Micro Physio Flashcards
basis of phylogenetic tree of life
comparative analysis of small subunit ribosomal RNA gene sequences showing evolutionary relationships
3 relevant features of prokaryotes
- nuclear membranes are absent, which allows couple transcription and translation
- smaller than eukaryotic
- cytoplasmic membrane is multifunctional in prokaryotes and represents the defining structure of the cell
5 superpyhla of archaea
nanoarchaeota, euryarchaeota, thaumarchaeota. crenarchaeota, korarchaeota
contains most cultured species of archaea, metabolically diverse and includes methanogens, halophiles, thermophiles and hyperthermo
euryarchaeota
contains nitrifying archaea; many members are uncultured, characterized by the use of 16s rrna genes
thaumarchaeota and cryptic archaeal phyla
represented by a single species; cannot grow in pure culture and only replicate when attached to the surface of their host organism (1)
nanorchaeota (DPANN), species- Nanoarchaeum equitans (one of the smalles cellular organism with smallest genome among species of archaea)
(1)Ignicoccus hospitalis- a hyperthermophilic species of crenarchaeota whose name means ‘the hospitable fireball’
nano attached to igni
many cultured isolates which are thermo/hyper using sulfur compounds as either electron donors or acceptor
crenarchaeota
t/f some archaea are natural flora in the human body
true
t/f there are archaea that cause diseases
f, no conclusive evidence
what domain is similar to archaea in terms of transcription machinery specifically in promoter recognition and initiation of transcription;
eukarya
only has one characterized species; recovered from obsidian pool a hot spring in yellowstone national park; species yet to be grown in pure culture
korarchaeota; Korarachaeum cryptofilum ‘ the secret filament of youth’
major composition difference in cell wall of bacteria vs archaea
presence of NAG and NAM in bacteria with beta 1-4 glycosidic linkage
while NAG and NAT in archaea with beta 1-3 glycosidic linkage
major composition difference in cell membrane of bacteria vs archaea
B= phospholipid bilayer, esther linked unbranched fatty acid to glycerol
A= branched isoprene chains, lipid monolayer in some archaea
the subunit composition and architecture of archaeal RNA polymerase is strikingly similar to
eukaryotic RNAPII
examples of DNA transfers in archaea
transformation in euryarchaeota
vesicle transport in thermococcales
transduction in archaea
conjugation in sulfolobaceae
cell fusion in haloarchaea
chromosomal DNA exchange in crenarchaeota
polymers of repeating units of glycerol or ribitol joined by phospohates; amino acids (D-ala) or sugars (glu) ar attached to gly/rib; covalently linked to murein through muramic acid; connected/ embedded in PG layer to membrane lipids
teichoic acids
linear polymers of 16-40 phosphodiester-linked glycerophosphate residues covalently linked to the cell membrane
lipoteichoic acid
properties and importance of teichoic acid
highly antigenic
anchors the wall to cell membrane
provides high density of regularly oriented charges
storage of phosphorus
facilitates attachment of bacteriophage
inhibits the activity of autolytic enzymes which hydrolyze the murein
cell wall substances: acidic polysaccharides containing uronic acids
teichuronic acids
cell wall substances: important in classification of some gram +
neutral polysaccharides
cell wall substances: may substitute for whatever function of LTA
other glycolipids
waxy lipids found in mycobacterium
mycolic acids
unique in the gram neg cell wall
LPS
gneg lps; embedded in the membrane as part of the lipid bilayer; hydrophobic; composed of 2 glucosamine residues linked B-1,6 backbone with 4 identical fatty acids
lipid A
gneg lps; shows high to moderate variability consists of hexoses
outer core
gneg lps; shows low structural variability; consists of 2-keto-3- deoxyoctonate (KDO), heptose, ethanolamine, and galactose
inner core
gneg lps; short polysach extending outward from the core; consist of peculiar sugars which varies between bacterial strains; not essential for variability
LPS o antigen
gneg lps importance
avoidance of host defenses (o antigen)
contributes to the neg charge on the cell’s surface
stabilizes membrane structure
acts as endotoxin
gneg lps; mediate interconnection between the OM and murein
lipoprotein
outer envelope; form small hydrophilic channels through the outer envelope allowing the diffusion of neutral charged solutes MW < 600 daltons; 3 identical units; associate to form membrane holes; transmembrane
porins
