midterm 1 Flashcards
(162 cards)
1
Q
Hooke
A
published first drawing of microbe in Micrographia
2
Q
Van Leeuwenhoek
A
“father of microbiology”, detailed drawings and descriptions, sent to Royal Society of London
3
Q
members of microbial world
A
Bacteria
Archaea
Eukarya (protists: algae, protozoa, slime molds, water mold; fungi)
viruses
4
Q
5 Kingdoms
A
Monera, Protista, Fungi, Animalia, Plantae
5
Q
basis for Woese’s classification
A
16S/18S rRNA sequence –> 3 domains
viruses lack rRNA, not in domain
6
Q
3 domains
A
Bacteria, Archaea, Eukarya
7
Q
taxonomic ranks
A
Domain, Kingdom, phylum, class, order, family, genus, species, strain
8
Q
Carolus Linnaeus
A
binomial system: Genus species
9
Q
Pasteur
A
sterile, fermentation, rabies vaccine
10
Q
Koch
A
bacteria cause disease from study of anthrax, Koch’s postulates, tuberculosis
11
Q
Fleming
A
penicillin
12
Q
Winogradsky
A
soil microbiology
13
Q
Beijerinck
A
virology, microbial ecology, nitrogen fixing bacteria
14
Q
resolution depends on
A
wavelength and lens ability (numerical aperture)
15
Q
Abbe equation
A
d = .5(wavelength) / nsin(theta)
16
Q
immersion oil
A
increases numerical aperture
17
Q
bright field
A
dark image against bright background
gross morphology of stained bacteria, dead cells
18
Q
dark field
A
light reflected by specimen
living unstained cells and internal structures, larger euk. microbes (fungi, algae)
19
Q
phase contrast microscope
A
out of phase light waves amplify differences in refractive index of cells and water
living unstained cells, internal structures, larger
20
Q
fluorescent microscope
A
light emitted by specimen
use fluorescent antibodies to identify 1 organism from many
21
Q
differential interference contrast (DIC)
A
out of phase light produce interference and form image
2 beams of polarized light by prisms
live unstained cells, colored and 3D
22
Q
confocal scanning laser microscope
A
laser beams to illuminate specimen, scans many sections, detector/computer put together, 3D image
23
Q
light microscope
A
uses light, condensers, eye
24
Q
electron microscope
A
uses electron beam, electromagnets, photographic plate
disadvantages: no living specimen, altered morphology
25
transmission electron microscope (TEM)
100,000X, .5nm resolution
view internal structures, viruses, DNA
lenses and specimen under high vacuum, thin slices in plastic
*form image from radiation that has passed through specimen
26
scanning electron microscope
produces image from electrons released from atoms on object's surface
sample coated with thin layer of metal
gives realistic 3D image
27
electron cryotomography
rapid freezing (vitreous ice) and tilt series --> 3D inside and outside
28
scanning probe microscopes
sharp probe moves over surface, can view atoms
| scanning tunneling and atomic force microscopes
29
scanning tunneling microscope
type of scanning probe microscope
| steady current maintained between probe and sample, up/down of probe located atoms on surface
30
atomic force microscope
type of scanning probe microscope
| probe moves over specimen at constant distance, up/down creates image, used with surfaces that don't conduct electricity
31
2 basic shapes of bacteria
coccus - round
| bacillus - rod
32
coccus arrangements
diplococcus - pairs
streptococcus - chains
staphylococcus - clusters
tetrads - squares, groups of 4
33
bacillus arrangements
diplobacillus
| some strepto-, never staphylo-
34
vibrios
comma shaped, single curve
35
spirilla
rigid spirals
36
spirochetes
flexible spirals
37
mycelium
network of hyphae
38
fruiting body
complex structure, bacteria
39
cell envelope
plasma membrane and all surrounding layers external
40
basic roles of bacterial plasma membrane
selectively permeable barrier, performs metabolic processes, communication with environment
41
ethanolamine
bacterial hydrophilic phosphate of phospholipid
