Bacteria

Bacteria, despite their apparent simplicity, contain a well developed cell structure which is responsible for many of their unique biological properties. Many structural features are unique to bacteria and are not found among archaea or eukaryotes. Because of the simplicity of bacteria relative to larger organisms and the ease with which they can be manipulated experimentally, the cell structure of bacteria has been well studied, revealing many biochemical principles that have been subsequently applied to other organisms.

Cell morphology

Perhaps the most elemental structural property of bacteria is cell morphology (shape). Typical examples include: 
* coccus (spherical) 
* bacillus (rod-like)  
* spirillum (spiral) 
* filamentousCell shape is generally characteristic of a given bacterial species, but can vary depending on growth conditions. Some bacteria have complex life cycles involving the production of stalks and appendages (e.g. "Caulobacter") and some produce elaborate structures bearing reproductive spores (e.g. "Myxococcus", "Streptomyces"). Bacteria generally form distinctive cell morphologies when examined by light microscopy and distinct colony morphologies when grown on Petri plates. These are often the first characteristics observed by a microbiologist to determine the identity of an unknown bacterial culture.

The bacterial cell wall

As in other organisms, the bacterial cell wall provides structural integrity to the cell. In prokaryotes, the primary function of the cell wall is to protect the cell from internal turgor pressure caused by the much higher concentrations of proteins and other molecules inside the cell compared to its external environment. The bacterial cell wall differs from that of all other organisms by the presence of peptidoglycan (poly-"N"-acetylglucosamine and "N"-acetylmuramic acid), which is located immediately outside of the cytoplasmic membrane. Peptidoglycan is responsible for the rigidity of the bacterial cell wall and for the determination of cell shape. It is relatively porous and is not considered to be a permeability barrier for small substrates. While all bacterial cell walls (with a few exceptions e.g. intracellular parasites such as "Mycoplasma") contain peptidoglycan, not all cell walls have the same overall structures. There are two main types of bacterial cell walls, Gram positive and Gram negative, which are differentiated by their Gram staining characteristics. For both Gram-positive and Gram-negative bacteria, particles of approximately 2 nm can pass through the peptidoglycan. [cite journal | author=Demchick PH and Koch AL | title=The permeability of the wall fabric of Escherichia coli and Bacillus subtilis | journal=Journal of Bacteriology | year=1996 | pages=768–73| volume=178 | issue=3 [http://jb.asm.org/cgi/reprint/178/3/768] ]

The Gram positive cell wall

The Gram positive cell wall is characterized by the presence of a very thick peptidoglycan layer, which is responsible for the retention of the crystal violet dyes during the Gram staining procedure. It is found exclusively in organisms belonging to the Actinobacteria (or high %G+C Gram positive organisms) and the Firmicutes (or low %G+C Gram positive organisms). Bacteria within the Deinococcus-Thermus group may also exhibit Gram positive staining behaviour but contain some cell wall structures typical of Gram negative organisms. Embedded in the Gram positive cell wall are polyalcohols called teichoic acids, some of which are lipid-linked to form lipoteichoic acids. Because lipoteichoic acids are covalently linked to lipids within the cytoplasmic membrane they are responsible for linking the peptidoglycan to the cytoplasmic membrane. Teichoic acids give the Gram positive cell wall an overall negative charge due to the presence of phosphodiester bonds between teichoic acid monomers.

The Gram negative cell wall

Unlike the Gram positive cell wall, the Gram negative cell wall contains a thin peptidoglycan layer adjacent to the cytoplasmic membrane, which is responsible for the cell wall's inability to retain the crystal violet stain upon decolourisation with ethanol during Gram staining. In addition to the peptidoglycan layer, the Gram negative cell wall also contains an additional outer membrane composed by phospholipids and lipopolysaccharides which face into the external environment. As the lipopolysaccharides are highly-charged, the Gram negative cell wall has an overall negative charge. The chemical structure of the outer membrane lipopolysaccharides is often unique to specific bacterial strains (i.e. sub-species) and is responsible for many of the antigenic properties of these strains.

