Bacterial Cell Diagram: Labeled 3D Model, Parts and Functions

A bacterial cell is a single prokaryotic cell with no nucleus and no membrane-bound organelles. Every bacterium has a plasma membrane, cytoplasm, ribosomes and DNA in a region called the nucleoid, and almost all have a cell wall made of peptidoglycan. Many also have a capsule, plasmids, storage granules, fimbriae, a sex pilus and one or more flagella.

This page uses Escherichia coli as the reference cell. It is a rod-shaped (bacillus), Gram-negative bacterium that lives in the gut of humans and other warm-blooded animals and is the standard organism of bacterial genetics. As a Gram-negative cell it has two membranes, an inner plasma membrane and an outer membrane, with a thin peptidoglycan wall in the gel-filled space between them, the periplasm. Where Gram-positive bacteria such as Staphylococcus or Bacillus differ, the text says so.

Bacteria are small. Most prokaryotic cells are 0.1–5 µm across, while typical plant and animal cells are 10–100 µm. Small size gives a large surface area for the volume, so nutrients and wastes can move in and out by diffusion fast enough to serve the whole cell. (OpenStax Biology 2e, 4.2 Prokaryotic cells.)

A labeled diagram of a bacterial cell shows, from the outside in: the capsule, the cell wall (in a Gram-negative cell the outer membrane, periplasm and peptidoglycan layer), the plasma membrane, and the cytoplasm with its nucleoid, plasmids, ribosomes and granules. Attached to the surface are fimbriae, a sex pilus and flagella, each flagellum with a hook and a basal body.

In the 3D model above, switch on All labels to see every part named at once, or click a part to zoom to it. The right-hand pole of the model shows the motor of one flagellum, with its rings set into each layer of the envelope.

Each part of a bacterial cell has one main job. The table lists every structure on a typical exam diagram, what it does, and whether all bacteria have it.

This is the text version of the 3D model: every labeled structure of the E. coli cell, grouped by region, with what it does. Use it as a study list or to check a bacterial cell labeling worksheet.

Bacterial cell walls come in two main types. A Gram-positive wall is a thick mesh of peptidoglycan, 30–100 nm and many layers deep, threaded with teichoic acids and lying directly on the plasma membrane. A Gram-negative wall is a peptidoglycan layer only a few nanometres thick, sitting in the periplasm under a second, outer membrane. (Silhavy, Kahne & Walker (2010): The bacterial cell envelope, Cold Spring Harbor Perspectives in Biology.)

Peptidoglycan, also called murein, is made of long sugar chains of alternating NAG (N-acetylglucosamine) and NAM (N-acetylmuramic acid), cross-linked by short peptides into one giant bag-shaped molecule around the cell. Teichoic acids can make up over 60% of the mass of a Gram-positive wall; wall teichoic acids are bonded to the peptidoglycan, and lipoteichoic acids are anchored in the membrane. (OpenStax Microbiology, 3.3 Unique characteristics of prokaryotic cells; Silhavy et al., 2010.)

How the Gram stain works. Crystal violet stains every cell purple; Gram's iodine locks it in as a crystal violet–iodine complex; alcohol or acetone then washes the dye out of cells with a thin wall but not from cells with a thick one; and the red counterstain safranin colors the cells that lost the purple. So Gram-positive cells end purple and Gram-negative cells end pink. Mycobacteria, such as the tuberculosis bacterium, are a third case: a waxy outer layer of mycolic acids makes them hard to Gram stain, so they are identified with an acid-fast stain instead. (OpenStax Microbiology, 2.4 Staining microscopic specimens.)

On a bacterial cell diagram, the endotoxin is found in the outer membrane of Gram-negative bacteria: it is lipid A, the fatty anchor of lipopolysaccharide (LPS) that forms the outer leaflet of that membrane. In the 3D model it is the thin dark-orange skin over the outer membrane; the green fuzz above it is the O antigen, and the short gold stalks between are the core oligosaccharide.

