Prokaryotic cell structure

Prokaryotic cell structure

Prokaryotes are single-celled organisms that are the earliest and most primitive forms of life on earth. The prokaryotic cell structure differs from the eukaryotic cell structure. Prokaryotes can be introduced as the initiative lives on earth. By studying the prokaryotic cell structure, we can get an idea of the origin of past life According to the Carl Woese classification; prokaryotes include Bacteria and Archaea. Some prokaryotes are photosynthetic organisms and are capable of photosynthesis.

All prokaryotic cells are covered by a cell wall. Many also have a capsule or slime layer. Prokaryotes often have appendages on their surface. They have Flagella and pili which are used for motion, Fimbriae help the cell to stick on a surface, Sex pili are used for DNA exchange. 

Typical Prokaryotic cell​

Prokaryotic cell structure
The photo credit goes to - Ali Zifan / CC BY-SA (

The basis of Carl Woese classification of living organisms

An American biologist called Carl Woese proposed three system for the classification of living organisms. Any classification system will use characteristics of organisms that can be compared with other organisms. A characteristic which is present only in some organisms would not be a suitable characteristic that can be used in a classification system. Instead a characteristics present in all the organisms will be ideal for comparison. The sequence of DNA or the gene responsible for the sysnthesis of ribosomal RNA (r-RNA) is present in all organisms (Because all organisms have ribosomes). The function of the ribosomes is the same function in all organisms that means the gene has not changed a lot during the course of evolution.

However there are some differences in the sequence of base pairs in the r-RNA genes different organisms. Carl Woese compared the r-RNA gene sequence of organisms and found that there are three main group of organims based on the r-RNA sequence. 

Relationship between three domain and six kingdom system

Prokaryotic cell structure

Bacterial cell size, shape and cell arrangements

Most bacteria range from 0.2-2.0 µm in diameter and from 2-8 µm in length. There are three basis shapes of bacteria.

  1. Spherical or ovoid in morphology is called a coccus (Plural – cocci)
  2. A cylindrically shaped cell is called a rod or a bacillus (Plural – bacilli)
  3. Spiral

They can be divided again according to their cell structure.

Cocci – They are usually round but can be oval or elongated.

  • Monococcus – They are also called micrococcus and represented by single.

Ex – Micrococcus flavus

  • Diplococci – Cocci that remain in pairs after dividing.

Ex Diplococcus pneumoniae

  • Streptococci – Those that divided and remain attached in chain like patterns.

Ex Streptoccus pneumoniase

  • Tetracocci – Those that remain in groups of four.
  • Sarcina – Those remain in attached in cube like groups of eight.

Ex Sarcina lutea

  • Staphylococcus – Those that form grapelike clusters of broad sheets.

Ex Staphylococcus aureus

Bacilli – Often forms long twisted chains of cells.

  • Single bacillus – Most bacilli appear as single rods.
  • Diplobacilli – Appear in pairs after division.
  • Streptobacilli – Those occur in chains.
  • Coccobacilli – Those who are oval and look so much like cocci.

Spiral – They are never straight and they have one or more twists.

  • Vibrio – Those that like curved rods.
  • Spirilla – They have helical shape and fairly rigid bodies.
  • Spirochete – They have helical and flexible bodies.
Prokaryotic cell structure

Bacterial Cell Wall

Bacterial cells have cell walls. The shape of the bacterial cell is determined by the cell wall. The bacterial cell wall structure is unique in the biosphere. Although bacterial cell walls are not present in other organisms. One example is peptidoglycan. It is a polymer of N-Acetyl glucosamine, N-Acetyl muramic acid and some amino acids. This compound has a shape of a three – dimensional network.

The peptidoglycan network has chains composed of N-Acetyl muramic acid and N-Acetyl glucosamine molecules present one after the other as a chain. There are many rows of these chains and it is called the backbone of the polymer. Each of these chains has side chains which are composed of amino acids. The side chains of one backbone chain are linked with the side chains of the next backbone chain cross links. In this manner the peptidoglycan polymer is arranged as a rigid 3D structure with some spaces within it.

Relationship of Cell Wall Structure to the Gram Stain

Some bacterial cells have peptidoglycan about 80% – 90% of their volume of the cell wall volume. Other bacteria have peptidoglycan only about 10% of their cell wall volume. Because of this difference in the peptidoglycan content these two types of bacteria stain differentially during the Gram’s staining procedure.

As the Gram’s staining helps to differentiate between two types of cell walls of bacteria it can be called as differential staining. The basis of this is the amount of peptidoglycan within the cell wall. In Gram’s staining on a glass side. The dye (Crystal violet) has to be left there for a few minutes, until it moves into the cell wall. Then iodine is added and is left until iodine make a complex with crystal violet. The large crystal violet + iodine complex molecules will be trapped within peptidoglycan network. The next step is an attempt to decolorize the cell wall. As Gram negative cell walls do not have a lot of peptidoglycan, they get decolorized easily, within 30 seconds or so.

Gram positive cells will retain the crystal violet + iodine color because those molecules are trapped with peptidoglycan. Ethanol can shrink the peptidoglycan network to a certain extent. After the decolorization step Gram negative cells become colorless and Gram-positive cells retain the dark purple color of Crystal violet + iodine complex. Using a light colored safranine cannot change the color of Gram-positive cells but it color rises the Gram negative cells with pink color.

The back bone of the peptidoglycan network is known as glycan. The side chains are composed of amino acids and therefore the side chains are called peptide side chains.

