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LSM2232 > DLW03 - Phage Lambda > Flashcards

DLW03 - Phage Lambda Flashcards

1
Q

Define “lytic cycle”

A

The lytic cycle entails the infection of a bacterium by a phage that ends in the destruction of the bacterium with release of the progeny phage.

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2
Q

Define “lysogeny”

A

Lysogeny refers to the ability of a phage to survive in a bacterium as a stable prophage component of the bacterial genome.

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3
Q

Define “prophage”

A

A prophage refers to the phage genome that has covalently integrated into the bacterial chromosome as a linear part of it

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4
Q

Define “immunity” in phages

A

The ability of a prophage to prevent another phage of the same type from infecting a cell.

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5
Q

Define “phage induction”

A

Phage induction occurs when a prophage enters the lytic cycle as a result of destruction of the lysogenic repressor. This leads to excision of the phage DNA from the bacterial chromosome.

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6
Q

Define “temperate phage”

A

A phage that can choose between a lytic and lysogenic pathway of development.

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7
Q

Define “virulent phage”

A

A lytic phage that is unable to display lysogenic cycles.

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8
Q

State the function of the N protein

A

The N protein is an antiterminator protein that allows for the synthesis of cII and cIII genes.

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9
Q

State the promoter of the N gene.

A

P_L

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10
Q

State the promoter of the cro gene.

A

P_R

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11
Q

State the function of the cro protein

A

cro binds to OR and blocks PRM leading to:

  1. immediate early gene synthesis blocked
  2. cI lambda repressor cannot be synthesised anymore for repressor maintenance
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12
Q

State the function of the Q protein

A

Q is an antiterminator protein that allows for the synthesis of late (head and tail) genes.

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13
Q

Name the protein product encoded by the cI gene.

A

Lambda repressor

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14
Q

State the functions of the lambda repressor

A
  1. Auto-regulation of itself
    Binds to OL and OR in a sequential manner, 1 -> 2- > 3
    When bound to OL2 and OR2, it stimulates its own synthesis while when it is bound to OL3 and OR3, it inhibits its own synthesis.
  2. Inhibits synthesis of immediate early genes N and cro to block lytic cycle
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15
Q

Describe the structure of the lambda repressor monomer

A

As a monomer, the lambda repressor is composed of:

  1. N-terminal that contains helix-turn-helix motif for DNA binding
  2. Connector region that is susceptible to UV damage
  3. C-terminal dimerization domain
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16
Q

Explain the concept of cooperativity, using the lambda repressor as an example.

A

There are three operator sites, OL1,2,3 and OR1,2,3.

  1. Lambda repressor has highest affinity for OL1 and OR1 and binds there first
  2. Subsequently when OL1 and OR1 sites are filled, OL2 and OR2 sites start to get filled even at a lower concentration of free lambda repressor. This is called cooperativity.
17
Q

Describe how the lambda repressor maintains its own levels.

A

Binding of the lambda repressor at its operator results in the increase of its own synthesis (cI gene). There are three repressor binding sites. Binding to the first two results in the stabilisation of RNA polymerase at P_RM, which in turn increases the synthesis of the lambda repressor. This is positive autogenous regulation.
As the lambda repressor increases in concentration, it binds to the third repressor binding site (O_L^3 and O_R^3). This turns off transcription in a negative autogenous regulation.

18
Q

State the function of cII

A

cII stabilises RNA polymerase such that cI genes are transcribed. cII also silences cro expression.

19
Q

State the function of cIII

A

cIII protects cII from degradation.

20
Q

Describe how cII silences cro expression.

A

cII stabilises RNA polymerase at P_RE. However, the resultant mRNA synthesised for cI is very long and contains a 5’ UTR region which overlaps with the start of cro’s mRNA. As such, the mRNA produced by cII’s facilitation will function like a miRNA that inhibits cro mRNA from translation.

21
Q

Briefly summarise the lysogenic pathway of phage lambda.

A
  1. The immediate early gene, N is synthesised, serving as an antiterminator that allows the synthesis of cII and cIII.
  2. cII and cIII causes lambda repressor synthesis to be established.
  3. the lambda repressor turns off immediate and delayed gene expression and at the same time turns on the maintenance circuit for its own synthesis.
  4. lambda DNA is eventually integrated into the bacterial genome.
22
Q

Briefly summarise the induction of the lytic phase in phage lambda.

A
  1. The lytic cascade requires the cro protein, which directly prevents repressor maintenance by binding at O_R^3 (this blocks P_RM).
  2. cro binding also blocks the expression of immediate early genes (such as N), indirectly blocking repressor establishment.
  3. Q is expressed, an antiterminator that allows the expression of late genes.
23
Q

When plating phages, the formation of plaques on a bacterial lawn indicate the presence of the phage. However, some plaques are cloudy instead of clear. Why is this so?

A

A mixture of wild-type phages often cause turbid or cloudy plaques. This is because they contain some cells that have established lysogeny instead of being lysed.

24
Q

Briefly describe how one would estimate the number of phages.

A
  1. Serial dilution is carried out, followed by plating on a bacterial lawn.
  2. The number of plaques can be used to estimate the original concentration of the phage.
25
Q

Lambda phages that replicate using both lytic and lysogenic cycles are known as temperate phages. TRUE or FALSE?

A

TRUE

26
Q

cII and cIII proteins are important for lysogenic infection owing to the prevention of lambda repressor synthesis being established, which in turn triggers the inhibition of late gene transcription. TRUE OR FALSE?

A

FALSE. cII and cIII establish the lambda repressor.

27
Q

E. coli cells carrying a prophage are immune to infection with an additional phage. Which mutation on the invading phage would allow an invading phage to overcome this immunity and infect lysogenic E. coli cells?

A

A loss of function mutation in operator sequences

28
Q

In phage replication, the whole phage particle enters the cell and the outer protein coat is removed. TRUE or FALSE?

A

FALSE.

29
Q

UV light can cause a phage in the lysogenic cycle to revert to the lytic cycle. TRUE or FALSE?

A

TRUE.

30
Q

After cro represses cI and all early genes, protein Q then activates late gene expression. TRUE or FALSE?

A

TRUE.

31
Q

The lambda repressor is able to function as a monomer. TRUE/FALSE?

A

FALSE. Lambda repressor is only functional after dimerizing because it requires two DNA binding N-terminal domains to bind to the operator region.

LSM2232 (9 decks)

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