• Lipid A (endotoxin): Anchors LPS in the membrane and makes the outer membrane a strong barrier. It is the endotoxin of Gram-negative bacteria: the part that triggers fever and, in severe infections, septic shock.
• Core oligosaccharide: Links the membrane anchor (lipid A) to the O antigen and helps make the outer membrane a tight barrier.
• O antigen: Forms a hydrophilic (water-loving) coat over the cell. Its exact sugars differ between strains and are recognised by antibodies, so it is used to type strains.
• Porins: Let water, ions, sugars, amino acids and other small hydrophilic molecules diffuse through the outer membrane.

Endotoxins differ from exotoxins. An exotoxin is a protein that a living bacterium secretes, such as tetanus or cholera toxin, and it can come from Gram-positive or Gram-negative species. An endotoxin is a structural part of the Gram-negative wall and is released mostly when the cell dies or is broken apart. Gram-positive bacteria have no LPS and so no endotoxin. The research section below explains how lipid A triggers fever and septic shock.

The bacterial cell membrane (plasma membrane) is a phospholipid bilayer studded with proteins that wraps the cytoplasm. It controls what enters and leaves the cell, and because bacteria have no mitochondria, it also carries the respiratory chain and ATP synthase that make ATP. It anchors the flagellar motors, and it is where the cell builds new membrane and wall.

Small molecules cross it by simple diffusion, facilitated diffusion through channel and carrier proteins, active transport using ATP, or group translocation, in which the molecule is chemically changed as it crosses, as in the phosphotransferase system that brings in sugars. (OpenStax Microbiology, 3.3 Unique characteristics of prokaryotic cells.) To see how a membrane drives ATP synthesis, see the cellular respiration diagram.

Inside the membrane, the cytoplasm is a crowded gel of water, ions, enzymes, RNA and ribosomes. With no nucleus, transcription and translation happen side by side in the same space.

Inside a bacterial cell, the DNA is in the nucleoid, a region of cytoplasm with no membrane around it. It holds one circular chromosome. Extra genes may sit on small DNA rings called plasmids. Proteins are made on 70S ribosomes, and reserves are kept in inclusions (storage granules).

• Nucleoid (chromosome): Carries the cell's genes. The DNA is copied before the cell divides, and genes are transcribed into mRNA right in the cytoplasm.
• Plasmids: Carry extra genes that are useful but not essential, such as antibiotic resistance, toxins or the genes for a sex pilus. They copy themselves independently and can be passed to other cells.
• 70S ribosomes: Translate messenger RNA into proteins.
• Glycogen granules: A store of carbon and energy that the cell can break down when food runs short.
• Volutin granules: Store phosphate, and energy in its phosphate bonds, for making DNA, RNA, ATP and membranes.

Inclusions vary between species. Besides glycogen and volutin (polyphosphate), bacteria store polyhydroxybutyrate (PHB) in Bacillus and Pseudomonas and sulfur in Thiobacillus. Some water bacteria have gas vacuoles for buoyancy, magnetotactic bacteria carry chains of magnetic crystals (magnetosomes), and photosynthetic bacteria pack the CO₂-fixing enzyme RuBisCO into carboxysomes. (OpenStax Microbiology, 3.3 Unique characteristics of prokaryotic cells.)

Bacteria have three kinds of surface appendage. Flagella are long helical filaments turned by a motor and used for swimming. Fimbriae are many short, thin bristles used to stick to surfaces. The sex pilus (F pilus) is a single long tube used to pull another cell close for DNA transfer.

• Flagellum (filament): Rotates like a propeller to push the cell through liquid.
• Hook: Acts as a universal joint, passing the motor's rotation to the filament at an angle.
• Rod (drive shaft): Transmits torque from the rotor in the plasma membrane out to the hook.
• L ring: Acts as a bushing (bearing) that lets the rod spin through the outer membrane.
• P ring: A second bearing for the rotating rod.
• MS ring: The foundation of the motor; it turns with the rod and carries the C ring.
• C ring: Part of the rotor and the switch: when the signalling protein CheY-P binds, the motor flips from counter-clockwise to clockwise rotation.
• Stator units (MotA/MotB): The motor's engine: protons flowing into the cell through the stators (the proton motive force) push on the rotor and turn it.
• Fimbriae: Attach the bacterium to surfaces and to host cells, for example the lining of the urinary tract or gut.
• Sex pilus: Reaches out to a recipient cell, then retracts to pull the two cells together so a copy of a plasmid can pass between them (conjugation).

