Term
| Essentials for Prokaryotic Environment |
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Definition
-liquid water
-energy source (food)
-minerals
*water can be liquid at more extreme temps, and salinity if at high pressure |
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easy environment
ground stays relatively constant
warm water less dense, rises. In summer can create anaerobic conditions at bottom, no mixing. |
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thermally stratified-
epilimnion
thermocline
hypolimnion |
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Definition
rivers move naturally, always mixing, alway aerobic
rivers more likely to get runoff
Surface Area to water ratio different
need surface to attach to
nutrients from falling leaves |
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near the top, lots of organic matter for food
when water not available, bacteria can form endospores or cysts to survive dry spells |
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deeper layers have less nutrients and ogygen, therefore types and abundances of organisms change
O horizon
A1
E
B
C
R (bedrock) |
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salt
temp
radiation
pH
pressure
sea ice
underground, sub sea floor
inside rocks |
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effects the way the proteins fold- activity
inclusions in sea ice are salt-water and therefore liquid |
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| effects protein folding- activity |
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| damages DNA- can repair DNA |
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| protein clumping in foreign pH (ex.. orange juice and milk) |
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| estimated that over 1/2 microbial life is under the sea floor |
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showed sulphide forming behavior (reduced form of sulphate also found) inside rock
more activity in sandstone-porous
more activity near shale- organic materials
*probably not representative of first bacteria because they were eating organic material |
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Definition
human eye can resolve 0.1 mm
typical prokaryote is .001mm
theoretical best of light microscope- 0.2µm |
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Definition
| light source, condenser, stage (specimen), objective, ocular |
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Definition
d=0.61(lambda)/nsinø
lambda- wavelength
n- refractive index of suspending medium
sinø- angular aperture of objective (from outside of lens down to light source) |
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| phase contrast microscope |
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Definition
can be alive-
uses optical tricks to play up small amount of refractive difference btw bacteria and water |
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Definition
| condenser lens difracts light so that it lights the specimen from the side- appears bright on dark background (light passing through specimen but not objective) |
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small tip runs over specimen, laser and receptor record movement- 3D surface image
dead specimen |
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preferentially bind to specific structures to make them visible-
dead specimen |
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Definition
| fuorescent molecule is excited by one wavelength and emits another- |
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Term
| confocal fluoresence microscope |
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Definition
dichromatic mirror reflect some wavelengths and let others through (so only emitted light is seen)
has a pinhole aperture only allowing visualization of 'in focus' plane of light
if sample is alive, you can make 2D movie of a specific plane
if sample is dead you can generate 3D image |
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Definition
TEM- e- pass through metal stained samples (metal makes them electron dense
SEM- coat samples with think metal to visualize surface detail
expensive, difficult to do well, need a lot of prep, must be dead
gives resolution of 2X diameter of H atom
e- wavelength is 0.005 nm |
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Definition
coccus- sphere
rod- cylindrical
spirillum- twisty
spirochete- long spirillum-like
budding and appendaged- stalk and hypha
filamentous |
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Definition
grape-like cluster= staphylococcus
2 joined together= diplococcus
a chain= streptococcus
a sheet
eight-cell packet= sarcina |
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Definition
bent rod= vibrio
spirillum= rigid
spirochete= flexible |
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Definition
form complex networks with branching= mycelium
trichome- associated cells in a 'filament'
specialized cells
*heterocyst-N fixation
*akinete- resting stage
-multicellular organism? differentiation.. |
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Definition
| nucleic acids, proteins, small molecules, ions, water |
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Definition
typically circular, 'nucleoid' no nucleus, usually approx 4 million base pairs
sometimes have plasmids for antibacterial resistence |
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Definition
| hard to pack so densly- negatively charged backbone |
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two subunits- 30s and 50s
bacterial and archaebacterial are very similar- show different reactions to antibiotics
not membrane associated- transcription and translation can occur at the same time |
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Definition
ribosomes like prokaryotes, own DNA like prokaryotic DNA
show antibiotic sensitivity
chloroplasts~ cyanobacteria
mitochondria~ proteobacteria |
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Definition
| major categories- enzymes, structural, and membrane |
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Definition
subunits of macromolecules
-nucleic acids
-proteins
-lipids
Storage
-sulfur granules
-starch (some PHB)
-polyphosphate molecules
-cyanophycin (store nitrogen in cyanobacteria)
stored as chains, polymers or granules because decreases osmolarity (too high osmolarity would increase H20 movement in) |
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Definition
| used to create correct solute conditions, and are used as cofactors for enzymes |
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enzymes->catalyze reactions
structural->physical structure of cell
membrane->specifically membrane functions (signalling etc.) |
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Definition
| nucleoid, ribosomes, cytoplasm, cytoplasmic membrane, peptidoglycan layer, outer membrane(in some), capsule |
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concentrated DNA- supercoiled, and plasmids
enzyme to 'pinch' a section while another is uncoiled for transcription |
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formed by some under starvation conditions
(try to find food first)
*can survive -heat-dehydration-radation-chemical disinfectants- when in endospore form (can last millions of years)
10-30% water (analagous to a seed)
changes refractive index- shows up as bright spot on phase microscope |
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Definition
| DNA divides, forespore is smaller DNA thats membrane enclosed. Other membrane engulfs it, sporangium releases endospore |
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Definition
