Prokaryotic Cell Structure PDF

Prokaryotic cell structure Cell morphology Small Seemingly limited amount of shapes Basic shapes Coccus (sphere), bacillus (rod), spirillum (spiral) Pleomorphic Common cell morphology Variety of prokaryotic shapes and sizes Why are prokaryotes small? Average size is...

Prokaryotic cell structure Cell morphology Small Seemingly limited amount of shapes Basic shapes Coccus (sphere), bacillus (rod), spirillum (spiral) Pleomorphic Common cell morphology Variety of prokaryotic shapes and sizes Why are prokaryotes small? Average size is 1 µm Theoretical limits „Must be large enough to house the total amount of needed stuff“ (Koch) 250-300 nm in diameter Prokaryotes must rely on diffusion to bring nutrients into the cell Surface-to-volume ratio Rate for transporting nutrients into a cell is a function of the amount of exposed surface area Smaller cells have higher surface-to-volume ratio Decreased amount of cytoplasm that has to be supported In growing cells, the volume increases faster than the surface à need for division Shape and nutrient uptake Coccus has the smallest surface-to-volume ratio In a rod, elongation does not change surface-to-volume ratio significantly but aids in nutrient uptake Bacterial shape is plastic Depletion of nutrients drives cocci to filaments What about very large cells? mechanisms that reduce volume (vacuole) Other mechanisms that drive bacterial shape cell division and segregation play with the cellular diameter and the division will be abberant attachment to surfaces it is much easier to wash down a coccus from a surface than an elongated rod passive dispersal stellar bacteria float more easily than cocci active motility smaller diameter moves faster the need to escape predators too small or too big are not readily eaten Cellular components The cytoplasm Water (80%), nutrients, wastes, enzymes, gases, inorganic ions Ribosomes Small (70S) both in archaea and bacteria Dispersed throughout the cytoplasm Circular chromosome and plasmids  Features of plasmids Extrachromosomal elements Circular or linear molecules capable of independent replication Frequently contain genes that give advantage in a given environment Some may integrate into genome à episomes May be transferred among bacteria  Selectivelly permeable barrier that encloses the cell Holds and separates the cytoplasm from the exterior Its components differ with respect to interior and exterior side The membrane Site of enzymatic reactions, cellular component distribution, cellular division  Lipid bilayer is fluid and elastic à fluid mosaic Membrane is a two-dimensional liquid that restricts the lateral diffusion of The membrane membrane components. Membrane may break and reassemble Membrane may rearrange its components Molecular structure Present in all membranes Hydrophilic polar head connected to hydrophobic fatty acid tails through glycerol linkage Allow organization into a bilayer Compose up to 30% of membrane dry weight  Other membrane components Sterol ring Cholesterol Hopanoid 1. Lipids are inserted into the membrane to increase rigidity/fluidity Sterols in eukaryotes Cyclic hopanoids in prokaryotes 2. Proteins constitute up to 60% of membrane A sea of lipids with protein icebergs Types of membrane proteins with respect to location Integral proteins Locked into membrane, may span it several times Hydrophobic amino acid regions embedded in membrane Hydrophilic regions located outside the membrane Often act as receptors or transfer signal Types of membrane proteins with respect to location Peripheral proteins Attract to the phosphate heads of the lipid molecules or to integral proteins No hydrophobic regions and have several polar amino acids Hydrophilic amino acids on the surface prevent them from being sucked into membrane Types of membrane proteins with respect to location Peripheral proteins Provide support Maintain and communicate with cytoskeleton Transfer signals to integral proteins May act as enzymes or transfer molecules Can detach/reattach in response to a signal Main membrane functions Membrane as a permability barrier Water is the only biologically meaningful compound that passes freely Lipid-soluble small compounds may pass Strict control of transport is orchestrated by carrier proteins Polar molecules and ions pass with substantial difficulty Transported using facilitated diffusion or active transport  Membrane as a protein anchor 1. Receptors relay signal between the cell‘s exterior and interior 2. Enzymes have many activities 3. Adhesion molecules identify and interact with other cells 4. Transport proteins move molecules and ions across the membrane  The necessity of transport proteins Simple