The bacterial cytoplasmic membrane

The bacterial cytoplasmic membrane is composed of a phospholipid bilayer and thus has all of the general functions of a cell membrane such as acting as a permeability barrier for most molecules and serving as the location for the transport of molecules into the cell. In addition to these functions, prokaryotic membranes also function in energy conservation as the location about which a proton motive force is generated. Unlike eukaryotes, bacterial membranes (with some exceptions e.g. "Mycoplasma" and methanotrophs) generally do not contain sterols. However, many microbes do contain structurally related compounds called hopanoids which likely fulfill the same function. Unlike eukaryotes, bacteria can have a wide variety of fatty acids within their membranes. Along with typical saturated and unsaturated fatty acids, bacteria can contain fatty acids with additional methyl, hydroxy or even cyclic groups. The relative proportions of these fatty acids can be modulated by the bacterium to maintain the optimum fluidity of the membrane (e.g. following temperature change).

As a phospholipid bilayer, the lipid portion of the outer membrane is impermeable to charged molecules. However, channels called porins are present in the outer membrane that allow for passive transport of many ions, sugars and amino acids across the outer membrane. These molecules are therefore present in the periplasm, the region between the cytoplasmic and outer membranes. The periplasm contains the peptidoglycan layer and many proteins responsible for substrate binding or hydrolysis and reception of extracellular signals. The periplasm it is thought to exist as a gel-like state rather than a liquid due to the high concentration of proteins and peptidoglycan found within it. Because of its location between the cytoplasmic and outer membranes, signals received and substrates bound are available to be transported across the cytoplasmic membrane using transport and signalling proteins imbedded there.

Other bacterial surface structures

Fimbrae and Pili

"Main article:" Pilus

Fimbrae are protein tubes that extend out from the outer membrane in many members of the Proteobacteria. They are generally short in length and present in high numbers about the entire bacterial cell surface. Fimbrae usually function to facilitate the attachment of a bacterium to a surface (e.g. to form a biofilm) or to other cells (e.g. animal cells during pathogenesis)). A few organisms (e.g. "Myxococcus") use fimbrae for motility to facilitate the assembly of multicellular structures such as fruiting bodies. Pili are similar in structure to fimbrae but are much longer and present on the bacterial cell in low numbers. Pili are involved in the process of bacterial conjugation. Non-sex pili also aid bacteria in gripping surfaces.

-layers

"Main article:" S-layer

An S-layer is a cell surface protein layer found in many different bacteria and in some archaea where it serves as the cell wall. All S-layers are made up of a two-dimensional array of proteins and have a crystalline appearance, the symmetry of which differs between species. The exact function of S-layers is unknown, but it has been suggested that they act as a partial permeability barrier for large substrates. For example, an S-layer could conceivably keep extracellular proteins near the cell membrane by preventing their diffusion away from the cell. In some pathogenic species, an S-layer may help to facilitate survival within the host by conferring protection against host defence mechanisms.

Capsules and Slime Layers

"Main article:" Slime layer

Many bacteria secrete extracellular polymers outside of their cell walls. These polymers are usually composed of polysaccharides and sometimes protein. Capsules are relatively impermeable structures that cannot be stained with dyes such as India ink. They are structures that help protect bacteria from phagocytosis and desiccation. Slime layers are somewhat looser, fibrous structures generally involved in attachment of bacteria to other cells or inanimate surfaces to form biofilms. Slime layers can also be used as a food reserve for the cell.  
*An example of how a bacterial cell uses their slime layer to attach to a surface is in the Streptococcus mutans. Streptococcus mutans attaches to the teeth with a slime layer and forms a sticky film that traps food particles and other bacteria on the teeth (dental plaque). The bacteria then metabolizes the trapped food particles and release acids (thus possibly causing tooth decay).

