Virus Basics

Question 1

What is a bacteriophage

Answer 1

Virus that infects bacteria

Question 2

Why are viruses difficult to study?

Answer 2

Need a living organism to grow

Can’t be seen with a light microscope

Question 3

Why are bacteriophages important to study?

Answer 3

Easy to cultivate in lab
Model for relationships between animal viruses and their host
Vehicle for horizontal gene transfer in bacteria
Kill bacteria (limit bacteria population)

Question 4

Can a virus have DNA and RNA

Answer 4

Not one single virus can have both. But some have DNA and some have DNA, never both

Question 5

What are spikes

Answer 5

Protein structures on animal viruses that allow them to attach to the host cell

Question 6

Virus characteristics

Answer 6

Can’t metabolize, replicate, or move

Contains genetic info in a protein coat

Question 7

How do bacteriophages infect during the lytic cycle (productive infection)?

Answer 7

Attachment by receptors
Genome entry by using lysosome enzyme on its tail to break down the peptidoglycan on the cell way (then injects its genome. Nucleotide separates from capsid.
Synthesis of phage proteins and genome
Late proteins like the tail and capsid are later made
Lysosome digests the host cell from within which leads to it being lysed.

Question 8

If a culture is infected with a temperate phage, will it go through the lytic or lysogenic stage?

Answer 8

Both. Depends on environment. Nutrient limiting environment will usually lysogenize their host.

Question 9

What does integrase do?

Answer 9

It integrates the phage particle into the host chromosome

Question 10

What is a Repressor

Answer 10

A protein that prevents expression of the gene required for excision.

Question 11

What is phage induction

Answer 11

When the phage escapes from a damage host (results in lytic cycle)
When the DNA from the host cell is damaged (can be by ultra violet light), the SOS repair system comes into play, and it destroys the Repressor protein needed to prevent the lytic cycle

Question 12

Consequences of lysogenize

Answer 12

Immunity to superinfection (by the same phage) 
Lysogenic conversion (certain phages change the phenotype of the lysogen...ex clostridium botulinum lysogens produce the botulinum toxin...normal wild type C. Botulinum don't)

Question 13

Filamentous phage

Answer 13

Attaches to f pilus
Capsomeres integrated into host cell membrane
Extrudes the membrane and gains the capsid
DOESNT LYSE THE BACTERIA

Question 14

Types of horizontal gene transfer

Answer 14

Generalized transduction and specialized transduction

Question 15

Generalized transduction

Answer 15

Results from a packaging error during phage assembly
Bacterial DNA can be packaged inside the head of a phage particle
Called generalized transduction particles
DNA is integrated into new cell through homologous recombination.

Question 16

Specialized transduction

Answer 16

When the temperate phage goes from the lysogenic stage to the lytic stage, some of the bacteria that is directly next to the integrated phage is excised instead and this is synthesized into the head of the phage particle.
This is specialized because only the genes right next to the phage are incorporated (in generalized it’s random bacteria DNA, you don’t know exactly which genes you’ll get)
Phage DNA becomes defective (can’t produce more productive infection)

Question 17

What are bacterias defense mechanisms against phages?

Answer 17

Altering receptor sites (capsules and slime layers can cover sites), restriction modification systems (quickly degrade incoming foreign DNA using restriction enzymes and modification enzymes) , and the CRISPR system

Question 18

Restriction modification system

Answer 18

Restriction enzymes recognize specific short nucleotide sequences of foreign DNA and cut them.
Modification enzymes protects the host cells own DNA from the restriction enzyme cutting it. By adding methyl groups because restriction enzymes can’t degrade methyl groups.
Sometimes the modification enzyme methylates the foreign DNA so it is not degraded and enters the cell and replicates and lyses it.
Used in biotechnology

Question 19

CRISPR System

Answer 19

Uses spacer DNA (phage DNA cut from a bacterial cell) from cas protein to allow the bacteria to recognize and then block subsequent infections by the SAME type of phage or a phage the bacteria has encountered in the PAST

Question 20

Why is it important to understand animal virus replication?