diffusion is not enough for cell functions Nutrient concentration outside the cell is low Simple diffusion can not occur against gradient Uptake against the gradient is necessary and is mediated by carrier Figure: 04-22 proteins Relationship between uptake rate and external concentration in diffusion and transport. Note that in the carrier-mediated process, the uptake rate shows saturation at relatively low external concentrations  The classes of membrane- transporting systems Simple transporters transport substances without chemical modification Group translocation requires phosphorylation of the transported substance ABC system couples the energy of ATP binding and hydrolysis to substrate transport. Types of transport events Uniport Unidirectional transport of a molecule Symport transport of a substance along with another substance, frequently a proton Antiport Transport of two substances in opposite directions  Energy generation and conservation accross the membrane Membrane potential a difference in electric potential between the interior and the exterior of a biological cell allows formation of proton motive force its generation involves two types of proteins Ion transporters actively push ions across the membrane and establish concentration gradient behave like a battery Ion chanells allow ions to move across the membrane down the concentration gradient behave like resistors  Proton motive force is used to obtain energy for processes for signaling and processing information  The cell wall Represents the outermost boundary of bacterial cells Very important to prokaryotes Solute accumulation within the cells generates turgor pressure which balances the osmotic pressure difference between the interior and exterior In Gram-negative cells this pressure amounts to 2 atmospheres! Removal results in spherical form, lysis in hypoosmotic medium, difficult divison and no motility There are only a few prokaryotes without cell wall Either intracellular parasites or possess unique membrane (lipoglycan)  The cell wall Unusual in many ways One of the few bidimensional polymers in nature Just one molecule can make a rigid container Very dynamic, synthetized and degraded constantly  The cell wall Multifunctional: Prevents osmotic lysis Maintains cellular shape Provides sufficient stability, but elastic enough to allow growth Enables communication with the environment Enables cellular of septum during cellular division Permeability barrier (in Gram-negatives) Provides motility (anchors flagella)  (NAM) Peptidoglycan structure (NAG) Polymer backbone: Alternative residues of sugars NAG and NAM L-alanine A four-aminoacid peptide (both D- and L-aa) is connected to carboxyl group of NAM D-aa rare in prokaryotes à resistance to peptidases D-glutamine Many bacteria substitute diaminopimelic acid at third position with another (L-Lys) But the bridge always resembles a diaminoacid Diaminopimelic acid NAG – N-acetyl-glucosamine NAM – N-acetyl-muramic acid D-alanine Connected through β (1-4) glucosidic bond Peptidoglycan structure  The problems of peptidoglycan synthesis 1. Fairly large precursors must be delivered accross the membrane 2. The synthesis must take part on the outside of the membrane, where there is no ATP  Solutions 1. Construct energetically rich units of peptidoglycane Results in formation of Park nucleotide à UDP-N-acetylmuramyl pentapeptide  Solutions 2. Use the conveyor belt Undecaprenol (bactoprenol) is a membrane lipid carrier Attach Park nucleotide to it, and it becomes a lipid Assemble the unit on the conveyor belt Flip it to the other side  Solutions 3. Insert into existing peptidoglycan Use transglycosylases to insert and link new monomers into the breaks in peptidoglycan Use transpeptidases to cross-link the peptidoglycan Both reactions transfer bond energy, without the need for ATP  Cell wall distinguishes Gram-positive from Gram- negative bacteria Klebsiella pneumoniae Streptococcus pneumoniae Features of Gram-positive cell wall Thick, multilayered, mainly peptidoglycan Needs structural stability Glycopolymers teichoic and lipoteichoic acids (anchored in the membrane) give structural stability Teichoic and lipoteichoic acids regulate autolytic cell-wall enzymes à maintain shape Nutrient transport How to bring in the nutrients over this thick wall? Small substances diffuse through the cell wall Synthesize and deliver exoenzymes which will degrade complex nutrients on the outside à bring in smaller components Features of Gram-negative cell wall Much more complex Peptidoglycan is thin Embedded in periplasm Over the peptidoglycan there is another layer à the outer membrane Outer membrane is unique to G- bacteria and is assymetric to