Prokaryote Morphology and Structure: 3050 Section 2 Slides PDF

The components and structures of microbes Chapters 2, 15  Prokaryote morphology many different shapes and structures found in prokaryotes cell shape is a genetic trait, usually mediated by specific proteins that determine the shape of the cell wall material as it is being synthe...

The components and structures of microbes Chapters 2, 15  Prokaryote morphology many different shapes and structures found in prokaryotes cell shape is a genetic trait, usually mediated by specific proteins that determine the shape of the cell wall material as it is being synthesized e.g., Escherichia coli RodA protein - if you make a mutant strain that doesn’t have the rodA gene the cells are spherical  Geeking out on morphology one very common structure is the “curved rod” why is this shape so common? scientists analyzed bacteria with this shape in terms of curvature versus length  Geeking out on morphology one very common structure is the “curved rod” why is this shape so common? swimming chemotaxis ”difficulty” to studied the properties of cells with make the cell different curvatures versus lengths shape for performance in different functions Geeking out on morphology swimming efficiency  Geeking out on morphology conclusions: there is a trade-off between the different properties, so there is no “perfect shape”, and evolution will act on different species to produce the shape that is most suited to their habitat  Relative sizes of prokaryotes prokaryotes are generally small, but there is a very large range of sizes changes in size dramatically affect the cell volume  The importance of being small cells need to get things in and out to survive transport rates in and out of the cell are related to cell’s surface area so, the size of the cell affects rates that nutrients and wastes pass in and out, and bigger cells have higher transport “potential” but you need to have the appropriate concentration of nutrients to meet the needs for growth  The importance of being small cells need to get things in and out to survive transport rates in and out of the cell are related to cell’s surface area so, the size of the cell affects rates that nutrients and wastes pass in and out, and bigger cells have higher transport “potential” but you need to have the appropriate concentration of nutrients to meet the needs for growth smaller cells have larger surface/volume ratios makes them more efficient and capable of faster growth and larger population sizes  Relative sizes of prokaryotes surface:volume ratios: P. ubique 22 E. coli 4.5 E. fishelsoni 0.05 P. ubique is the most abundant bacterium in the ocean and therefore one of the most abundant bacteria on the planet  Sizes of prokaryotes Epulopiscium fishelsoni ~0.6 mm long this large size is rare, limited to specific environments and physiologies for this bacterium, each cell contains 100s of copies of the DNA genome – needed to provide enough mRNA and protein throughout the huge interior volume of the cell  Sizes of prokaryotes this tiny bacterium is ~1/150 the size of E. coli passes through a 0.22-um filter (often used to sterilize liquids) was found in anaerobic groundwater that originated in the deep subsurface is this super small size an advantage in its nutrient-poor environment? Prokaryote cell structures - the wall The cell wall is extremely important for the functioning of cells  The cytoplasmic membrane directly surrounds the cell’s cytoplasm phospholipid bilayer 6-8 nm thick  Structure of phospholipids structures of phospholipids are different in the different domains Phospholipid = hydrophilic “head” + hydrophobic “tails” Bacteria: head = glycerol + phosphate tails = fatty acids connected by ester linkage  Structure of phospholipids structures of phospholipids are different in the different domains connected by Archaea: ether linkage head = glycerol + phosphate tails = phytanyl (repeated isoprene units linked together)  Structure of phospholipids structures of phospholipids are different in the different domains different Archaea have different tail structures some have lipid some have lipid monolayers made monolayers made of of crenarchaeol biphytanyl  Archaeal membranes lipid monolayers are widespread among hyperthermophilic Archaea more resistant to higher temperatures because the two halves cannot be separated  Cytoplasmic membrane many proteins: ~ half the membrane space is made up of proteins (enzymes, transport proteins, etc.) integral proteins: inserted into the membrane peripheral proteins: associated with membrane surface lipoproteins: attached to the membrane by a lipid molecule Cytoplasmic membrane functions the CM performs many important functions for the cell  Transport vs. diffusion some things pass through membranes easily (e.g., water), but charged molecules cannot go through on their own cells need to get many charged molecules in and out of the cell in order to function actively bring substances across the membrane with specific transporters the transporters are much more efficient at getting things across the membrane in comparison with waiting for diffusion to happen, but transport requires energy Transport across membranes transport requires energy simple transport: substance is transported across membrane using energy of proton motive force Transport across membranes transport requires energy ABC transporters: 3 protein components: periplasmic binding protein, transporter, ATP-hydrolyzing protein (energy from ATP) ABC system = ATP-Binding Cassette Transport across membranes transport requires energy group translocation: substance is altered as it crosses the membrane and uses energy from a phosphate bond  Prokaryotic cell walls cell wall