Phages

Question 1

How are phages classified?

Answer 1

by their morphology and nucleic acid type

Question 2

What are some key characteristics of bacteriophages?

Answer 2

route for genetic exchange via transduction
parasites
only alive inside bacterial cells
can alter the properties/phenotype of infected cells when not in lytic phase
can coexist within bacterial cells
lytic phages are virulent

Question 3

What is meant by a temperate phage?

Answer 3

can choose to replicate and burst the host cell (lytic phase) or choose to integrate into the host (lysogenic phase) depending on environmental conditions

Question 4

What is meant by the terms episome and prophage DNA?

Answer 4

episome: can replicate independently and also in association w chromosome if integrated
prophage: integrated into chromosomes, dormant

Question 5

How do phages insert their DNA into a bacterium?

Answer 5

1. adsorption onto cell surface: adherence protein receptors are specific to certain bacteria
2. cell wall is dissolved to make a hole where the phage’s nucleic acid is inserted

Question 6

What is the life cycle for a lysogenic phage?

Answer 6

nucleic acid is integrated into a plasmid, or the nucleic acid is used to make new phage particles

Question 7

What is the life cycle for a lytic phage?

Answer 7

1. early genes activate and allow control of bacterial genes
2. mid gene expression allows synthesis of new virions
3. late genes allow DNA packaging and lysis of host cell

Question 8

What is the life cycle of a chronic phage?

Answer 8

1. infects cell and synthesises new virions
2. does not lyse cell but continues to release new phages from cell

Question 9

What are non-essential genes in the context of phages?

Answer 9

genes that are already part of the host bacterial genome

Question 10

What is phage protein splicing?

Answer 10

instead of RNA splicing
after translation, inteins are removed and exteins are fused together

Question 11

Give examples of host defense systems in bacteria.

Answer 11

1. restriction enzymes
2. crispr/cas systems

Question 12

Give examples of host defense subversion systems in bacteriophages.

Answer 12

• nucleic acid modification
• anti-host restriction proteins
• restriction of host chromosomes eg I-protein shuts down bacterial protein synthesis and speeds up phage protein synthesis
• modification/inactivation of host RNAP

Question 13

Why are phages of medical importance?

Answer 13

1. phages encode toxins that cause disease which they can pass onto bacteria and make them virulent
2. phages could be used as an alternative to antibiotics in getting rid of an infection as they are highly specific

Question 14

What is the infection process of Bacteriophage T7?

Answer 14

• makes hole in bacteria and inserts only early genes
• uses host RNApol and DNApol at this point
• first protein made is anti-restriction enzyme proteins, protein 0.3
• shuts down host RNApol and makes its own
• makes DNApol and other proteins
• T7 has linear genome which has terminal redundancy (TR) ends that are complimentary to each other
• R loop forms w two replication forks and genome replication occurs
• as TR ends are complementary they can hybridise and create long genomes
• when enough proteins and machinery has been synthesised, genome is cleaved into normal sized genomes at pac sites

Question 15

What is the infection process of Bacteriophage M13?

Answer 15

• Bacteriophage M13 infects E.coli by recognizing the pili on the cell surface and injecting its DNA through the cell membrane
• The M13 genome is a single-stranded DNA that circularizes to protect itself from host nucleases. However, it cannot be used to make proteins.
• M13 uses host DNA polymerase to make its genome double-stranded, known as the Replicative Form (RF), and then uses host RNA polymerase to make proteins.
• M13 produces several proteins, including p2, which is a control protein that ensures enough genomes are made and separated out.
• M13 also nicks positive strands of DNA generated by the host at the right site, pulls it away from the replication machinery, and cyclizes it into a single positive strand, which can be packaged into viral particles.
• The ratio of p2 to p10 determines whether p2 should keep separating out positive strands until there is enough to package into all viral particles.
• After enough positive strands have been made, p5 attaches to the single-stranded DNA, changing it into a filamentous form that can be put into viral particles.
• p5 also plays a role in shutting down the replication process.
• The DNA is passed through a specialized channel, and M13 also produces many proteins that play a role as structural proteins in the E.coli membrane

Question 16

What is the infection process of Bacteriophage λ?

