Exam 1 Mindmap Flashcards
1
Q
endosymbiosis
A
bacteria and archaea was engulfed and evolved to be mitochondria and chloroplasts in eukaryotes
2
Q
koch’s postulates
A
rules for determining the link between microbe and disease
1. microbe is present in ill cells and not in healthy cells
2. when isolated and cultured inside hosts, no other microbes are present
3. healthy people injected with isolated microbe become sick
4. microbe can be isolated and cultured from those newly sick individuals
3
Q
pasteur’s experiment
A
a broth was boiled and microbes were killed, and after 100 years, no microbes were present in broth but they accumulated in an attached tube
once the gathered microbes were tipped into the nutritious broth, they multiplied quickly (disproves spontaneous generation)
4
Q
common ground between archaea and bacteria
A
no nucleus or membrane bound organelles
5
Q
common ground between bacteria and eukaryotes
A
membrane composition
6
Q
common ground between eukaryotes and archaea
A
genetic makeup and machinery
7
Q
microscope purpose
A
useful to see how microbes interact with eachother
8
Q
resolution
A
smallest distinguishing distance between 2 things
9
Q
detection
A
ability to determine prescence of object
10
Q
magnification
A
(what we resolve through) increase in apparent size to distinguish objects
11
Q
spherical bacteria
A
coccus
12
Q
rod shaped
A
bacillus
13
Q
box shaped
A
arcula
14
Q
appendaged
A
additive portion of bacteria
15
Q
what gives us information on the type of bacteria?
A
shape of bacteria and colonies
16
Q
what can we see with light microscopes?
A
eukaryotes, prokaryotes sometimes (without sub cellular structures), NOT phages and viruses (too small)
17
Q
conditions to resolve an object
A
contrast, wavelength, magnification
18
Q
wavelength rule
A
can be maximum 2x the object (the size of the object must be at least half of the wavelength)
19
Q
focal point
A
where refracted light meets (and where we can see)
20
Q
immersion oil
A
use with microscope’s 100x lens, it has the same refractive index as glass (so it cancels), more waves absorb and less escape
21
Q
wet mount bacteria
A
in its natural state
22
Q
smear bacteria
A
stained and dead
23
Q
simple stain
A
colors cells
ex: methylene blue
24
Q
differential stain
A
stains some cells and not others (to differentiate)
ex: gram stain
25
fluorescence microscopy
specimen absorbs light and emits longer wavelengths
used to identify specific bacteria if they are too small to resolve
26
chemical imaging
detects activity of cells and uses its mass to identify microb
27
dark field
used when size is too small to resolve with light or when the cytoplasm is transparent (uses phase contrast and scattered light)
28
electron microscopy
2 types: transmission and scanning
electrons are equal to lightwaves and the object (which is fixated and coated with metal - besides cyro EM) absorbs electrons. used to observe shapes
29
transmission EM
observes internal structures
30
scanning EM
observes externally
31
fundamental traits of bacteria
think and complex outer envelope, compact genome, tightly coordinated functioning (for efficiency and quick replication in compact state)
32
cytoplasm
gel with DNA, RNA, proteins and solutes (unique structural filaments: MinC and MinD)
33
cell membrane
encloses cytoplasm
34
nucleoid
non membrane bound area of cytoplasm containing chromosomes (looped coils)
35
cell wall
rigid external structure to prevent bursting
36
specialized structures
flagellum and chemosensors for motility
37
gram negative bacteria
lots packed into the plasma membrane- the cell envelope is key to interaction with host and environment
38
cell components
water, proteins, nucleic acids, peptidoglycan, essential ions (dictactes what is transported across the envelope)
39
membrane composition of bacteria
phospholipids: made up of glycerol (carb), with ester links to hydrophobic tails and phospholipid head group
40
phospholipids in archaea
more rigid, more ether links
41
fluidity of bacterial membranes
adaptable by modifying fluidity
unsaturated (cis) bonds increase fluidity
cyclic structures reduce fluidity (more rigid)
42
teichoic acids
found in gram positive bacteria, holds together the layers of peptidoglycan and consists of glycerol and phosphodiester chains
43
Gr+ cell envelope
cell membrane, peptidoglycan, S layer, glycosyl chains
44
Gr- cell envelope
inner membrane, peptidoglycan (periplasm), outer membrane, liposacchrides
45
liposacchrides
found in Gr- bacteria: endotoxins that are healthy for bacteria but if the cell is lysed, dangerous for host (difficult to target because antibiotics repel due to hydrophobicity)
46
inner membrane proteins
YjpP and YjgQ (transport liposacchrides to the surface of the cell)
47
mutations in the cytoskeleton
can cause shape change, function, complications, and death!
