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BIMM 120 - Microbio > Midterm 2 material > Flashcards

Midterm 2 material Flashcards

1
Q

Define: F0F1 ATPase

goal?
characteristics? 3 total
where is it found?

A

goal: to pump protons to other side of mem

Reversible process
Ubiquitous + highly conserved
F1 and F0 oriented in opposite directions

Found in mito mem of eukaryotes OR mem of prokaryotes

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2
Q

location of F1 + F0 in the cell and their role

A

F1 - free in the outside of cell
It’s the catalytic site for ATP synthesis

F0 - bound to interior of mem
acts as a rotary motor powered by the flow of protons

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3
Q

what are the subunits of F0?

A

F0: 3 subunits - all are integral mem components
1. A - embedded in mem
2. B - connects F0 + F1
A + B = Provide a channel for proton flow + interacts with the rotor to generate torque
3. C also known as C ring - has 12 subunits

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4
Q

what are the subunits of F1?

also something is impaled

A

F1: Gamma + Epsilon - 2 total philic subunits acting as a rotating rod
Alpha - has NO catalytic function; Only holds structure together
Beta - hydrophilic w/ small hydrophobic region; Phobic region = anchor
Alpha + beta subunits impaled by gamma

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5
Q

What is the rotor + stator of F0F1 ATPase? what subunits form each part?

A

Rotor + stator - a combination of subunits from both F0 and F1

Rotor: c subunit (from F0) + gamma subunit (from F1)
- Rotating component

Stator: a + b subunit (from F0) + alpha + beta subunit (from F1)
- Stationary component

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6
Q

What is the driving force of F0? F1?

A

F0 = PMF
F1 = ATP hydrolysis
proton gradient generates ATP

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7
Q

what happens to the F1 ATPase normally + when it changes direction? what happens per
revolution?

A

Normally, F0 forward + F1 in reverse; ATP synthesis driven by PMF

F1 moving forward, towards ATP hydrolysis; 3 ATP hydrolyze/revolution

F1 moving in reverse; 3 ATP synthesized/revolution

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8
Q

what is the bacterial flagella?

A

hair like structures that propel bacteria through liquid environments

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9
Q

what is the bacterial flagella made of?

A
  1. basal region w/ 4 rings…
  2. A pipe
  3. Hook
  4. HAP1 + 3
  5. HAP2
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10
Q

rings associated w/ the basal region of the bacterial flagella? 4 total rings

A

(A) C ring associated w/ motor

(B) M ring associated w/ mem

(C) P ring (peptidoglycan binding motif) associated w/ stator - Allows for motor to be stabilized via anchoring

(D) L ring associated w/ LPS - Lipopolysaccharide

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11
Q

what is the purpose of the bacterial flagella’s pipe? 3 points

A

Allows transport of export substrate
Leads to lengthening of tail
Goes through all the rings

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12
Q

what is the purpose of HAP1 + 3 and HAP2?

A

HAP1 + 3 - Responsible for linking hook + basal region
HAP 2 - Cap that causes flagellum to stop growing

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13
Q

What is the order of synthesis of the bacterial flagellum? what is the driving force?

A

(first) basal region → hook → flagellum (last)

Driving force… proton motive force

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14
Q

What is the direction of the flagellum?

A

flagella move in direction of something good + away from bad things

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15
Q

What is the purpose of MotAB? what do they make up?

A

Components A+B s crucial for the function of the bacterial flagellar motor

make up the stator, acting as channel for proton

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16
Q

What forms a complex that interacts w/ MotAB? what happens if no comples interaction? 3 points

A

FliG, M, N form a complex that interacts w/ MotAB
No complex interaction, then…
1. No intact flagella
2. Intact flagella w/ no motor
3. Intact flagella w/ no chemotaxis

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17
Q

how is the flagella constructed + what can control its length?

A

T3SS (Type 3 secretory system) - crucial for assembly of components outside of mem
- Components that traveled through hollow flagellum tube added to end of tail

Capped by HAP2 - stop growth
- Completion of Hook + basal body = crucial checkpoint

FliK regulates hook length - an internal “ruler”

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18
Q

what happens when the switch between swarming + swimming occurs? how do the swarming cells looks?

