week 9 Flashcards
monotrichous
one (monocle)
amphitrichous
one on each end (both)
lophotrichous
tuft
petritrichous
flagella all over (around)
monotrichous flagella movement
single flagella
forward = counter clockwise
reverse = clockwise
turns by “flicking” = quick start/stop cycles
peritrichous or lophotricous flagella movement
RUN
counter clockwise helices bundle = forward
TUMBLE
clockwise = bundles break apart = erratic movement
amphitrichous flagella movement
forward movement = 1 flagella CW, 1 flagella CCW
cell flexes/turns = flagella rotate same direction
chemotaxis
movement of a cell towards or away from a stimulus
chemoattraction
bacteria attracted to a chemical gradient
positive chemotaxis
chemorepulsion
bacteria repelled away from chemical gradient
negative chemotaxis
chemoeffectors
different chemicals that attract or repel bacteria
two behaviors that are combined to travel
forward motion
random change in direction
why is chemotaxis important?
helps bacteria maintain optimal environment niche
bacteria change behaviors through differential gene expression using a combination of…… (3 things)
sigma factors
activators
repressors
how do bacteria know when to activate or repress gene expression if the signal is external?
2-component regulatory systems
2- component regulatory systems
- sensory kinase
- response-regulator protein
number of 2-component systems encodes on the genome is correlated to the…….
size of the genome
sensor kinase
membrane- bound protein
extracellular receptor for a metabolite
signals the intracellular communication pathway via phosphorylation of a Histidine residue
response- regulator protein
cytoplasmic protein (usually)
relays signal from the sensor kinase
activated/deactivated when sensor kinase adds/removes a phosphate
activates or represses transcription
PHO system
sensor kinase: PhoR
response regulator: PhoB
major genes expressed by PHO system
phoA
phoE
Pst system (5 proteins)
many genes for uptake/breakdown of various organophosphorus compounds
phoA
phosphatase that cleaves phosphate from organic phosphate esters
phoE
outer membrane porin channel to increase phosphate uptake
Pst system
high-affinity phosphate uptake system
the Pho system under phosphate abundant conditions
abundant inorganic phosphate binds to a phosphate binding protein (PstS)
PstS binds to phosphate transporter PstABC
PstABC imports the phosphate and forms a repressor complex w/the kinase sensor (PhoR)
while repressed, PhoR dephosphorylates the regulator response protein (PhoB), keeping the PHO regular inactive
the Pho system under limiting phosphate conditions
PstS no longer binds to PstABC, resulting in activation of PhoR
PhoR autophosphorylates and then phosphorylates PhoB
phosphorylated PhoB positively regulates the PHO regulon
the PhO regulon regulates 38 genes required during phosphate limitation
porins
protein channels found in the outer membrane of Gram-negative bacteria
OmpC
NARROW-channel porin expressed in HIGH osmolarity media
Hi-C juice box:)
OmpF
WIDE-channel porin expressed in LOW osmolarity media
OmpF and OmpC are associated with…… (3 things)
nutrient uptake
cell homeostasis
outer membrane integrity
EnvZ/ OmpR rules
- both porins have separate promoters
- the regulator response protein (OmpR) activates the expression of both OmpF and OmpC
a. inactive OmpR activates OmpF expression
b. active OmpR activates OmpC expression and represses OmpF expression
EnvZ
sensor kinase that spans the inner membrane and has 2 pairs of helical domains
as membrane pressure increases, EnvZ…..and this causes:
compresses
hydrogen bonds form between adjacent helices and are further stabilized by increased osmolyte concentration inside the cell
following EnvZ compression, how does the EnvZ/ OmpR system work
compressed form of EnvZ auto-phosphorylates by accepting a phosphate from ATP
phosphorylated EnvZ then activates the regulator response protein OmpR by transferring the phosphate
activated OmpR activates the expression of OmpC and represses the expression of OmpF
the signal is reset by EnvZ. under low osmolarity, EnvZ removes the phosphate from activated OmpR
inactive OmpR
non-phosphorylated
activates the expression of OmpF
active OmpR
phosphorylated
activates OmpC and represses OmpF
how do we determine the function of a gene/protein?
