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367 molecular biology > pp 13 > Flashcards

pp 13 Flashcards

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1
Q

What does the sigma factor recognize?

A

-10 and -35 promoter elements (similar sequences to a consensus)

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2
Q

What does time dependent programming of gene expression result from?

A

switching sigma factor of the holoenzyme. Turning on transcription of multiple genes driven by promoter is recognized by a new sigma factor.

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3
Q

What are examples of sigma factor switching?

A

T4 phage infection, formation of endospores

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4
Q

How does the infection of B.subtilis by phage SPo1 start?

A

it has a long genome and has time-dependent programmed gene transcription pattern upon infection. Temporal control of transcription is divided into three parts, early, middle and late genes. During each phase, RNA polymerase holoenzyme with a different sigma factor is used that recognizes different classes of promoters

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5
Q

Sporulation involes switching on sporulation genes and switching off many vegetative genes, how?

A

By changing the sigma factors, Of, Oe, Oh, Oc, Ok act with Oa. This shows sigma factor switching is important

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6
Q

How does sigma-factor switching happen in E.coli?

A

E.coli ises the sigma factor O70 from their transcriptional activity, but it stationary phases or in starvation, alternative signma factors drive transcription of genes to respond.

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7
Q

What is the importance of sigma factor switches during heat shock?

A

E.coli turns on 17 genes called heat shock genes that code for molecular chaperones and proteases. They bind to misfolded proteins and fold them properly. The heat shock proteins are regulated by sigma factor 32.

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8
Q

What is nitrogen starvation?

A

switches on expression of o54 and o38

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9
Q

What is anti-sigma factors?

A

high temperatures and high osmolarity, E.coli makes regulator of Sigma D (rsd). This will bind to o70 and prevent it from binding housekeeping promoters.

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10
Q

Why is RNA polymerase switching important?

A

T7 phage the infects E.coli has three phases of transcription. Host RNA polymerase and o70, transcribes class I early phase genes. T7 polymerase genes are there allowing it to transcribe class II and III genes.

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11
Q

How does Phage Y infect?

A

regulates programmed gene expression using anti-termination. Since it is a temperate phage, (doesnt aways kill its host) it can undergo lysis or lysogeny.

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12
Q

What is the Lytic pathway?

A
  1. replication of phage DNA, breaking down host DNA
  2. New phage particles are produced
  3. Assembly of progeny phage
  4. Phage released from host cell by lysis
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13
Q

What is the lysogenic pathway?

A
  1. Phage DNA duplicated with host DNA
  2. Phage DNA passed on to host progeny
  3. Cycle repeated for many generation
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14
Q

What causes cell to enter lysogenic pathway?

A

integration of phage DNA into host DNA: low nutrient levels and high MOI

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14
Q

What causes lysogenic cells to re-enter lytic pathway?

A

Prophage induction: stress conditions

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14
Q

How does the lysogenic mode work?

A
  1. CI is the Y repressor, shuts down all phage gene expressions which favours lysogeny
  2. Cro: represses CI expression
14
Q

What is lysogen?

A

bacterium harboring integrated phage DNA

15
Q

What is a prophage?

A

Integrated DNA

16
Q

What is the lytic mode?

A

-results in viral replication and rupture of host cells releasing phage particles
- it has three phases, immediate, delayed and late, if any of these are interrupted, it goes back to lysogenic pathway

17
Q

Who is lytic mode time-dependent transcription pattern controlled by?

A

Antitermination. Genes of these phases are arranged sequentially on the page DNA

18
Q

How does transcription of immediate genes in Y phage work?

A
  • transcription begins with immediate early genes from P1 and Pr promoters
  • transcription stops at terminator downstream of N gene, downstream of cro gene
  • N expression allows for subsequent transcript to bypass terminators
  • N: anti-terminator
19
Q

How is N an anti-terminator?

A

Requires nut site on RNA transcript, and when it is complexed to transcript, termination signal is ignored, downstream genes can be transcribed

20
Q

What is N-dependent anti-termination?

A

Switches gene expression program from immediate early to delayed early

21
Q

What is Q-dependent anti-termination?

A

responsible for switching from delayed early program to late program.
- Q is delyaed early gene, that binds to DNA. If Q isnt there, RNA polymerase will stall. Q binds with qut when it is present.

22
Q

What is the order of events of promoter fro repressor establishment (Pre)

A
  1. RNA polymerase expresses immediate early genes cro and N
  2. N protein is produced enabling delayed early gene expression, including cII and cIII
  3. cII acts as a transcription activator for Pre, enabling cI transcription
  4. cI binds to operators O1 and Or (repress transcription of cro, CI can also act as an activator for second promoter Prm)
23
Q

What is the role of the promoter for repressor maintenance Prm?

A

Binding Y repressor to Or2 works to activate transcription from PRM through protein-protein interactions with RNA polymerase that stabilizes formation of promoter complex. If Y repressor binds Or3, it blocks transcription of cI.

24
Q

How is cI autoregulated?

A
  • when there is a lot of cI, it can downregulate its own Y repressor protein.
  • O1 mutations abolish repression (negative feedback)
25
Q

How do we determine the fate of Y infection

A

Need to check the cI and cro as they act against each other

26
Q

What happens if a Y pahge particle enters a lysogen?

A
  1. cI gene binds Or1 and Or2 repressing P1 and Pr driven transcription of immediate early gene (favours lysogeny)
  2. the cro gene binds Or3 repressing Pre and Prm driven transcription of cI (favours lysis)
  3. gene product CI or Cro to first reach threshold concentration determines cell fate
27
Q

What is the lysogenic induction?

A

mutagenic chemicals and radiation stresses the cell, inducing recA gene (recombination repair). It acts as a co-protease stimulation a latent protease autoproteolytic activity in cI. The proteolysis of CI releases negative regulation leading to lytic cycle.

28
Q

What types of phages can escape potentially lethal damage to host cell?

A

Phages replicated virally and progeny

367 molecular biology (10 decks)

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