A

Switch between swarming + swimming = change in morphology

Swarming cells more elongated + flagellated

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19
Q

differences between archaea + bacterial flagellum

6 points

A

-diff structure + function
-Driven by ATP hydrolysis NOT PMF or SMF
-Slower + thinner than bacteria
-Archaea has no peptidoglycan in cell wall
-New subunits assemble @ base andare diff (Bacteria subunits assemble @ tip)
-Flagellum - no hollow space

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20
Q

similarities between archaea + bacterial flagellum

A

-have Flimanet + basal region + hook too
- Use the same homologous chemotaxis proteins

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21
Q

compare the motors between archaea + flagellum

what aa are used?

A

Motors are diff
Bacteria: use proton/sodium channels + serine or threonine

Archaea: they use ATP to drive the process
- Its an aspartate + asparagine aa derivative

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22
Q

sodium motive force (SMF)

what does it do?

A

-provide energy
-bacteria useS PMF to power the rotation of the flagellum for motility
- archaea uses SMF to indirectly help ATP synthesis

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23
Q

what does motility Type IV pili (T4P) controls + how?

A
  • movement over surfaces w/o flagella
  • Uses cell propulsion
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24
Q

steps in cell propulsion. 3 total

A
  1. pilus extension
  2. Attachment to a surface
  3. Retraction
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25
Q

why is the assembly of pili rapid?

A

due to genome economics - Rapid assembly from newly synthesized monomers due to high rate of new protein synthesis

recycles primary pilA

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26
Q

what is Gliding movement? what is it powered by? what protein does it use? what is the motor comprised of?

A

a type of lateral movement on solid surfaces, Powered by PMF

Uses SprB adhesin - an adhesive organelle used to grab onto something

Motor used in gliding movement comprised of GLD proteins

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27
Q

function of SprB aka what does it attach to? what allows for movement? when does movement occur? it rotates over what?

A

-attaches itself to the surface
-undergoes conformational changes that allow for movement
- Movement occurs during retraction conformational stage
-SprB rotates over lateral surface

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28
Q

what is lateral movement? what is an example aside from gliding? what is it powered by?

A

made up of several diff sideways movements
Ex. twitching
Powered by ATP hydrolysis

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29
Q

define the two forms of motility: S + A motility

A

S motility - a type of twitching motility
A motility - polysaccharide secretion generates propulsion; Slime trail left behind

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30
Q

what 2 things can be secreted to produce cell propulsion

A
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31
Q

what uses the centipede + inchworm motility methods?

what is it?

A

Mycoplasma - tiny bacteria w/ simple genome + asymmetric built - move w/ head direction

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32
Q

explain centipede + inchworm motility

A

Gli proteins localized @ neck allow for Leg like function leading to centipede like movement

Are able to glide in the direction of terminal organelle where terminal cytoskeleton forms dynamic motor; Leads to inch worm like confirmation changes

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33
Q

why does the outside of a cell have a pH of 5.5?

A

outside of cell more acidic bc of high [H+] protons; [high] given protons are pumped out of cell producing proton gradient

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34
Q

why is the F0F1 ATPase reversible?

A

because of two possible energy sources, ATP hydrolysis + PMF

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35
Q

which way is the F0F1 ATPase rotating to promote the PMF? ATP synthesis?

A

ATP hydrolysis + CW rotation = PMF
PMF + CCW rotation = ATP synthesis

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36
Q

which AA residue is essential for transferring H+ ions (protons)

A

Aspartate/Aspartic acid (D)

D61

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37
Q

which AA residues are essential for the channel to function

A

D61 + Arginine (R)/R210

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38
Q

where does the ATP binds + the general steps in the F1 component

A

ATP binds beta subunit

General steps
1. ADP + Pi binds
2. ATP synthesis
3. ATP leaves

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39
Q

why is the flagellar motility energetically significant?

A

Bc it takes half of all energy to rotate flagella + to allow movement

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40
Q

what functions together to produce the torque in the flagellar motor?

A

C-terminal domain of FliG interacts w/ MotAB to produce the torque

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41
Q

negative cooperativity

A

binding of 1 or more ligand molecules to a multimeric receptor makes it difficult for other ligand molecules to bind

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42
Q

what is negative cooperatively due to?

A

receptor clumping +
(receptor) methylation

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43
Q

why is chemotaxis so important?

A

important amongst bacterial flagella for successful host colonization + infection

Generally, important for survival + growth + directed movement away from bad environment, towards good environment

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44
Q

how is tumbling caused? how can tumbling direction change? CW or CCW rotation?

