microbiology (8) (Kevin Purdy) Flashcards
(88 cards)
1
Q
number of domains
what are they?
A
3
bacteria
archaea
eukaryotes
2
Q
bacteria size
A
1-6 μm
largest are visible (almost mm)
lots cell space, storage - makes big
3
Q
archaea
A
once thought to be bacteria
lots are extremophiles - 1st non extremophile found in 2004
no known pathogenic ones
found everywhere
4
Q
fungi
what is it and size?
A
eukaryote
size varies enormously
largest is 10,000kg because spreads
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
6
Q
how many cells of microbes on Earth?
A
4.6 x 10^30
more than the number of stars
7
Q
what gases are mostly inside microbes?
A
nitrogen and phosphorous
8
Q
phototroph
A
E from light
9
Q
organotroph
A
use organic compounds like sugars as electron donors
e.g. humans
10
Q
lithotroph
A
use inorganic compounds like water as electron donors
11
Q
autotroph
A
use CO2 as carbon source
fixes own carbon
12
Q
heterotroph
A
use organic carbon as a carbon source
13
Q
chemotroph
A
energy from chemical bonds
14
Q
cyanobacteria
A
maybe original chloroplasts
photolithoautotrophs (plants are also this)
15
Q
E.coli and animals are classed as what in terms of how they use electrons to pass energy around?
A
chemoorganoheterotroph
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
17
Q
complex media
A
like blood, milk, or yeast, of biological origin
exact chemical composition is unknown so complex media is undefined
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)
19
Q
phases of bacterial growth
A
lag phase
log phase
stationary
death
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
21
Q
selective media
A
allow growth of only some organisms
to identify pathogens from clinical sample
22
Q
differential media
A
identification based on growth and appearance on medium
colour differences from pH can identify if pathogenic
23
Q
enzyme activity
A
Apizym test - for pathogens, grow and put cells into wells, compare colour against database
24
Q
surface origin hypothesis
A
warm little pond
primordial soup
high UV
meteor strikes, volcanic activity (evidence that organic molecules can form spontaneously)
25
subsurface origin hypothesis
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
26
time of domains
eukaryote was 2 billion years ago - more recent than bacteria/archaea
27
formation of RNA
```
self-replicating
catalyse cheical reactions
produce proteins
make ribozymes (enzymes)
unstable - too many functions
```
28
LUCA
last universal common ancestor
| from this evolution splits to archaea and bacteria
29
what do bacteria and archaea make from H and CO2
B - acetate
| A - methane
30
anoxygenic photosynthesis
without oxygen
produce sulfur as waste
by purple and green sulfur bacteria
31
phylogenetics
| and how to measure
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
32
how closely related are the 3 domains?
archaea closer related with eukaryotes than bacteria is to both of them
33
endosymbiotic theory
defo true - chloroplasts came from phototrophic cyanobacteria into eukaryotic cell
debatable - aerobic chemo-organotrophic bacteria became mitochondria in host cells
34
some bacteria examples (8)
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
35
systematics
study of diversity of organisms and their relationships
| links phylogeny and taxonomy
36
bacteria taxonomy
phenotypic comparisons - what they did
37
bacterial names
reflects shape/what they do
staphylococcus epidermis - bunch of group clusters, coccus-shaped, from skin
bacillus thermophilus - rod, at high temp
38
microbiology species
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
polyphasic bacterial taxonomy
phenotype - what do, morphology, metabolism, physiology, chemicals
and genotype
and history - phylogenetic evolutionary relationships
40
morphology
motility
nutrition
shape of cells
Gram stain
phase-contrast microscopy, some swim
what grow on
41
decomposition of simple carbohydrates
acid from glucose turns pH indicator from red to yellow
| see if gas produced - info about metabolism
42
enzymes that decompose large molecules
tested in agar plates
| starch used up so stain with iodine
43
colony characteristics
```
shape
margin
surface
texture
colour
odour
```
44
```
acidophile
alkaliphile
microaerophile
barophile
halophile
facultative anaerobe
obligate anaerobe
psychrophile
mesophile
thermophile
hyperthermophile
```
```
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
molecular analysis
```
FAME
DNA-DNA hybridisation
DNA profiling (PCR, AFLP)
MLST
GC base ratios
```
46
outer layer of microbes
capsule/ S-layer
47
Gram +ve
| Gram -ve
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
capsules
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
function of capsule
```
carbon store
prevent desiccation
capture nutrients
attach to surfaces
biofilm
defense
difficult for immune system to recognise - resist phagocytosis
```
50
S-layer
paracrystalline outer wall layer composed of protein/glycoprotein
external to cell wall
protect
51
peptidoglycan (murein)
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
lysozyme
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
penicillin's effect on bacterial walls
inhibits peptidoglycan synthesis so better against Gram +ve
54
archaeal cell walls
```
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
membranes
stiff - hopanoids/sterols sit alongside fatty acids (too flexible) so stabilise
no hopanoids in archaea
56
archaeal membranes
isoprene hydrocarbons attached to glycerol by ether link not ester (bacteria/eukarya)
branched/rings - function same as hopanoids/sterols
57
lipopolysaccharide (LPS)
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
Lipid 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
core polysaccharide/R-antigen
sugar residues
| side chains of NAG, phosphate, ethanolamine
60
O side chain
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
functions of LPS on bacteria
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
endotoxin
produced by pathogen when cells are attacked and destroyed or during cell division/lysis
63
what does LPS of bacteria cause in our body?
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
porins
protein channels
65
protein export to periplasm
sec
| TAT
66
flagella
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
how does flagella get longer?
growth at tip, adds at end, channel allows flagellin to pass up to tip to grow
68
types of flagella (4)
monotrichous (1 end)
amphitrichous (2 ends)
lophotrichous (multiple at 2 ends)
peritrichous (everywhere, like E.coli)
69
aerotaxis
chemotaxis
magnetotaxis
phototaxis
towards O2
to nutrients and away from toxins
along lines of magnetism
towards lights
70
how do bacteria sense changes in nutrient conc.
transmembrane proteins
71
MCP
how many does E.coli have?
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
Che B
methylesterase
73
what happens to MCP in low conc. attractant?
```
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
what happens to MCP in high conc.attractant?
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
what happens to MCP in high conc. repellent?
methylated MCP leads to longer runs, less tumblr and leaves env.
76
which sequences of receptors are conserved and which vary?
cytoplasmic domains of all receptors are highly conserved
| periplasmic sensing domains vary
77
Gliding
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
Twitching
via type IV pilus
extend then retract so drag cell
powered by ATP
79
Gas vesicles
in planktonic bacteria/archaea
| float to right level in water
80
Fimbriae/Pili e.g. CFA
adhesion
7 groups
virulence, resist phagocytes, antigenic
adhesion to epithelial cells
81
type 1 fimbriae
properties
types of proteins involved
how is it made?
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
type 4 pili
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
F pilus
conjugation?
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
endospore
dormant stage/dispersal stage to survive difficult conditions
only Gram +ves
stain with Malachite green
resistant to 150 degrees
85
human microbiome
ecological community of commensal, symbiotic, and symbiotic, and pathogenic MOs that share our body space
shield against pathogens
86
virulence factors
anything that allows bacteria to avoid detection and stick to cell
toxins, adhesins, surface capsules, enzymes, LPS
secretion machineries, siderophones, catalases counteract phagocytes
87
who invented vaccines?
Edward Jenner
88
Louis Pasteur
infected chicken with old culture and didn't affect them, then new culture didn't either
