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BIMM 120 - Microbio > Final exam material - W9/10 > Flashcards

Final exam material - W9/10 Flashcards

1
Q

what are Persister cells? what does dormancy grant them?

A

cells that show recurrence of chronic bacterial infection through the displayed dormant pheno that’s metabolically reduced

dormancy grants them tolerance to antimicrobial agents

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2
Q

3 main ways of persister cell eradication?

SIMPLE version

A
  1. Direct killing
  2. Re-sensitising persister cells to conventional antimicrobials
  3. Prevention of persister formation through lab findings that have been translated to clinical practice
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3
Q

what methods can be used to complete each of the 3 eradication processes

A
  1. targeting of bacterial cell wall w/ periodic exposure to antimicrobials
  2. encourage resuscitation within dormant pop to actively produce targets + Stimulate metabolism of persisters, causing a phenotypic switch from dormant type to antibiotic sensitive
  3. targeting cell’s response to an alarmone - (p)ppGpp, preventing its accumulation
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4
Q

is it resistance or tolerance that allows persisters to survive antibiotics?

A

tolerance

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5
Q

what is the level of genotypic variation in cell pops that then generates a subset of them to become persister cells?

A

no genotypic variation in the pop but rather a phenotypic adaptation triggered by environmental cues (stress)

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6
Q

characteristics of the persister dormant state?

what is reduced? what does it grant the cell?

A

dormant state = drastically reduced metabolic activity allowing survival upon exposure to antimicrobial drugs

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7
Q

what kinds of genes experience an increase/decrease in level of expression in persister cells?

A

downregulation in biosynthesis genes

upregulation in toxin/antitoxin (TA) genes

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8
Q

What is the TA system?

A

intrinsically linked genes (2 (bicistronic) or more) responsible for encoding toxic protein + its corresponding antitoxin

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9
Q

Function of toxins? antitoxins? which is stable? which is easily degradable by proteases?

A

toxin protein = stable
antitoxin = easily degradable

Toxins function: down-regulate protein synthesis + involved in bacterial dormancy and tolerance

Antitoxin Function: controls autoregulation of TA bicistronic operons

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10
Q

functions of (p)ppGpp?

A

acts as an alarmone + triggers release of toxins from TA systems

downregulation of protein synthesis via interaction with RNA poly

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11
Q

3 main ways that antibiotics/antimicrobials work?

A
  1. Direct killing of metabolically dormant persister cells
  2. Sensitizing persisters to conventional antibiotics by promoting resuscitation
  3. Comprising of molecules linked to the induction of persister cells
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12
Q

how do the levels of ATP in either the stationary phase or exponential phase affect the generation of persister cells?

A

stationary phase = reduced ATP levels = persister formation

exponential phase = increased ATP levels = exponential growth of non persister, normal cells

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13
Q

what is persister resuscitation? can a relapse in infection occur? what is the most significant trigger for resuscitation?

A

Persisters eventually return to a functional state from their dormant state, and a relapse in infection can occur

Significant trigger - Ala (an aa)

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14
Q

how do chemotaxis change in persister cells? when does greatest awakening of dormant cells occur?

hint: what needs to be produced

A

chemotaxis down-regulated in dormant persister cells

greatest awakening (of dormant cells) occurred in cells producing the chemotaxis response regulators CheY + CheA

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15
Q

what are bacterial endospores? how long can they survive AND w/o what? formation happens close to what?

A

most resilient types of cells known

can survive very long periods of time w/o any nutrients

Spore formation happened close to a single cell pole

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16
Q

endospores - what conditions cause spore formation? characteristics?

A

lack of nutrients and boiling periods

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17
Q

what is sporulation? germination?

A

S: process in which normal growing cells (Vegetative cells) turn into spores

G: process in which spores turn into vegetative cells

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18
Q

step 0+1 of sporulation?

A

Stage 0: Vegetative Growth where chromo + mem + peptidoglycan are visible

Stage I: Chromosome Condensation where DNA replicates into 2 chromes that form an axial filament spanning the long axis of the cell; division sites shift to polar positions

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19
Q

What is stage 2 of sporulation? what does the polar septum do?

A

Stage II: Asymmetric Septation - Only 1 division site forms a septum, generating a larger mother cell + a smaller forespore

polar septum traps the forespore chromo to transport it by the SpoIIIE DNA translocase

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20
Q

what is the engulfment step in sporulation? what starts assembling?

A

the mem of the mother cell migrates around the forespore in a phagocytosis-like process

A proteinaceous coat around the forespore

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21
Q

What is stage 3 of sporulation?