provides structure and shape, and protects cell from osmotic forces Bacteria can be divided into two groups based on cell wall structure: Gram-negative Gram-positive Bacteria and Archaea have different cell wall structures  Cell wall functions one of the important functions of the cell wall is to protect the cell from lysing due to osmotic forces one of our body’s innate anti-bacterial defenses is to produce the enzyme LYSOZYME in our secretions (e.g. tears, saliva) which breaks open the cell wall and then the bacterium gets lysed by osmotic forces  Cells without walls some Bacteria, the Mollicutes (= soft), which includes the genus Mycoplasma, do not have cell walls and are only surrounded by membranes also some Archaea in the genus Thermoplasma  Bacterial cell walls Gram-positive cells have a a thick layer of peptidoglycan surrounding their cytoplasmic membrane  Bacterial cell walls Gram-negative cells have a a thin layer of peptidoglycan outside the cytoplasmic membrane and then an outer membrane surrounding that  Peptidoglycan peptidoglycan (also called murein) is only found in Bacteria made of sugars (glycans) NAG (N-acetylglucosamine) NAM (N-acetylmuramic acid) and a short peptide (often 4 amino acids, but varies among species) glycans peptide Peptidoglycan neighbouring chains of the glycans are linked by covalent attachments between peptide chains  Peptidoglycan the structures of peptidoglycan from Gram-negative and Gram-positive bacteria are different due to use of different peptides and cross-linking  The peptidoglycan layer the connections between the glycans along the chain and then between peptide chains make peptidoglycan into 1 very large molecule that surrounds the cell and it is very strong in all directions Gram-positive cell walls thick layer of peptidoglycan surrounding the CM G+ cell walls also contain teichoic acids, and some are covalently linked to lipids to form lipoteichoic acids, which attach the peptidoglycan layer to the membrane  Gram-negative cell walls more complex than G+ walls thin layer of peptidoglycan (outside CM, in periplasm) also an outer membrane, which is very different than the cytoplasmic membrane - phospholipids, proteins, and lipopolysaccharide (LPS)  The periplasm space between inner and outer membranes is called the periplasm, and a lot of important cell functions happen there contains: peptidoglycan, water, compounds that diffuse across the outer membrane also proteins such as: sensors, binding proteins for ABC transporters, enzymes, peptidoglycan synthesis machinery  Lipopolysaccharide (LPS) LPS makes up the outer leaflet of the outer membrane = lipid (Lipid A) + sugars Lipid A is a toxin (“endotoxin”): causes fever, inflammation, shock, and blood clotting when in tissues and blood; vomiting and diarrhea when in the gastrointestinal tract  Porins the outer membrane of Gram- cells is much more permeable than the cytoplasmic membrane contains protein channels called porins that allow small molecules in and out by diffusion  Cell walls in Archaea Bacterial cell walls: G+, G-, or nothing (just CM) Many more different types of cell wall structures in Archaea: Pseudopeptidoglycan Protein layers Polysaccharide Glycoprotein layers  Cell walls in Archaea no peptidoglycan but some have pseudopeptidoglycan similar to peptidoglycan but different glycan structures, different bonds between the glycans, and different peptides  Lysozyme and cell walls bacterial PG is broken by lysozyme pseudoPG has a lysozyme- insensitive structure no archaeal pathogens are known  Beyond the wall capsules and slime layers many cells secrete gelatinous, sticky substances outside cell usually made of polysaccharides capsule: rigid, tight matrix, firmly attached slime layer: not rigid, more difficult to see, loosely attached used for attachment to surfaces, also protect cells from desiccation can prevent some pathogens from being recognized by immune system  Beyond the wall - Fimbriae Fimbriae: proteinaceous extensions used for adherence, not for motility - up to hundreds per cell - shorter than flagella - important for biofilm formation, pathogenesis  Beyond the wall - Pili protein filaments, usually not very numerous on the cell many different types of pili that have different functions: movement (“twitching motility”) attachment (to surfaces, host cells, etc.) gene exchange (transfer of plasmids) conjugation pilus: connects two cells for transfer of DNA plasmids  Beyond the wall - Hami similar to pili, made by some archaea cells hami cells in biofilm have a grappling hook structure at the end, used for attachment to surfaces and to other cells to form a biofilm in their environment  Beyond the wall - Flagella complex, whip-like structure extending beyond cell surface can also be important for disease with some pathogens different species have different numbers and arrangements of flagella peritrichous polar monotrichous lophotrichous  Beyond the wall - Flagella flagella are very thin and impossible to see under bright-field microscopy without staining dark field microscopy phase contrast treated with a microscopy “flagella stain”  Flagella some species can have different polar, monotrichous numbers and arrangements under different conditions Rhodocista centenaria has a polar monotrichous flagellum in liquid broth but forms “swarmer cells” with peritrichous flagella when growing on agar plates and moves towards light across the surface peritrichous  Flagellar machinery is in the wall FILAMENT the flagellum is a complex molecular motor uses a large amount of protein resources to make HOOK and a lot of energy to rotate BASAL BODY  Flagellar function depends on the cytoplasmic membrane the flagellum is turned using energy from the