42
lecithin
eukaryotic hydrophilic phosphate of phospholipid
43
sterols
eukaryotic part of plasma membrane, gives rigidity
44
hopanoids
bacterial part of plasma membrane, sterol-like, unique to bacteria
45
macroelements
carbon, oxygen, hydrogen, nitrogen, sulfur, phosphorus
46
micronutrients
manganese, zinc, cobalt, molybdenum, nickel, copper
47
growth factors
must be obtained from environment
| amino acids, purines/pyrimidines/ vitamins
48
transported by passive diffusion
glycerol, H2O, O2, CO2
49
primary active transport
```
ABC transporters (ATP binding cassette)
membrane binding domain/transporter, solute binding/binds substrate, ATP binding domain
```
50
secondary active transport
uses potential energy of ion gradients, co-transporters, include major facilitator superfamily (MFS) proteins
symport and antiport
51
symport
same direction
| ex: lactose uptake, lactose + proton
52
antiport
opposite directions
| ex: sodium leaves, proton enters
53
group translocation
involves chemical modification of substrate
sugar phosphotransferase system (PTS) - sugar transported while being phosphorylated
phosphoenolpyruvate (PEP) - phosphate donor
54
siderophores
secreted by cell, bind ferric ion, supply to cell
| ferrichrome, enterobactin
55
murein
peptidoglycan
56
basic PG structure
N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) alternate in chains, link together
tetrapeptide attached to NAM
57
tetrapeptide in PG
L-alanine
D-glutamine
L-lysine or meso-diaminopimelic acid
D-alanine
58
tetrapeptide cross links
direct or through peptide interbridge (5 glycines)
59
gram + cell wall
thick, fluffy, PG 60-100%
peptide interbridge - 5 glycines in crosslink
teichoic acid/lipoteichoic acid
periplasmic space?
60
gram - cell wall
PG 5-10%
direct linkage - no additional amino acid
not all tetrapeptides linked
outer membrane linked to plasma membrane by Braun's lipoprotein or contact sites
lipopolysaccharide (LPS)
permeability - porin
periplasmic space
61
lipopolysaccharide (LPS)
```
hair like, outermost layer of gram neg.
lipid A + core polysaccharide + O antigen
attachment
O antigen = protection
Lipid A = endotoxin
```
62
gram stain mechanism
crystal violet (+ charge), iodine (dye retention), ethanol (decolorization), safranin ( - charge)
63
protoplasts
complete loss of cell wall
64
spheroplasts
gram neg. cells w/out PG
| still have OM and plasma membrane
65
bacteria that lack PG in cell wall
Chlamydiae and Planctomycetes
66
mycoplasmas
lack cell wall, sterols in plasma membrane, osmotically sensitive
67
outside bacterial cell wall...
capsules, slime layers, glycocalyx, s layer,
68
capsules
well organized, hard to wash off
| polysaccharides, help pathogens resist phagocytosis, protect against desiccation, exclude viruses and hydrophobic toxins
69
slime layers
diffuse/unorganized, easy to remove
| polysaccharides, facilitates motility (gliding bacteria)
70
glycocalyx
can include capsule and slime layers
network of polysaccharides extending from surface
attachment to solid surfaces
71
S layer of bacteria
not part of cell wall
regularly structured, protein or glycoprotein
protection, shape, cell adhesion
72
FstZ
bacterial cytoskeleton protein
septum formation
euk = tubulin
73
MreB/MbI
bacterial cytoskeleton protein
maintain bacilli cell shape, PG synthesis
euk = actin
74
CreS (crescentin)
bacterial cytoskeleton protein
maintain spiral call shape
euk = lamin and keratin
75
examples of internal membranous structures of bacteria
thylakoids of cyanobacteria - photosynthesis
internal membranes of nitrifying bacteria - nitrification (ammonia --> nitrate)
anammoxosomes of Planctomyces - anaerobic ammonia oxidation
76
purpose of inclusions found in bacteria
storage of carbon, inorganic compounds, energy
| reduction of osmotic pressure
77
glycogen
branched chain of glucose units