A

forespore is enclosed within the mother-cell cytoplasm, defined by 2 membranes

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22
Q

What are the 2 mems within the mother cell cyto found in stage iii?

A

An inner mem that is the og forespore membrane

An outer mem derived from the mother cell engulfing mem

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23
Q

What is stage 4 of sporulation?

A

Cortex Formation made of peptidoglycan - synthesized between the inner + outer forespore membranes

Small acid soluble proteins (SASPs) start building chromo

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24
Q

What is stage 5 of sporulation?

A

Coat Formation + complete assembly

forespore chromo is compacted + saturated w/ SASPs to protect DNA

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25
Q

What is stage 6 of sporulation?

A

Maturation where a molecule - DPA - is synthesized in the mother cell and is then loaded into the forespore

forespore core partially dehydrated

spore becomes heat-resistant

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26
Q

What is stage 7 of sporulation?

A

Lysis where mother cell lyses and the spore is released into environment where it remains dormant until conditions are appropriate for germination

Different structural features

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27
Q

what is Spo– mutant? what it means in regards to how development is blocked?

A

Asporogenous + oligosporogenous

spo- mutants block sporulation @ diff stages

28
Q

3 conclusions made regarding cell-specific gene expression?

A
  1. Most developmental genes are not expressed in growing cells, and their expression is induced at different times
    during sporulation
  2. dependency hierarchy in developmental gene expression where expression of genes that participate in later sporulation pathway events tend to depend on the expression of genes that participated in earlier events
  3. The majority of the sporulation genes are expressed in only 1 of the 2 cells required to form a spore, either the mother cell or the forespore
29
Q

what is a sigma factor? what about the hierarchy regarding the sigma factors? how are diff sigma factors acitivated in alternating cellular components

A

a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoter

activation of diff sporulation 𝝈 factors follows a hierarchical order

diff 𝝈 factors sequentially activated in alternating cellular compartments

30
Q

what’s the relationship between the mother cell and the forespore? how does the mother cell aid the forespore?

A

mother cell nurtures forespore by implementing a cell-specific protein degradation system that also relies on cell-specific gene expression

31
Q

what’s the important progress that was made regarding SpoIIIE?

A

mutations in spoIIIE prevented complete segregation of the forespore chromosome

32
Q

quorum sensing, what it depends on, what kinds of molecules are used, as well as the specificity of the molecules for each species. Know about quorum sensing and biofilm formation.

A

bacterial cells socialization via chemical signals

depends on cell density to even begin biofilm constuction

quorum sensing molecules specific to a species

33
Q

how does M. xanthus move?

A

does not swim

instead, they attach to surfaces and move via gliding motility, and commonly form biofilm

34
Q

what’s cellecell signaling

A

helps ensure that pop makes an informed decision before it engages in the energetically costly process of development

35
Q

whats EPS and the importance of fibrils?

A

ExoPolySaccharides = EPS

Fibrils play a key role in cell-cell adhesion, motility, recognition and development

36
Q

what species uses A and S motility?

2 motility systems that drive gliding known as adventurous + Social

A

M. xanthus

37
Q

what’s the connection between the complexity of Myxobacteria and their genomes?

A

complexity of myxobacterial social interactions is mirrored by their genomic complexity

38
Q

how can certain mutants be rescued as a result of signal complementation?

A

A signaling-defective mutant can be rescued when co-cultured w/ a strain that produces the missing signal

39
Q

what are the characteristics of A-signal, when is it initiated? what does the signal monitor and why? as well as RodK?

5 points

A

Initiated under starvation conditions

signal serves as a nutritional + quorum sensor

Monitors pop density ensuring min # of starving cells are present

reaching threshold concentration tiggers expression of A-signal
dependent genes and the developmental program proceeds

RodK, regulates temporal and spatial processes during development + links A/C signaling

40
Q

what are the characteristics of the C-signal and its connection to motility (what happens when the C-signaling level is low, intermediate, or high)

A

low = induces rippling

Intermediate = induces aggregation

High = induces sporulation

41
Q

why are cell-cell interactions important? how does it relates to S-motility?

A

important in gliding motility given swarm expansion rates increase at higher cell densities

S-motility itself requires cell-cell contact for cell movement

42
Q

PilA and PilT

A

PilA - bind fibril EPS directly on neighboring cells or in the ECM

PilT - an ATPase that powers retraction

43
Q

what’s the relationship between biofilms and exchange of materials

A

Myxobacteria in a structured biofilm fuse their OMs (outer membranes) and exchange contents

44
Q

what’s the process of rescuing in regards to donors and recipients

A

stimulation requires that the “donor” strain contain the wild-type gene that is mutated in the “recipient.”

45
Q

what’s the requirements for protein transfer?