Flagella are arranged in four patterns: monotrichous (one at one pole), amphitrichous (one at each pole), lophotrichous (a tuft at one pole) and peritrichous (scattered all over the cell). E. coli is peritrichous, with about three or four flagella per cell. (OpenStax Microbiology, 3.3 Unique characteristics of prokaryotic cells; Turner, Ryu & Berg, 2000.)

In conjugation, a donor cell carrying the F plasmid extends its sex pilus to a recipient, the pilus retracts to draw the cells together, and a single strand of the plasmid is copied across. R plasmids carrying several antibiotic-resistance genes spread the same way, even between species, which is one reason resistance spreads so fast. (OpenStax Microbiology, 11.6 How asexual prokaryotes achieve genetic diversity.)

An endospore is a tough, dormant structure that some Gram-positive bacteria, notably Bacillus and Clostridium, form inside the cell when conditions turn bad. E. coli does not make endospores, which is why there is none in the model. Inside the spore is a dehydrated copy of the chromosome, wrapped in a double membrane, a thick cortex rich in calcium and dipicolinic acid, a protein coat and, in some species, an outer exosporium. Endospores survive heat, radiation, drying and many disinfectants, and germinate when conditions improve. (OpenStax Microbiology, 3.3 Unique characteristics of prokaryotic cells.)

Endospores do not take up the Gram stain and look like clear holes in a Gram-stained cell. The Schaeffer-Fulton stain drives green malachite green into them with heat, so spores show green inside pink cells. Diseases caused by spore-formers include anthrax (Bacillus anthracis), tetanus and botulism (Clostridium). (OpenStax Microbiology, 2.4 Staining microscopic specimens.)

Bacteria come in three basic shapes: round cocci, rod-shaped bacilli and spiral spirilla. In-between forms include the short, oval coccobacillus, the comma-shaped vibrio and the long, flexible spirochete. The cell wall, helped by internal cytoskeleton proteins, holds each shape. (OpenStax Microbiology, 3.3 Unique characteristics of prokaryotic cells.)

Cells that stay joined after dividing form typical arrangements: pairs (diplococci), chains (streptococci and streptobacilli), grape-like clusters (staphylococci) and squares of four (tetrads). The names of many bacteria come straight from this: Streptococcus grows in chains, Staphylococcus in clusters. A coccal bacterial cell has the same parts as the rod in the model, just packed into a sphere.

Bacteria are prokaryotic cells: they have no nucleus and no membrane-bound organelles, and their DNA is usually a single circular chromosome. Eukaryotic cells (animals, plants, fungi and protists) keep their linear chromosomes in a nucleus and divide their cytoplasm into organelles such as mitochondria and the endoplasmic reticulum.

The 70S ribosomes and bacterial-like DNA inside mitochondria and chloroplasts are key evidence that these organelles began as bacteria living inside an ancestral eukaryotic cell (the endosymbiotic theory). (OpenStax Microbiology, 3.4 Unique characteristics of eukaryotic cells.) Compare the double membrane of a chloroplast in our chloroplast structure model, and see eukaryotic single cells in the amoeba and Euglena diagrams.

Plant, animal and bacterial cells all have a cell membrane, cytoplasm, ribosomes and DNA. Plant and animal cells are eukaryotic and share a nucleus and mitochondria. Plant and bacterial cells both have a cell wall, but plant walls are cellulose and bacterial walls are peptidoglycan. Only bacterial cells lack a nucleus.

Sources for the plant and animal columns: OpenStax Biology 2e, which notes that animal cells each have a centrosome and lysosomes whereas most plant cells do not, and that plant cells have a cellulose wall, chloroplasts and a large central vacuole. (OpenStax Biology 2e, 4.3 Eukaryotic cells.)

