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Microbiology > Virus/Phage > Flashcards

Virus/Phage Flashcards

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Biology 101 flashcards
1
Q

Why are viruses considered unicellular?

A

Psych. They are considered acellular

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2
Q

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

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

A

All of those processes require the hosts machinery

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3
Q

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

A

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

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4
Q

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

A
  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
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5
Q

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

A
  • Viruses do not all share 1 common trait -
    • like the 16s rRNA in bacteria…or the sexual reproduction in Eukaryotes
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6
Q

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

A

Virion

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7
Q

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

What is the 3rd “form”

A
  • Helical (rod)
  • Spherical
    • Icosahedral
  • Complex
    • Helical portion + Icosahedral portion
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8
Q

Define:

Capsid

Capsomere

Nucleocapsid

A
  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!
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9
Q

Can the Nucleocapsid contain other proteins besides capsomeres?

A

yes

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10
Q

How are nucleocapsids usually packaged? (2 types)

A
  1. Naked
  2. Enveloped (partial to Eukaryotes)
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11
Q

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

A
  • Plants and bacteria have cell walls.
  • the enveloped virus are better at getting through the plasma membrane of animals.
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12
Q

Does and enveloped virus kill its host?

A
  • It doesnt have to.
  • The virus basically ‘blebs” out covering itself in the membrane of the host.
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13
Q

What determines the shape of enveloped proteins?

A

Capsomeres

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14
Q

Bacteriophage normally have what type of structure…?

What is a widely studied bacteriophage?

A

Complex

The T4 that attacks E.coli

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15
Q

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

A
  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?
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16
Q

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

A

Birth size

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17
Q

What are the 5 steps in Virus Replications?

A
  1. Attachment
  2. Penetration
  3. Synthesis
  4. Assembly
  5. Release
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18
Q

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
A
  1. Viral Attachment Protein
  2. receptor….co-receptor
  3. Evolve/change….host jump?
19
Q

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

A
  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
20
Q

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

Why are these necessary?

A
  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.
21
Q

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?

A
  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
22
Q

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?

A
  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.
23
Q

Do viruses carry ribosomes?

A

No

24
Q

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

A
  • 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
25
Q

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

A
  • 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
26
Q

What are the 2 “lifestyles” for a virus?

A
  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
27
Q

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

A
  • Self-assembly of all proteins into virion form inside the cytoplasm of host cell.
28
Q

What are 2 methods of release for a virus?

A
  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
29
Q

What are methods Eukaryotes use to halt viral synthesis?

A
  • RNA interference-recognizes viral DNA and leads to degredation
  • Innate and adaptive memory of previous pathogens and antibody production
30
Q

What are ways that bacteria fight off viral infection?

A
  • CRISPR - memory based short DNA fragments interference
  • Restriction endonucleases - recognizes and clips DNA at certain sequences (palindromic sequences and methylated sequences)
31
Q

Bacteriophage Facts

  • Genome type?
  • Enveloped?
  • Physical Type?
  • Life Style?
  • Types?
A
  1. dsDNA
  2. naked
  3. Complex (head and tail)
  4. Lytic and lysogenic lifestyle
  5. Virulent Phage and Temperate Phage
32
Q

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 []
A
  1. rapidly
  2. T4 - infects E.coli
  3. tRNA
  4. hydroxymethylcytosine, restriction modification
  5. Endonuclease (chops up host DNA for use by virus)
33
Q

Temperate Phage

  • Capable of [] via lysogeny
  • Exists as a [] in the genome
  • Can be [] to become lytic
  • Most well studied example - [] ?
A
  1. non-killing
  2. prophage
  3. induced
  4. bacteriophage lambda
34
Q

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?
A
  1. cos
  2. att
  3. lytic or lysogenic
  4. Linear DNA will be killed in E.coli
35
Q

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

A
  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
36
Q

What is a defective virus?

A
  • It is a virus that has lost the ability to do 1 of the 5 steps in teh viral process
  • Requires a helper virus
37
Q

What is a viroid?

A
  • infectious RNA, LACKS CAPSID
  • Found only in plants
  • 246 to 339 nt long
38
Q

What is a Prion?

A
  • Infectious proteins that cuase aggregation or misfolding of host proteins
39
Q

What makes a normal protein a “prion”?

A
  • 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
40
Q

2 examples of examining viruses in vitro?

A
  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
41
Q

What is the “Regressive/Reduction Hypothesis?”

A

Viruses are remnants of cellular organisms that lost their features.

42
Q

How could retrotransposons be tied to viral evolution?

A
  • mobile genetic elements may have evolved to travel between cells therby becoming infectious entities
43
Q

Do viruses possess any hallmark genes?

A
  • Yes
  • There are many genes shared by different viruses.

Microbiology (11 decks)

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