week 10 Flashcards
what is a biofilm
community of microbial cells that are attached to a surface by an extracellular polymeric matrix (EPM)
true or false: about 95% microorganisms live in biofilms as long as there is at least a minimal amount of water and nutrients
true
the architecture of a biofilm supports the transport of…….
nutrients
biofilms:
provide habitat………
facilitate resource…..
promote community……..
protect cells from……..
diversity
capture
interconnectivity
environmental hazards
why are cells in biofilm 100-1000x more resistant to antibiotics
-physical barrier
-charged matrix
-horizontal gene transfer
- degradation of antibiotics
-persister cells
- diversity
what kinds of surfaces can biofilms form on
living tissues, indwelling medical devices, natural/ industrial systems, etc.
the NIH estimates that what percent of infections are caused by microorganisms growing in a biofilm?
80%
bacteria growing in biofilms help remove…….from wastewater
dissolved organics (unwanted)
how does growing attached to a surface improve fitness
close to other bacteria/ communities to communicate/ share resources
why can biofilms cause industrial systems to fail?
can cause localized corrosion in fuel storage tanks
quorum sensing identifies…….
population density
sequence of formation of biofilm
- organic/inorganic molecules + ions pre-condition the surface
- planktonic cells reversibly adhere to surface
-initial attachment by adhesins surface proteins
-hydrophobic/ hydrophilic + Van der Waals interactions
-contact through pili/fimbriae - nutrients available = cells irreversibly attach to surface
-adhesive EPM - cells begin to replicate + produce EPM
-quorum sensing triggers binding to form microcolonies - 2ndary colonizers partition the biofilm into niches/ water channels
- external parts of the biofilm may detach
dispersal is triggered by 3 major factors
- starvation: depletion of C or N, intracellular starvation signals
-density: quorum sensing mediated release
-toxins: reactive oxygen species, particularly NO
mechanical stress can also cause biofilms to disperse
3 distinct varieties in which biofilm dispersal occurs
- erosion: release of single cells or small clusters of cells at low levels
- sloughing: sudden detachment of large portions of the biofilm
- seeding: rapid release of a large number of cells following the formation of hollow, fluid-filled cavities inside biofilm
many bacteria produce hollow biofilms, filled with……and…..
fluids
planktonic cells
two main strategies for managing problematic biofilm formation
- inhibition
- dispersal
-physical
-chemical
-enzymatic
3 main variables important to cell attachment, biofilm formation development
- adhesion surface
-texture
-charge
-hydrophobocity - bulk fluid
-flow velocity
-pH
-temp
-nutrient - cell
-appendages
-EPM
-signaling molecules
3 methods to get rid of biofilms
physical removal
chemicals to dissolve
enzymes to disperse
Shelford’s law of tolerance
max. and min. limits of an organism control their abundance and distribution
5 environmental stressors that bacteria
- pH
- temp
- osmolarity
- oxygen
- starvation
-log(Ka) =
pKa
when pH = pKa…..
concentration of dissociated and undissociated acids will be equal
when pH > pKA….
more molecules will dissociate
when pH < pKA….
fewer molecules will dissociate
all C-termini and N-termini can…..
donate/ accept protons
at pH > pKa…. amino acids will…..
donate protons
If the pH strays too far from optimum, the presence of H+ or OH– ions will disrupt……..
bonds in the tertiary structure
how can pH affect the properties of an R-group
electrostatic attraction between molecules of solution + R groups = decreased enzyme affinity
bacteria prevent denaturation or lowered enzyme affinity by…..
maintaining a consistent internal pH
neutrophile pH
internal 7.5-8
external 6-8
acidophile pH
internal 6.5-7
external 1-4
alkaliphile pH
internal 8.4-9
external 9-12
true or false: acids can diffuse very quickly through the membrane bc of the negative charge
FALSE acids diffuse slowly c of the positive charge
at low pH, concentration of H+ ions…….the pressure
increases
To adapt to internal pH changes, bacteria must be able to do two different things:
alkalize cytoplasm
acidify cytoplasm
4 ways to alkalize cytoplasm:
- proton pumping
- potassium pumping
- reduce membrane permeability
- produce ammonia
2 ways to acidify cytoplasm:
- Na+/ H+ anti-porting
- K+/ H+ anti-porting
if cytoplasm is too acidic, then….
more protons are pumped out than in
………..limits the amount of H+ that can be moved to outside the cell
accumulation of + charges outside the cell
to balance the internal charge when protons are pumped outwards, cells……
pump K+ ions back inside the cell
saturated fatty acids are more hydro…… than unsaturated
hydrophobic
saturated fatty acids are…….permeable to H+ ions
less
bacteria can increase the pH with enzymatic……
activity
example of enzymatic activity to increase pH
producing ammonia from urea with urease
deaminase can increase pH by…….
removing the amine group from an amino acid or nucleotide
alkaliphiles acidify the cytoplasm by…….
supplementing normal H+ pumping with Na+/ H+ anti-porters
high temps cause proteins to……and membranes to become more…….
denature
permeable
low temps……membrane permeability and……chemical reaction rates
reduce
reduce
at higher temps, bacteria modify membrane fatty acids to contain…..saturated fatty acids
more
saturated fatty acids have……melting points
higher
many bacteria produce………to restore protein function after high temps
heat shock proteins (Hsps)
newly synthesized proteins need the help of……. to fold into
chaperone proteins
Hsp70
heat-shock chaperone protein that helps fold proteins using energy from ATP
Hsp70 is activated by binding ATP, which…….
opens the active site to the unfolded polypeptide
Hsp40
binds unfolded polypeptides and delivers them to Hsp70
Hsp70 closes around the unfolded protein and provides energy from……and a suitable environment for protein folding
ATP hydrolysis
a…….replaces ADP with ATP , which triggers Hsp70 to release the newly folded protein
nucleotide exchange factor
in addition to folding new proteins, Hsp70 can…..
help refold denatured proteins
unfolded proteins can form……usually due to exposed hydrophobic domains
aggregates
some Hsps, like……. are able to disentangle aggregates before feeding polypeptides to Hsp70 and Hsp40
ClpB
if misfolded proteins cannot be refolded, then……
they are degraded to prevent the toxic accumulation of aggregates
there are at least……ATP-dependent proteases Hsp’s
6
most bacteria live in ……tonic solutions
hypo
turgor pressure
pressure exerted on the cell wall from water expanding inside the cell
isotonic solution
no net movement of water
cell membrane attached to cell wall
hypertonic solution
water particles move out of the cell
cell membrane shrinks and detaches from cell wall
shrunken cell
hypotonic solution
water particles move into the cell
cell wall counteracts osmotic pressure swelling + lysis
4 mechanisms bacteria use to respond to changes in osmolarity
- salting out
- accumulation of compatible solutes
- expression of aquaporins
- opening/ closing of mechanosensitive channels
when turgor pressure is too high, bacteria can “salt-out” by……
trasnsporting Na+ out of the cell
when turgor pressure is too low, bacteria…..
accumulate compatible solutes
compatible solutes include
any non-toxic osmolytes in cytoplasm
can be organic or inorganic
after increasing intracellular K+, cells…….
switch to other organic compatible solutes
sugars, poly-acids, amino acids
osmolarity formula
osmolarity = moles ions/ L solution