A

Tumbling is a result of temporary reversal in the rotary direction of flagellar motors

increasing repellent causes tumbling to go another direction

Bacteria disperse in CCW rotating leading to tumbling

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45
Q

which step of the signal transduction rxn is faster? which is sower? is faster attributed to tumbling or swimming? how about slower?

A
  1. Activation step = fast
    Fast rxn for tumbling, heading in a different direction
  2. Adaptation step = slow
    Slow rxn for swimming, heading in the correct direction
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46
Q

what is the role or CheA? CheW? what do they accomplish together?

A

CheA - histidine kinase
CheW - adaptor protein

CheA+CheW = form complex that primarily clusters @ poles to control clumping

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47
Q

CheR + CheB’s purpose? what are the domains of CheR? CheB? Hint: both have 2 domains

A

de/methylate specific residues

CheR has 2 domains
1. N for MCP binding only
2. C for MCP binding + catalysis

CheB has 2 domains
1. Phosphorylatable receiver/regulatory domain
2. Catalytic methylesterase domain

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48
Q

connection between chemotaxis and environmental niches?

A

Bacteria use chemotaxis to accumulate in environmental niches that provide optimal conditions for growth

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49
Q

significance of nutrient or repellent gradients? aka what movement happens if there is an increase in attractant/nutrient? an increase in repellent

A

Both act as signals

An increase in attractant (nutrient) leads to smooth swimming; For moving towards nutrient rich environments

An increase in repellent (toxic substance) leads to tumbling; For moving away from toxic environments

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50
Q

trade-off between nutrients and motility

A

Accumulation of nutrients leads to increased nutrient uptake
-Advantage: Leads to enhanced growth + swimming motility
-Disadvantage: requires high investment of cellular resources
-Solution: swim for food when it’s abundant but conserve energy when food is scarce

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51
Q

significance of cAMP? what happens under high cAMP?

A

cAMP is important for determining regulation of flagellar genes

Reflects growth rate under carbon limited conditions

High cAMP under limited conditions activates alternative uptake + metabolism routes for diff energy sources

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52
Q

connection between trade-offs and variability as well as niche formation? when does variability decrease?

A

chemotactic performance variability in bacterial pops exists

Run + tumble of bacterial swimming + chemotactic sensitivity = varies within cells

Variability decreases @ high levels of chemoattractants

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53
Q

when is tradeoff in flagellar motility + chemotaxis of bacterial pathogens most beneficial? what will happen later in the process ?

A

beneficial @ early stages of infection

Later becomes too much given flagellum = major antigen thats recognized by immune system

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54
Q

why is the flagellum detrimental to pathogens?

A

Flagellum = major antigen recognized by immune system

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55
Q

Chemotactic responses occur due to…

what type of patterns

A

emergence of higher complexity patterns

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56
Q

what is the chemotactic response? what does it lead to?

A

Bacteria responding to chemicals released by other bacteria

Leads to chemotactic self-attraction, generating aggregative processes

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57
Q

what happens at higher densities of cells and swimming?

A

cell swimming leads to physical interactions between bacteria

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58
Q

how is the flagellum beneficial at surfaces?

A

Flagellum promotes initial attachment to a surface

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59
Q

why is the flagellum beneficial for pathogenic bacteria? 3 reasons?

A

Higher interaction w/ mucus layer

Increased chance of penetration into host cell

Helps w/ colonization

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60
Q

what is the Rhizosphere? what taxis does it use? what is the purpose?

A

-an area in the soil surrounding plant roots

-Rhizosphere pathogenic bacteria uses chemotaxis

-Purpose is to accumulate towards nutrient rich environment around plant route

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61
Q

Adhesion to the surface helps w/…

adhesion to surface is what stage in the development of biofilms?

A

resistance to antibiotics via enhancing stability of plasma mem

It is the initial stage in development of biofilms

62
Q

Biofilms are important for…

A

survival + proliferation + protection against agents

63
Q

concept of flagella impedance?

A

Where surface sensing is mediated via proximal surface interfeing w/ rotation of bacterial flagella

64
Q

characteristics of Type IV pili (T4P): what are they? how are they extended? what kind of motility used?

A

They are mem bound filamentous structures

Extended via polymerization by an assembly ATPase

Perform twitch motility

65
Q

Pseudomonas aeruginosa

what are they?
what kind of injury is it common w/?
what sickness can it cause?
what kind of flagella does it contain?
can it attach to the surface? detach? for how long?

