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1st year: AID > microbiology (8) (Kevin Purdy) > Flashcards

microbiology (8) (Kevin Purdy) Flashcards

1
Q

number of domains

what are they?

A

3
bacteria
archaea
eukaryotes

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2
Q

bacteria size

A

1-6 μm
largest are visible (almost mm)
lots cell space, storage - makes big

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3
Q

archaea

A

once thought to be bacteria
lots are extremophiles - 1st non extremophile found in 2004
no known pathogenic ones
found everywhere

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4
Q

fungi

what is it and size?

A

eukaryote
size varies enormously
largest is 10,000kg because spreads

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5
Q

protists

what is it and size?

A 
eukaryote
most eukaryotes are protists, very diverse
usually microscopic and unicellular
1-150 μm
e.g. Paramecium
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6
Q

how many cells of microbes on Earth?

A

4.6 x 10^30

more than the number of stars

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7
Q

what gases are mostly inside microbes?

A

nitrogen and phosphorous

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8
Q

phototroph

A

E from light

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9
Q

organotroph

A

use organic compounds like sugars as electron donors

e.g. humans

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10
Q

lithotroph

A

use inorganic compounds like water as electron donors

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11
Q

autotroph

A

use CO2 as carbon source

fixes own carbon

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12
Q

heterotroph

A

use organic carbon as a carbon source

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13
Q

chemotroph

A

energy from chemical bonds

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14
Q

cyanobacteria

A

maybe original chloroplasts

photolithoautotrophs (plants are also this)

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15
Q

E.coli and animals are classed as what in terms of how they use electrons to pass energy around?

A

chemoorganoheterotroph

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16
Q

bacteria are what kind of trophs (can be 2 types)?

and what does this mean

A

prototroph - synthesise all their own cellular components like AAs nucleotides and vitamins

fastidious - need to give them some components in media

some microbes have to be grown in eukaryotic cells if require complex media

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17
Q

complex media

A

like blood, milk, or yeast, of biological origin

exact chemical composition is unknown so complex media is undefined

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18
Q

bacterial growth: asexual reproduction

A

binary fission or budding
double in size then split
exponential growth
sometimes fail to separate so pairs and long chains

all organisms limited by carrying capacity of medium (space/nutrients)

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19
Q

phases of bacterial growth

A

lag phase
log phase
stationary
death

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20
Q

measurements of bacterial growth

A

turbidmetry - light scattered so becomes cloudy (turbid)
weigh biomass
total viable count, colony forming unit - dilute so can count colonies, assume colonies from single cell

identify MOs - microscopy+staining, selective media, test substrates/enzymes for growth, cell characteristics of chemical constituents, sequence genes

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21
Q

selective media

A

allow growth of only some organisms

to identify pathogens from clinical sample

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22
Q

differential media

A

identification based on growth and appearance on medium

colour differences from pH can identify if pathogenic

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23
Q

enzyme activity

A

Apizym test - for pathogens, grow and put cells into wells, compare colour against database

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24
Q

surface origin hypothesis

A

warm little pond
primordial soup
high UV
meteor strikes, volcanic activity (evidence that organic molecules can form spontaneously)

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25
Q

subsurface origin hypothesis

A

hydrothermal vents at ocean floor from volcanic activity
gases out of floor
more stable because surrounded by water
constant sources of energy - reduced inorganic compounds from ocean crust and vents
more likely for life to survive

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26
Q

time of domains

A

eukaryote was 2 billion years ago - more recent than bacteria/archaea

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27
Q

formation of RNA

A 
self-replicating
catalyse cheical reactions
produce proteins
make ribozymes (enzymes)
unstable - too many functions
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28
Q

LUCA

A

last universal common ancestor

from this evolution splits to archaea and bacteria

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29
Q

what do bacteria and archaea make from H and CO2

A

B - acetate

A - methane

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30
Q

anoxygenic photosynthesis

A

without oxygen
produce sulfur as waste

by purple and green sulfur bacteria

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31
Q

phylogenetics

and how to measure

A

relationships of organisms

can’t allow gene transfers or will carry info of where it’s been
must be homologous

look at production of protein via ribosomal RNA
other markers: ATPase, EF-Tu, RecA

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32
Q

how closely related are the 3 domains?

