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microbio > week 9 > Flashcards

week 9 Flashcards

1
Q

monotrichous

A

one (monocle)

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2
Q

amphitrichous

A

one on each end (both)

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3
Q

lophotrichous

A

tuft

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4
Q

petritrichous

A

flagella all over (around)

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5
Q

monotrichous flagella movement

A

single flagella

forward = counter clockwise
reverse = clockwise

turns by “flicking” = quick start/stop cycles

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6
Q

peritrichous or lophotricous flagella movement

A

RUN
counter clockwise helices bundle = forward

TUMBLE
clockwise = bundles break apart = erratic movement

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7
Q

amphitrichous flagella movement

A

forward movement = 1 flagella CW, 1 flagella CCW
cell flexes/turns = flagella rotate same direction

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8
Q

chemotaxis

A

movement of a cell towards or away from a stimulus

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9
Q

chemoattraction

A

bacteria attracted to a chemical gradient

positive chemotaxis

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10
Q

chemorepulsion

A

bacteria repelled away from chemical gradient

negative chemotaxis

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11
Q

chemoeffectors

A

different chemicals that attract or repel bacteria

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12
Q

two behaviors that are combined to travel

A

forward motion
random change in direction

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13
Q

why is chemotaxis important?

A

helps bacteria maintain optimal environment niche

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14
Q

bacteria change behaviors through differential gene expression using a combination of…… (3 things)

A

sigma factors
activators
repressors

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15
Q

how do bacteria know when to activate or repress gene expression if the signal is external?

A

2-component regulatory systems

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16
Q

2- component regulatory systems

A
  1. sensory kinase
  2. response-regulator protein
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17
Q

number of 2-component systems encodes on the genome is correlated to the…….

A

size of the genome

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18
Q

sensor kinase

A

membrane- bound protein

extracellular receptor for a metabolite

signals the intracellular communication pathway via phosphorylation of a Histidine residue

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19
Q

response- regulator protein

A

cytoplasmic protein (usually)

relays signal from the sensor kinase

activated/deactivated when sensor kinase adds/removes a phosphate

activates or represses transcription

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20
Q

PHO system

A

sensor kinase: PhoR
response regulator: PhoB

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21
Q

major genes expressed by PHO system

A

phoA
phoE
Pst system (5 proteins)
many genes for uptake/breakdown of various organophosphorus compounds

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22
Q

phoA

A

phosphatase that cleaves phosphate from organic phosphate esters

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23
Q

phoE

A

outer membrane porin channel to increase phosphate uptake

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24
Q

Pst system

A

high-affinity phosphate uptake system

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25
Q

the Pho system under phosphate abundant conditions

A

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

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26
Q

the Pho system under limiting phosphate conditions

A

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

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27
Q

porins

A

protein channels found in the outer membrane of Gram-negative bacteria

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28
Q

OmpC

A

NARROW-channel porin expressed in HIGH osmolarity media

Hi-C juice box:)

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29
Q

OmpF

A

WIDE-channel porin expressed in LOW osmolarity media

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30
Q

OmpF and OmpC are associated with…… (3 things)

A

nutrient uptake
cell homeostasis
outer membrane integrity

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31
Q

EnvZ/ OmpR rules

A
  1. both porins have separate promoters
  2. 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
32
Q

EnvZ

A

sensor kinase that spans the inner membrane and has 2 pairs of helical domains

33
Q

as membrane pressure increases, EnvZ…..and this causes:

A

compresses

hydrogen bonds form between adjacent helices and are further stabilized by increased osmolyte concentration inside the cell

34
Q

following EnvZ compression, how does the EnvZ/ OmpR system work

A

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

35
Q

inactive OmpR

A

non-phosphorylated

activates the expression of OmpF

36
Q

active OmpR

A

phosphorylated

activates OmpC and represses OmpF

37
Q

how do we determine the function of a gene/protein?

A
  1. observe a phenotype
  2. disable a gene and observe a change in phenotype
  3. restore the original phenotype in the same organism
38
Q

tracers

A

fused with protein products to detect if, when, where a protein product is produced

39
Q

our first step to link a phenotype to a protein is to…..