A

-Pathogen w/ acute or chronic effects
-Common w/ infections of burns
-Can cause cystic fibrosis
-Contains polar flagella
-Attaches + detaches to surface temporarily

66
Q

what if P aeruginosa remain attached to the surface? what kind of surface is required?

A

if attached, then its irreversible, halting flagella rotation

Require physically rigid surface, not specific chemical surface composition

67
Q

what is quorum sensing?

A

Sensing of cell pop density, regulating gene expression

68
Q

E. coli and its characteristics

is it commensal or harmful bacteria?

how does it regulate virulence?

what 3 things does it use to mediate diseases as virulence factors?

what happens in response to changes in physical force?

A

Can be commensal bacteria + common health concerns as a virulent strain

Regulates via mechanosensors

Uses type 3 sec system + adhesins + toxins

Expression of virulence factors are altered

69
Q

what is the motility speed of E coli in soft agar?

A

Pathogenic strains had increased motility, Commensal bacteria had normal motility speed

70
Q

What does mechanosensing of E coli help with? how? what is motility useful for?

A

helps w/ successful host colonization via increasing expression of flagella in early infection stages

Motility useful in promoting contact w/ epithelial cells during early stages of infection

71
Q

what happens when V. Cholerae cannot use the flagella

A

Defective motility leads to enhanced expression of virulence factors like toxins

72
Q

what are the functions + characteristics of pili based nanowires? 3 total

A

Conductive in absence of native metal cofactors + added metals

Function as conduits for long range e- transport → extracellular terminal e- acceptors

More conductive due to higher aromatic aa abundance

73
Q

how can certain amino acid residues increase conduction

A

Close packing of aromatic aa during filament assembly forms aromatic-to-aromatic e- conduction paths thereby increasing conduction

74
Q

what are some of the devices that use bacterial nanowires? 3 total

A

Sensors, electricity production, and memristors

75
Q

MCPs and CheA - is activity stimulated or inhibited? when bound to repellent/attractant

A

Repellent-bound MCPs stimulate autokinase activity of CheA

Attract-bound MCPs inhibit autokinase activity of CheA

76
Q

what happens when you add a repellent or an attractant

A

Add attractant, Leads to dimerization of TM1/TM2 monomers

Add repellent, monomers dissociate

77
Q

what controls clumping?

A

CheA + CheW

78
Q

methylation and clumping in negative cooperatively. What does negative cooperatively mean? what is it due to?

A

Negative cooperativity refers to the ability of sensing a [range]

Negative cooperativity due to clumping of receptors @ poles + receptor methylation

79
Q

what components can control methylation

A

CheR + CheB

80
Q

components of attractant binding + MCP methylation?

hint: what does binding create and becomes what to what? What is the purpose of SAM?

A

Binding creates conformational changes such that MCP = poor substrate of CheB but good substrate for CheR

SAM increases methylation, reducing attractant affinity by removing (-) charge thereby returning protein to inactive/condensed form

81
Q

what induces lateral flagella use? six points

A
  1. Increase viscosity = decrease rotation of polar flagella
  2. Decrease rotation for growth on surfaces
  3. Decrease rotation when antibody binds to polar flagellum
  4. Decrease rotation when Na+ channels are blocked
  5. Prevent rotation when there are muts in the flagellum constituents, blocking assembly
  6. Prevent rotation when muts are in motor
82
Q

what induces swarmin?

A
  1. Halting cell division
  2. Cell elongation
  3. Induction of all swarmer cell genes
  4. Induction of surfactin genes
83
Q

what is TolQRA responsible for? how is it involved in drug resistance?

A

-responsible for transport of LPS to outer surface

-Indirectly involved in drug resistance as Tol mutants have leaky outer mems, altering drug sensitivities

84
Q

Tsr, Tar, Trg and Tap which kinds of thermosensors are they?

A

Tsr + Trg = warm sensors
Tar - warm + cold sensors
Tap - cold sensor

85
Q

what kind of motility is induced when warm or cold sensors experience changing temperatures?

A

Warm sensors experience temp decrease, they tumble

Cold sensors experience temp decrease, then smooth swimming

86
Q

obligate and facultative bacteria [Oxygen]? what happens in high levels of O2 in Facultative?

