Comparison of Prokaryotic & Archaeal Cell Structures: Walls, Flagella, Fimbriae, Membranes, Study notes of Health sciences

Download Comparison of Prokaryotic & Archaeal Cell Structures: Walls, Flagella, Fimbriae, Membranes and more Study notes Health sciences in PDF only on Docsity! Bacterial Physiology HSCI 5607 Chapter 1 Structure and Function Introduction: Prokaryotes do not contain organelles such as nuclei, mitochondria, chloroplast, Golgi apparatus etc. Nevertheless, their metabolic activities are still compartmentalized. Compartmentallization is found in multicomponent enzymes, within periplasm, in intracellular membranes and the cell membranes and within the inclusion bodies which store various enzymes, pigments and storage products. Prokaryotic cells do contain well developed cell walls, and surface appendages such as fimbriae, pili and flagella. Prokaryotes are divided into two distinct groups: 1. Bacteria 2. Archaea Archaea differ from bacteria in ribosomal RNA sequences, in cell chemistry as well as certain physiological aspects. Archaea commonly belong to one of the three phylogenetic groups: 1.Methanogenic; 2.Extremely halophilic; 3.Extremely thermophilic. Comparison of Archaea, Bacteria and Eukarya: 1. In Archaea the membrane lipids are long hydrocarbon chains are linked by ether-linkage to glycerol while in bacteria as well as in eukarya the fatty acids are ester linked to glycerol. 2. Archaea lack peptidoglycan, in their cell wall but some archaeal cell wall contain compound known as ‘Pseudomurein’ which is not found in bacterial cell wall. 3. Archaea contain histones similar to that is found in eukarya. Histones bind archaeal DNA into compact structures like nucleosomes. 4. The Archaea contain RNA polymerase (8-10 subunits) different than bacterial RNA polymerase (4 subunits) but is similar to that of eukaryotic RNA polymerase (10-12 subunits). 5. Archaeal protein synthesis differs from bacterial protein synthesis. The archaeal ribosomes are not sensitive to the antibiotics affecting bacterial ribosomes indicating the structural differences in their ribosomes. 6. The halophilic archaea have light driven ion pumps not found in bacteria. 7. The methanogenic archaea have several unique coenzymes that are not found in bacteria. These are used for the reduction of CO2 to methane and formation of Acetyl CoA from H2 and CO2. Cell Appendages: Cell appendages include: 1. Flagella, which is used for motility. 2. Fimbrae (pili), used for adhesion on different surfaces. 3. Sex pili, used for mating by some bacteria. Flagella: Motile bacteria contain one or more flagella on the cell surface. Some bacteria can move without flagella by gliding. The flagellum is a semirigid, long helical(right or left handed) filament which rotates like a propeller. The number and arrangement of flagella vary in different species. Bacterial flagella is different than eukaryotic flagella. The most studied bacterial flagella are those of E.coli and S.typhimurium. Functions: 1. Flagella helps the motile bacteria to drive towards nutrients, light and electron acceptor or drive away from toxic environments. 2. Plays important role in bacterial virulence, e.g. movement of Treponema pallidum through connective tissues. Flagella (General Structure): The flagellum consists of mainly three parts: A. Basal body, B. A hook, and C. A filament and additional proteins required for motor function. The flagellum is made up of approximately 20 different types of polypeptides and requires almost 40 different genes for its assembly and function. The motor rotates either clockwise or counterclockwise determining the direction of swimming and it also responds to chemotactic signals. Exceptionally in Rhodobacter sphaeroides and Rhizobium meliloti, the flagella rotate only in one direction. The Hook: The central rod which originates from the base is attached to a curved hook that is made of multiple copies of protein known as ‘Hook protein’ a product of flgE gene. There are additional hook-associated proteins HAP1 and HAP3 products of flgK and flgL genes respectively. These proteins are necessary to form junction between the hook and the filament. The HAP2 protein which is a product of flgD gene caps the the flagellar filament. Mutants lacking these proteins secrete flagellin