the inside of the cell it is made of phospholipids Outer membrane is unique to G- bacteria and is assymetric to the inside of the cell, it is made of phospholipids To the outside, it is composed of lipopolysaccharide Outer membrane is unique to G- bacteria and is assymetric to the inside of the cell, it is made of phospholipids To the outside, it is composed of lipopolysaccharide It is attached to the peptidoglycan by lipoprotein Outer membrane is unique to G- bacteria and is assymetric to the inside of the cell, it is made of phospholipids To the outside, it is composed of lipopolysaccharide It is attached to the peptidoglycan by lipoprotein It is connected to the cytoplasmic membrane by adhesion sites It is held together by divalent cations and hydrophobic interaction à stiff and strong  Lipopolysaccharide (LPS, endotoxin) Major component of outer membrane Contributes to the structural integrity pili of the cell Protects the membrane from certain chemical attacks Increases the negative membrane charge Plays a role in surface adhesion, phage sensitivity and predator interaction  Lipid A Basic component, essential for viability Responsible for endotoxin activity (arouses immune system) Phosphorylated glucosamine dissacharide backbone with fatty acids anchoring the structure One carbohydrate chain is attached to the disaccharide backbone and extends away from the bacteria.  The core polysaccharide Branched polysaccharide of 9 to 12 sugars. Most of the core region also essential for structure and viability Contains an unusual sugar, 2-keto-3- deoxy-octanoate (KDO) and is phosphorylated.  The O-antigen Attached to the core Long, linear polysaccharide 500-100 repeating units of 4-7 sugars per unit. Species-specific Example serotype E. coli O157:H7 (O antigen:flagellin) à hemolytic-uremic syndrome  Nutrient transport No exoenzymes Periplasm contains transport systems for ions, protein, sugars These are degraded by periplasmatic enzymes Porins traverse entire cell wall and allow diffusion of small hydrophobic molecules Secretion systems At least six types of secretion systems differing in complexity, mechanisms of secretion and the substrates they secrete Examples: Type I composed of three parts, secretes in one step Type III is a molecular syringe  Alternative cell wall structures 1. Mycobacteria (tuberculosis) Peptidoglycan intertwined with arabinogalatan Surrounded by wax-like lipid coat of mycolic acids Can not be stained using Gram à acid-fast staining 2. Mycoplasma (‚walking‘ pneumonia, phylum Tenericutes) Have no cell wall, but incorporate host steroids into membrane to achieve rigidity The membrane is three-layered Evolved from G+ bacteria that lost their cell wall 3. Thermoplasma Free living but has unusual lipoglycan as an alternative Internal structures Cytoskeleton Haloquadratum walsbyi Inclusions Carbon storage Glycogen Poly-β-hydroxybutyrate (PHB) Inorganic storage Polyphosphate granules Sulfur globules Other Gas vacuoles made out of vesicles (buoyancy) Magnetosomes composed of magnetite (orientation in geomagnetic field)  Icosahedral inclusions with protein shell Carboxysome Contains RuBisCO, main enzyme of CO2 fixation Annamoxosome Microcompartments Contains enzymes needed for annamox reaction (NH4+ + NO2− → N2 + 2H2O) Allows bacteria to gain energy Important in N cycle Chlorosome Light-harvesting complex found in photosynthetic bacteria  Found only in Clostridium and Bacillus, G+ bacteria Produced under hostile conditions from vegetative cells Develop within the vegetative cell Dormant stage Visible under microscope à spore position species-specific Germinate under favorable conditions in 6-8 hours Removed only by autoclaving Endospores Endospores Formation of endospore  Completed in 6 hours Triggered by an environmental change which initiates gene expression Germinationof Three stages: endospore Activation Germination Outgrowth  Surface structures of bacteria 1. Capsule Tigthly packed polysaccharide or protein layer Protects the bacterium from the host immune response Removed by immune cells produced by the spleen à infections in asplenic individuals often result in death Promotes adhesion to host surfaces Promotes formation of biofilm à bacteria embedded in polysaccharides are protected from antibiotics and host defense  Surface structures of bacteria 2. Slime layer Loosely packed polysaccharide layer that is easily removed from the cell 3. S-layer Composed of proteins or glycoproteins Highly organized, anchored into cell wall Provides rigidity, cell shape, protection from environmental changes, predators Hexagonal S-layer Structures outside of the cell wall 1. Fimbriae Numerous extensions composed of protein pilin