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agents of infectious disease > 1-8 microbio > Flashcards

1-8 microbio Flashcards

1
Q

what 4 classes of organisms are said to be microbes?

A
  • bacteria
  • archaea
  • fungi
  • protists
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2
Q

how much microbial carbon, nitrogen and phosphorus is there in comparison to plants? (measuring using biomass)

A
  • microbial carbon equals that of plants
  • microbial nitrogen and phosphorus are over 10x what is found in total plant biomass
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3
Q

what reasons are there for such a large number of microbes in the environment?

A
  • 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
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4
Q

what nutritional categories can microbes be classified using?

A
  • sources of energy
  • electron donors
  • cell carbon
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5
Q

what are the two microbe classifications using sources of energy?

A
  • phototrophs - gain energy from light
  • chemotrophs - gain energy from chemical bonds
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6
Q

what are the two microbe classifications using electron donors?

A

organotrophs - uses organic compounds as electron donors
lithotrophs - uses inorganic compounds as electron donors

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7
Q

what are the two microbe classifications using cell carbon?

A

autotrophs - use CO2 as their carbon source
heterotrophs - use organic compounds as their carbon source

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8
Q

what are the primary nutrients required by microbes?

A

the primary nutrients are:
- macronutrients (e.g. C,HO,N,S,K.Na)
- micronutrients (trace metals) (e.g. B,Cr,Co,Fe)

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9
Q

can phototrophs synthesise all their own cellular components?

A

yes

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10
Q

can fastidious bacteria synthesis their own cellular components?

A

no

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11
Q

what are the 4 main stages of microbial growth?

A
  • lag phase
  • log/exponential phase
  • stationary phase
  • death phase
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12
Q

why do colonies enter the stationary phase?

A

growth is inhibited by the limitation of nutrients and build up of waste products

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13
Q

why may there be some cell division in the death phase?

A

when cells lyse in the death phase, other cells can feed off these cells in the media

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14
Q

how can growth of a colony be measured?

A
  • cell number
  • optical density
  • fresh/dry weight
  • protein
  • DNA
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15
Q

what is the problem with identification of microorganisms?

A
  • there is limited morphological diversity, so most microbes look similar down a microscope
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16
Q

what are the traditional methods of microorganism identification?

A
  • microscopy and staining
  • growth on selective/differential media
  • resting substrate spectrum supporting growth
  • testing enzyme activity
  • characteristics of cell chemical constituents
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17
Q

what occurs in modern methods of microorganism identification?

A
  • mainly based on sequencing the specific conserved genes
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18
Q

what is the test used for measuring enzyme activity called and how is it carried out?

A

-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

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19
Q

describe the surface origin hypothesis

A
  • 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
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20
Q

describe the subsurface origin theory

A
  • life began in hydrothermal vents at the ocean floor
  • there was a constant source of energy present from reduced inorganic compounds
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21
Q

what is the current timeline given for the origin of cellular life?

A

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

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22
Q

what are the requirements for a molecule to be used as a molecular marker?

A
  • 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
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23
Q

how is it theorised that mitochondria, chloroplast, and nuclei were acquired to produce eukaryotic organisms?

A
  • 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
    78
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24
Q

what is the hydrogen hypothesis?

A
  • 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
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25
Q

describe the aquifex organism

A
  • isolated from a hot spring (hyperthermophilic)
  • one of the deepest branching bacterial phyla
  • chemolithoautotroph
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26
Q

what is the unique feature of deinococcus?

A

they are extremely radiation resistant by very rapidly assembling radiation damaged DNA

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27
Q

define microbial systematics

A

the study of the diversity of organisms and their relationships

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28
Q

why can the definition of a species used for higher organisms not be applied to microbiology?

A
  • asexual reproduction
  • lateral gene transfer
  • phenotypic and genotypic plasticity of microorganisms
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29
Q

what is the current definition of species used for microorganisms?

A

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

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30
Q

how is phenotypic analysis used to define bacterial taxonomy?

A
  • results are compared with a type culture
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31
Q

how is morphology used in bacterial taxonomy?

A
  • Gram stain
  • presence of flagella, capsules, staining reactions etc
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32
Q

what physiological properties are used to compare bacterial strains?

A
  • growth pH
  • barophiles (requiring high pressures)
  • halophiles
  • response to oxygen
  • hyperthermophiles
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33
Q

describe the structure of the capsule of microbial cells

A
  • made up of polysaccharide components outside of the cell wall
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34
Q

what is the glyocalyx involved in?

