Prokaryotes and Their Structure

General Features

Nucleoid Region

The most defining feature of a prokaryotic cell is its lack of a nucleus. Instead, prokaryotic DNA floats around in the cell in a specialized region called the nucleoid region.

Circular DNA

If we looked closer at the DNA present there we would notice another striking difference between prokaryotes and eukaryotes. Prokaryotic DNA is comprised of a single circular double-stranded DNA molecule.


Outside of the nucleoid region, we would also find small sets of circular DNA called plasmids. These plasmids aren’t required for prokaryotes to survive but often contain virulence factors that increase a bacteria’s ability to thrive. Often these virulence factors confer antibiotic resistance, produce toxins, or evade the host immune system which increases a bacteria’s overall fitness.

Smaller Ribosomes

In addition to lacking a nucleus prokaryotic cells also lack membrane-bound organelles. They still contain ribosomes which allow bacteria to produce a wide variety of different proteins. However, these ribosomes are smaller than those found in eukaryotes. Here the large subunit is 50s and the small subunit is 30s for an overall sedimentation of 70s.

Cell Membrane + Cell Wall = Envelope

Last but not least the cell membrane is different in prokaryotes. In addition to a lipid bilayer, prokaryotes also have a cell wall and collectively the cell wall and cell membrane are called the envelope.

The cell wall creates an additional compartment separating the inner cytoplasm from the environment. This creates an additional protective barrier for the cell and gives the cell greater control over the molecules it brings in from the external environment. Lastly and importantly the cell membrane is the site of the prokaryotic electron transport chain. Here the space between the membranes allows for the generation of an H+ gradient that will power ATP synthase.


Additionally, some bacteria possess flagella which allow them to move around in their environments. While eukaryotes also possess flagella the two structures are significantly different from one another. In the eukaryote the flagella is composed of a collection of microtubules that wave back and forth.

In contrast the prokaryotic flagella is composed of flagellin and spins in a circle. Structurally the prokaryotic has three major components: the filament, hook, and basal body.

Now that we have explored the general features of prokaryotes let’s look at their subclassifications: archaea and bacteria.


Archaea are visually similar to bacteria but possess functions only found in eukaryotes. While they lack a nucleus their DNA interacts with histones that are absent in all bacteria. Furthermore, they share some of the same metabolic pathways as eukaryotic cells.

Despite these similarities, one of the biggest differences that distinguish archaea from both bacteria and eukaryotes is their ability to live in extreme environments. As extremophiles, they can be found in volcanic vents and extremely acid hot springs. There they live off inorganic compounds such as sulfur or nitrogen-based compounds. It is rare to see this content come up on the MCAT, but if it does you should only need a broad understanding or passage-based information to answer the question correctly.


Bacteria encompasses a diverse set of unicellular organisms. All of them have the basic prokaryotic features: nucleoid region, 70s ribosomes, and cell membrane + cell wall with some bacteria having flagella. Since bacteria are of interest in medicine the MCAT expects us to know more about them than archaea.

We will begin by exploring three different ways of classifying bacteria and why each is important.


The most salient classification of bacteria is by shape. Bacteria are sorted into three large categories: spherical, rod-shaped, and spiral. Spherical bacteria are called cocci after the Latin word for berry since colonies of cocci tend to form colonies that look like a cluster of berries. Rod-shaped bacteria are called bacilli after the Latin name for stick and spiral-shaped bacteria are called spirilli for the Latin word coil which was pretty predictable.

Cell Wall

Bacteria also possess two different types of cell walls with different thicknesses and different compositions. The naming convention used for these two classifications are gram-positive and gram-negative and refer to what happens when they undergo Gram staining.

Gram Positive

Gram-positive bacteria contain a thick peptidoglycan layer with lipoteichoic acid running throughout. As the name suggests peptidoglycan is a polymer of amino acids (peptido) and sugars (glycan). The thick peptidoglycan layer provides substantial physical and chemical protection to the bacteria. However, both molecules are also foreign to eukaryotic organisms and serve as antigens that our immune systems can respond to.

The peptidoglycan layer also absorbs violet dye during the Gram staining process causing Gram-positive bacteria to appear bright purple under light microscopy.

Gram Negative

Gram-negative bacteria lack the thick peptidoglycan layer found in Gram-positive bacteria as a result they uptake violet dye poorly during Gram-staining and appear bright pink under light microscopy.

Instead, the cell wall of a gram-negative bacteria is comprised of a very thin peptidoglycan layer followed by an additional lipid bilayer composed of phospholipids and lipopolysaccharides. Since eukaryotic cells lack lipopolysaccharides found on the outer membrane of Gram-negative bacteria these also trigger an immune response.


The last way of characterizing a bacteria is by its metabolism. Specifically a bacteria’s ability to use oxygen. In this way bacteria are grouped into aerobes that can utilize oxygen and anaerobes that are unable to use oxygen.

From here the groups are further divided into obligate aerobes that must have oxygen to survive and obligate anaerobes that are killed by oxygen. Additionally there are aerotolerant anaerobes who can’t use oxygen but aren’t killed by it either and lasty facultative anaerobes that prefer oxygen but can survive without it too.

You might be wondering why does oxygen kill some bacteria but not others? During metabolism oxygen readily forms reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) or the free radical superoxide (O2). These well, react with important proteins and biological molecules causing widespread damage to the cell. Aerobic bacteria and eukaryotic cells have antioxidants that preferentially react with these ROS neutralizing them before they can damage the cell.