Block D Lecture 2: Viruses of Archaea and Bacteria

Question 1

What does the latent period of a virus life cycle encompass?

Answer 1

The eclipse and maturation periods
(Slide 7)

Question 2

When does the eclipse period start?

Answer 2

As soon as the virus enters the host cell
(Slide 7)

Question 3

What does “burst size” refer to?

Answer 3

The number of virions released from an infected host cell
(Slide 7)

Question 4

What is a bacteriophage (sometimes known as a phage)?

Answer 4

A type of virus which infects (and replicates) within bacteria
(Slide 9)

Question 5

What genomes do most bacteriophages use?

Answer 5

dsDNA genomes
(Slide 9)

Question 6

What components do bacteriophages contain?

Answer 6

Heads
Tails
Other components
(Slide 9)

Question 7

What do viruses which infect archaea resemble?

Answer 7

Those which infect enteric bacteria
(Slide 12)

Question 8

What type of viruses are the only type which have been identified to infect archaea?

Answer 8

dsDNA viruses
(Slide 12)

Question 9

What is the oldest known predator-prey interaction?

Answer 9

Bacteria and bacteriophages
(Slide 14)

Question 10

Why is attachment of a virion to a host cell highly specific?

Answer 10

As it requires complementary receptors on the surface of the host and virus cells
(Slide 15)

Question 11

What does the attachment of a virus to its host cell result in?

Answer 11

Changes in both the virus and the host cell’s cell surface that facilitate penetration
(Slide 16)

Question 12

What bacteria does the bacteriophage T4 infect?

Answer 12

E.coli
(Slide 16)

Question 13

How does the T4 bacteriophage attach to E.coli?

Answer 13

Via its tail fibres which interact with polysaccharides on the E.coli cell envelope
(Slide 16)

Question 14

What happens after T4 bacteriophage tail fibres attach to polysaccharides on the E.coli cell surface?

Answer 14

The tail fibres retract, and the tail core makes contact with the E.coli cell wall
(Slide 16)

Question 15

What happens after the T4 bacteriophage tail core makes contact with the E.coli cell wall?

Answer 15

A Lysozyme-like enzyme forms a small pore in the peptidoglycan layer
(Slide 16)

Question 16

What happens after the bacteriophage T4 uses a lysozyme-like enzyme to form a pore in the peptidoglycan layer?

Answer 16

The tail sheath contracts, and viral DNA passes into the cytoplasm by travelling down the central tail tube
(Slide 16)

Question 17

What 2 features does the doubled stranded DNA genome of the T4 bacteriophage have?

Answer 17

It is circularly permuted and terminally redundant
(Slide 17)

Question 18

What does the T4 bacteriophage having a dsDNA genome that is circularly permuted and terminally redundant affect?

Answer 18

Genome packaging
(Slide 17)

Question 19

What does circularly permuted mean?

Answer 19

Circular permutation involves breaking and re-joining the circular molecule at different positions along its backbone, resulting in a new circular molecule with a different starting point for the sequence
(Slide 17)

Question 20

What does terminally redundant mean?

Answer 20

That it contains identical or nearly identical sequences at both ends of the genome
(Slide 17)

Question 21

Many eukaryotes can utilise RNA interference to diminish virial infections. What is RNA interference?

Answer 21

It is a natural cellular process that regulates gene expression by degrading or inhibiting the translation of specific messenger RNA (mRNA) molecules
(Slide 17)

Question 22

What are 3 examples of mechanisms which prokaryotes can use to combat virial infections?

Answer 22

CRISPR (similar to RNA interference)
Restriction modification system
Restriction enzymes
(Slide 17)

Question 23

What is the restriction modification system?

Answer 23

A DNA destruction system which is only effective against dsDNA viruses
(Slide 17)

Question 24

How can bacteria prevent restriction enzymes they use as defence against bacteria from damaging their own DNA?

Answer 24

By modifying their own DNA at restriction enzyme recognition sites
(Slide 17)

Question 25

What are 3 virial mechanisms that T4 ( and other viruses) can use to evade bacterial restriction systems?