proton motive force (moving H+ across the CM) and interactions between the motor and ring proteins  Flagellar machinery is in the wall flagella are built in an ordered fashion, inside to outside requires many genes and proteins energetically expensive to make and use filament = 20,000 copies of a protein called flagellin also functions as a protein export machine because the outer protein components travel through the proteins in the wall to get outside  Swimming with Flagella how the cell moves is determined by the the direction the flagellum/flagella turn, which is controlled by molecular interactions involving the motor inside the cell peritrichous flagella: counter-clockwise (CCW) rotation makes the cells swim (called a “run”) and clockwise (CW) makes them stop swimming and jiggle around (called a “tumble”)  Swimming with Flagella how the cell moves is determined by the the direction the flagellum/flagella turn which is controlled by molecular controls acting on the motor inside the cell polar flagellum: cells reorient in the liquid when rotation stops and then swim in a different direction  Archaella archaea have structures similar to flagella, called archaella similar functionally, but genetically distinct from flagella more closely related to bacterial pili thinner than flagella, the cells cannot swim as fast as bacteria with flagella use ATP for energy  Taxis – movement with a purpose cell movements are not usually just random most mobile microbes make directed movements toward or away from stimuli sensory response controls the flagellar rotation chemotaxis: response to chemicals via chemoreceptors phototaxis: response to light via photoreceptors  Taxis – movement with a purpose cells move towards things they want/need: nutrients (e.g. sugars, amino acids), oxygen (for aerobes) = attractants and away from things that are harmful = repellents  Chemotaxis in the absence of chemical stimuli, e.g. an attractant such as a food source, movements random in the presence of an attractant, runs become biased so that the cell moves towards it Observing chemotaxis in “the real world” tracking bacterial cells’ movements near an algal cell that is producing oxygen and releasing nutrients the bacteria use the bacterial cells are concentrated closer to the algal cell and their movements biased to keep them close Phototaxis many microbes that use light as their energy source (phototrophs) will swim towards light, and even towards specific wavelengths of light they sense specific wavelengths of light, which can be observed under the microscope when the different wavelengths are distributed across the slide Movement with intracellular structures: gas vesicles some cells that live in aquatic environments can regulate their buoyancy with gas vesicles e.g., many cyanobacteria the cells are not actively swimming, but changing their buoyancy changes the depth they will be at in the water (can go up or down) Movement with intracellular structures: gas vesicles can often see gas vesicles in the microscope because they refract light and appear bright fairly simple structure made of proteins that form a “bag” that’s filled with gas so makes the cells float higher in the water  Movement using magnets magnetosomes: made of magnetite (Fe3O4), surrounded by a membrane, make bacteria act like small magnets hypothesized that they are used to sense the Earth’s magnetic field, which directs the bacteria downward in the water or sediment (in place of sensing gravity) they migrate along magnetic field lines: magnetotaxis like environments with a small amount of O2 and also reduced inorganic nutrients  Other intracellular structures other chunks of stuff are often seen in cells, many of which function in storage of energy/carbon reserves e.g., poly-hydroxyalkanoates (PHAs = lipid-like polymers) chunks of sulfur polyphosphate (in the periplasm)  Endospores produced by some Gram+ bacteria- e.g., Bacillus and Clostridium sporulation transforms vegetative cell into endospore: spores form when the bacterium runs out of nutrients and begins to starve - the spore is not physiologically active and can survive for long periods of time germination happens when the spore senses better conditions: endospore germinates to become a new vegetative cell  Endospores stable resting state for the organism resistant to drying, heat, radiation, and toxic chemicals viable for an indefinite time spores are very different than vegetative cells  Endospores different species form their spores at different locations in the cells like cell shape, this is a genetic trait  Endospores versus other spores formation of endospores is restricted to some species within the Gram-positive lineage of Bacteria (not all G+ bacteria make endospores) some other bacteria, such as Streptomyces, form spores but they are different from endospores and function in dispersal, not as a shut-down resting stage  Eukaryotic cell structure depending on the type, eukaryotic cells can contain many different intracellular organelles and compartments, and extracellular structures  Eukaryotic flagella and cilia -completely different structure and mechanism of movement compared to bacterial flagella -much larger, made up of microtubules -move like a whip, not by rotation like bacterial flagellum cilia look like fimbriae, but they function like small “oars” for movement of the cell  Eukaryotic structures mitochondria: evolved from a bacterium site of respiration, oxidation of organic compounds (i.e. TCA cycle)  Eukaryotic structures phototrophic eukaryotes contain chloroplasts, which evolved from cyanobacteria pigments fluoresce use light energy to energize electrons that drive the synthesis of ATP and allow the conversion of CO2 to glucose