2.1 Membrane Atlas of Bacterial and Archaeal Cell Structure Home
Source: Lam Nguyen


Phospholipids have a hydrophilic head (colored here) and hydrophobic tails (grey); in water they spontaneously pack side-by-side and tail-to-tail to shield their tails from unfavorable interactions with water. This results in closed double-layered bags: membranes. One key difference between archaea and bacteria (and with them, eukaryotes) is the kind of lipid in their membranes. Hybrid membranes containing both these lipid types can be made artificially, and it is possible that the last universal common ancestor of all cells on Earth contained both types, with specialization occurring later.

Membranes also contain many proteins. Some have hydrophobic regions that embed them into the lipid bilayer. Other proteins are fused, or tethered, to the lipids. In fact, cells’ “lipid” membranes are made up of roughly equal parts phospholipids and proteins.

Source: Sobti et al. (2016) Structure: PDB 5T4O

ATP Synthase

Cells take advantage of the phospholipid bilayer’s impermeability to charged molecules to establish an ion gradient across the membrane, using a chain of electron-carrying proteins in the membrane to pump protons out of the cell. Protein complexes in the membrane called ATP synthases, like this one from Escherichia coli [20], use the resulting ion potential to generate energy. The portion of the complex in the membrane provides a conduit for protons to flow down their potential, producing a “proton-motive force” that spins the rotor, generating energy that is chemically stored in Adenosine Triphosphate (ATP), the energetic currency of the cell. (You can watch an animation illustrating this process on YouTube.)

For this reason, we say that the membrane is “energized.” Holes in the membrane allow the ion gradient to equilibrate, destroying the cell’s means of generating energy, and thus its life.


Most of the metabolic work of the cell is performed by proteins. The translation of messenger RNA into new proteins, however, is performed by a hybrid complex containing both proteins and RNA molecules. (You can watch an animation illustrating the process on YouTube.) This ribosome from Escherichia coli contains ~50 different protein molecules (shown in cyan) and 3 RNA molecules (in grey) [21]. Electrons interact more strongly with RNA than with protein, making ribosomes stand out darker than surrounding proteins in cryo-EM images. You will also notice their abundance; each cell employs up to tens of thousands of ribosomes to churn out its protein workforce.


The fundamental unit of life is the cell–a contained self-replicating assembly. For many species, including all bacteria and archaea, the organism consists of a single cell. And for nearly all species, no matter how many cells an organism eventually contains (probably around 10 trillion in your case), it started life as a single cell (an egg, in your case). The details vary, but every cell on Earth is the same at heart–a DNA-based replicating machine built from just four macromolecules: nucleic acids, proteins, lipids and carbohydrates. In the environment, molecules interact rarely and randomly. Bringing them together enables the reproducible reactions required for life. So no matter what the first self-replicating molecules were (likely ribonucleic acid, or RNA), they were not a cell until they acquired a container.

How would you build a container for a cell? You would probably want a porous material that allowed you to sort specific molecules from the environment. Evolution agrees. All cells are enclosed by a selectively permeable membrane, made of phospholipids and proteins (Learn More ⇩), that allows them to separate their contents from the environment. The chemical properties of phospholipids make membranes impermeable to ions and large or hydrophilic molecules (but not to water). This property is a critical feature for the life of the cell (⇩).

With a membrane, your cell now has a clearly delineated exterior and interior. The interior is called the cytoplasm (“cell substance,” from the Latin for something molded, in this case by the membrane). Almost all archaea and many bacteria, like these Mycoplasma genitalium cells, are monoderms (“single skin”). This means that their cytoplasm is enclosed by a single membrane. At this resolution, the membrane looks like a single dark line, but remember that it is really a bilayer, as you will be able to see in some later examples. The cytoplasm contains the many macromolecules that carry out the various functions of the cell’s metabolism. The most prominent are the ribosomes, which produce new proteins (⇩).

Other structures you see in this cell function in motility and will be explained in Chapter 6. Remember that tomograms show cells in their entirety, so the example we choose to illustrate one feature will likely highlight others as well. For now, focus on the feature being discussed. Later, when you have learned about other features, you may want to use the Feature Index to find additional examples of them. To help orient you, feature labels in movies are color-coded according to the chapter in which they are discussed. Chapter colors appear in the Navigation Menu (top left).

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