Help bacteria attach 2. Pili Longer than fimbriae, attachment Conjugative pili participate in DNA exchange Type IV pili enable twitching motility  Bacterial flagellum The most complex structure in the bacterial cell Largest gene cluster (~50 genes) in the genome dedicated to its synthesis Turns clockwise (CW) or counter- clockwise (CCW) à swimming  Bacterial flagellum Rotary nanomachine (45 nm) composed of motor and flagellum (10 nm) Rotates like outboard motor Rotation rate of motor 16000 rpm (centrifuge), may reach 100000 rpm (ultracentrifuge) Rotation rate with filament ~1000 rpm Turns clockwise or counter-clockwise à swimming  Flagellum structure Hollow tube (20 nm) made up of protein flagellin A hook allows its axis to point away from the cell A shaft runs between the hook and the basal body passing though a series of rings that embed it in the membrane and connect it with the motor The motor is powered by H+ or Na+ flux  Flagellar rotation Directionality of rotation controlled by switch at motor base CCW rotation results in straight-line runs 1 s, as helix screws through medium Moves 10-20 body-lengths CW rotation: results in tumbling Random changes in direction of swimming Helical flagellar filaments fly apart If no gradient random movement: runs, tumbles, runs in random new direction  Chemotaxis Movement towards the attractant or away from the repellent using the flagellum Orchestrated by bacterial chemoreceptors Attachment of the molecule phosphorylates/methylates the receptor à activation of protein pathway The affects the flagellum swimming It becomes biased towards CCW rotation (runs) The movement remains random, but results in movement towards the attractant  Corkscrew motility Endoflagella put torsion on the entire cells Other types of Spirochaeta locomotion Gliding Does not require flagella, observed on surfaces Provided by surface layer proteins or slime  Biofilm formation In a biofilm, bacterial cells are embedded in extracellular polysaccharide, making them particularly resistant to environmental conditions Many surfaces can be colonized by biofilm – Human urinary tract – Water pipes – Cathethers  Biofilm formation Pioneer cells attach to the surface through adhesins, fimbriae of extracellular polysaccharides Other cells are attracted to the biofilm Cells are kept at distance by polysaccharide molecules with small water channels allowing exchange of water and nutrients Protected from dessication, antibiotics, immune system Bacterial classification Classification distinguishes different types of Bacteria Nomenclature distinguishes by name and is binomial Genus name (capitalized) is followed by species name (never capitalized) Species are designated by biochemical and other phenotypic criteria and by DNA relatedness Strains are a category below species level and are classified below by serotyping, enzyme typing, identification of virulence factors, characterization of plasmids, protein patterns, or nucleic acids. Bacterial classification Classification distinguishes different types of Bacteria Nomenclature distinguishes by name and is binomial Genus name (capitalized) is followed by species name (never capitalized) Species are designated by biochemical and other phenotypic criteria and by DNA relatedness Strains are a category below species level and are classified by serotyping, enzyme typing, identification of virulence factors, characterization of plasmids, protein patterns, or nucleic acids. Clinical laboratories work only with known species à their aim is to rapidly identify organisms How to identify a microorganism Given that distribution of pathogens is niche- dependant, clinical laboratories canoften assume which organisms to expect Step 1. Observing the colony morphology Microbes grow as colonies, which are clones of a single bacterium and contain up to 109 organisms. Colonies differ in shape, organization, and smell. How to identify a microorganism Step 2. Using differential staining to observe cellular morphology Gram stain differentiates bacteria into two major groups based on the thickness of cell- wall. Cellular morphology is a useful tool Bacteria differ in cell shape, cellular organisation, presence of capsule, flagella  How to identify a microorganism Morphological information is often not sufficient and is supplemented with: Metabolic examination Ability to use oxygen Ability to degrade nutrients and produce enzymes Ability to grow at different pH values and at different temperatures Other methods: use of bacterial viruses “bacteriophages” use of serology: antibody – antigen reactions Genetic differentiation Based on sequence of 16S rRNA gene (not usual in clinical settings) DNA hybridization, PCR