A

biofilm formation

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35
Q

what is the difference between a capsule, a glycocalyx, and a slime layer?

A
  • a capsule is more tight and organised than a glycocalyx and is not easily removed
  • slime layers are more unorganised and easily removed
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36
Q

what is the role of a capsule?

A
  • 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
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37
Q

what is the S-layer?

A
  • 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
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38
Q

what is murein made up of?

A
  • 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
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39
Q

what are the non-protein amino acids involved in peptidoglycan?

A
  • D-glutamic acid
  • D-alanine
  • DAPA
  • D-amino acids protect against degradation by proteases
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40
Q

what is the difference between Gram negative and Gram positive cell walls?

A

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

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41
Q

what are lysozymes?

A
  • they are ‘antibacterial enzymes’
  • they degrade the beta 1,4-glycosidic bonds in the peptidoglycan backbone
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42
Q

how are archaeal cell walls different to bacterial cell walls?

A
  • they do not contain peptidoglycan
  • some methanogens contain pseudomurein
  • other archaeal cell walls contain other polysaccharide, glycoproteins, or S-layers
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43
Q

what are hopanoids?

A
  • they are present in bacterial cell membranes
  • they are rigid planar molecules which stabilise the membrane structure
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44
Q

what are hopanoids?

A
  • they are present in bacterial cell membranes
  • they are rigid planar molecules which stabilise the membrane structure
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45
Q

what structures are used in archaea instead of hopanoids?

A

isoprene structures

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46
Q

describe the outer membrane of bacterial cells

A
  • the OM is only present in Gram -ve cells
  • Braun lipoproteins are the most abundant proteins in the OM are are linked to peptidoglycan
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47
Q

describe the structure of archaeal membranes

A
  • branched chain hydrocarbons are attached to glycerol by ether links rather than fatty acid-ester links
  • isoprene comes off the side
48
Q

what is lipopolysaccharide made up of?

A
  • it is a large complex molecule containing lipid and carbohydrate
  • it is made up of Lipid A, core polysaccharide, O side chain
49
Q

what is lipopolysaccharide called when it is free in the host?

A

endotoxin

50
Q

what can endotoxin induce in the host?

A

septic shock

51
Q

what is lipid A made up of?

A
  • 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
52
Q

what is the core polysaccharide comprised of?

A
  • it often has side chains of NAG, phosphates, and ethonolamine
53
Q

in what bacteria does the core polysaccharide contain unusual sugar residues?

A

salmonella

54
Q

what is the O side chain and what is it made of?

A
  • it is a variable region responsible for the antigenic makeup of bacteria
  • it extends outwards from the cell
55
Q

what trait of bacteria is dependent on the O side chain length?

A

whether the bacteria is rough or smooth

56
Q

what is the function of LPS?

A
  • 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
57
Q

are rough or smooth bacterial variants more susceptible to phagocytosis?

A

rough

58
Q

when is endotoxin released?

A

it is released during cell division or by lysis of bacterial cells

59
Q

what are the specific properties of endotoxin?

A
  • it is heat stable
  • it is toxic in nanogram amounts
60
Q

how does endotoxin interact with the innate immune system?

A
  • it can trigger the release of cytokines in a cascade
  • it activates transcription factors such as tumor necrosis factor and interferon B
61
Q

what makes the outer membrane of bacteria more permeable than the inner membrane

A

porins

62
Q

what are porins?

A

protein channels that permit the passage of small molecules

63
Q

what is the periplasm?

A

it is the space between the outer membrane and cytoplasmic membrane

64
Q

what enzyme activity occurs in the periplasm?

A
  • nutrient acquisition
  • energy conservation
  • peptidoglycan synthesis enzymes
  • periplasmic binding proteins deliver specific compounds to ABC transporters
65
Q

how is the Sec pathway used in the protein export into the periplasm?

A
  • it exports nascent polypeptide through the cytoplasmic membrane using a translocase
  • folding of the pathway occurs after translocation
66
Q

how is the TAT pathways used to export protein into the periplasm?

A
  • it exports fully folded enzymes across the cytoplasmic membrane
  • proteins have a twin arginine in the n terminal region
67
Q

define what a flagella is

A

long thin extracellular helical structures made of protein subunits that aid in mobility

68
Q

what is the general structure of a flagella?

A
  • 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
69
Q

how is the flagella motor driven?

A
  • the motor is driven due to the transfer of protons through the ring structure
  • the power is provided by the basal structures
70
Q

where does growth occur in flagella?

A
  • at the tip
71
Q

what is the order in which structures are synthesised to produce flagella?