Answer 16

temperate phage, can follow lytic cycle or lysogenic cycle so needs to be able to switch off and on certain genes
linear DNA, has cohesive ends at 5’ (cos) which are complementary
1. adsorption
2. entry of linear DNA
3. pairing of cos elements -> nicked circle
4. -> ligated circle by DNA ligase
5. supercoiling by topoisomerase
6. θ replication
7. θ replication
8. rolling circle replication -> concatemers
9. cleavage of concatemers at cos sites; packaging into head
10. addition of tail

Question 17

What is meant by P and P’ in bacteriophage λ being complementary to B and B’ in E coli?

Answer 17

-In bacteriophage lambda, the P and P’ genes code for proteins that are complementary to the B and B’ genes in E. coli
-This means that the proteins encoded by the P and P’ genes can interact with and regulate the expression of the B and B’ genes in the host bacterium
-The B and B’ genes in E. coli are involved in the synthesis of the bacterial cell wall, which is necessary for the bacterium’s survival
-The P and P’ proteins of lambda phage can interfere with the expression of the B and B’ genes, allowing the phage to take over the host cell and use its resources to replicate and produce more phage particles
-This regulation of host gene expression by viral genes is a common strategy used by bacteriophages to co-opt the host cell’s machinery for their own replication and survival

Question 18

How does the regulatory system that decides the phase of Bacteriophage λ work?

Answer 18

• In the absence of any triggers favoring the lytic cycle, the cI gene is expressed, and the CI protein is synthesized
• This results in the establishment of a lysogenic state in which the phage DNA integrates into the host chromosome and replicates along with it
• If the host cell is under stress or other conditions favoring the lytic cycle, the levels of CI protein decrease, allowing the cro gene to be expressed
• This leads to the expression of phage genes that are involved in the synthesis of new phage particles, lysis of the host cell, and release of the phage particles.

Question 19

What is the function of the proteins in the cl and cro regulatory system?

Answer 19

CI: represses lytic cycle by shutting down the promotion of excision proteins by binding to cro, and prevents infection by another phage (superinfection immunity) - LYSOGENIC
N: blocks terminators allowing v long mRNA sequences which code for CRO, CII, O, P, Int, Xis - LYTIC???
CII: delays late transcription and binds to promoters which causes the production of more proteins, CI, alpha-cro, alpha-Q - LYSOGENIC
CIII: complexes w CII, stabilising it, allowing CI production. also produces chromosomal integration proteins - LYSOGENIC
— complex can be broken by host proteases (RecA) as part of SOS response or UV light, stops CI and INT production allowing phage to become lytic
Cro: inhibits transcription, blocking production of CII and CIII
Q: antiterminator that allows head and tail synthesis - LYTIC

CI and Cro inhibit each other, levels of each decide cycle outcome, called a bistable genetic switch

Question 20

What are some other predators of bacteria?

Answer 20

1. protists
2. BALOs (Bdellovibrio and like organisms)

Question 21

What are BALOs?

Answer 21

gram negative bacteria that prey on other gram negative bacteria
do not go fully into cytoplasms but instead stay in periplamsic space

Question 22

How does Vampirococuss prey on bacteria?

Answer 22

gram negative bacteria that preys on freshwater purple sulfur bacteria
uses a type IV secretion system to inject hydrolytic enzymes to break down material within hos and use nutrients to replicate
replicates outside the cell

Question 23

How does Daptobacter prey on bacteria?

Answer 23

gram negative bacteria that preys on freshwater purple sulfur bacteria
penetrates into cytoplasm and degrades it, using nutrients to replicate within the cytoplasm