22.2 Structure of Prokaryotes: Bacteria and Archaea

Prokaryotic Cell Structure and Components

Prokaryotes are the simplest cellular organisms, yet their structures are remarkably efficient. Understanding how bacteria and archaea are built helps explain why they dominate so many environments on Earth, and it also clarifies why certain antibiotics work against some microbes but not others.

Components of Prokaryotic Cells

Every prokaryotic cell has a few core components: a cell envelope, a nucleoid region, ribosomes, and sometimes inclusion bodies. Here's what each one does.

Cell Envelope

The cell envelope includes the plasma membrane and the cell wall together. It provides structural support, protection from the outside environment, and selective permeability (controlling what gets in and out).

Cell Wall

• A rigid structure surrounding the plasma membrane that maintains cell shape and protects against osmotic stress
• In bacteria, the wall is composed of peptidoglycan, a polymer made of sugars cross-linked by short amino acid chains
• Archaea have chemically different cell walls (more on this below)

Plasma Membrane

• A phospholipid bilayer with hydrophilic (water-loving) heads facing outward and hydrophobic (water-fearing) tails facing inward
• Acts as a selectively permeable barrier, controlling the passage of nutrients in and waste out
• Contains embedded proteins that handle transport, energy production (like ATP synthase), and signal transduction

Nucleoid

Prokaryotes don't have a membrane-bound nucleus. Instead, their genetic material sits in a region of the cytoplasm called the nucleoid.

• The DNA is circular and highly condensed, associated with DNA-binding proteins (HU proteins in bacteria, histones in archaea)
• Contains all the essential genes for cell function and replication
• Plasmids, small circular DNA molecules separate from the main chromosome, may also float in the cytoplasm. These often carry genes for antibiotic resistance or other survival advantages.

Ribosomes

• Carry out protein synthesis
• Prokaryotic ribosomes are 70S, smaller than eukaryotic ribosomes (80S). This size difference is why certain antibiotics can target bacterial ribosomes without harming human cells.

Inclusion Bodies

• Storage structures that hold reserve nutrients or metabolic products
• Examples: glycogen granules (energy storage), sulfur granules, and gas vesicles (buoyancy control in aquatic prokaryotes)

Cell Wall Comparisons in Microorganisms

The composition of the cell wall is one of the biggest structural differences between Gram-positive bacteria, Gram-negative bacteria, and archaea. The Gram stain is a lab technique that distinguishes bacteria based on these wall differences.

Gram-Positive Bacteria (e.g., Streptococcus, Staphylococcus)

• Thick cell wall with many layers of peptidoglycan (up to 90% of the wall)
• Contains teichoic acids, which add rigidity and play a role in immune recognition
• Retains the crystal violet dye during Gram staining, appearing purple under the microscope

Gram-Negative Bacteria (e.g., Escherichia coli, Salmonella)

• Thin peptidoglycan layer (only 10–20% of the wall)
• Has an outer membrane on top of the peptidoglycan that contains lipopolysaccharides (LPS). LPS can act as endotoxins, triggering strong immune responses in humans.
• A periplasmic space sits between the outer membrane and the plasma membrane, housing enzymes and transport proteins
• Does not retain crystal violet dye; stains pink/red with the counterstain (safranin)

Archaea (e.g., Methanococcus, Halobacterium)

• Cell wall composition varies widely among species
• Some have pseudopeptidoglycan (similar structure to peptidoglycan but with different chemical linkages)
• Others have an S-layer (a single layer of glycoproteins), and some lack a cell wall entirely (e.g., Thermoplasma)
• Because they lack true peptidoglycan, archaea are naturally resistant to antibiotics like penicillin and cephalosporins that target peptidoglycan synthesis

Prokaryotic Cytoskeleton and Membrane Structures

Prokaryotic Cytoskeleton

For a long time, scientists thought only eukaryotes had cytoskeletons. Prokaryotes actually have homologs of eukaryotic cytoskeletal proteins, including FtsZ (similar to tubulin, critical for cell division) and MreB (similar to actin, helps maintain cell shape).

Mesosomes

• Infoldings of the plasma membrane once thought to play roles in cell division and energy production
• Current evidence suggests mesosomes are likely artifacts of chemical fixation during sample preparation, not true structures in living cells. You may still see them mentioned in older sources.

Prokaryotic Reproduction and Genetic Exchange

Prokaryotes reproduce asexually, but they have several ways to exchange genetic material with other cells. This genetic exchange isn't reproduction; it's a way to increase genetic diversity without producing offspring.

Binary Fission

Binary fission is the primary method of prokaryotic reproduction. It produces two genetically identical daughter cells.

1. The circular chromosome attaches to the plasma membrane and replicates
2. The cell elongates, pulling the two copies of the chromosome apart
3. The plasma membrane and cell wall pinch inward at the center (septum formation)
4. The cell divides into two equal daughter cells

Under favorable conditions, this happens fast. E. coli can divide every 20 minutes, meaning a single cell could theoretically produce millions of descendants in just a few hours.

Horizontal Gene Transfer

Prokaryotes can acquire new genes from sources other than their parent cell through horizontal gene transfer (HGT). This is a major reason bacteria can adapt so quickly to antibiotics and new environments. There are three main mechanisms:

Transformation

• A cell takes up free-floating ("naked") DNA from the surrounding environment
• Only competent cells (those with the right surface proteins) can do this
• The incorporated DNA can be expressed and passed to daughter cells
• Example organisms: Streptococcus pneumoniae, Bacillus subtilis
• This process is also used in genetic engineering to introduce recombinant DNA into bacterial cells

Transduction

• A bacteriophage (virus that infects bacteria) accidentally packages bacterial DNA and transfers it to a new host cell
• Two types:
  • Generalized transduction: any piece of bacterial DNA can be packaged into the phage
  • Specialized transduction: only DNA adjacent to the phage's insertion site gets transferred
• A key mechanism for spreading antibiotic resistance genes between bacteria

Conjugation

• Direct cell-to-cell transfer of DNA through a structure called a pilus (also called an F pilus)
• Requires physical contact between a donor cell and a recipient cell
• Typically transfers plasmids, especially the F plasmid (fertility plasmid), though conjugative transposons can also move this way
• Allows antibiotic resistance and virulence factors to spread through bacterial populations