1-8 microbio Flashcards
what 4 classes of organisms are said to be microbes?
- bacteria
- archaea
- fungi
- protists
how much microbial carbon, nitrogen and phosphorus is there in comparison to plants? (measuring using biomass)
- microbial carbon equals that of plants
- microbial nitrogen and phosphorus are over 10x what is found in total plant biomass
what reasons are there for such a large number of microbes in the environment?
- rapid growth rate
- many chances of speciation through random mutation
- lateral gene transfer
- every available niche is occupied by specifically adapted microbes
- long evolutionary history
what nutritional categories can microbes be classified using?
- sources of energy
- electron donors
- cell carbon
what are the two microbe classifications using sources of energy?
- phototrophs - gain energy from light
- chemotrophs - gain energy from chemical bonds
what are the two microbe classifications using electron donors?
organotrophs - uses organic compounds as electron donors
lithotrophs - uses inorganic compounds as electron donors
what are the two microbe classifications using cell carbon?
autotrophs - use CO2 as their carbon source
heterotrophs - use organic compounds as their carbon source
what are the primary nutrients required by microbes?
the primary nutrients are:
- macronutrients (e.g. C,HO,N,S,K.Na)
- micronutrients (trace metals) (e.g. B,Cr,Co,Fe)
can phototrophs synthesise all their own cellular components?
yes
can fastidious bacteria synthesis their own cellular components?
no
what are the 4 main stages of microbial growth?
- lag phase
- log/exponential phase
- stationary phase
- death phase
why do colonies enter the stationary phase?
growth is inhibited by the limitation of nutrients and build up of waste products
why may there be some cell division in the death phase?
when cells lyse in the death phase, other cells can feed off these cells in the media
how can growth of a colony be measured?
- cell number
- optical density
- fresh/dry weight
- protein
- DNA
what is the problem with identification of microorganisms?
- there is limited morphological diversity, so most microbes look similar down a microscope
what are the traditional methods of microorganism identification?
- microscopy and staining
- growth on selective/differential media
- resting substrate spectrum supporting growth
- testing enzyme activity
- characteristics of cell chemical constituents
what occurs in modern methods of microorganism identification?
- mainly based on sequencing the specific conserved genes
what is the test used for measuring enzyme activity called and how is it carried out?
-ApiZym
- mainly optimised towards pathogens and comparing pathogenic and benign strains
1 - a culture of the bacteria is grown
2 - cells are resuspended in a buffer
3 - the resulting colour in the test strip is compared against a database
describe the surface origin hypothesis
- it describes an environment where all the nutrients were available that were needed for life and that organic molecules formed spontaneously
- this in unlikely due to hostile surface conditions at that time
describe the subsurface origin theory
- life began in hydrothermal vents at the ocean floor
- there was a constant source of energy present from reduced inorganic compounds
what is the current timeline given for the origin of cellular life?
1 - in subsurface vents, thermal energy can drive the production of compounds from organic elements
2 - self replicating RNA (ribozymes) and enzymatic proteins are present so lipid bilayers form around this material
3 - some organisms began using amino acid compounds as well as ribozymes and began to produce proteins
4 - DNA begins to be used as the genetic code and biochemical pathways begin to evolve
5 - the Last Universal Common Ancestor is formed and the lineage splits by division of lipid biosynthesis and of cell walls to produce bacteria and archaea
what are the requirements for a molecule to be used as a molecular marker?
- it must be universal
- it must contain variable and conserved regions
- it must not be subject to horizontal gene transfer
- it must be truly homologous
how is it theorised that mitochondria, chloroplast, and nuclei were acquired to produce eukaryotic organisms?
- mitochondria may have been acquired by endosymbiosis
- chloroplast were nearly certainly acquired by endosymbiosis
- nucleus formation is more likely to have been a physical event
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what is the hydrogen hypothesis?