into the medium. The Filament: Filament is semirigid and helical structure attached to the hook. It is made up of protein flagellin. Thousands of copies of flagellin are present. The type of flagellin varies from species to species. Their molecular weight vary from 20 to 65 kD in different species. They show homology at the N and C terminal regions while the central part may vary considerably. The flagellin subunits are arranged in such a manner that there is a central 60 angstrom unit hole. This hole may play important role in transporting flagellin during flagellar growth at the tip. 2. Mechanism of Motor Function: The rotational force which originates in the MS ring with the help of Mot proteins rotates the central rod and eventually the filament. The mechanism through which the Mot proteins generate rotational force using proton efflux is not yet understood. One of the set of rings must act as stator in order to hold the motor in place and allowing the torque to rotate the filament. 3.Growth of Flagella: The flagellum grows at the tip. This has been demonstrated by the use of fluorescent amino acids or radioisotopes. The flagellin monomers are supposed to be transported through the central hole to the site of growth(assembly) at the tip of the filament. Fimbriae, Pili, Filaments, and Fibrils: The filamentous structures called fimbriae or pili or filaments or fibrils are commonly observed in gram negative bacteria but also found in gram positive Corynebacterium renale and Actinomyces viscosus. Their length vary from short (0.2 m) to long (20 m) while their thickness ranges from 3 to 14 nm or greater. They are made up of protein ‘Pilin’. Some of them originate from the basal body in the cell membrane but in most of the cases it is not known how are they attached to the cell surface. They are commonly found in freshly isolated culture but tend to be lost during subculturing and handling. Usually they are classified into two groups: 1.Fimbriae and 2. Sex Pili. Fig. 1.3 Electron micrograph of a metal- shadowed preparation of Salmonella typhi showing flagella and fimbriae. The cell is about 0.9 wm in diameter. Source: Reprinted with permission of J. P. Duguid.  1. Fimbriae: The filamentous structures which mediate attachment of bacterial cells on various cell surfaces including that of other bacteria, animal, plant, or fungi are called fimbriae. Thus they play important role in colonization of bacteria. They are also referred to as ‘Adhesive pili’. They posses adhesins on their tips which help them to stick to other surfaces. Adhesins are the proteins at the tip that recognize specific receptors on the cell surface. The receptors on animal cell surface include, glycolipids and glycoproteins embedded in the cell membranes in such a way that their oligosaccharide moieties are presented on the surface. Their cell adhesive properties are very useful in medical diagnostics, e.g. hemagglutination where fimbriae is used to attach to the surface of red blood cells. The Glycocalyx: ‘Glycocalyx’ is the term used to describe the outer most layer surrounding the cell wall. The glycocalyx may be in the form of S layers, capsules, or slime. S layers: S layers are the array of protein or glycoprotein subunits on the cell wall surface. They are found in wide range of gram positive and gram negative eubacteria. They are also found in archaea, where the S layer sometimes covers the cell membrane and serves as the cell wall itself. Capsules: Capsule is a extracellular fibrous material which is either loosely or tightly attached to the surface of bacteria. When it is loosely attached to the cell surface , it is also referred to as slime layer or slime capsule or extracellular polysaccharide. Capsule is covalently attached to either phospholipid or lipid A embedded in the cell surface. Chemical composition of Capsule: Most of the glycocalyces are made up of polysaccharides but some are made up of protein. The example of polypeptide capsule is the polymer of D-glutamate found in B.anthracis. Polysaccharide capsules are diverse in chemical composition and structure. Some are homopolymers while others are hetropolymers. The monosaccharides involved are linked to each other by glycosidic linkage to form straight or branched chains. The chemical composition of