a separate compartment between the cell membrane and outer membrane in g neg bacteria; site of redox reactions, osmotic regulations, solute transport, protein secretion, hydrolysis
periplasm
usually composed of only 1 or a few subunits self organized into repeating structures, which can have hexagonal, tetragonal, or trimeric symmetry; forming a rigid yet permeable paracrystalline lattice
s-layers
another confirmatory tests for gram reactions; 3% KOH (lysing agent); gneg more susceptible due to thin lipid content in the OM
gregersen’s method
uses carbolfuschin for primary stain; methylene blue for counterstain; for staining bacteria which cell wall contains high lipid concentrations thus are waxy, hydrophobic, and impermeable to gram staining; also for bacteria resistant to acid and alcohol (AFB and/or AAFB)
acid fast staining
small cell wall-less bacteria but possess distinct morphologies; have internal protein cytoskeleton that determines and maintains cell shape; cytoplasmic membrane are more stable than that of other bacteria due to sterols; uses lipoglycans to stabilize cell membrane; parasitic and pathogenic
mollicutes- mycoplasma. spiroplasma, acholeplasma
cytoplasmic membrane functions
serves as permeable barrier
protein anchor
for energy conversation
lipid biosynthesis and cell wall
protein secretion
secretion and uptake of intracellular signals
responses to environmental signals
major phospholipid in the cytoplasmic membrane; formed from glycerol-3-P, serine and fatty acids in the ratio 1:1:2
phosphatidylethanolamine
next most prevalent phospholipid in the cytoplasmic membrane; formed from glycerol-3-P and fatty acids in equimolar ratios
phosphatidylglycerol
cytoplasmic membrane components; embedded in the CM;amphipathic; bound to the fatty acids of the phospholipids via hydrophobic bonding
integral proteins
cytoplasmic membrane components; attached to membrane surfaces by ionic interactions
peripheral proteins
archaeal membrane distinction from bacterial and eukaryotic membranes
ether linkages
isoprenoid side chains
branched side chains
lipid monolayer composition examples in archaea
diglycerol tetraethers
crenarchaeol
contains of aqueous solution of three groups of molecules- maromolecules (proteins, mRNA, tRNA etc), small molecules which serves as energy sources, precursors of macromolecules, metabolites or vitamins, various organic and inorganic ions and cofactors; structural components: nucleoid, ribosomes, inclusion bodies
cytoplasm
isolated compartments where specialized conditions are maintained to perform chemical process not possible in the cytoplasmic space (ie. anammoxosome, carboxysome, acidocalcisomes); densely packed membrane structures that facilitate higher throughput for membrane-dependent metabolic processes by increasing the available surface in a cell (ie thylakoid, chlorosome, membranous structure in methane, nitrite, and ammonia oxidizer)
intracytoplasmic membranes (ICM)
complex structures made of both protein and ribonucleic acid; present in the cytoplasmic matrix or loosely attached to the plasma membrane; site of protein synthesis
ribosomes
site of DNA and RNA synthesis; DNA tightly coiled; DNA binding ‘nucleoid’ proteins that bend and compact DNA
nucleoid
general term for the thick cover or layer of polymers deposited outside the cell
glycocalyx
well organized glycocalyx; attached firmly to the cell wall; compact; excludes particles like india ink
capsule
zone of diffused, unorganized material; loose association; does not exclude particles
slime layer
capsule staining procedure; use of acidic dye, nigrosin/ india ink; stains the background brownish to black; capsules clear zones or colorless around refractile cells
negative staining/ Duguid’s method
capsule staining procedure; use of crystal violet as primary stain and 20% copper sulfate as decolorizer and counterstain; capsules appear light or blue or colorless, cells are dark purple
anthony’s method
capsule staining procedure; uses congo red as ph indicator; stain component- 1% acid fuchsin which stains cell cytoplasm, 5% phenol which increases penetration power of stain, 30% FeCl3 which is a chemical fixative, 20% acetic acid which changes the background from red to blue
maneval’s staining method
hairlike substructure on the surfaces of prokaryotic cell; composed of protein sub-units called ‘pilins’
pili/fimbriae
types of pili; involved in attachment of cells to surfaces; composed of a single protein; major determinant of bacterial virulence; up to 1000 per cell
adhesion pili
types of pili; vehicles for transfer of genetic information between bacteria; composed of phosphoglycoprotein; about 1-10 per cell
conjugation pili