Bacteria divide by binary fission: the cell copies its chromosome, grows longer, builds a wall across its middle and splits into two identical daughter cells. Under ideal laboratory conditions E. coli can divide every 20 minutes. (OpenStax Microbiology, 9.1 How microbes grow.)

1. Replication. Copying of the circular chromosome begins at a single site, the origin of replication, and runs both ways around the circle until the two forks meet at the terminus.
2. Segregation and growth. The cell lengthens and the two copies of the chromosome move apart, so each half of the cell gets one complete copy.
3. Z ring. The protein FtsZ assembles into a ring on the inside of the plasma membrane at mid-cell. It marks the plane of division and recruits other proteins to form the divisome.
4. Septum. The divisome builds new peptidoglycan and membrane inward, forming a cross-wall (septum) that pinches the cell in two.
5. Separation. Enzymes split the shared wall and two daughter cells of similar size separate, each with a copy of the parent's genome.

Binary fission is not mitosis. There is no nucleus to break down, no spindle and no condensed chromosomes. Each division doubles the population, which is why bacterial numbers rise exponentially when food is plentiful.

For a simple GCSE bacterial cell diagram, draw a rod or oval with a cell wall around a cell membrane, fill it with cytoplasm, and draw the DNA as one large loop lying free (no nucleus), one or two small plasmids, dots for ribosomes, and a tail-like flagellum. Label each part and state that a bacterial cell is prokaryotic and much smaller than a plant or animal cell.

• GCSE must-knows: cell membrane, cell wall, cytoplasm, chromosomal DNA as a single loop, plasmids, ribosomes, flagellum; no nucleus, no mitochondria, no chloroplasts. Most bacteria are a few micrometres long at most, about ten times or more smaller than a typical plant or animal cell.
• A-level additions: 70S ribosomes (vs 80S), a murein (peptidoglycan) cell wall, capsule, pili and plasmids; binary fission; the Gram-positive vs Gram-negative wall and its link to antibiotic action.
• Common mistakes: drawing a nucleus; calling the cell wall cellulose; drawing mitochondria; giving ribosomes a membrane; drawing the DNA as several linear chromosomes.
• Mesosomes: some older textbooks show folds of the membrane called mesosomes. They turned out to be artefacts of preparing cells for the electron microscope, so most courses no longer include them.

Bacteria are not viruses. A virus has no cytoplasm, ribosomes or cell membrane and cannot reproduce on its own. Compare the two in our virus structure diagram.

A bacterial flagellum does not wave like a whip. It spins. At its base is a rotary motor of about 25 different proteins that spans the whole cell envelope. A shaft called the rod runs through the middle; the MS ring in the plasma membrane and the C ring below it form the rotor; the L ring in the outer membrane and the P ring in the peptidoglycan act as bushings; and a ring of stator units, each made of the proteins MotA and MotB, sits around the rotor and drives it. About 12 stators fit around the E. coli motor. (Guo & Liu (2022): The bacterial flagellar motor, Frontiers in Microbiology.)

The energy comes from protons, not ATP. The cell pumps protons out across its plasma membrane, and as they flow back in through the stator channels they push on the rotor. Rotation rates are on the order of 100 revolutions per second, which drives filaments about 20 nm thick and several micrometres long. (Turner, Ryu & Berg (2000): Real-time imaging of fluorescent flagellar filaments, Journal of Bacteriology.)

E. coli steers by switching the motor's direction. When the motors turn counter-clockwise, the left-handed filaments wrap into one bundle behind the cell and it swims straight, a 'run' that lasts about a second. When one or more motors reverse to clockwise, the bundle flies apart for about a tenth of a second, the cell 'tumbles', and it sets off in a new random direction. Filming fluorescently labelled filaments showed that a change in just one filament can cause a tumble. (Turner, Ryu & Berg (2000): Real-time imaging of fluorescent flagellar filaments, Journal of Bacteriology.)

By making runs longer when it moves towards food and shorter when it moves away, the cell drifts up a nutrient gradient. This is chemotaxis. The signal reaches the motor through the protein CheY: when it is phosphorylated (CheY-P), it binds the C ring and flips the motor to clockwise. (Guo & Liu (2022): The bacterial flagellar motor, Frontiers in Microbiology.)