A

disable the gene

40
Q

to prove a gene has a specific function, we need to……

A

restore that gene and see if the function returns

41
Q

……..are one common strategy used to restore functions

A

expression vectors

42
Q

……… can be used to link sensor kinases to their regulator response proteins

A

radioactive ATP

43
Q

……..can provide clues as to which genes are associated with a particular phenotype

A

RNA sequencing

44
Q

6 steps of RNA sequencing

A
  1. isolate RNA from samples
  2. fragment RNA into short segments
  3. convert RNA fragments into cDNA
  4. ligate sequencing adapters and amplify
  5. perform NGS sequencing
  6. map sequencing reads to the transcriptome/ genome
45
Q

…….. can be used to identify regulator response-DNA interactions

A

reporter genes

46
Q

5 main components of bacterial flagella

A
  1. Basal Body: attachment to membrane, transport proteins for assembly, structure to allow rotation
  2. the Motor: rotation
  3. the Switch: allows for changing of rotation (C-ring)
  4. the Hook: connects the filament to the basal body
  5. the filament and capping proteins: structural proteins
47
Q

the basal body is the…..

A

base of the flagellum and anchors the structure to the membrane(s)

48
Q

a……..passes through the rings and connects the hook to the motor

A

protein rod

49
Q

the motor of the flagellum has two parts:

A

stator (non-rotating)
rotor (rotating)

50
Q

Mot protein complex

A

facilitates the diffusion of proteins into the cell to transfer the energy required to turn the flagella

51
Q

2 possible models for motion in Mot protein complex

A
  1. protons interact w/ rotor proteins
  2. protons interact w/ stator proteins
52
Q

the motion generated by the motor causes the….., which……

A

rod to spin

turns the hook, hook associated proteins, and filament

53
Q

the filament is a…….,……filament that acts as a

A

hollow, helical
propeller

54
Q

the filament is made of the protein……and ends in a…..protein

A

flagellin
Cap

55
Q

the turns in the helix are…… which generate……

A

counter clockwise
propulsion

56
Q

angled helical arrangement of flagellin proteins…….. the cell when……

A

propels
rotated

57
Q

chemotaxis requires 4 processes to occur

A
  1. sense presence/absence of a chemoeffector (MCP)
  2. signal the motor to change direction (CheA, CheW, CheY)
  3. return to the forward direction (CheZ)
  4. sensory adaptation (CheB + CheR)
58
Q

chemoeffectors are detected by…….

A

methyl accepting chemotaxis proteins (MCPs)

59
Q

MCPs

A

bind specific ligands, result in conformational change that starts or stops tumbling

60
Q

Tar

A

towards aspartate + maltose

away from nickel + cobalt

61
Q

Tsr

A

towards serine

away from leucine + indole + weak acids

62
Q

Trg

A

towards galactose + ribose

63
Q

Tap

A

towards dipeptides

64
Q

MCPs are localized towards the…….

A

front of the cell

65
Q

if the attractant is present, the cell continues to…….

A

move in a straight line

66
Q

what does the CheW protein do

A

arranges MCPs into large chemosensory arrays

67
Q

attractant is absent sequence

A
  1. unbound MCP allows sensor kinase CheA to autophosphorylate
  2. phosphate is transferred to CheY = activates CheY-P
  3. CheY-P binds to C-ring = flagellum motor turns clockwise = tumble
  4. 1 sec = CheZ removes the phosphate from CheY-P and counterclockwise rotation resumes = run
  5. CheY cycles between phosphorylated/ unphosphorylated = short runs + tumbles
68
Q

attractant is bound to the MCP =

A

CheA does not phosphorylate + the cell continues to run

69
Q

the cell’s ability to detect chemoeffectors is limited by……

A

the number of MCP receptors in the membrane

70
Q

to continue moving to higher concentrations, the cell needs to…..

A

activate

71
Q

sensory adaptation

A

allows bacteria to fine tune their motility

72
Q

sensory adaptation is regulated by……

A

2 cytoplasmic proteins, CheR + CheB

73
Q

the enzyme…. adds methyl groups slowly to MCP bound to attractants, activating CheA

A

CheR

74
Q

methylated MCPs can be inactivated at higher concentrations of chemoattractants when MCPs can……..

A

bind multiple chemoattractants at once

75
Q

methylation by CheA is a slow process and doesn’t occur frequently unless……

A

all the MCPs are bound to at least one effector molecule

76
Q

MCPs

A

microbio (5 decks)

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