- association of an archaeal host using hydrogen as an energy source with an aerobic bacteria producing hydrogen as a waste product
- the archaeal cell completely surround bacteria
describe the aquifex organism
- isolated from a hot spring (hyperthermophilic)
- one of the deepest branching bacterial phyla
- chemolithoautotroph
what is the unique feature of deinococcus?
they are extremely radiation resistant by very rapidly assembling radiation damaged DNA
define microbial systematics
the study of the diversity of organisms and their relationships
why can the definition of a species used for higher organisms not be applied to microbiology?
- asexual reproduction
- lateral gene transfer
- phenotypic and genotypic plasticity of microorganisms
what is the current definition of species used for microorganisms?
a group of strains that show a high degree of overall similarity and differ considerably from related strain groups with respect to many independent characteristics
how is phenotypic analysis used to define bacterial taxonomy?
- results are compared with a type culture
how is morphology used in bacterial taxonomy?
- Gram stain
- presence of flagella, capsules, staining reactions etc
what physiological properties are used to compare bacterial strains?
- growth pH
- barophiles (requiring high pressures)
- halophiles
- response to oxygen
- hyperthermophiles
describe the structure of the capsule of microbial cells
- made up of polysaccharide components outside of the cell wall
what is the glyocalyx involved in?
biofilm formation
what is the difference between a capsule, a glycocalyx, and a slime layer?
- a capsule is more tight and organised than a glycocalyx and is not easily removed
- slime layers are more unorganised and easily removed
what is the role of a capsule?
- not required for growth or reproduction
- they are carbon stores
- provide protection against desiccation
- may be involved in the capture of nutrients
- attachment to surfaces
- often resist phagocytosis
what is the S-layer?
- a paracrystalline outer wall layer composed of protein or glycoprotein
- a regularly structured layer which is external to the cell wall
- may protect against ion and pH fluctuation. osmotic stress, associated with predators
what is murein made up of?
- it is made up of alternating residues of NAG and NAM
- they are arranged in dimers which are crosslinked by amino acid side chains creating amide bonds
what are the non-protein amino acids involved in peptidoglycan?
- D-glutamic acid
- D-alanine
- DAPA
- D-amino acids protect against degradation by proteases
what is the difference between Gram negative and Gram positive cell walls?
gram + cell walls are thicker than Gram - , 90% of the thickness of the cell wall is peptidoglycan in Gram +ve and 10% in Gram -ve
what are lysozymes?
- they are ‘antibacterial enzymes’
- they degrade the beta 1,4-glycosidic bonds in the peptidoglycan backbone
how are archaeal cell walls different to bacterial cell walls?
- they do not contain peptidoglycan
- some methanogens contain pseudomurein
- other archaeal cell walls contain other polysaccharide, glycoproteins, or S-layers
what are hopanoids?
- they are present in bacterial cell membranes
- they are rigid planar molecules which stabilise the membrane structure
what are hopanoids?
- they are present in bacterial cell membranes
- they are rigid planar molecules which stabilise the membrane structure
what structures are used in archaea instead of hopanoids?
isoprene structures
describe the outer membrane of bacterial cells
- the OM is only present in Gram -ve cells
- Braun lipoproteins are the most abundant proteins in the OM are are linked to peptidoglycan
describe the structure of archaeal membranes
- branched chain hydrocarbons are attached to glycerol by ether links rather than fatty acid-ester links
- isoprene comes off the side
what is lipopolysaccharide made up of?
- it is a large complex molecule containing lipid and carbohydrate
- it is made up of Lipid A, core polysaccharide, O side chain
what is lipopolysaccharide called when it is free in the host?
endotoxin
what can endotoxin induce in the host?
septic shock
what is lipid A made up of?
- it is made up of glucosamine residues linked to fatty acids and phosphate
- it anchors LPS into the membrane
- remaining LPS projects from the cell surface
what is the core polysaccharide comprised of?
- it often has side chains of NAG, phosphates, and ethonolamine
in what bacteria does the core polysaccharide contain unusual sugar residues?
salmonella
what is the O side chain and what is it made of?
- it is a variable region responsible for the antigenic makeup of bacteria
- it extends outwards from the cell
what trait of bacteria is dependent on the O side chain length?
whether the bacteria is rough or smooth
what is the function of LPS?