Answer 20

Viruses need enzymes to replicate. So antiviral drugs destroy these enzymes resulting in a slower replication. This gives the host’s defense mechanisms time to eliminate the virus before the symptoms appear.

Question 21

Difference between phage and animal virus attachment

Answer 21

Animal- receptors made of glycoproteins
Uses spikes or proteins to attach
More than one receptor is usually needed for attachment
Receptors are specific and some hosts don’t have them. Humans can be infected but cats might not be. Or dogs might get infects but humans don’t. Depends on if they have the receptor

Question 22

Differences between animal and phage viruses in penetration and un coating

Answer 22

Animal- entire virion is taken into cell

Phage - only nucleic acid is taken into cell

Question 23

Enveloped animal viruses entry

Answer 23

Receptor mediated Endocytosis; normal process by which cells bring certain extra cellular material into the cell (viral proteins bind to receptors)
Fusion of envelope with cytoplasmic membrane of host cell, nucleocapsid is released into cytoplasm.

Question 24

Nonenveloped viruses

Answer 24

Cannot fuse with cytoplasmic membrane due to its lack of envelope
Only uses Endocytosis
Nucleic acid ALWAYS separated from capsid before it replicates (called uncoating)

Question 25

Replication of DNA viruses

Answer 25

Encodes its own DNA polymerase to replicate
mRNA is a plus strand. Plus strand is needed for translation of RNA into proteins.
Single stranded DNA is made into Double stranded DNA then is made into single stranded positive strand MRNA which makes protein

Question 26

Replication of RNA viruses

Answer 26

Need a virally encoded RNA polymerase called replicase.
Replicase can synthesize a strand of RNA from an RNA template.
RNA positive strands already has the mRNA needed and can bind to host cell ribosomes and be translated to make proteins. It encodes for proteins that make replicase, which synthesizes more mRNA.
MRNA can be packaged to make new virions as well.
Single stranded negative RNA needs replicase because it cannot be translated into mRNA without it. When new virions are made replicase and negative strands can be packaged
Double stranded RNA also needs its own replicase

Question 27

What is the consequence of replicase?

Answer 27

It lacks proofreading ability so it makes more mistakes and mutations. Leads to antigenic variation and allows some RNA viruses to adapt to selective pressures. You can be protected from the influenza one year but not the not be protected from the variant the next year

Question 28

Antigenic shift

Answer 28

Reassortment of different strains of the viruses into one.

Creates new subtype of virus

Question 29

Replication of reverse transcribing viruses

Answer 29

Encodes the enzyme reverse transcriptase (synthesizes DNA from an RNA template)
Retroviruses (ex: HIV) have a plus strand RNA that carries reverse transcriptase within the virion.
The DNA is then integrated and can stay latent in the genome of the cell or begin production of new virions. Once DNA is copied it cannot be eliminated from cell

Question 30

When do the viruses mature?

Answer 30

Non enveloped viruses mature in cytoplasm

Enveloped viruses may mature when the virion leaves the cell

Question 31

How are the viruses released?

Answer 31

Enveloped viruses are released by budding (process in which virus acquires its envelope). Matrix protein forms
Some get their envelope from an organelle like the Golgi apparatus or RE reticulum…cell doesn’t die when enveloped virus escapes
Non enveloped viruses are only released when cell dies. These viruses trigger apoptosis instead of what phages trigger (lysis)
Immune response of animal trying to destroy virus can trigger apoptosis. Viruses can leave from feces, urine, genital secretions, blood, mucus, saliva.

Question 32

Categories of animal virus infections

Answer 32

Acute: sudden onset of symptoms of a short duration…result from a burst of virions being released from infected host cell.
Persistent: continues with or without symptoms for years, or even the lifespan of the host…result from the continuous production of low levels of viral particles…
Latent infections: viral genome remains silent within the host cell but can reactivate to cause a productive infection…some replicate outside of the host DNA (like a plasmid) …called a protovirus (CANT BE ELIMINATED FROM BODY)…ex shingles and herpes cold sores…it reoccurs