Bacteriophages

Question 1

What are bacteriophages?

Answer 1

Typically highly specific viruses (species/strain) that infect bacteria

Question 2

What makes bacteriophages significant?

Answer 2

good models for animal viruses
Evolution via Horizontal gene transfer in bacteria (transduction)
Medical applications

Question 3

What are the medical applications of bacteriophages?

Answer 3

Diagnostics - phage typing
Treatment - phage therapy
Research - phage display

Question 4

What are the types of phage structures?

Answer 4

Head-tail
filamentous / helical
Icosahedral

Question 5

What are the four main stages of phage replication?

Answer 5

1. Adsorption and Penetration
2. Transcription and Translation
3. Replication
4. Assembly and Release

Question 6

What is involved in the Adsorption and penetration step of phage replication?

Answer 6

Specific receptors on host cell wall
Genome injection
Entry via bacterial feature

Question 7

What is involved in the Transcription and Translation step of phage replication?

Answer 7

Expression of Viral RNA
And production of viral proteins
(by host ribosomes)

Question 8

What can be involved in the Replication step of phage replication?

Answer 8

Terminal redundancy
Rolling circle
Lysogeny

Question 9

What is involved in the Assembly and Release step of phage replication?

Answer 9

Follows a pathway and potentially uses lytic enzymes

Question 10

What happens in Adsorption?

Answer 10

Tail fibres bind specific receptor in host cell wall

Question 11

How does receptor interactions affect adsorption of bacteriophages?

Answer 11

Affects host specificity

Question 12

What are the ways that bacteria develop resistance to phage?

Answer 12

Modify receptors
Hide receptors
Modify O/K antigen

Question 13

What is an example of a bacteria producing a protein to mask receptors from phage adsorption?

Answer 13

Staphylococcus aureus produces protein A

Question 14

How do phages with a sheath penetrate the bacterial envelope?

Answer 14

Phages with a sheath e.g. T4: irreversible binding of the phage to the bacterium results in the contraction of the sheath

the hollow tail fiber is pushed through the bacterial envelope

remainder of phage stays on the outside (some exceptions)

Question 15

If a phage doesn’t have a sheath what is a mechanism they could use to get through the bacterial cell envelope?

Answer 15

Using enzymes that digest various components of the bacterial envelope

Question 16

For bacteriophages what do class I genes do?

Answer 16

Set cell up for replication

Question 17

For bacteriophages what do class II genes do?

Answer 17

Phage genome replication

Question 18

For bacteriophages what do class III genes do?

Answer 18

encode structural components or lytic enzymes (produced very late)

Question 19

What is the main problem when replicating linear DNA?

Answer 19

Replicating the end sequences

Question 20

What is a strategy to avoid the problem of replicating end sequences regarding linear DNA?

Answer 20

Terminal redundancy

Question 21

What is a strategy to avoid the problem of replicating end sequences regarding circular DNA?

Answer 21

No ends in circular DNA!

Rolling circle replication

Question 22

What is a strategy to avoid the problem of replicating end sequences regarding Passive replication within host genome?

Answer 22

Lysogeny

Question 23

What is Rolling circle replication?

Answer 23

Endonuclease nicks a strand
3’ end extended by DNA polymerase
Displacing complimentary strand which is then copied in short segments by DNA polymerase
Replication proceeds until one new copy is made

Question 24

What is a concatemer?

Answer 24

long continuous DNA molecule that contains multiple copies of the same DNA sequence linked in series

Question 25

What is Terminal Redundancy?

Answer 25

Terminal repeated sequences that can anneal to form concatenated forms of the genome cut at the overlapping sequences every genome length to leave a 5’ overhang suitable for polymerisation to complete the ends

Question 26

How are phage structures assembled?

Answer 26

Often via specific pathways involving sub-structures (such as the pro-head)

Question 27

How is a transducing phage produced?

Answer 27

A mistake in incoorporation of DNA causes bacterial DNA to be packaged as a transducing phage

Question 28

Is incoorporation of DNA during phage assembly specific?

Answer 28

YES

Question 29

Are the assembly and release process for bacteriophages active or passive?

Answer 29

Both are active!

Question 30

What is an example of a bystander protein during assembly of bacteriophage?

Answer 30

Scaffolding proteins

Question 31

What are Holins?

Answer 31

protein that disrupts hosts cytoplasm membrane

Question 32

What do lysozymes do?

Answer 32

degrade cell wall

Question 33

What are the steps of the packaging process?

Answer 33

1. Terminase binds viral genome 2. Terminase-DNA binds procapside portal 3. DNA translocation 4. contamer cleavage and packaging completion

Question 34

What is an example of phages that use accessory proteins in the assembly process?

Answer 34

Phage lambda

Question 35

What does lysin do?

Answer 35

punches holes in bacterial outer cell wall

Question 36

What is a Lytic bacteriophage?

Answer 36

capable of replication via lytic cycle only

Question 37

What is a Temperate / lysogenic bacteriophage?

Answer 37

able to integrate genome in host genome and replicate passively when host divides, or establish lytic infection depending on environmental conditions

Question 38

What is a prophage?

Answer 38

term used to describe lysogenic phage when it has integrated in host genome and is mostly repressed and inactive

Question 39

What is a Lysogen?

Answer 39

term used to describe bacterial cell in which a phage has integrated its genome in dormant state (i.e. as prophage)

Question 40

What are examples of lytic phages?

Answer 40

T2 and T4

Question 41

What are the steps of the lytic cycle?

Answer 41

1) attachment 2) insert of phage DNA and degradation of host DNA 3) synthesis of viral genomes and proteins 4) assembly 5) release

Question 42

What happens during lysogeny?

Answer 42

Phage genome integrates at specific site into host chromosome phage still present as prophage Under certain conditions, such as UV irradiation, it becomes active and resumes a lytic replicaiton cycle

Question 43

What is a prophage?

Answer 43

phage present in the cell as an integrated copy of the genome

Question 44

What is an example of a prophage that goes through the lysogenic cycle?

Answer 44

Phage lambda

Question 45

How is circulisation of the phage lambda genome achieved?

Answer 45

by complementary base pairing of the ss overhangs

Question 46

For phage lambda what is the site at which it integrates into the host genome?

Answer 46

Integrates at specific site (attB) in host genome | att site opposite cos site required for integration

Question 47

What genes serve as the lambda repressor switch?

Answer 47

``` Lambda repressor protein (cI) Cro protein (control of repressor operator) ```

Question 48

What does the lambda repressor protein (cl) do?

Answer 48

activates the lysogenic pathway

Question 49

What does the Cro protein (control of repressor operator) do?

Answer 49

activates the lytic pathway

Question 50

Why are lysogens immune to "super infection" by more phage?

Answer 50

they are full of cI repressor

Question 51

How is the lytic virus replication activated?

Answer 51

Certain environmental stimuli (e.g. UV light) indirectly inactivate the cI repressor (via activation of bacterial RecA protein)

Question 52

Why is lysogenic replication sometimes preferred to lytic replication?

Answer 52

Poor growth of host = wise to wait for better times (likely to be limited new hosts available for progeny phage)

Question 53

M13 causes chronic infection of host cells how does it achieve this?

Answer 53

Rolling circle replication | Does not cause lysis of host cell