Virus/Phage

Question 1

Why are viruses considered unicellular?

Answer 1

Psych. They are considered acellular

Question 2

For which process will a virus require their host cells machinery?

replication, energy, metabolic intermediates, genome replication, protein synthesis?

Answer 2

All of those processes require the hosts machinery

Question 3

By which method would a virus that normall injects itself into E.coli infect Shigella?

Answer 3

Viruses show high levels of specificity. If it normally infects E.coli it wont infect Shigella

Question 4

What are the 2 classifications of virus? How do they differ?

Answer 4

1. Baltimore Classification
   
   1. Based on Genome and mRNA production methods
   2. 7 classes
2. ICTV Classification
   
   1. Based on phenotypes
      
      1. morphology
      2. nucleic acids
      3. mode of replication
      4. host organisms
      5. diseases
   2. Still 3,000 known viruses unclassified

Question 5

What makes it hard to “classify” all the different viruses?

Answer 5

• Viruses do not all share 1 common trait -
  
  • like the 16s rRNA in bacteria…or the sexual reproduction in Eukaryotes

Question 6

What is the term used to describe the virus outside of a cell, or in the external environment?

Answer 6

Virion

Question 7

What are the 2 primary forms the nucleocapsid of the virus will take?

What is the 3rd “form”

Answer 7

• Helical (rod)
• Spherical
  
  • Icosahedral
• Complex
  
  • Helical portion + Icosahedral portion

Question 8

Define:

Capsid

Capsomere

Nucleocapsid

Answer 8

1. Capsid - protein structure encasing the RNA/DNA of virus
2. Capsomere - indivudual proteins making up the capsid
3. Nucleocapsid - The Capsid and DNA/RNA all in one unit!

Question 9

Can the Nucleocapsid contain other proteins besides capsomeres?

Answer 9

yes

Question 10

How are nucleocapsids usually packaged? (2 types)

Answer 10

1. Naked
2. Enveloped (partial to Eukaryotes)

Question 11

Why do enveloped virus “generally” not infect plants or bacteria?

Answer 11

• Plants and bacteria have cell walls.
• the enveloped virus are better at getting through the plasma membrane of animals.

Question 12

Does and enveloped virus kill its host?

Answer 12

• It doesnt have to.
• The virus basically ‘blebs” out covering itself in the membrane of the host.

Question 13

What determines the shape of enveloped proteins?

Answer 13

Capsomeres

Question 14

Bacteriophage normally have what type of structure…?

What is a widely studied bacteriophage?

Answer 14

Complex

The T4 that attacks E.coli

Question 15

What are 4 examples of, common, protiens found within a virus?

Answer 15

1. Adhesion proteins
   
   1. ALL viruses need these to help find/target specific host cells
2. Lysozyme
   
   1. breaks down NAG-NAM in peptidoglycan
   2. Punctures cell walls
3. Polymerases
   
   1. Needs to replicate nucleic acids once inside a cell
   2. Reverse Transcriptase - turns RNA into DNA
4. Neuraminidases
   
   1. Break glycoproteins and glycolipids in cell walls to free virions?

Question 16

What is the term for the amount of “offpspring” from a virus?

Answer 16

Birth size

Question 17

What are the 5 steps in Virus Replications?

Answer 17

1. Attachment
2. Penetration
3. Synthesis
4. Assembly
5. Release

Question 18

Viral Attachment:

1. Mediated by:
2. Each Virion will recognize a specific [] and maybe even a []
3. VAPs can []. with their host and even evolve to [] in a certain population

Answer 18

1. Viral Attachment Protein
2. receptor….co-receptor
3. Evolve/change….host jump?

Question 19

What are the way a virus will penetrate the host cell?

Answer 19

1. Injection
   
   1. this is used for hosts wil cell cells
   2. Complex virus (like T4) use this
2. Fusion
   
   1. Used mainly by enveloped virus
   2. Also can be endocytosed
   3. Requires uncoating of nucleocapsid

Question 20

What are 2 options for an RNA virus to replicate in the host cell?

Why are these necessary?

Answer 20

1. Convert their RNA genome to dsDNA
   
   1. Reverse transciptase, Retroviruses
2. Bring their own RNA-dependent RNA polymerase (RdRp)
   
   1. recognized RNA templates, makes copies of RNA
3. this is Necessary because host cells do not have machinery to use RNA as a template. Needs to be converted to DNA first.

Question 21

How does a Class II (+ ssDNA) virus replicate its genome?

How does a Class III (+/- dsRNA) virus replicate its genome

How does a Class IV (+ ssRNA) replicate its genome?

Answer 21

1. Class II- makes a 2nd copy of its ssDNA and then uses host machinery
2. Class III (+/- dsRNA)- Uses RdRp to transcribe - side into a + mRNA
3. Class IV (+ ssRNA) - Can be used as mRNA

Question 22

How does a Class V (- ssRNA) virus replicate its genome?

How does a Class VI (+ ssRNA) virus replicate its genome?

How does a Class VII (+/- dsDNA) virus replicate its genome?