types of pili; structure for motility
type IV pili
distinct bodies that may occupy a substantial part of the cytoplasm; may be organic or inorganic; some lie free in the cytoplasm or enclosed by a shell consisting of proteins or a membranous structure composed of proteins and phospholipids; usually used for storage
inclusion bodies
motility structures and mechanisms; swimming in aqueous environment; swarming on solid surface
flagella
motility structures and mechanisms; twitching motility
type 4 pili
motility structures and mechanisms; swimming without flagella
cytoskeleton
motility structures and mechanisms; buoyancy; movement in water column
gas vesicle
flagellar composition; a hollow rigid cylinder constructed of a single protein called flagellin; consists of a thousand copies of flagellin
flagellar filament
flagellar composition; connects filament to cell; structurally related to filament, made of different protein, FLgE; less rigid than filament; junction proteins between hook and filament
flagellar hook
motile bacteria move in response to different environmental stimuli
taxis
unique about flagella of spirochetes
located in the periplasm
function by rotating in the periplasmic space
expressed throughout the cell’s life cycle and are believed to have vital skeletal and motility functions
leads into corkscrew motility
surface motility; requires ATP hydrolysis to extend to several micrometers and then retract the cell to move forward; movement occurs in discrete movements
twitching motility by type IV
surface motility; requires a helical intracellular protein track that interacts with the gliding motors and extracellular adhesion proteins; rotation driven by PMF that translate the force to the helical track causing adhesion protein to move in a helical pattern; results in a continuous forward motion and clockwise rotation of the cell
gliding motility
surface appendages; means tuft in latin; first identified functional amyloids; extracellular protein fibers produced by many enteric bacteria (E. coli, S. enterica); crucial in biofilm formation, colony patterning, and interactions with host factors; morphology is characterized by highly coiled and aggregative thin fibers randomly distributed on the cell surface; resistant to degradation by proteases and denaturation by detergents
bacterial curli
surface appendages; tubular surface appendages broadly found in gram-negative bacteria; extend without apparent connection to the cytoplasm and are attached to the cell surface by proteins; for long-distance communication among bacteria, mediating exchanges in intercellular signals; randomly distributed on the cell surface
bacterial spinae
surface appendages; hollow tubules; small reed or cane in latin; connects the cells of pyrodictium to each other; highly resistant to heat and denaturing agents; entered the periplasmic space but not the cytoplasm; function unclear whether used for nutrient and genetic exchange or provide a means for anchoring
archaeal cannulae
surface appendages; prickle, claw, hook, barb / fishing rod in latin; structurally resemble type IV pili except for their barbed terminus; affix cells to a surface to form a networked biofilm; function as miniature grappling hooks to attach cells to a surface or to one another; archaeal cells that bear these fibers are found in macroscopically visible string-of-pearls like arrangements among bacterial filaments
archaeal hami
anatomy of the spore; loosely cross-linked peptidoglycan
cortex
anatomy of the spore; forms complex with small acid-soluble proteins (SASP); binds to DNA and protects it from UV desiccation and dry heat; carbon and energy source for outgrowth of new vegetative cell during germination; contains high levels of dipicolinic acid and other ions; dehydrates the spore conferring resistance to chemicals and inactivates enzymes
core
anatomy of the spore; possesses ridges and valleys; appears as fold in cross-section (TEM); prevents entry of large degradative molecules, toxic small reactive molecules, and predation by other microbes; when unfolded accommodate the increase in volume of that accompanies germination
coat
anatomy of the spore; outermost layer of the spore; contiguous shell surrounding the coat, and separated from it by a gap (interface); proteins present are candidates for vaccine and spore detection and important interaction with the environment
exosporium
do not possess photosystem II, thus do not produce O2; do not fix CO2 thus, do not require carbohydrates and reductants from vegetative cells; do not divide; site of nitrogen fixation, nitrogen gas to ammonia
heterocysts in anabaena
