Phages

Question 1

What are bacteriophages?

Answer 1

Viruses that only infect bacteria

Question 2

Where can phages replicate?

Answer 2

Inside metabolically active cells as hosts

Question 3

Does the phage use its own proteins and materials for replication?

Answer 3

No, come from the bacteria

Question 4

What are phages made of?

Answer 4

Protein and nucleic acid

Question 5

Can phages only use DNA for their genome?

Answer 5

No, they can use double or single stranded RNA or DNA. But not both

Question 6

How does the length of the phage genome correlate with its complexity?

Answer 6

Larger genomes have more complicated structures

Question 7

Why would a phage bother making a more complex structure?

Answer 7

Easier to infect a host

Question 8

How does the size of a phage genome compare to a bacterial genome?

Answer 8

Phage genome is smaller, about 300 000 base pairs while a small bacterium would have about a million bp

Question 9

How do phages protect themselves from restriction enzymes?

Answer 9

Chemically modified bases that prevents the enzymes from cutting

Question 10

How does T4 modify its bases to avoid being cut by EcoR1?

Answer 10

EcoR1 can only cut unmethylated DNA, so T4 replaces all its cytosines with hydroxymethylcytosine so EcoR1 can’t cut

Question 11

What are the 2 parts of the phage protein coat?

Answer 11

Capsid and tail

Question 12

Does every phage have a capsid?

Answer 12

Yes, in a variety of shapes and sizes

Question 13

What does the capsid of a phage do?

Answer 13

Protective covering for the nucleic acid

Question 14

Does every phage have a tail?

Answer 14

No, only the more complex ones with larger genomes

Question 15

What does the tail of a phage do?

Answer 15

Used for infection, makes it easier for the phage genome to get into the host cell

Question 16

How are phages classified?

Answer 16

Based on structural and genome properties

Question 17

What is a plaque?

Answer 17

Region of clearing on a bacterial lawn caused by lytic growth

Question 18

If a phage underwent the lysogenic cycle, would it form a plaque?

Answer 18

No

Question 19

What is a phage stock?

Answer 19

Solution of identical bacteriophages

Question 20

How do you make a phage stock?

Answer 20

Pick a phage from a plaque, mix it in with a solution of bacteria, wait, then clean out the cell debris

Question 21

What is the titre?

Answer 21

Concentration of a phage stock

Question 22

Why does the plaque counting method underestimate the number of phage in the stock?

Answer 22

Same reasons as with bacterial plate counts. Not every phage will form a plaque so units are pfu/ml

Question 23

What is the efficiency of plating?

Answer 23

How many phage particles in a stock form plaques

Question 24

What does it mean if the efficiency of plating is 1?

Answer 24

Every phage in the stock forms a plaque

Question 25

What is the efficiency of plating for a virulent phage?

Answer 25

0.3 to near 1 - very high

Question 26

What is the efficiency of plating for a temperate phage?

Answer 26

«<1. They’ll usually integrate in lab strains except for a few that randomly undergo the lytic cycle

Question 27

What is the multiplicity of infection?

Answer 27

Number of phage per bacterial cell

Question 28

Can more than 1 phage infect a bacteria at a time?

Answer 28

Yes

Question 29

What does it mean when the multiplicity of infection is less than 1?

Answer 29

Bacteria outnumber phage, so not every cell will be infected

Question 30

What does it mean when the multiplicity of infection is more than 1?

Answer 30

Phage outnumber bacteria, each cell will be infected by multiple phage

Question 31

What is the host range of a phage?

Answer 31

Host bacteria species/strains that can be infected by a specific strain

Question 32

What are the 3 reasons why phages are so specific to their hosts?

Answer 32

1. bacteria and phage receptor compatibility
2. promotor and machinery compatibility
3. Phage modifications to avoid restriction enzymes

Question 33

What is a host range mutant?

Answer 33

A phage that can infect a bacteria that WT phage can’t infect

Question 34

How do you generate an h mutant?

Answer 34

1. Mix WT E coli and WT phage at a high MOI
2. Find any mutant cells that mutated to survive the infection
3. Mix the mutant E coli and WT phage
4. Anything that forms a plaque is an h mutant since it had a mutation to match the E coli mutation

Question 35

What are the 6 reasons why phages are good genetic models?

Answer 35

1. Haploid
2. Short generation times
3. Multiply clonally
4. Easy to cross phage strains
5. Easy to select mutants
6. Simple systems with small genomes

Question 36

How can we cross phage strains?

Answer 36

Co-infection at a high MOI, so bacteria get infected by two different phages and can swap DNA

Question 37

Why are most mutations in phages lethal?

Answer 37

The mutation is lethal if the phage can’t replicate, and almost everything in the phage genome involves replication

Question 38

Why is it so easy to select mutant phages?

Answer 38

Can plate millions under selective conditions and only the mutant will grow (like an h mutant)

Question 39

Why is having a small simple genome advantageous to genetic studies?

Answer 39

Easy to connect gene to phenotype because there’s not very much stuff