Answer 22

1. Class V (- ssRNA)- uses RdRp to make a dsRNA and then replicate genome
2. Class VI (ssRNA +) - Retroviruses
   
   1. Uses reverse transcriptase to make RNA–> DNA
   2. Then makes ssDNA into dsDNA and then can use host machinery
3. Class VII (dsDNA +) - hepatic viruses
   
   1. Starts with dsDNA –> RNA –> ssDNA –> dsDNA
   2. Uses host polymerase to make RNA –>then uses viral polymerase with reverse tranciprtase and DdDp to make dsDNA.

Question 23

Do viruses carry ribosomes?

Answer 23

No

Question 24

What is the difference between positive RNA and negative strand RNA?

Answer 24

• Positive = sense
  
  • its the coding strand, has RBS and AUG codon
  • Must be positive to be recognized by ribosome
• Negative = antisense
  
  • template strand; reverse complement of coding strand

Question 25

Is there a "timing" for gene expression during viral synthesis/replication?

Answer 25

* Yes * you'll see early genes encode enzymes and regulatory protiens need to start viral replication * RTs, transcription factors for late genes, RdRp * You see late genes encod for structural proteins * capsid * VAP * tail proteins, envelope proteins

Question 26

What are the 2 "lifestyles" for a virus?

Answer 26

1. Lytic 1. Rapid progression through viral synthesis phase 2. No viral DNA incorporation into host genome 2. Lysogenic 1. Incorporates viral DNA into host DNA (but not expressed) 2. Virus lays dormant until conditions are right 3. "Activation" (stimulus) will swith it to Lytic cycle

Question 27

How does the virus assemble all of the proteins into its virion form?

Answer 27

* Self-assembly of all proteins into virion form inside the cytoplasm of host cell.

Question 28

What are 2 methods of release for a virus?

Answer 28

1. Budding 1. induved extrusion carrying host membranes with it 2. Lysis 1. late viral genes encode protesin that break down membranes/wall and allow release

Question 29

What are methods Eukaryotes use to halt viral synthesis?

Answer 29

* RNA interference-recognizes viral DNA and leads to degredation * Innate and adaptive memory of previous pathogens and antibody production

Question 30

What are ways that bacteria fight off viral infection?

Answer 30

* **CRISPR** - memory based short DNA fragments interference * **Restriction endonucleases** - recognizes and clips DNA at certain sequences (palindromic sequences and methylated sequences)

Question 31

Bacteriophage Facts * Genome type? * Enveloped? * Physical Type? * Life Style? * Types?

Answer 31

1. dsDNA 2. naked 3. Complex (head and tail) 4. Lytic and lysogenic lifestyle 5. Virulent Phage and Temperate Phage

Question 32

Virulent Phages * kill host [] * Best example [] * Encodes some of its own [] * T4 DNA contains 5 [] instead of cytosine = resistant to [] [] by hosts * Express their own []

Answer 32

1. rapidly 2. T4 - infects E.coli 3. tRNA 4. hydroxymethylcytosine, restriction modification 5. Endonuclease (chops up host DNA for use by virus)

Question 33

Temperate Phage * Capable of [] via lysogeny * Exists as a [] in the genome * Can be [] to become lytic * Most well studied example - [] ?

Answer 33

1. non-killing 2. prophage 3. induced 4. bacteriophage lambda

Question 34

Phage Lambda * Uses [] sites to cyclize * Inserts itself into host genome at [] sites (possesed by both virus and hose * Can be [] or [] * Why does Phage Lambda want to cyclize?

Answer 34

1. cos 2. att 3. lytic or lysogenic 4. Linear DNA will be killed in E.coli

Question 35

What are some of the possible outcomes of viral infections in Eukaryotes?

Answer 35

1. **Transformation** - normal cell to tumor cell and so on 2. **Lysis** - death of cell and release of virus 1. Influenze, Rhinovirus 3. **Persistant Infection** - slow release of virus without cell death 1. Rubella, Adenovirus 4. **Latent Infection** - viruse present but not replicating..until necessary or stimulated...could revert to lytic 1. Herpes, HIV 5. **Cell Fusion** 1. 2 cells become one and now the body cant locate the virus becomes it moves back and forth between the fused cells

Question 36

What is a defective virus?

Answer 36

* It is a virus that has lost the ability to do 1 of the 5 steps in teh viral process * Requires a helper virus

Question 37

What is a viroid?

Answer 37

* infectious RNA, LACKS CAPSID * Found only in plants * 246 to 339 nt long

Question 38

What is a Prion?

Answer 38

* Infectious proteins that cuase aggregation or misfolding of host proteins

Question 39

What makes a normal protein a "prion"?

Answer 39

* If the protein is misfolded, it can become infectious * Once misfolded - it can induce other near proteins to misfold leading toinsoluble protein aggregates * PrP^sc = infectious * PrP^C = normal protiein

Question 40

2 examples of examining viruses in vitro?

Answer 40

1. Plaque Formation - hole in the lawn of host in a agar tray = a plaque 2. Plaque Assay - infect layer of host cells with serial dilution froma virus stock 1. stain host cells and observe number of plaque and multiply by dilution factor. 2. in units of PFU/mL

Question 41

What is the "Regressive/Reduction Hypothesis?"

Answer 41

Viruses are remnants of cellular organisms that lost their features.

Question 42

How could retrotransposons be tied to viral evolution?

Answer 42

* mobile genetic elements may have evolved to travel between cells therby becoming infectious entities

Question 43

Do viruses possess any hallmark genes?

Answer 43

* Yes * There are many genes shared by different viruses.