- observe a phenotype
- disable a gene and observe a change in phenotype
- restore the original phenotype in the same organism
tracers
fused with protein products to detect if, when, where a protein product is produced
our first step to link a phenotype to a protein is to…..
disable the gene
to prove a gene has a specific function, we need to……
restore that gene and see if the function returns
……..are one common strategy used to restore functions
expression vectors
……… can be used to link sensor kinases to their regulator response proteins
radioactive ATP
……..can provide clues as to which genes are associated with a particular phenotype
RNA sequencing
6 steps of RNA sequencing
- isolate RNA from samples
- fragment RNA into short segments
- convert RNA fragments into cDNA
- ligate sequencing adapters and amplify
- perform NGS sequencing
- map sequencing reads to the transcriptome/ genome
…….. can be used to identify regulator response-DNA interactions
reporter genes
5 main components of bacterial flagella
- Basal Body: attachment to membrane, transport proteins for assembly, structure to allow rotation
- the Motor: rotation
- the Switch: allows for changing of rotation (C-ring)
- the Hook: connects the filament to the basal body
- the filament and capping proteins: structural proteins
the basal body is the…..
base of the flagellum and anchors the structure to the membrane(s)
a……..passes through the rings and connects the hook to the motor
protein rod
the motor of the flagellum has two parts:
stator (non-rotating)
rotor (rotating)
Mot protein complex
facilitates the diffusion of proteins into the cell to transfer the energy required to turn the flagella
2 possible models for motion in Mot protein complex
- protons interact w/ rotor proteins
- protons interact w/ stator proteins
the motion generated by the motor causes the….., which……
rod to spin
turns the hook, hook associated proteins, and filament
the filament is a…….,……filament that acts as a
hollow, helical
propeller
the filament is made of the protein……and ends in a…..protein
flagellin
Cap
the turns in the helix are…… which generate……
counter clockwise
propulsion
angled helical arrangement of flagellin proteins…….. the cell when……
propels
rotated
chemotaxis requires 4 processes to occur
- sense presence/absence of a chemoeffector (MCP)
- signal the motor to change direction (CheA, CheW, CheY)
- return to the forward direction (CheZ)
- sensory adaptation (CheB + CheR)
chemoeffectors are detected by…….
methyl accepting chemotaxis proteins (MCPs)
MCPs
bind specific ligands, result in conformational change that starts or stops tumbling
Tar
towards aspartate + maltose
away from nickel + cobalt
Tsr
towards serine
away from leucine + indole + weak acids
Trg
towards galactose + ribose
Tap
towards dipeptides
MCPs are localized towards the…….
front of the cell
if the attractant is present, the cell continues to…….
move in a straight line
what does the CheW protein do
arranges MCPs into large chemosensory arrays
attractant is absent sequence
- unbound MCP allows sensor kinase CheA to autophosphorylate
- phosphate is transferred to CheY = activates CheY-P
- CheY-P binds to C-ring = flagellum motor turns clockwise = tumble
- 1 sec = CheZ removes the phosphate from CheY-P and counterclockwise rotation resumes = run
- CheY cycles between phosphorylated/ unphosphorylated = short runs + tumbles
attractant is bound to the MCP =
CheA does not phosphorylate + the cell continues to run
the cell’s ability to detect chemoeffectors is limited by……
the number of MCP receptors in the membrane
to continue moving to higher concentrations, the cell needs to…..
activate
sensory adaptation
allows bacteria to fine tune their motility
sensory adaptation is regulated by……
2 cytoplasmic proteins, CheR + CheB
the enzyme…. adds methyl groups slowly to MCP bound to attractants, activating CheA
CheR
methylated MCPs can be inactivated at higher concentrations of chemoattractants when MCPs can……..
bind multiple chemoattractants at once
methylation by CheA is a slow process and doesn’t occur frequently unless……
all the MCPs are bound to at least one effector molecule
MCPs