48
bacillus mutation
mutated mreB (rods to bubbles)
49
creS mutation
makes curved cells straight
50
FtsZ
forms complex around middle of cell (Z-ring) to help develop round shape
51
MreB
guides peptidoglycan elongation
52
crescentin
polymerizes along inner curve to create curved shape
53
ribosomes
made of RNA and proteins in cytoplasm
54
svedburg units
measures size and density
bacterial ribosomes: 70S
eukaryote ribosomes: 80S
55
pilin
protein monomers that attach to envelope and cytoplasm (cause gonorrhea)
56
chromosome
double stranded circular DNA aggregated in the nucleoid (viruses can be single stranded)
57
plasmid
non essential pieces of DNA (important in genetic engineering which produced insulin production), passed onto offspring, exchange antibiotic resistance
58
O2 and CO2 (small and uncharged molecules)
passively permeate through the membrane
59
H2O transport
uses aquaporins (proteins) to cross membrane via osmosis
60
weak acid and base transport
pass uncharged through the membrane and then become charged
61
active transport
low concentration to high concentration (requires energy)
62
passive transport
high concentration to low concentration
63
coupled transport
uses concentration gradient of one substance to power another against its gradient (can be symport or antiport)
64
ABC transport
ATP binding proteins dephosphorylate (making ADP) and uses that released energy to transport across
65
sidrophores
used to transport rare nutrients
66
group translocation
fools gradient (uses phosphate)
67
what is resolution dependent on?
density of photoreceptors in observer's eye
68
peptidoglycan
a target for antibiotics, because it is in the cell wall of bacteria. a polymer of NAM and NAG sugars that are interconnected
69
S-layers
crystalline layers of proteins for extra protection
70
capsule
polysaccharides and glycoproteins- protect cell from drying out and being eaten (phagocytosis)
71
carboxysomes
bodies packed with Rubisco for CO2 fixation
72
gas vesicles
protein bound gas filled structures to make things float
73
flagella
spiral filament of protein monomers rotated by a proton motive force
74
chemotaxis
flagella moving!
clockwise = tumbles (flips/switches directions)
counterclockwise = moves forward
75
essential nutrients
must be supplied from the environment
76
macronutrients
major elements in cell macromolecules
77
cofactors
magnesium, iron, and potassium
78
micronutrients
trace elements necessary for enzyme function
79
autotrophs
fix CO2 and assemble into organic molecules (producers)
80
heterotrophs
use preformed organic molecules (consumers)
81
(chemo)organotrophs
use organic molecules for e- (most heterotrophs)
82
(chemo)lithotrophs
use inorganic molecules for e-
83
phototrophs
obtain energy from chemical reactions triggered by light
84
chemotrophs
obtain energy from redox reactions (two types: lithotrophs and organotrophs)
85
mixotrophs
can use multiple methods to exist
86
heterotrophy metabolism
external C sources cause energy transfer and C breakdown for other machinery (carbon cycle generates energy)
87
autotrophy metabolism
energy generated is used to fix CO2, molecules are reassembled into glucose
88
bacteria grown in liquid or broth
useful for studying the growth characteristics of a pure culture
89
solid
useful for trying to separate mixed cultures from clinical specimens or natural environments
90
dilution streaking
a loop is dragged across the surface of an agar plate
91
spread plate
serial dilutions are performed on a liquid culture, a small amount of each dilution is then plated
92
complex media
nutrient rich but poorly defined
93
minimal media
contains only nutrients that are essential for growth of a specific microbe
94
enriched media
complex media to which specific components are added
95
selective media
favors growth of one organism over another
96
differential media
exploits differences between species that grow equally well
97
growth factors
specific nutrients required by not all, but some species (needed to grow in lab media)
98
unculturable microbes
species that adapted so well to their environment that we cannot grow them in lab (may depend on growth factors that other species produce), or we may give too much!
99
optical density
measures growth in real time; bacteria in a tube of liquid medium can be detected by how cloudy medium appears as the cells scatter light
-quick and easy approximation of cell density
-decreased intensity of light due to scatter by a suspension is measured as optical density
100
light microscopy
direct counting of living and dead cells
-counted directly by placing dilutions on a special microscope (hemocytometer)
101
fluorescence microscopy
direct counting of living and dead cells
-living cells may be distinguished from dead cells using chemical dyes
(dead = red from propidium, live = green from syto-9 which can enter all cells)
102
flow cytometry and cell sorting
direct counting of living and dead cells
-light scatter correlates to cell size and granularity
-fluorescence measures live and dead cell content
103
how do most bacteria divide?
binary fission: one parent cell splits into two equal daughter cells
some divide asymmetrically (caulobacteria has a stalk and swimmer cell, and hyphomicrobium divides by budding)
104
growth rate
rate of increase in cell numbers or biomass is proportional to the population size at a given time (exponential growth never lasts indefinitley)
105
generation time
time it takes for a population to double
106
final cell number for binary fission equation
Nt = N0 x 2^n
Nt = final cell number
N0 = original cell number
n = number of generations
107
cyanobacterial heterocysts
every 10th anabaena cell- makes nitrogenase, forms a specialized barrier from O2, degrades photosynthetic machinery, allowing it to fix nitrogen anaerobically at night and maintain oxygenic photosynthesis during the day
108
gliding motility
myxococcus uses gliding motility - starvation triggers the aggregation of 100,000 cells which form a fruiting body (cells inside differentiate into dormant microspores)
109
what determines ability for rate and growth?