carbon storage (form in low nutrients, high carbon)
many or may not have membrane
78
polyhydroxyalkonate (PHA) granules
poly-b-hydroxybutyrate (PHB) granules
carbon storage
single layer membrane of protein and phospholipid
biodegradable plastic
79
polyphosphate granules
volutin, metachromatic granules
| phosphate storage, energy reserve or source
80
sulfur globules
source of e-
81
cyanophycin granules
composed of arginine and aspartic acid
| store extra nitrogen
82
microcompartments
a kind of inclusion
analogous to organelles, but not lipid bilayer
functions other than simply storing substances
relatively large polyhedrons formed by one or more different proteins, contain one or more enzymes
83
carboxysome
microcompartment in cyanobacteria (CO2 fixing bacteria)
| polyhedral protein coat, contain Rubisco enzyme, concentrates CO2
84
gas vacuole
composed of gas vesicles, construct or collapse as needed
85
magnetosome
```
membrane bound iron granules
transform extracellular iron to magnetite
make intracellular magnetic compasses
oriented in chain
found in aquatic microaerophiles
```
86
eukaryote vs. bacteria/archaea ribosomes
euk: 80S, bound to ER
| bacteria/archaea: 70S, free in cytoplasm
87
nucleoid
nuclear body, chromatin body, nuclear region
chromosomes and protein
usually single circle
highly folded/supercoiled
88
plasmids
circular extrachromosomal dsDNA
| less than 30 genes, 0-100 per cell, carry nonessential traits, replicate autonomously
89
episomes
plasmids that integrate into chromosomes
90
curing
loss of a plasmid
| spontaneously or induced (mutagens, radiation, thymine starvation, antibiotics, high growth temps)
91
major types of bacterial plasmids
conjugative - transfer copies to other bacteria during conjugation (F factor)
resistance - confer antibiotic resistance (R factor)
virulence - make bacteria more pathogenic
metabolic - provide enzymes to degrade substances
92
fimbriae/pili
attachment (movement)
fine hair like appendages, helically wound pilin
fimbriae - up to 1000
sex pilus - up to 10
93
bacterial flagella
motility
slender, rigid, hollow
protein = flagellin
use type III secretion system - grow from tip
94
bacterial flagella movement
```
rigid helix that rotates
ccw = run
cw = tumble
motor: base of flagellum, rotor turns in stator
power: proton motive force (PMF)
```
95
bacterial swarming
on moist surfaces, most have peritrichous flagella, produce characteristic colony morphologies
96
monotrichous
1 flagella, polar
97
amphitrichous
1 flagella at each end
98
lophotrichous
clusters of flagella at 1 or both ends
99
peritrichous
flagella all over
100
spirochete motility
axial fibril - multiple flagella at each end, wind around cell, covered with outer sheath
periplasmic flagella
cause corkscrew shaped outermembrane
101
twitching motility
short, jerky, intermittent motions
| only when cells in contact, use type IV pili
102
gliding motility
smooth, varies in rate
| more than 1 mech., use type IV pili, slime
103
attractant vs. repellant chemotaxis
attractants - response at low levels
repellant - response only at high levels
(must ignore past stimuli)
104
chemoreceptors
integral proteins
methylated or demethylated, conformational change
transfer chemotactic signal to flagella motor
105
2 forms of bacteria
vegetative - actively growing, easily destroyed
| endospore - non growing, resistant to eat, chemicals, etc.
106
endospores usually for..
gram +
| bacillus, clostridium, sporosarcina
107
endospores contain
DNA, RNA, ribosomes, enzymes, few small molecules
| no metabolic functions
108
layers of endospore
```
dehydrated core
inner membrane
germ cell wall
cortex
outer membrane
coat
exposporium
```
109
dehydrated endospore core
dipicolinic acid + calcium (Ca-DPA)
| stabilizes DNA
110
small acid soluble DNA binding proteins (SASPs)
stabilize critical components (DNA, ribosomes, etc.)