polysaccharide may vary in different strains of the same organism. For example there are more than 80 different types of polysaccharides found in E.coli strains. Sometimes same types of polysaccharides may be found in two different species. Functions: One of the most important function of capsule is adhesion to the other cell surfaces or on inanimate surfaces to form biofilm. Protection from phagocytosis and thereby increasing the virulence is another important function of the capsules. Other functions include prevention of dehydration of cell. Cell Wall: In most of the bacteria cell membrane is surrounded by a rigid wall like structure known as ‘cell wall’. Cell wall is responsible for specific shape and protects the cell from bursting. Most of the bacteria can be divided into two groups on the basis of the type of cell wall they contain. They can be distinguished on the basis of gram stain reaction. The one which retain gram stain are gram positive and the one which do not retain the stain are known as gram negative. The Gram Stain: Christian Gram invented gram staining procedure in 1884. According to the procedure the cells are divided into two groups on the basis of whether they can retain the Crystal violet-iodine complex or not. The one which retain are gram positive while the one which loose and are stained with counter stain safranin are gram negative. Peptidoglycan: The peptidoglycan is responsible for the strength and the rigidity of the bacterial cell wall. It is a glycoprotein made up of two types of sugar, N- acetyleglucosamine (GlcNAc or G), N-acetyl-muramic acid (MurNAc or M)linked with -1,4 linkage and a tetrapeptide attached to M. Two glycan chains are cross linked with peptide bonds between the tetrapeptides of two chains. Tetrapeptide usually consists of L-alanine, D-glutamate, a diamino acid, and D-alanine. Peptidoglycan forms three dimensional structure surrounding the cell membrane with covalent glycosidic and peptide bonds. The strength is due to the presence of many covalent bonds. Peptidoglycan…. In gram negative bacteria peptidoglycan layer is free and only noncovalently attached to the outer envelope which can be isolated as murein sac. In gram positive bacteria the peptidoglycan is bonded to various polysaccharides and teichoic acids and can not be isolated as pure peptidoglycan sac. In gram negative bacteria the diamino acid is generally the diaminopimelic acid (DAP) while it is present sometimes in gram positive bacteria. In gram negative bacteria the peptides are linked directly whereas in gram positive bacteria usually peptide bridge (e.g. pentaglycine bridge in Staphylococcus aureus) is present. Gram Positive Cell Walls: Relatively thick, about 15-30 nm wide and consist of several polymers and mainly peptidoglycan (PG). Nonpeptidoglycan polymers usually can consist of almost 50% of the dry weight of the gram positive bacterial cell wall. They are bound to the glycan chain of PG. The nonpeptidoglycan polymers include, Teichoic acids (polymers of ribitol or glycerol phosphates), Teichuronic acid (Acidic polysaccharides containing uronic acids), Neutral polysaccharides (common in Streptococci, Lactobacilli), lipoteichoic acids (Phosphodiester linked glycerol phosphate bound to lipid), glycolipids and Mycolic acid (common in genus Mycobacterium). Porins…. Since porins exclude molecules larger than 600 Da., gram negative outer membrane translocates larger molecules with the help of other proteins. For example LamB protein transports maltose and maltodextrins, BtuB transports vitamin B12, FepA transports ferricenterobactin a siderophore produced by E.coli, Tsx transports nucleosides and there are many more……. Archaeal Cell Wall: The main difference between the bacterial cell wall and archaeal cell wall is that the archaeal cell wall do not contain ‘Peptidoglycan’. The cell walls have different structures and they are made of either pseudopeptidoglycan, polysaccharide or protein (S layer). Pseudopeptidoglycan is made up of N-acetylglucosamine (same as PG) and N-acetyltalosaminuronic acid instead of N- acetylmuramic acid. The sugars are linked by -1,3 linkage instead of -1,4 as in PG. The tetrapeptide consists of L-aminoacid instead of D-amino acids as in PG. Periplasm: In gram negative bacteria, the space between