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A-Monotrichous;B-Lophotrichous;C-Amphitrichous;D-Peritrichous;]

Flagella

"Main article:" Flagellum

Perhaps the most recognizable extracellular bacterial cell structures are flagella. Flagella are whip-like structures protruding from the bacterial cell wall and are responsible for bacterial motility (i.e. movement). The arrangement of flagella about the bacterial cell is unique to the species observed. Common forms include: 
* Peritrichous - Multiple flagella found at several locations about the cell 
* Polar - Single flagella found at one or both cell poles 
* Lophotrichous - A tuft of flagella found at one cell pole 
Flagella are complex structures that are composed of many different proteins. These include flagellin, which makes up the whip-like tube and a protein complex that spans the cell wall and cell membrane to form a motor that causes the flagellum to rotate. This rotation is normally driven by proton motive force and are found in the body of the cell.

Intracellular bacterial cell structures

In comparison to eukaryotes, the intracellular features of the bacterial cell are extremely simplistic. Bacteria do not contain organelles in the same sense as eukaryotes. Instead, the chromosome and perhaps ribosomes are the only easily observable intracellular structures found in all bacteria. There do exist, however, specialized groups of bacteria that contain more complex intracellular structures, some of which are discussed below.

The bacterial chromosome and plasmids

"Main article:" Plasmid

Unlike eukaryotes, the bacterial chromosome is not enclosed inside of a membrane-bound nucleus but instead resides inside the bacterial cytoplasm. This means that the transfer of cellular information through the processes of translation, transcription and DNA replication all occur within the same compartment and can interact with other cytoplasmic structures, most notably ribosomes. The bacterial chromosome is not packaged using histones to form chromatin as in eukaryotes but instead exists as a highly compact supercoiled structure, the precise nature of which remains unclear. Most bacterial chromosomes are circular although some examples of linear chromosomes exist (e.g. "Borrelia burgdorferi"). Along with chromosomal DNA, most bacteria also contain small independent pieces of DNA called plasmids that often encode for traits that are advantageous but not essential to their bacterial host. Plasmids can be easily gained or lost by a bacterium and can be transferred between bacteria as a form of horizontal gene transfer.

Ribosomes and other multiprotein complexes

"Main article:" Ribosome

In most bacteria the most numerous intracellular structure is the ribosome, the site of protein synthesis in all living organisms. All prokaryotes have 70S (where S=Svedberg units) ribosomes while eukaryotes contain larger 80S ribosomes in their cytosol. The 70S ribosome is made up of a 50S and 30S subunits. The 50S subunit contains the 23S and 5S rRNA while the 30S subunit contains the 16S rRNA. These rRNA molecules differ in size in eukaryotes and are complexed with a large number of ribosomal proteins, the number and type of which can vary slightly between organisms. While the ribosome is the most commonly observed intracellular multiprotein complex in bacteria other large complexes do occur and can sometimes be seen using microscopy.

Intracellular membranes

While not typical of all bacteria some microbes contain intracellular membranes in addition to (or as extensions of) their cytoplasmic membranes. An early idea was that bacteria might contain membrane folds termed mesosomes, but these were later shown to be artifacts produced by the chemicals used to prepare the cells for electron microscopy.  Examples of bacteria containing intracellular membranes are phototrophs, nitrifying bacteria and methane-oxidising bacteria. Intracellular membranes are also found in bacteria belonging to the poorly studied Planctomycetes group, although these membranes more closely resemble organellar membranes in eukaryotes and are currently of unknown functionCytoskeleton

The prokaryotic cytoskeleton is the collective name for all structural filaments in prokaryotes. It was once thought that prokaryotic cells did not possess cytoskeletons, but recent advances in visualization technology and structure determination have shown that filaments indeed exist in these cells.logues for all major cytoskeletal proteins in eukaryotes have been found in prokaryotes. Cytoskeletal elements play essential roles in cell division, protection, shape determination, and polarity determination in various prokaryotes. 