- lipid A stabilises the outer membrane structure
- the core polysaccharide is charged and contributes to the negative charge on the surface
- protects against host defences
are rough or smooth bacterial variants more susceptible to phagocytosis?
rough
when is endotoxin released?
it is released during cell division or by lysis of bacterial cells
what are the specific properties of endotoxin?
- it is heat stable
- it is toxic in nanogram amounts
how does endotoxin interact with the innate immune system?
- it can trigger the release of cytokines in a cascade
- it activates transcription factors such as tumor necrosis factor and interferon B
what makes the outer membrane of bacteria more permeable than the inner membrane
porins
what are porins?
protein channels that permit the passage of small molecules
what is the periplasm?
it is the space between the outer membrane and cytoplasmic membrane
what enzyme activity occurs in the periplasm?
- nutrient acquisition
- energy conservation
- peptidoglycan synthesis enzymes
- periplasmic binding proteins deliver specific compounds to ABC transporters
how is the Sec pathway used in the protein export into the periplasm?
- it exports nascent polypeptide through the cytoplasmic membrane using a translocase
- folding of the pathway occurs after translocation
how is the TAT pathways used to export protein into the periplasm?
- it exports fully folded enzymes across the cytoplasmic membrane
- proteins have a twin arginine in the n terminal region
define what a flagella is
long thin extracellular helical structures made of protein subunits that aid in mobility
what is the general structure of a flagella?
- it is composed of a series of complex ring structures anchored into the membrane and cell wall or outer membrane
- the shaft, tip, and hook have different antigenic properties
- the filament is made of a single protein called flagellin
how is the flagella motor driven?
- the motor is driven due to the transfer of protons through the ring structure
- the power is provided by the basal structures
where does growth occur in flagella?
- at the tip
what is the order in which structures are synthesised to produce flagella?
1 - MS or C rings in the cytoplasmic membrane
2 - motor proteins
3 - P and L ring, hook, and cap
4 - the flow of flagellin through the hook to grow the filament
what is a monotrichous flagella?
a single flagella that protrudes out of one side of the cell
which pathogen possesses a monotrichous flagella?
Vibrio cholerae
what is an amphitrichous flagella?
a flagella that comes out both ends of the cell
which pathogen has an amphitrichous flagella?
Campylobacter jejuni
what are lophotrichous flagella?
- one or multiple flagella at both ends of the cell
- can be monopolar or bipolar
what are peritrichous flagella?
flagella everywhere?
what pathogen has peritrichous flagella?
E. coli
what occurs when a bacteria ‘runs’?
- the motor rotates anticlockwise
- the flagellar filaments form a bundle and propel the cell
what happens when a bacteria ‘tumbles’?
- the motor quickly reverses to clockwise motion
- this causes the bundle to fall apart
what is the use of running and tumbling for bacteria?
- it allows bacteria to move towards favourable conditions or move away from unfavourable conditions
define aerotaxis in bacterial movement
movement usually towards oxygen
define chemotaxis in bacterial movement
movement usually towards nutrients but also away from toxins
what transmembrane proteins in bacteria detect nutrient concentrations in the environment?
methyl accepting chemotaxis proteins
how do methyl accepting chemotaxis proteins interact with cytoplasmic proteins?
Che proteins interact with the turning of the motor to dictate runs and tumbles
describe signal recognition between methyl accepting chemotaxis proteins and Che proteins
1 - the signal is recognised by MCPs
2 - MCP interacts with CheA which can autophosphorylate
3 - phosphorylate CheA phosphorylates CheY
4 - phosphorylated CheY binds to the flagella motor, causing tumbling
how does MCP/CheA signal recognition adapt over time?
- the cell integrates a/r signals via MCP methylation by CheR
- fully methylated MCP is insensitive to any environmental attractant
- CheB is phosphorylated by CheA and demethylates MCP, increasing sensitivity to the attractant
- high concentrations of repellent result in longer runs and less tumbling
how does a cell glide without a flagella?