A

archaea closer related with eukaryotes than bacteria is to both of them

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33
Q

endosymbiotic theory

A

defo true - chloroplasts came from phototrophic cyanobacteria into eukaryotic cell

debatable - aerobic chemo-organotrophic bacteria became mitochondria in host cells

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34
Q

some bacteria examples (8)

A

aquifex - hyperthermophile, chemolithoautotroph
deinococcus - radiation resistant, bio-remediation
cyanobacteria
actinobacteria - heterotroph, antibiotic or pathogen
firmicutes - mostly heterotroph, probiotics or pathogen
chlamydia - parasite, infect eyes, STD
spirochaetes - spin, heterotroph, parasite
proteobacteria - very diverse

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35
Q

systematics

A

study of diversity of organisms and their relationships

links phylogeny and taxonomy

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36
Q

bacteria taxonomy

A

phenotypic comparisons - what they did

37
Q

bacterial names

A

reflects shape/what they do
staphylococcus epidermis - bunch of group clusters, coccus-shaped, from skin

bacillus thermophilus - rod, at high temp

38
Q

microbiology species

A

asexual so viable offspring definition doesn’t make sense, also lateral gene transfer occurs

groups of strains that show a high degree of overall similarity and differ considerably from related strain groups with respect to independent characteristics

issue: single mutation can change definition of species e.g. pleomorphism (exist in diff shapes)

39
Q

polyphasic bacterial taxonomy

A

phenotype - what do, morphology, metabolism, physiology, chemicals
and genotype
and history - phylogenetic evolutionary relationships

40
Q

morphology
motility
nutrition

A

shape of cells
Gram stain

phase-contrast microscopy, some swim

what grow on

41
Q

decomposition of simple carbohydrates

A

acid from glucose turns pH indicator from red to yellow

see if gas produced - info about metabolism

42
Q

enzymes that decompose large molecules

A

tested in agar plates

starch used up so stain with iodine

43
Q

colony characteristics

A 
shape
margin
surface
texture
colour
odour
44
Q 
acidophile
alkaliphile
microaerophile
barophile
halophile
facultative anaerobe
obligate anaerobe
psychrophile
mesophile
thermophile
hyperthermophile
A 
pH < 6
pH > 8
low O2 conc
high pressure
salty
better with O2 but can w/o
can't tolerate O2
low temp < 15
normal temp
high temp >50
very high > 80
45
Q

molecular analysis

A 
FAME
DNA-DNA hybridisation
DNA profiling (PCR, AFLP)
MLST
GC base ratios
46
Q

outer layer of microbes

A

capsule/ S-layer

47
Q

Gram +ve

Gram -ve

A

outer cell wall, 90% of cell wall is peptidoglycan

2 outer membranes with periplasmic space between (stores peptidoglycans)
10% peptidoglycan
lipoprotein attaches outer M to peptidoglycan covalently

48
Q

capsules

A

outside cell wall - glycocalyx/slime layers (polysaccharide components)

no stain on capsule with phase contrast miscroscopy (negatively staine with india ink so stain things not in cell)

loose network of polymer fibres extend from wall
form biofilms
capsule is organised, tight matrix, not easily removed

slime layer is unorganised, easily removed

49
Q

function of capsule

A 
carbon store
prevent desiccation
capture nutrients
attach to surfaces
biofilm
defense
difficult for immune system to recognise - resist phagocytosis
50
Q

S-layer

A

paracrystalline outer wall layer composed of protein/glycoprotein

external to cell wall
protect

51
Q

peptidoglycan (murein)

A

after plasma membrane
alternating NAG & NAM (sugar moieties)
dimers cross link by AA chains creating amide bonds
mesh-like polymer
stained in Gram stain (more in Gram +ve)
joined by cross links between peptides
cross links between carboxyl group of terminal D-alanine connected to amino group of DAPA
porous, elastic, stretchable

52
Q

lysozyme

A

antibacterial enzyme in saliva, tears, airways
targets peptidoglycan and degrades 1-4 glycosidic bonds between NAG & NAM
so makes bacteria sensitive to osmotic pressure so burst and die

53
Q

penicillin’s effect on bacterial walls

A

inhibits peptidoglycan synthesis so better against Gram +ve

54
Q

archaeal cell walls

A 
no pathogens
no peptidoglycan but some have pseudomurein
1-3 beta not 1-4
no D-amino acids in linker
not affected by penicillin/lysozyme
55
Q

membranes

A

stiff - hopanoids/sterols sit alongside fatty acids (too flexible) so stabilise

no hopanoids in archaea

56
Q

archaeal membranes

A

isoprene hydrocarbons attached to glycerol by ether link not ester (bacteria/eukarya)
branched/rings - function same as hopanoids/sterols

57
Q

lipopolysaccharide (LPS)

A

large complex molecules on surface of Gram -ve cells
contain lipid and carbohydrates - called endotoxin when free in host (us)

lipid A, core polysaccharide, O side chain

58
Q

Lipid A

A

2 glucosamine residues linked to fatty acid and phosphate/pyrophosphate
induces largest immune response
in outer membrane while the rest of LPS projects from surface

59
Q

core polysaccharide/R-antigen

A

sugar residues

side chains of NAG, phosphate, ethanolamine

60
Q

O side chain

A

variable region - antigenic make-up
make antibodies to this
different O serotypes linked to diseases
flexible
rough/smooth depending on side chain length
often phosphorylated and anchored into OM via lipid
R = more easily detected so phagocytosis - less pathogenic

61
Q

functions of LPS on bacteria

A

Lipid A - inflexible so stabilises outer membrane
core polysaccharide - -ve and hydrophilic so reduces permeability
loss of O-antigen means reduced virulence, diagnostic tool

62
Q

endotoxin

A

produced by pathogen when cells are attacked and destroyed or during cell division/lysis

63
Q

what does LPS of bacteria cause in our body?