A

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

72
Q

what is a monotrichous flagella?

A

a single flagella that protrudes out of one side of the cell

73
Q

which pathogen possesses a monotrichous flagella?

A

Vibrio cholerae

74
Q

what is an amphitrichous flagella?

A

a flagella that comes out both ends of the cell

75
Q

which pathogen has an amphitrichous flagella?

A

Campylobacter jejuni

76
Q

what are lophotrichous flagella?

A
  • one or multiple flagella at both ends of the cell
  • can be monopolar or bipolar
77
Q

what are peritrichous flagella?

A

flagella everywhere?

78
Q

what pathogen has peritrichous flagella?

A

E. coli

79
Q

what occurs when a bacteria ‘runs’?

A
  • the motor rotates anticlockwise
  • the flagellar filaments form a bundle and propel the cell
80
Q

what happens when a bacteria ‘tumbles’?

A
  • the motor quickly reverses to clockwise motion
  • this causes the bundle to fall apart
81
Q

what is the use of running and tumbling for bacteria?

A
  • it allows bacteria to move towards favourable conditions or move away from unfavourable conditions
82
Q

define aerotaxis in bacterial movement

A

movement usually towards oxygen

83
Q

define chemotaxis in bacterial movement

A

movement usually towards nutrients but also away from toxins

84
Q

what transmembrane proteins in bacteria detect nutrient concentrations in the environment?

A

methyl accepting chemotaxis proteins

85
Q

how do methyl accepting chemotaxis proteins interact with cytoplasmic proteins?

A

Che proteins interact with the turning of the motor to dictate runs and tumbles

86
Q

describe signal recognition between methyl accepting chemotaxis proteins and Che proteins

A

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

87
Q

how does MCP/CheA signal recognition adapt over time?

A
  • 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
88
Q

how does a cell glide without a flagella?

A
  • the cell pulls along slime extruded on the outside
89
Q

what bacteria are known to glide?

A

cyanobacteria

90
Q

what is twitching motility in bacteria?

A
  • type IV pili extend from the cell surface and then retract it and drag the cell along a surface
  • powered by ATP hydrolysis
91
Q

what are gas vesicles?

A
  • they are present in planktonic bacteria and some archaea
  • they confer buoyancy and allow cells to float up to oxygenated water or towards light
92
Q

are both fimbriae and pili bacterial adhesins?

A

yes

93
Q

do fimbriae or pili join 2 cells together?

A

pili

94
Q

can fimbriae and pili aid resistance to phagocytosis?

A

yes

95
Q

how do type IV pili use their adhesive tip protein?

A

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

96
Q

describe the structure and function of type I fimbriae

A
  • 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
97
Q

how does FimD act as an usher protein?

A

FimD catalyses FimA polymerisation at the base of the pili

98
Q

what are P-pili also known as?

A

Pyelonephritis-Associated-Pili

99
Q

describe the structure and function of P-pili

A
  • 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
100
Q

describe the distribution and structure of type IV pili

A
  • 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
101
Q

describe the roles of type IV pili

A
  • host cell adhesion
  • biofilm formation
  • forming microcolonies
102
Q

what are colonising factor antigens?

A
  • 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
103
Q

describe the structure and functions of the F pilus

A
  • 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
104
Q

what are bacterial endospores?

A
  • 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
105
Q

what is sporulation?

A
  • a complex series of cellular differentiation events
  • environmental triggers switch on sporulation genes
106
Q

describe the process of sporulation

A

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

107
Q

describe the structure of endospores

A
  • 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
108
Q

why does germination occur?

A
  • caused by the uptake of water and amino acids
109
Q

how do tears act as a barrier to infection?

A
  • lysozymes in tears dissolve cell walls
110
Q

how do airways act as a barrier to infection?

A
  • cilia remove small particles
  • the mucus suspends microorganisms in mucus
111
Q

how does the skin act as a barrier to infection?

A
  • a physical barrier
  • produces antimicrobial fatty acids, its normal flora inhibits pathogen colonisation
112
Q

how does the gut microflora act as a barrier to infection?

A

it competes with pathogens for nutrients

113
Q

how do blood proteins act as an infection barrier?

A

they inhibit microbial growth

114
Q

define what is thought of as a microbiome

A

the ecological community of commensal, symbiotic, and pathogenic organisms that share our body space

115
Q

what do virulence factors generally aid a pathogen in?

A
  • adhesion to and entry into cells
  • antiphagocytic activity, immune system evasion
  • production of toxins

agents of infectious disease (4 decks)

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