Nutrient storage structures

Most bacterial habitats do not live in environments that contain large amounts of essential nutrients at all times. To accommodate these transient levels of nutrients bacteria contain several different methods of nutrient storage in times of plenty for use in times of want. For example, many bacteria store excess carbon in the form of polyhydroxyalkanoates or glycogen. Some microbes store soluble nutrients such as nitrate in vacuoles. Sulfur is most often stored as elemental (S⁰) granules which can be deposited either intra- or extracellularly. Sulfur granules are especially common in bacteria that use hydrogen sulfide as an electron source. Most of the above mentioned examples can be viewed using a microscope and are surrounded by a thin nonunit membrane to separate them from the cytoplasm.

Gas vesiclesGas vesicles are spindle-shaped structures found in some planktonic bacteria that provides buoyancy to these cells by decreasing their overall cell density. They are made up of a protein coat that is very impermeable to solvents such as water but permeable to most gases. By adjusting the amount of gas present in their gas vesicles bacteria can increase or decrease their overall cell density and thereby move up or down within the water column to maintain their position in an environment optimal for growth.

Carboxysomes

Carboxysomes are intracellular structures found in many autotrophic bacteria such as Cyanobacteria, Knallgasbacteria, Nitroso- and Nitrobacteria. They are proteinaceous structures resembling phage heads in their morphology and contain the enzymes of carbon dioxide fixation in these organisms (especially ribulose bisphosphate carboxylase/oxygenase, RuBisCO, and carbonic anhydrase). It is thought that the high local concentration of the enzymes along with the fast conversion of bicarbonate to carbon dioxide by carbonic anhydrase allows faster and more efficient carbon dioxide fixation than possible inside the cytoplasm.Similar structures are known to harbor the coenzyme B12-containing glycerol dehydratase, the key enzyme of glycerol fermentation to 1,3-propanediol, in some Enterobacteriaceae (e. g. Salmonella).

Magnetosomes

Magnetosomes are intracellular structures found in magnetotactic bacteria that allow them to sense and align themselves along a magnetic field (magnetotaxis). The ecological role of magnetotaxis is unknown but it is hypothesized to be involved in the determination of optimal oxygen concentrations. Magnetosomes are composed of the mineral magnetite and are surrounded by a nonunit membrane. The morphology of magnetosomes is species-specific.

Endospores

"Main article:" Endospores

Perhaps the most well known bacterial adaptation to stress is the formation of endospores. Endospores are bacterial survival structures that are highly resistant to many different types of chemical and environmental stresses and therefore enable the survival of bacteria in environments that would be lethal for these cells in their normal vegetative form. It has been proposed that endospore formati

Acid-fastness is a physical property of certain bacteria (and, less commonly, protozoa), specifically their resistance to decolorization by acids during staining procedures.^[1][2]Acid-fast organisms are difficult to characterize using standard microbiological techniques (e.g. Gram stain - if an acid-fast bacillus (AFB) was gram stained, the result would be an abnormal gram positive organism, which would indicate that further testing was necessary), though they can be stained using concentrated dyes, particularly when the staining process is combined with heat. Once stained, these organisms resist the dilute acid and/or ethanol-based de-colorization procedures common in many staining protocols, hence the name acid-fast.^[2]The high mycolic acid content of certain bacterial cell walls, like those of Mycobacteria, is responsible for the staining pattern of poor absorption followed by high retention. The most common staining technique used to identify acid-fast bacteria is the Ziehl-Neelsen stain, in which the acid fast bacilli are stained bright red and stand out clearly against a blue background. Another method is the Kinyoun method, in which the bacteria are stained bright red and stand out clearly against a green background. Acid-fast bacteria can also be visualized by fluorescence microscopy using specific fluorescent dyes (auramine-rhodamine stain, for example).^[3] Some bacteria may also be partially acid-fast. The eggs of the parasitic lung fluke Paragonimus westermani are actually destroyed by the stain, which can hinder diagnosis in patients who present with TB-like symptoms.