A

Obligate aerobes - migrate to the air-water interface

Facultative aerobic bacteria - Seek optimal [oxygen] where high O2 levels can inhibit respiration

87
Q

what are Magnetosomes? what are they made of? size comparison across all organisms? what about chain + magnetic moment orientation?

A

small cubo-octahedral crystals made of magnetite + greigite

Crystal size the same across all organisms

Chains have same orientation - Magnetic moments thus are all in the same direction

88
Q

What does TatA do? How can TatA accommodate large/small subunits? when does it adjust to large subunits? what’s the purpose of TatC?

A

TatA - creates size adjustable pore by changing amount of TMSs; Adjusts to large substrates only as needed

TatC - energizer

89
Q

what are holins? what are they responsible for?

A

Form holes in mem - Are responsible for export of enzymes that cause cell wall degradation and eventually, cause lysis

90
Q

why it is bizarre that the LolA/LolB pieces have a similar 3D structure?

A

Bc one is in a hydrophobic environment and the other in a hydrophilic environment

91
Q

Explain how ABC systems (3 total) arose either in duplication of fusion + what they transport

Also explain how the 5 TMS of ABC 4 arose

A

ABC 1 - Duplicated or fused to other domains; Transport all substrates

ABC 2 - Rarely duplicated/fused; Export carbohydrates

ABC 3 - Often duplicated/fused to other domains w/ non-random arrangement; Transport peptides + proteins

5 TMS ABC 4 arose from either a 2 duplication plus 1 or 3 dup minus 1

92
Q

inner mem sec system: Type 1

A

Allows transport across both mems of gram-neg envelope in single step

TolC - Forms trimeric outer mem beta barrel pore structure + trans-periplasmic trimeric alpha helical conduit, connecting inner mem permease to outer mem pore

OMF itself provides trans periplasmic channel

MFP interlinks inner + outer mem transport pathways

93
Q

inner mem sec system: tat

TatABC?

A

Translocate redox enzymes

Are channels for protein translocation

TatABC - 1 B homologue + C required for function
C is the specificity determinant for complex

94
Q

inner mem sec system: Type 4

A

Made up of subunits that span 2 mems + peptidoglycan wall in gram-neg cell envelope + single mem pilus of gram-pos cell envelope

Export proteins + DNA protein complexes into cytoplasm of recipient cell + Also transfer DNA

95
Q

inner mem sec system: Type 3

What do they secrete?

Do they secrete proteins directly into host cell cytoplasm w/o exposure to extracellular environment + Secret virulent factors?

A

Allow secretion of cytoplasmically synthesized proteins across both mems of cell envelope

YES

96
Q

General secretory translocases (sec system) (type 2)

what are the e coli translocase constituents made up of? what are they know as?

What is the 2nd thing they are made up of? what are they known as?

A

Made up of heterotrimeric integral mem protein complex Known as SecYEG

Also made up of cytoplasmic ATPase known as SecA
Sec-dependent proteins export

97
Q

in the sec system, are Integral mem protein insertions driven by ATP/GTP hydrolysis?

A

YES

98
Q

What is the purpose of the PMF in the gen sec system?

A

PMF is stimulatory + functions in translocating C-terminal parts of unfolded proteins

99
Q

Outer mem sec systems: FUP

A

Function: biogenesis of fimbriae/pili in gram-neg bacteria

Fimbrium specific periplasmic chaperone protein + outer mem usher protein

Pilus subunits bound to chaperone proteins; Prevents self assembly of pili in periplasm

100
Q

Outer mem sec systems: TPS

A

They are large proteins w/ adhesive activities linked to bacterial virulence

Passenger domain exported across outer mem via transport constituents

101
Q

Outer mem sec systems: AT-1

A

Made up of single protein w/ N-terminal sec type signal peptide + central passenger domain + C-term beta domain

Passenger domains determined by function of exo proteins

102
Q

Outer mem sec systems: AT-2

A

Has YadA

Linker needed for stability + translocation of passenger domain through outer mem

103
Q

Outer mem sec systems: OmpIP

what is it and what are the outer membrane proteins assembled from?

what are they involved in?

what happens if you decrease OMP83?

A

They are gram-neg bacterial outer mem proteins assembled from periplasm into outer mem

Involved in lipid biosynthesis

Decrease of Omp85 leads to accumulation of LPS in inner mem + loss in outer mem

104
Q

are proteasomes found in eukaryotes? Archaea? bacteria? w/ what function?

