Phages Flashcards
What are bacteriophages?
Viruses that only infect bacteria
Where can phages replicate?
Inside metabolically active cells as hosts
Does the phage use its own proteins and materials for replication?
No, come from the bacteria
What are phages made of?
Protein and nucleic acid
Can phages only use DNA for their genome?
No, they can use double or single stranded RNA or DNA. But not both
How does the length of the phage genome correlate with its complexity?
Larger genomes have more complicated structures
Why would a phage bother making a more complex structure?
Easier to infect a host
How does the size of a phage genome compare to a bacterial genome?
Phage genome is smaller, about 300 000 base pairs while a small bacterium would have about a million bp
How do phages protect themselves from restriction enzymes?
Chemically modified bases that prevents the enzymes from cutting
How does T4 modify its bases to avoid being cut by EcoR1?
EcoR1 can only cut unmethylated DNA, so T4 replaces all its cytosines with hydroxymethylcytosine so EcoR1 can’t cut
What are the 2 parts of the phage protein coat?
Capsid and tail
Does every phage have a capsid?
Yes, in a variety of shapes and sizes
What does the capsid of a phage do?
Protective covering for the nucleic acid
Does every phage have a tail?
No, only the more complex ones with larger genomes
What does the tail of a phage do?
Used for infection, makes it easier for the phage genome to get into the host cell
How are phages classified?
Based on structural and genome properties
What is a plaque?
Region of clearing on a bacterial lawn caused by lytic growth
If a phage underwent the lysogenic cycle, would it form a plaque?
No
What is a phage stock?
Solution of identical bacteriophages
How do you make a phage stock?
Pick a phage from a plaque, mix it in with a solution of bacteria, wait, then clean out the cell debris
What is the titre?
Concentration of a phage stock
Why does the plaque counting method underestimate the number of phage in the stock?
Same reasons as with bacterial plate counts. Not every phage will form a plaque so units are pfu/ml
What is the efficiency of plating?
How many phage particles in a stock form plaques
What does it mean if the efficiency of plating is 1?
Every phage in the stock forms a plaque
What is the efficiency of plating for a virulent phage?
0.3 to near 1 - very high
What is the efficiency of plating for a temperate phage?
«<1. They’ll usually integrate in lab strains except for a few that randomly undergo the lytic cycle
What is the multiplicity of infection?
Number of phage per bacterial cell
Can more than 1 phage infect a bacteria at a time?
Yes
What does it mean when the multiplicity of infection is less than 1?
Bacteria outnumber phage, so not every cell will be infected
What does it mean when the multiplicity of infection is more than 1?
Phage outnumber bacteria, each cell will be infected by multiple phage
What is the host range of a phage?
Host bacteria species/strains that can be infected by a specific strain
What are the 3 reasons why phages are so specific to their hosts?
- bacteria and phage receptor compatibility
- promotor and machinery compatibility
- Phage modifications to avoid restriction enzymes
What is a host range mutant?
A phage that can infect a bacteria that WT phage can’t infect
How do you generate an h mutant?
- Mix WT E coli and WT phage at a high MOI
- Find any mutant cells that mutated to survive the infection
- Mix the mutant E coli and WT phage
- Anything that forms a plaque is an h mutant since it had a mutation to match the E coli mutation
What are the 6 reasons why phages are good genetic models?
- Haploid
- Short generation times
- Multiply clonally
- Easy to cross phage strains
- Easy to select mutants
- Simple systems with small genomes
How can we cross phage strains?
Co-infection at a high MOI, so bacteria get infected by two different phages and can swap DNA
Why are most mutations in phages lethal?
The mutation is lethal if the phage can’t replicate, and almost everything in the phage genome involves replication
Why is it so easy to select mutant phages?
Can plate millions under selective conditions and only the mutant will grow (like an h mutant)
Why is having a small simple genome advantageous to genetic studies?
Easy to connect gene to phenotype because there’s not very much stuff