A

cells must be in physical contact on a hard surface

46
Q

TraAB proteins? TraA and TraB specifically?

A

proteins required for coupled transfer of lipid + proteins

A: serves as a cell surface receptor/adhesin and can bind to glycans on neighboring cells (LPS/EPS).

B: binds to TraA to facilitate its subcellular localization

47
Q

what helps with the fusion of outer membranes? how does it leads to destabilization?

A

tight cellecell binding between cell poles may help catalyze fusion bc its where membrane curvature is
highest; leads to its destabilization

48
Q

whats the relationship between Myxobacteria and their social perspectives? especially in regards to how they can tell their own species from another

A

relationship: Myxobacteria are highly antagonistic toward other related species and subspecies

The OM exchange may represent one layer for self-recognition.

The OM exchange is likely to play a role in what is known as kin selection

49
Q

what are directed mutations?what kinds of mutations are seen in this process

A

where organisms could respond to stresses by purposely altering genes

mutations that relieved the stress that caused them present w/ increased freq

50
Q

why is the theory of directed mutations controversial?

A

They realized that directed mutation did not cause directed point mutations independently, rather, for
transposon-mediated mutations - goes against the dogma.

51
Q

what are transposons? what are IS elements?

A

jumping genes

IS elements: small transposons that encode the transposase that catalyzes the hopping event

52
Q

can IS elements activate or inactivate genes? how does that idea relates to H-NS?

A

YES

Losing H-NS reduces transposon hopping in E. coli bc there is no way to downregulate the detrimental transposition event + can also keep certain operons silenced until the
transposition event w/ one of the IS elements occurs

53
Q

what is (IS) insertion Hotspots as well as what type of genomic regions have a higher frequency of transposition events

A

regions of supercoiling stress-induced DNA duplex destabilization (SIDDs) that occur in intergenic regions @ a higher freq

54
Q

what’s the flhDC flagellar master switch? what mutation is most common for the switch to be activated.

A

Directed Mutation of the Operon Encoding the Flagellar Master Switch - flhDC

directed muts only when environmental conditions allow swarming, or when cells form communal biofilms

55
Q

Zinc resistance?

A

Cupriavidus metallidurans - Zinc induces transposition of several diff IS elements where insertion events give rise to zinc resistance

56
Q

how does a cell respond to stress to then adapt to that stress?

in terms of IS elements

A

IS elements can be induced to hop by various stresses to promote adaptation to the very stresses that cause
appearance of the adaptive mutations

57
Q

what’s the concept of evolution learning from the past

A

evolution progresses from past selection as do learning systems when they acquire knowledge based on past experiences

58
Q

what’s the Multilayer Regulatory SpoIIAB-SpoIIAA-SpoIIE System and their functions? what does spo2E allow for in terms of forespore differentiation

A
  1. SpoIIAB (Anti-Sigma Factor): SpoIIAB binds to σF, inhibiting its activity
  2. SpoIIAA (Anti-Anti-Sigma Factor): SpoIIAA, when dephosphorylated, binds to SpoIIAB, neutralizing its inhibitory effect on σF, thereby allowing σF to become active
  3. SpoIIE (Anti-Anti-Anti-Sigma Factor): SpoIIE is a phosphatase that dephosphorylates SpoIIAA allowing SpoIIAA to bind to SpoIIAB, thus freeing σF from inhibition. This allows controlled initiation of the forespore differentiation
59
Q

does the sigma cascade starts with sigma H?

A

YES

60
Q

What are the shapes of spores vs vegetative cells

A

Spores = round
Vegetative = elongated + rod-shaped

61
Q

what’s the fruiting body and how it’s formed

hint: what’s scares?

A

aggregation of myxobacterial cells when nutrients are scarce

using Structural cells to form fruiting body + cells destined to become spore cells

62
Q

embryogenesis and cell fate

A

E: If two early embryonic cells are separated, two identical siblings result

Cell fate not fixed early during embryogenesis, and it depends on cell-cell interaction

63
Q

what’s the correlation between complementation and genetic exchange

A

No genetic exchange needed given we have phenotypic complementation

64
Q

concepts regarding directed/non-random mutations?

A

Directed muts might shift the course of evolution in a non-random and accelerated way

65
Q

what’s the relationship between transposons and IS elements and how they can inactivate or activate genes,
specifically, where they need to hop to cause different outcomes

A

can inactivate a gene if the transposon hops into IS

can activate expression if it hops into upstream regulatory region of IS

66
Q

about IS5, its preferred target, IRs and the transposase.

A

preferred target site is CTAG

need IRs bc that is what the transposase recognizes

BIMM 120 - Microbio (6 decks)

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