A

Eukaryotes + archaea use proteasomes for protein degradation

Only certain bacteria have proteasomes with diverse functions

105
Q

how is the function + structure similar and different to chaperones

A

Chaperone proteins fold unfolded proteins into native state while proteasomes degrade misfolded proteins

106
Q

do proteasomes require ATP to function?

A

YES BUT NOT ALL

107
Q

where do GQYL motifs insert themselves? why?

A

between alpha subunits to open M tuberculosis 20S CP gate

108
Q

Proteolytic specificity is determined by…

A

the chemical nature of the pocket surrounding the active site.

109
Q

nitric oxide (NO) resistance. what does it depend on? what does it damage? what are the effects of the damage?

A

NO resistance dependent on proteasomal degradation

NO can damage lipids + proteins + nuc acids, inhibiting microbial growth

110
Q

copper (Cu) resistance. what is the expression of Copper inducible genes controlled by? what does it link? what is Cu considered? when is Rice activated?

A
  • expression of copper-inducible genes controlled by a single transcriptional repressor, RicR, links proteasome-dependent degradation to copper (Cu) homeostasis
  • Cu can be a nutrient but also a potent source of toxicity

-RicR is activated under conditions of elevated Cu

111
Q

bacteria are not…

A

just a “bag of enzymes”

112
Q

2 enzymes required for pupylation? what are they considered?

A

Dop (deamidase of Pup) + PafA (proteasome accessory factor A)

both are depupylases

113
Q

is pupylation always involved in degradation?

A

NO

114
Q

connection between propeptideless PrcB and 20S CP assembly?

A

Production of a propeptideless PrcB subunit significantly lowers the rate of 20S CP assembly

115
Q

what are Mpa and ARC considered? what unfolding is a requisite for survival during iron starvation?

A

Both are AAA ATPases

ARC unfolding

116
Q

when does quicker degradation occur?

A

Quicker degradation when bacteria grow under nitrogen starvation

117
Q

Proteotoxic stress uses HspR, a regulon,…

A

required for heat shock resistance

118
Q

what are the 2 halves of the internal cavity in bacteriorhodopsin? what parts do they compromise?

A

its divided into half channels
-cytoplasmic + external half channels
-comprise the two parts of the transmembrane H+ pathway

119
Q

what 2 things produce torque? force exerted to what?

A

Large clusters of MotAB homologs interacting w/ MreB

exerted force to the surface

120
Q

is retraction required for movement to occur?

A

YES

121
Q

Do twitch + gliding motility require a surface or another cell to attach to?

A

YES

122
Q

what stops random peptides from entering the proteasome and being degraded?

A

Alpha subunits of 20S CP harbor N terminal extension, preventing peptides from entering central protease chamber

123
Q

3 essential functions of the proteasomal ATPases

A
  1. Specific recognition of substrates
  2. ATPase-driven unfolding
  3. Engagement with 20S CPs to induce gate opening
124
Q

What is AAA? what does it power? what is its defining feature of AAA ATPase unfoldases?

A

A domain that powers substrate delivery into the 20S CP

defining feature: a conserved aromatic-hydrophobic-glycine motif known as the pore loop

125
Q

where does the pore loop extend into? what does it make direct contact w/?

A

into the channel of the ATPase
Makes direct contact with substrates.

126
Q

what is Dop + what happens if its non functional + what does that demonstrate?

A

a depupylase

there will still be Pupylation but vast majority of Pup + substrates were degraded

illustrates requirement of DOP for removal + recycling of pup before proteasomal degradation

127
Q

what is MPA + what happens if its non functional + will depupylation occur in the presence of MPA

A

Participates in depupylation

w/o Mpa, overproduction of Pup results in fast accumulation of pupylated ino1

depupylation occurs in the presence of Mpa

128
Q

what discover did ATP independent proteasome activity lead to? what activator and amino acid motif is needed?

A

discovery of a non-ATPase proteasome activator PafE
or Bpa

activator: Bpa

motif: a c-terminal motif needed for 20S CP gate opening, specific to PafE which is only a gate opener, not unfoldase

129
Q

bacterial cytoskeleton components + what are they key elements for?