| protection
111
germ cell wall
PG for germination
112
cortex
```
spongy peptidoglycan (missing tetrapeptides)
involved in dehydration process
```
113
endospore coat
several protein layers, resistance to chemicals, lytic enzymes
114
exposporium
thin other covering
115
7 steps of sporulation
1. DNA replicated
2. inward folding of cell membrane, enclose part of DNA, produce forespore septum
3. mother cell engulfs immature endospore in 2nd membrane
4. cortex in space between 2 membranes, calcium and dipicolinic acid accumulated
5. protein coat formed around cortex
6. maturation of endospores
7. lytic enzymes destroy sporangium, release spore
116
endospore to vegetative state
activation : prep (reversible)
germination: breaking of dormant state (irreversible)
outgrowth: vegetative cell emerges from spore coat
117
morphologies or archaea
coccus, bacillus, curved rods, spiral shapes, pleomorphic
no spirochete or mycelial
unique: branched forms, square
118
archaea plasma membrane
branched hydrocarbons from isoprene units (vs. fatty acids)
attached to glycerol by ether links (vs. ester links)
bilayer or monolayer (more rigid)
119
glycerol diether lipids
archaea lipids
2 hydrocarbons attached to glycerol
C20 diethers
120
diglycerol tetraether lipids
archaea lipid
2 glycerols linked by 2 long hydrocarbons
C40 tetraethers
121
archaea cell wall
variety, lack PG
| S-layer: glycoprotein or protein, main part of cell wall
122
s layer + protein sheath
possible pressure regulator
123
s layer + methanochondroitin
```
polysaccharide layer (similar to component in animal connective tissue)
cause cell-cell adhesion
```
124
s layer + psuedomurein
PG like molecule (s-layer is outermost)
| resistant to lysozyme, penicillin
125
N-acetyltalosaminuronic acid
in pseudomurein instead of NAM
126
no S-layer in archaea cell wall
```
polysaccharide layer (pseudomurein or something else)
resemble gram + bacteria
```
127
archaea with no cell wall
slime layer or outermost layer
128
archaeal ribosomes
70S, similar to bacteria
| different shape, sequence, additional rRNA, more proteins
129
3 groups of archaeal ribosomes
in all 3 domains
unique to archaea
observed in archaea and eukaryotes
130
unique archaeal nucleoid
can be polyploidy
| condensing proteins: HU homologues, alba, histones
131
archaea pili
made of pilin homologues
have central lumen
allow for attachment
132
cannulae
unique to archaea
hollow, tube like
form cell network
133
hami
unique to archaea
| filaments with grapping hook for attachment
134
archaea flagella
```
rotates like bacteria
powered by ATP
cw: pushed forward
ccw: pulls back
not hollow
flagellar proteins similar to bacterial type IV pili proteins
added to base of filament
```
135
bacterial vs. archaea pili
bacteria: attachment and conjugation
| archaea : attachment
136
size range of viruses
10nm to 400nm, need EM
137
general structure of viruses
nucleocapsid: nucleic acid (DNA or RNA)and capsid (made of protomers)
138
protomers
capsid proteins
139
viral capsid shapes
helical - hollow tubes
icosahedral - regular polyhedron (20 triangular faces, made of capsomers)
complex
140
capsomers
clusters of protomers (5-6)
ring of knob shaped
make up icosahedral shape
141
viral envelopes
from host cell membrane
modified to infect next cell
envelope proteins: spikes or peplomers
142
ssRNA plus/positive strand
identical to mRNA
143
ssRNA minus/negative strand
complementary to mRNA
144
dsRNA
red flag to cell, doesn't have it
| must be a virus
145
steps in viral multiplication
```
adsorption
entry into host cell
synthesis
assembly of virus
release of virus
```
146
adsorption
attachment of virus to specific host receptors on host
147
bacteriophage
injection of nucleic acid only
148
3 modes of entry for euk. virus
1. fusion of viral envelope with host membrane, nucleocapid enters cell
2. by endocytosis
3. nucleic acid injection
149
location of assembly of virus in bacteria/archaea
cytoplasm
150
location of assembly of virus in euk.
cytoplasm or nucleus
151
methods to release virus
lysis of host
| budding: common in enveloped viruses
152
2 types of viral infection in bacteria/archaea
lysis (lytic cycle) and lysogen (lysogenic cycle)
153
lytic cycle
caused by virulent phage
154
lysogenic cycle
caused by temperate phage
| 2 options: lysis at end or remain in host
155
prophage
form of virus that remains in host
| integration of viral genome into host chromosome
156
lysogens or lysogenic bacteria
infected bacteria
157
lysogenic conversion
change of host phenotype
158
induction
switch to lytic cycle
159
4 types of viral infections in euk.
acute (cytocidal) - cell lysis
latent - host not harmed
chronic - slow release of virus w/out lysis, budding
transformation into malignant cell
160
bacterial/archaea virus cultivation
broth or agar cultures
| plaques = clearing in lawn due to cell lysis
161
plant virus cultivation
infection of host plant, tissue culture, separate cells, protoplasts
necrotic lesions - rapid death to cells
162
animal virus cultivation
```
host animal, fertilized egg, tissue culture
plaques = localized areas of cell destruction
cytopathic effects (CPE) - abnormalities in cells or tissue
```