The endotoxin of a Gram-negative bacterium is not a secreted poison; it is part of the cell wall. Lipopolysaccharide (LPS) has three regions: lipid A, a hydrophobic anchor that forms the outer leaflet of the outer membrane; a non-repeating core oligosaccharide; and the long O-antigen polysaccharide on the outside. Lipid A is the part that carries the endotoxin activity. An E. coli cell carries about a million lipid A molecules. (Raetz & Whitfield (2002): Lipopolysaccharide endotoxins, Annual Review of Biochemistry.)

Our innate immune system detects lipid A through the receptor TLR4 and its helper protein MD2. A small amount of LPS is a useful alarm that switches on defences. Released in large amounts in the bloodstream in severe sepsis, it can drive the over-production of inflammatory mediators and clotting factors that leads to Gram-negative septic shock. Synthetic E. coli lipid A on its own reproduces these effects in animals, which is how scientists know lipid A is the active part. (Raetz & Whitfield (2002): Lipopolysaccharide endotoxins, Annual Review of Biochemistry.)

LPS also explains why the outer membrane is such a good barrier. The outer membrane is a lipid bilayer, but not a phospholipid bilayer: phospholipids are confined to its inner leaflet, while the outer leaflet is mostly LPS. Hydrophilic molecules can only cross through porins such as OmpF and OmpC, which let through molecules smaller than about 700 daltons. That is one reason many antibiotics that work on Gram-positive bacteria fail against Gram-negative ones. (Silhavy, Kahne & Walker (2010): The bacterial cell envelope, Cold Spring Harbor Perspectives in Biology.)

A useful rule of thumb is that an E. coli cell is about 1 µm across and 2 µm long, with a volume of about 1 µm³ (one femtolitre) and a mass of about 1 picogram. Treating the cell as a cylinder with rounded ends gives a slightly larger volume, about 1.3 µm³. Cells that grow faster are bigger: dry mass ranges from about 148 fg in cells that divide every 100 minutes to 865 fg in cells that divide every 24 minutes. (Milo & Phillips, Cell Biology by the Numbers: How big is an E. coli cell and what is its mass?.)

Ribosome numbers rise steeply with growth rate, because a fast-growing cell needs to make protein quickly. Measurements on E. coli B/r at 37 °C give about 6,800 ribosomes per cell at a 100-minute doubling time and about 72,000 at a 24-minute doubling time. The 3D model above shows only about 300, enlarged, on the cut faces of the cytoplasm. (BioNumbers 101441: ribosomes per E. coli cell at different growth rates (Bremer & Dennis).)

The chromosome of the standard laboratory strain, E. coli K-12, is 4,639,221 base pairs long and codes for 4,288 annotated proteins. At about 0.34 nm per base pair, that DNA would stretch to about 1.6 mm, roughly 800 times the length of the cell, which is why it must be folded into the compact nucleoid. (Blattner et al. (1997): The complete genome sequence of Escherichia coli K-12, Science (Europe PMC).)

E. coli is also the host of the best-studied bacterial viruses. See how one injects its DNA through the envelope in our bacteriophage T4 diagram.

Test yourself with this blank bacterial cell diagram. Write the name of each of the 16 numbered parts, then open the answer key. For a quick quiz, turn off the labels in the 3D model, click parts at random and name them before you read the panel.

Short-answer questions:

1. Name four structures found in every bacterial cell. (Plasma membrane, cytoplasm, ribosomes, DNA/nucleoid.)
2. What are the two subunits of a bacterial ribosome? (30S and 50S, making a 70S ribosome.)
3. Which layer of a Gram-negative cell contains the endotoxin? (The outer membrane: lipid A of LPS.)
4. Why do Gram-positive cells stay purple in a Gram stain? (Their thick peptidoglycan keeps the crystal violet–iodine complex.)
5. What is the difference between a fimbria and a sex pilus? (Fimbriae attach; the sex pilus joins cells for DNA transfer.)
6. Name the protein that forms the ring at the division site. (FtsZ.)