5 components + 4 key elements

A

tubulins (FtsZ) + actins (MreB and ParM) + intermediate filaments (IF and crescentin) are key
elements for
1. cell division
2. chromosome + plasmid separation
3. cell shape and polarity maintenance,
4. organelle-like structure distribution

130
Q

what are the pieces that organize DNA components + their role? 3 total

A

TubZ - a tubulin for plasmid segregation

PhuZ - replicates bacteriophage DNA in the cell’s center

Crescentin - helps keep the helical shape of some strains

131
Q

what is the role of SopA P-loop ATPase? does the polymerization of SopA occur @ the same rate for either chromosomal and plasmid segregation?

A

to segregate plasmids in E. coli

yes

132
Q

which piece is the flagellar switch?

A

FliM(NFG) complex comprises the switch (gear box) + part of the motor

133
Q

Sec systems are…
They are the…form

A

Universal; basic

134
Q

function of carboxysomes? hint: what do they concentrate (2 things)? how (2 things)?

A

concentrate bicarbonate and CO2

use transport systems in the cell membrane + the
microcompartment

135
Q

function of RuBisCO? is it considered the most prevalent enzyme on Earth? is its activity fast or slow? how much of this enzyme is needed?

A

CO2 fixation

YES, most prevalent enzyme on Earth

acts slowly

cells need a lot of it

136
Q

what does Ethanolamine Utilization sequester? 2 things

A

volatile + toxic metabolites

137
Q

what is in the sulfur granules (2 things)? can the sulfur in the granules be used as electron donor or acceptor in subsequent redox processes? Are they protective organelles?

A

redox-dependent energy generation and sulfur storage is the sulfur granule

YES

YES

138
Q

What is the function of SecYEG? why is men transport harder for gram-negative bacteria?

A

SecYEG channel complex - where substrate proteins must pass to enter external surface of men or to be inserted into the mem

because it has 2 membranes

139
Q

What is the ratchet system used for? Are polysaccharides rapidly propelled?

A

For cells to move rapidly over surfaces, Gld proteins are thought to comprise the multicomponent motor that propels the surface adhesin SprB.

YES

140
Q

Adventurous motility vs social motility

A

Adventurous gliding motility (A-motility) involves movement of a single cell

Social motility - motility of a
mass of cells

141
Q

what is the purpose for gas vacuoles to house air in the cytoplasmic membrane?

A

for floatation

142
Q

characteristics of GroES and GroEL? what is unique about the surface of GroEL? what interaction of GroEL drives the folding of proteins? which one is the Cap or barrel?

A

GroES + GroEL = hydrophobic

surface of GroEL is hydrophilic

half hydrophilic + half hydrophobic interaction

GroES - the lid

143
Q

do most of the “Somes” have lipid membranes, or at least traditional lipid membranes?

A

NO

144
Q

Is Glucose the most thermodynamically stable sugar? Does this make it is the most prevalent sugar on the planet?

A

YES; YES

145
Q

Is Cellulose an insoluble fibrous polymer of glucose? it is important for the formation of what?

A

YES
for biofilm formation

146
Q

What can anammoxisomes do? what are the runs used for? why kind of unique lipids are they composed of?

A

where anammox reactions occur and are used for microbial nitrogen cycles

ladderane lipids

147
Q

why did it take so long to discover anammoxisomes?

A

grow extremely slowly given unique lipid

148
Q

why do Carboxysomes concentrate CO2?

A

to help with the inefficiency

149
Q

exosomes/degradosomes: what do they degrade? what do they process?

A

RNA
process/modify small stable RNAs

150
Q

cellulosomes: what is their function? how many domains in cohesive + what are they known as? what is the purpose of DD? what does cellulose bind?

A

function: Contain cellulose binding domains for binding crystalline cellulose, and a duplicated dockerin domain

-9 massive cohesive domains, known as cohesins

-large Dockerin Domain (DD) - anchors the protein to the cell wall

-Cellulose binds to a hydrophobic/hydrophobic interface in the scaffoldin’s cellulose binding domain (CBD)

151
Q

about the 20S Core Particle (CP)

Is it a protease component of all proteasomes?

Is the mechanism of proteolysis by 20S CPs universal among proteasomes?

What lowers the rate of 20S CP assembly ?

A

YES

YES

production of a propeptideless PrcB subunit significantly

152
Q

is 20S Core particle gated to prevent nonspecific entry of proteins?

In all domains of life, is the 20S CP a 28 subunit complex consisting of 4 stacked rings?

Are pupylation components always encoded by 20S CP subunit genes?

A

YES

YES

NO

BIMM 120 - Microbio (6 decks)

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