Peptidoglycan = Peptide + Glycan

Most proteins in living organism are composed of L amino acids. However, peptide chains of peptidoglycan have D amino acids in addition to L amino acids. Some bacteria have Diaminopimelic acid (DAP). The cross links between peptide chains make differ from bacteria to bacteria. Usually in Gram-negative cells an amino acid of the peptide side chain joins with the next peptide side chain directly with the peptide bond.

In Gram-positive bacteria the cross link between peptide side chains can be a peptide bridge with the chain of amino acids.

The above diagrams are only examples of the composition of peptidoglycan. They vary from bacteria to bacteria. Although, the backbone structure is the same. The differences are in the sidechains and cross links.

Gram-positive cell wall

Gram-positive bacteria usually have another compound known as Teichoic acid. These molecules found within the peptidoglycan structure. Some teichoic acids molecules are linked with the lipids of cell membrane. These ae known as lipo-teichoic acid. In addition to teichoic acids and peptidoglycans the Gram-positive cell wall can have proteins and lipids within the cell wall. There can be upto 25 layers of peptidoglycan in a Gram-positive cell. And it can tolerate even about 1 atm pressure.  Penicillin group of antibiotics inhibit the synthesis of peptidoglycan. Therefore, new cells will not develop a proper cell wall and therefore, they cannot withstand the pressure caused by intake of water into cell. Under the atmospheric pressure these cells burst and die.

Teichoic acids are composed of the following components.

  • Sugar alcohols such as glycerol or ribitol
  • Phosphate groups connected to sugar alcohols
  • Sugar like glucose
  • D-Alanine

Molecules composed of these compounds are linked together with phosphate ester bonds. Because of the presence of phosphate groups teichoic acids are negatively charged. Because of the presence of the presence of teichoic acids Gram-positive cell walls has negative charges. So, these cell walls can bind positively charged ions such as Ca2+ and Mg2+ and H helps the bacteria to take these ions into the cells.

Gram-negative cell wall

Gram-negative cell walls have only about 10% peptidoglycan in their cell walls. This peptidoglycan layer is present outside the cell membrane within the periplasm (the space between the cell wall and membrane). There is a unique cell wall protein in Gram-negative bacteria outside the periplasm.

This is structurally similar to the cell membrane and therefore is known as the outer membrane. Gram-negative cell walls are composed of outer membrane and peptidoglycan. Peptidoglycan layer is there in the periplasm. Periplasm in the Gram-negative cell is the space between outer membrane and the cell membrane. In addition to peptidoglycan it contains many proteins most of which are enzymes used for the degradation of large molecules. Outer membrane has some similarities to the structure of cell membrane. It is also a bilayer and the inner layer is composed of phospholipids. Just like in the cell membrane.

Lipopolysaccharides (LPS) which form the outer layer of outer membrane has a lipid protein and a polysaccharide portion. Lipid part of LPS called Lipid-A and it is oriented towards the phospholipid layer. The polysaccharide part of the outer layer of the outer membrane is oriented towards outside.

Lipid-A of LPS

Lipid-A is not a glycerol lipid, it is a lipid that consists of N-Acetyl glucosamine not glycerol. Fatty acid molecules and phosphate groups form esters with N-Acetyl glucosamine (Not with glycerol). In addition to providing shape and strength to the cell like any other cell wall component, lipid A can act as a toxin inside host tissues. For example, Salmonella Lipid A causes fever (High temperature in human bod. As it is a part of the structure it is called an endo-toxin).

Polysaccharide part of LPS

The polysaccharide part of LPS has two parts.

  1. Core-Polysaccharide
  2. O-Specific polysaccharide

O specific polysaccharide of LPS determines antigenic properties. Ex: Some salmonella species can have hundreds of different varieties depending on the differences in the O specific polysaccharide structure. These different varieties are called serovars (serological varieties). They can be identified using serological tests (Antigen-antibody reactions).

Bacteria have either Gram-positive or Gram-negative cell wall. However sometimes a culture may not give a clear result for Gram staining. For example, an old culture with many dead and decaying cells would not give a clear result for Gram staining. Some bacterial species are known as Gram variable. Because, they also do not show clearly whether they are on their cell wall structure which may have different peptidoglycan contents. There are some bacterial species are pathogens who do not have cell wall at all.

Ex- Mycoplasma and Thermoplasma

These bacteria have stronger cell membranes usually sterols within the membrane.

Gram-positive bacteria Vs Gram-negative bacteria

Characteristic Gram-positive Gram-negative
Gram’s reaction
Stain dark violet or purple
Stain pink.
Peptidoglycan layer
Thick (Multilayers)
Thin (Single layered)
Teichoic acid
Periplasmic space
Outer membrane
Lipid and Lipoprotein content
Toxins production
Primarily exotoxins
Primarily endotoxins
Antibiotic resistance
More resistant
More susceptible
Resistance to physical disruption


Michael T. Madigan, John M. Martinko, Kelly S. Bender, Daniel H. Buckley, D. A. S. (2015). BROCK BIOLOGY OF MICROORGANISMS (14th ed.). Pearson Education,Inc

Eugene W. Nester; Denise G. Anderson; C.Evans Roberts; Nancy N. Pearsall; Martha T. Nester,(2004). Microbiology: A Human Perspective (4th ed.). McGraw-Hill Education.

Article By,

Pasindu Chamikara – Microbiologist

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