| inner membrane- cortex and spore wall (peptidoglycan, dif cross-linking) - outer membrane - spore coat (laminated spore coat proteins) - exosporium (think protein coat) |
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Definition
10-30% water, dipicolinate and ca++ associate with DNA (heat stabilizatioN)
Small Acid-soluble Spore Proteins compact DNA protecting from heat, radiation, dessication
become C and energy sources during germination |
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Definition
| absorb water, swell out of layers, release ca dipicolinate, break down SASP's, return to vegitative growth |
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Definition
largely in photosynthetic bacteria
make organism float
cork and wack with hammer, increase pressure burst vesicles, organisms sank |
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hydrophobic amino acids
95% gvpA Beta sheets
5%gvpC alpha helices
gasses diffuse into rigid vesicles-whatever is in the medium |
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Definition
| typically grow better in low O2- magnetosomes allow orientation to find lower O2 environment |
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Definition
| transport system(chemotaxis, secretion, solutes), barrier, site of energy generation, site of lipid synthesis, cell wall synthesis, helps segregate replicated DNA |
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| typical phospholipid- ester linkages |
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Definition
ether linkage (no C=O bonds at fatty acids-glycerol)
fatty acids have 20-carbon isoprenoid(phytane) groups
some make monolayer (connect two layers, *40 C fatty acids, 2 glycerols)
-beneficial at high temp, wont come apart |
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Definition
rigid structure- prevents osmotic lysis
also creates shape
(those without cell walls have sterols to strengthen membranes, high solute intracellular) |
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Definition
rigid structure- prevents osmotic lysis
also creates shape
(those without cell walls have sterols to strengthen membranes, high solute extracellular) |
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Definition
| crystal violet, iodine treatment, wash with ethanol(stain removes from gram -), counter stain with safranin |
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Definition
usually amino acids are L config(eukaryotes). some D in bacteria.
lysine forms 3 peptide bonds because R group has NH2- can form another bond --> giving 2D polymer around the cell |
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Definition
layers(up to 50) peptidoglycan are linked by teichoic acid cross links
in gram -, only 1 or 2 layers, no teichoic acid |
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Term
| archaebacterial cell walls |
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Definition
no peptidoglycan- some methanogens produce psuedomurein
-polysaccharide
-protein
-glycoprotein/s-layer
*other cell wall options |
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Term
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Definition
lipo-polysaccharides- endotoxins(make pathogenic)
also have porins- for smoall molecules
lipo-proteins in inner leaflet of outer membrane anchors membrane to peptidoglycan |
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Definition
high concentration of proteins, enzymes
site of cell wall synthesis and nutrient uptake |
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Definition
| capsule, slime layer, sheath, s-layer |
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Definition
most are polysaccharides, some are of polypeptides(D-glutamic acid)
*prevents desiccation
*attachment to substrate
*prevent virus attachment
*defense against phagocytes(can't recognize, hides antigens) |
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Definition
polysaccharide, glycoprotein, glycolipid
exudes polymer, absorbs water and 'pushes' along
may protect from chemicals and dessication |
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Definition
| tube structure- allows adhesion of colony in flowing water |
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Definition
lattice of protein- mostly in archaea
sometimes only layer beyond membrane
will self assemble in vitro-no organism |
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Definition
rotates to move to more favorable environment
10-20nm wide, 5-20µm long |
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Definition
proteinacous
basal structure- hook- filament
Mot(or) protein provides rotational movement powered by Proton Motive Force(H+
S(haft) and M(otor) rings join shaft and motor-transmit movement
L ring(lipopolysaccharide layer) and P(eptidoglycan) rings act as bearing, spinning shaft
*can spin in either direction
protein subunits secreted to tip through hook to grow |
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Definition
| begins at MS ring- motor proteins- p ring - L ring- eary hook- cap- filament |
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chemotaxis (thermo, photo..)
'tumbling' |
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Definition
elicit response by gradient.
at increasing concentration autophosphorylation of CheA is suppressed, suppresses CheB(which methylates receptors, desensitizing them) low CheA also means longer runs(counter clockwise)
at stable concentrations CheA authophsphorylates, phosphorylating CheY, binds to flagella making it reverse and tumble |
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Definition
proteinaceous, adhesion to other cells or host organism, mating, 'twitching mobility' or rudder-like in currents
*grow at membrane, can depolymerize and 'pull' along for movement |
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Definition
| signal sequence directs incompletely translated protein to membrane- either remains in membrane, or is cleaved and secreted |
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| hydrophilic proteins prevented from folding by secB- directed to membrane, secreted |
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Definition
| made in inner membrane via secA pathway- shuffled to outer membrane |
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Definition
prtoeins completely assembled in cytoplasm- bound to cofactor
proton motive force drive movement of protein out
*in gram + bacteria proteins can diffuse through cell wall |
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Definition
(C-terminal signal sequence) binds to ABC triggers structure assembly- MFP crosses periplasm to OMP excreted- folds outside cell
*ATP driven |
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Definition
N-terminal sequence -> to periplasm via Sec. - folded protein is secreted
*structure looks like pilus
*important for many pathogens |
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Definition
secretion directly into host via 'needle'
N-terminal signal
machinery spans both membranes
driven by ATPase
similar to flagellar structure-(remember flagella grow by secretion) |
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Definition
directly into other cells (can inject DNA)
even gram + cells have it (even though only one membrane)
driven by ATP hydrolysis
similar to bacterial mating machinery |
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sec pathway- folds in periplasm
inserts self into outer membrane- passenger domain goes through own created pore, may or may not be cleaved |
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Definition
not well understood- looks like viral tail
used to secrete directly into host cell for pathogenesis |
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