- the cell pulls along slime extruded on the outside
what bacteria are known to glide?
cyanobacteria
what is twitching motility in bacteria?
- type IV pili extend from the cell surface and then retract it and drag the cell along a surface
- powered by ATP hydrolysis
what are gas vesicles?
- they are present in planktonic bacteria and some archaea
- they confer buoyancy and allow cells to float up to oxygenated water or towards light
are both fimbriae and pili bacterial adhesins?
yes
do fimbriae or pili join 2 cells together?
pili
can fimbriae and pili aid resistance to phagocytosis?
yes
how do type IV pili use their adhesive tip protein?
1 - they establish initial contact to the host cell
2 - the adhesive tip protein binds to a receptor
3 - the pili depolymerizes and pulls the bacterium close to the host cell
describe the structure and function of type I fimbriae
- important virulence factor in many pathogens
- thin
- made up of 500-3000 subunits of FimA protein stacked in a helical cylinder
- FimH is the tip adhesin which binds to b-mannose containing structures
- FimF and FimG link the Fim71 adhesin onto the fimbriae
- in the export system FimC acts as a chaperone and FimD as an usher protein
how does FimD act as an usher protein?
FimD catalyses FimA polymerisation at the base of the pili
what are P-pili also known as?
Pyelonephritis-Associated-Pili
describe the structure and function of P-pili
- it is a critical virulence factor of uropathogenic E.coli
- similar in structure and assembly to type I fimbriae but uses PapG as the tip adhesin
describe the distribution and structure of type IV pili
- widely distributed in Gram negative bacteria, but also in some Gram positive
- typically longer and only a few pili per cell
- often aggregate laterally to form bundles
describe the roles of type IV pili
- host cell adhesion
- biofilm formation
- forming microcolonies
what are colonising factor antigens?
- they are pili that E.coli possess
- allows the bacteria to adhere to tissues such as the small intestine and the urinary tract where they produce toxins
describe the structure and functions of the F pilus
- found on many Gram negative bacteria (all of which are plasmid encoded)
- has a channel in the middle
- involved in the transfer of genetic information
- forms a helical arrangement
- attracts via the tip and retracts to bring the cells together
what are bacterial endospores?
- they form inside the bacterial cell
- represent a dormant stage in the bacterial life cycle
- extremely resistant to heat, desiccation, and radiation
- form when stress occurs in a vegetative cell
- disperse through wind, water, and faeces
- only produced by Gram positive cells
what is sporulation?
- a complex series of cellular differentiation events
- environmental triggers switch on sporulation genes
describe the process of sporulation
1 - a vegetative cell comes under stress so DNA organises along the cell axis
2 - forespore is produced which a genome copy which is engulfed in a second membrane by the cell membrane
3 - the cortex between membranes becomes dehydrated
4 - complete exosporium layers are produced and the spore matures which complex cortical layers
5 - cell lyses releasing the spores
describe the structure of endospores
- the exosporium is a thin layer of protein for dispersal
- the spore coat consists of spore specific proteins
- they possess a peptidoglycan cortex
- the inside contains the genome, cytoplasm, and ribosomes but is metabolically inactive
- ## small acid soluble proteins maintain genome integrity
why does germination occur?
- caused by the uptake of water and amino acids
how do tears act as a barrier to infection?
- lysozymes in tears dissolve cell walls
how do airways act as a barrier to infection?
- cilia remove small particles
- the mucus suspends microorganisms in mucus
how does the skin act as a barrier to infection?
- a physical barrier
- produces antimicrobial fatty acids, its normal flora inhibits pathogen colonisation
how does the gut microflora act as a barrier to infection?
it competes with pathogens for nutrients
how do blood proteins act as an infection barrier?
they inhibit microbial growth
define what is thought of as a microbiome
the ecological community of commensal, symbiotic, and pathogenic organisms that share our body space
what do virulence factors generally aid a pathogen in?
- adhesion to and entry into cells
- antiphagocytic activity, immune system evasion
- production of toxins