Answer 25

Chemical modification of virial DNA (via glycosylation or methylation) Production of proteins which inhibit host cell restriction system T4 specifically contains a modified base, called 5-hydroxymethylcytosine which is resistant to almost all known restriction enzymes (Slide 18)

Question 26

What 3 things do T4 bacteriophage early proteins code for?

Answer 26

Enzyme for the synthesis and glucosylation of the T4 base 5-hydroxymethylcytosine Enzymes that function in T4 replisome Proteins which modify host RNA polyremase (Slide 20)

Question 27

What does a replisome refer to?

Answer 27

The molecular machinery responsible for DNA replication (Slide 20)

Question 28

What are T4 middle proteins?

Answer 28

Additional proteins which modify host RNA polymerase (Slide 20)

Question 29

What do T4 late proteins code for?

Answer 29

Proteins of the virus coat Structural components (Slide 21)

Question 30

How is the T4 genome packaged?

Answer 30

Precursor of head is assembled Packaging motor is assembled dsDNA is pumped into head under pressure using ATP (Slide 21)

Question 31

What occurs after the dsDNA of the T4 genome is pumped into the head?

Answer 31

The T4 tail, tail fibres and other components are added (Slide 21)

Question 32

What 2 modes can a virus life cycle be?

Answer 32

Virulent and temperate modes (Slide 22)

Question 33

What is the virulent mode?

Answer 33

Viruses lyse host cells after infection (Slide 22)

Question 34

What is the temperate mode?

Answer 34

Viruses replicate their genomes in tandem with the host genome and do so without killing the host cell (Slide 22)

Question 35

What relationship can temperate viruses form with the host cell?

Answer 35

A stable genetic relationship (Slide 22)

Question 36

What is lysogeny?

Answer 36

A state where most virus genes are not expressed and the virial genome (known as a prophage) is replicated with the host chromosome (Slide 22)

Question 37

What is a lysogen?

Answer 37

A bacterium containing a prophage (Slide 22)

Question 38

What may lysogenic viruses do?

Answer 38

They may revert back to the lytic pathway and begin producing virions under certain conditions (Slide 22)

Question 39

What kind of genome does the bacteriophage lambda have?

Answer 39

A linear, dsDNA genome (Slide 23)

Question 40

How can the bacteriophage lambda genome from a double-stranded circle?

Answer 40

It contains single-stranded regions at the 5' terminus of each strand and upon penetration of a cell, these DNA ends base-pair, which forms the cos site, and then the DNA ligates and forms a double-stranded circle (Slide 23)

Question 41

What can bacteriophage lambda do when it is lysogenic?

Answer 41

Integrate its gene into E.coli chromosome at the lambda attachment site (Slide 23)

Question 42

What does bacteriophage lambda do once it enters the lytic pathway?

Answer 42

It synthesises long, linear concatemers of DNA using rolling circle replication (Slide 25)

Question 43

What is a concatemer?

Answer 43

A long DNA molecule that consists of multiple copies of the same DNA sequence linked end to end (Slide 25)

Question 44

How are lysogenic and lytic events regulated in bacteriophage lambda?

Answer 44

By a complex genetic switch containing 2 repressor proteins called the cl protein and the Cro repressor (Slide 26)

Question 45

What does the cl protein do?

Answer 45

It is also known as the lambda repressor and causes repression of lambda lytic events resulting in the activation of lysogeny (Slide 26)

Question 46

What does the cro repressor do?

Answer 46

It controls activation of lytic events by repressing lysogenic genes (Slide 26)

Question 47

What is key to the balance of cl protein and cro repressor in the cell of the bacteriophage lambda?

Answer 47

The physiology of the bacterial host (Slide 26)

Question 48

What is transduction?

Answer 48

The transfer of DNA from one cell to another due to host cell DNA being mispackaged into a phage, which then "infects"another cell with the previous host cell's DNA (Slide 27)

Question 49

What does transduction drive?

Answer 49

Bacterial evolution (Slide 27)

Question 50

What are the 2 modes of transduction?

Answer 50

Generalised and Specialised transduction (Slide 27)

Question 51

What is the difference between generalised and specialised transduction?

Answer 51

Generalised transduction is when DNA from any portion of the host genome is packed inside the virion Specialised transduction is when DNA from a specific region of the host chromosome is integrated directly into the virus genome (Slide 27)