the inner membrane and the outer membrane is termed as ‘Periplasm’. It is filled with aqueous solutions containing proteins, oligosaccharides, salts and also the PG layer. Many specialized functions like oxidation-reduction, osmoregulation, nutrient transport, protein secretion and enzymatic hydrolyses are carried out in this space. Periplasmic space contains many solute binding proteins involved in transport, component of electron transport e.g. cytochrome C, hydrolytic enzymes like phosphatases and nucleases, and detoxifying enzymes like -lactamase. Another important protein partially located in periplasm is TonB. This protein is anchored to inner membrane but extends to the periplasm. It is involved in energy transduction to many transport processes including iron and vitamin B12 transport. It is also involved in energizing drug efflux systems in bacteria. Recently it has been reported that even gram positive bacterial cell perhaps possesses compact periplasmic space. Functions of CM: There are more than 100 proteins located in CM involved in diversified functions such as proton pump in ATPase (ATPsynthesis), movement of flagella, electron transport, nutrient transport, photosynthesis, biosynthesis of lipids, cell wall polymers, secretion of proteins and signal transduction. The phospholipid bilayer also acts as a permeability barrier to most of the water soluble solutes. Archaeal Cell membrane: The lipids found in archaeal membranes are different than the ones found in bacteria. They consist of isopranoid alcohols either 20 or 40 carbon long. The isopranoid alcohols are either ether-linked to glycerol to form monoglycerol diethers or to two glycerols to form diglycerol tetraethers. Not many archaeal membrane proteins have been studied except ‘Bacteriorhodopsin’ and ‘Halorhodopsin’ both involved in light driven functions. The thermoacidophilic and some methanogenic archaea have tetraether glycerolipid having polar end at both the ends. These lipids form lipid monolayer which are resistant to high temperature. This is the only example of membrane having lipid monolayer. A: Monoglycerol Diether B: Diglycerol tetraether Isopranoid alcohols in Archaeal Cell membranes 5. Ribosomes: They are the site of protein synthesis. They are made up of three different types of RNA (23S, 16S, and 5S) and 50 different types of proteins. Their approximate size is 22nm by about 30nm. On the basis of sedimentation rate both bacterial and archaeal ribosomes sediment at 70S but archaeal ribosomes are still different structurally than bacterial ribosomes. 6. Nucleoid: It is an area where an amorphous mass of DNA is located almost in the center of the cytoplasm bound to the membrane. Sometimes in rapidly growing bacterial cells you can observe two such area containing single copy of chromosome. The DNA present in the nucleoid is tightly coiled. DNA string if stretched would be 500 times longer than the length of the cell. DNA is also bound to RNA which is freshly transcribed and many proteins including, enzyme RNA polymerase, several DNA binding proteins. 7. Multienzyme complexes: There are many large multienzyme complexes located within the cytoplasm. The examples are: 1. Pyruvate dehydrogenase from E.coli is a complex of three enzyme consist of total 50 proteins having total size of 4.6-4.8 x 106 Da. The enzyme complex oxidizes pyruvate to acetyl CoA and CO2. 2. -Ketoglutarate dehydrogenase also consists of three enzymes and made up of 48 proteins having total size of 2.5 x 106 Da. This enzyme oxidizes -Ketoglutarate to succinyl CoA and CO2. Cytosol: The cytosol is a liquid portion of the cytoplasm which can be isolated by centrifuging the broken cells at 105,00 x g for 1 to 2 hours. Centrifugal force separates soluble fraction of the cytoplasm (the Cytosol) as supernatant from the membranes, protein aggregates, and DNA as a sediment. Cytosol contains all the soluble enzymes responsible for catalyzing thousands of biochemical reactions of carbohydrate, lipid, protein and nucleotide metabolism. Therefore the protein concentration of cytosol is very high making it very viscous. Analogues to tubulin and actomyosin: There are increasing evidence that there is a presence of ‘Cytoskeleton’ like structures made up of proteins like tubulin are present in bacteria.