A

small amounts are fine because trigger immune system
high levels lead to septic shock
trigger cytokines - activates transcription factors
inflammation, fever, coagulation of blood

it’s heat stable

64
Q

porins

A

protein channels

65
Q

protein export to periplasm

A

sec

TAT

66
Q

flagella

A

extracellular helical structure
protein
motor spins
longer than cell

rings and hook of flagella = rigid and attached
shaft = easily removed, signle protein flagellin
motor driven by transfer of protons through rings
base = hook (diff proteins)
single protein connects shaft to motor

Gram -ve: L ring in lipopolysaccharide of OM, P ring in peptidoglycan, S-M ring on membrane, C ring in cytoplasm

67
Q

how does flagella get longer?

A

growth at tip, adds at end, channel allows flagellin to pass up to tip to grow

68
Q

types of flagella (4)

A

monotrichous (1 end)
amphitrichous (2 ends)
lophotrichous (multiple at 2 ends)
peritrichous (everywhere, like E.coli)

69
Q

aerotaxis
chemotaxis
magnetotaxis
phototaxis

A

towards O2
to nutrients and away from toxins
along lines of magnetism
towards lights

70
Q

how do bacteria sense changes in nutrient conc.

A

transmembrane proteins

71
Q

MCP

how many does E.coli have?

A

Methyl-accepting chemotaxis proteins (transducer protein)
interact with cytoplasmic proteins and change toxic behaviour of cell by interacting with rings of motor

E.coli - 5 transducers to sense different compounds

72
Q

Che B

A

methylesterase

73
Q

what happens to MCP in low conc. attractant?

A 
attractant decreases CheA-P
so low conc, means high CheA-P
high CheB-P (which removes methyl from MCP)
demethylation of MCP
increased sensitivity to attractant
74
Q

what happens to MCP in high conc.attractant?

A

low CheA-P, low CheB-P, methylated MCP
decreased sensitivity
if harder and harder to sense - know going up conc. gradient
if no sensitivty - short runs and tumble and stay in env.

75
Q

what happens to MCP in high conc. repellent?

A

methylated MCP leads to longer runs, less tumblr and leaves env.

76
Q

which sequences of receptors are conserved and which vary?

A

cytoplasmic domains of all receptors are highly conserved

periplasmic sensing domains vary

77
Q

Gliding

A

pulls along slime extruded on outside
little feet
3 gld proteins - ABC transporters
5 lipoproteins in membranes

dsrupting gld genes means loss of motility, lose ability to digest chitin, increase resistance to bacteriophage infection

78
Q

Twitching

A

via type IV pilus
extend then retract so drag cell
powered by ATP

79
Q

Gas vesicles

A

in planktonic bacteria/archaea

float to right level in water

80
Q

Fimbriae/Pili e.g. CFA

A

adhesion
7 groups
virulence, resist phagocytes, antigenic
adhesion to epithelial cells

81
Q

type 1 fimbriae

properties

types of proteins involved

how is it made?

A

thin (7nm), short (1-2μm), only attached to outer membrane

FimA protein stacked in helical cylinder
FimC chaperone
FimD usher protein (catalyse FimA polymerisation at base of pili)
Fim F,G,H - adhesin onto fimbriae
FimH - tip adhesin binds to D-mannose containing structures

don’t have middle channel so grow from base
proteins transported into periplasm via sec translocase then fold to fimbriae

82
Q

type 4 pili

A

lots in Gram -ve, some in +ve, long, both ends of cell, twitching motility

aggregate to form bundles which causes virulence

e.g. CFA in E.coli (K antigen), ETEC interacts with mucosal epithelium but no CFA so not pathogenic

83
Q

F pilus

conjugation?

A

10μm long, 8nm wide, central 2nm channel, in Gram -ve, plasmid encoded

adhesion like type 4 pili

e.g. E.coli F pilus

conjugation - only attach if other cells have no F-pilus, remember video shown of attaching to other cells and giving them pilus (attachment, retraction, exchange F pilus genes)

84
Q

endospore

A

dormant stage/dispersal stage to survive difficult conditions

only Gram +ves

stain with Malachite green

resistant to 150 degrees

85
Q

human microbiome

A

ecological community of commensal, symbiotic, and symbiotic, and pathogenic MOs that share our body space
shield against pathogens

86
Q

virulence factors

A

anything that allows bacteria to avoid detection and stick to cell
toxins, adhesins, surface capsules, enzymes, LPS
secretion machineries, siderophones, catalases counteract phagocytes

87
Q

who invented vaccines?

A

Edward Jenner

88
Q

Louis Pasteur

A

infected chicken with old culture and didn’t affect them, then new culture didn’t either

1st year: AID (5 decks)

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