverse functions, including ribosomes, the protein synthesis factories. A eukaryotic cell differs from a prokaryotic cell, therefore, in having physical separation of transcription (within the nucleus) and translation (in the cytoplasm). Even the cytosol, the soluble portion of the cytoplasm, is highly organized. It has an internal scaffold of protein filaments, the cytoskeleton, that provides stability, generates the forces needed for movement and changes in cell shape, facilitates the intracellular transport of organelles, and allows communication between the cell and its environment.