nutrients available, physical parameters, chemical and biological control agents (may stress response or adapt)
110
normal conditions
pressure: sea level
temperature: 20-40 degrees C
pH: near neutral
salt concentration: 0.9%
ample nutrients
111
what can microbes control?
pH, osmolarity, sometimes O2
112
what can microbes not control?
internal temperature and pressure
113
microbe temperature
matches its environment ---> affects nutrient transporters, DNA/RNA stability, enzyme structure and function
114
osmolarity
number of solute molecules (opposite of water activity)
115
water activity
how much water is available (becomes water as solutes increase, fungi can grow with lower activity)
116
hypertonic medium
osmolarity greater inside than outside the cell, water flows inside
117
hypertonic medium
osmolarity greater outside than inside, water flows outside
118
how do halophiles avoid high internal salt concentration?
using Na+/K+ antiporters (special ion pumps excrete sodium and replace it with a compatible solute)
119
mechanosensitive channels
leak ions out of cell to avoid an influx of water
120
how do alkaliphiles maintain a neutral internal pH?
rely on Na+/H+ antiporters to bring protons into the cell, peptidoglycan and lipid modifications reduce OH permeability, has sodium motive force (to power flagella motility)
121
how do acidophiles maintain a neutral internal pH?
proton motive force is present, membrane permeability changes to reduce H+ entrance, K+(in)/H+(out) antiporters
122
strict anaerobes
die in the presence of oxygen *have different acceptor in the electron transport chain*
123
aerotolerant
can grow in O2 while functioning in fermentation
124
microaerophiles
only grow at low O2 concentration
125
faculatative
can grow with or without O2 (both types of respiration)
126
probiotics
restore balance in intestinal microbiome
127
phage therapy
aims to treat infectious diseases with a virus targeted to a pathogen
128
halophile
high salt
129
barophile
high pressure
130
hyperthermophile
above 80 degrees C
131
thermophile
between 50-80 degrees C
132
disinfection
killing/removing antigens from inanimate objects
133
sterilization
kills all living cells, spores, and viruses
134
antisepsis
kills/removes pathogens from surface of living tissues
135
antimicrobials
bacteriostatic = inhibits growth
bactericidal = kills bacteria
136
lag phase
bacteria are preparing cell machinery for growth
137
log phase
growth approximates an exponential curve
138
stationary phase
cells stop growing and shut down their growth machinery while turning on stress responses to retain viability
139
death phase
cells die with a "half life" similar to that of radioactive decay, a negative exponential curve
140
rod shape
envelope elongates + peptidoglycan chains track around the cell (DNA synthesis, then separation)
141
sphere
septation by Z ring generates cell envelope (splits then expands)
142
archaea
more closely related to Eukarya
- unique DNA compaction
-unique and chemically distinct cell walls
-certain genetic sequences only found in rRNA
143
psychrophiles
cold
144
what shows distance in ancestry?
nitrogen bases in rRNA
145
macronutrients
C, H, N, O, P, S
146
micronutrients
Co, Cu, Mn, Zn, Mb, Ni
147
cations necessary for enzyme function
cofactors: K+, Fe2+, Mg2+
cell signaling: Ca2+
148
autotrophs
fix carbons for themselves through CO2 (glucose through fixation)
149
heterotrophs
obtain carbon for organic molecules (to glycolysis)
150
phototrophs
energy from light
151
chemotrophs
energy from redox reactions
152
chemolithotrophs
use inorganic molecules for electrons
153
chemoorganotrophs
use organic molecules for electrons
154
how are bacteria defined?
by similarities within traits
155
serotype
stimulate distinct response of antibiotics
156
subspecies/strain/type
same species with different characteristics
157
growth cycle
bacteria divides by binary fission; one cell divides into 2 equal daughter cells (some divide asymmetrically)
158
growth factors
specific nutrients required by some but not all species
159
mixotrophs
can use multiple methods to obtain energy and carbon
160
liquid culture
best to see growth
161
solid culture
best to see seperation of species
162
isolation techniques
streaking and spread plate (dilution)
163
batch culture
liquid culture within a closed system (best for seeing change in environments)
164
continuous culture
all cells in a population achieve a steady state, which allows detailed study of bacterial physiology
adds and removes equal amounts of culture medium (ex: stomach)
165
biofilms
protect the cells from drying out; specialized, surface attached communities (defense against stress). can be cued by environmental signals in different species (pH, iron, temperature, oxygen, amino acids)
166
steps to forming biofilms
1. a signal induces a genetic program in planktonic cells, cells attach to surfaces
2. adhered cells. coat surface and more cells attach, communicate via quorum sensing
3. cells form extracellular matrix (polysacchrides, DNA, proteins)
4. columns, streaks, and channels form
5. individuals detach when nutrients become scarce
167
