Virology > Virus Structure and Replication > Flashcards

Virus Structure and Replication Flashcards

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1
Q

What is a Virus?

A
  • Obligate intracellular parasite
  • Small
    • submicroscopic “filterable” infectious agent
  • Possesses genetic material
    • DNA or RNA
    • ds or ss
  • Infectious to a variety of living organisms:
    • Humans, animals, plants, bacteria, invertebrates, fungus
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2
Q

What is the size of viruses?

A
  • 100 nm
    • vs bacteria at >300nm
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3
Q

What is special about Viral DNA/RNA?

A
  • Have DS DNA & RNA
  • Have SS DNA & RNA
  • vs Animals, plants, etc DS = DNA SS = RNA
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4
Q

How are viruses classified?

A
  • Originally classified by size
  • Then classified by pathogenic properties, transmission ecology, or organ tropism
    • Yellow fever, Hep A, B, &C, Rift valley fever would all be hepatitis viruses
  • NOW:
    • Order -virales
    • Family -viridae
    • Sub-family -virinae
    • Genus -virus
    • Species (Common Name) - viruses “share common features” (molecular/structural)
    • Isolate, strain, etc.
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5
Q

What are the types of viral genomes?

A
  • Composition: DNA or RNA
  • Form: SS or DS
    • Polarity of SS RNA:
      • Positive
      • Negative
      • Ambisense
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6
Q

How do viruses replicate?

A
  • Viral genomes MUST make mRNA that can be read by the host ribosomes
  • mRNA is (+)sense RNA
  • mRNA can be translated into a protein
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7
Q

What is Reverse Transcriptase?

A
  • Unique to retroviruses
  • Cells do NOT have a polymerase to turn RNA to DNA - A virus MUST bring its own
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8
Q

What are the Coding Regions of the Viral Genome?

A
  • Genes that produce proteins
  • Open Reading Frame (ORF):
    • has start codon
    • stop codon
    • intervening sequence that codes for a polypeptide of at least 100 amino acids
      • Non-structural proteins
      • Structural Proteins
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9
Q

What are the Non-coding regions of the Viral genome?

A
  • Normally referred to as “untranslated regions” (UTRs)
  • Contain:
    • Regulatory elements
    • Scaffolding
    • Terminal repeats
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10
Q

What are Non-structural Viral Proteins?

A
  • Participate in processes important to the virus
    • Viral replication
    • Regulating gene expression
    • Replication of the genome
    • Facilitating the assembly of the virus particle
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11
Q

What are viral structural proteins?

A
  • Components of the virion
    • envelope proteins
    • matrix proteins
    • capsid proteins
    • additional virion-associated proteins
    • provide receptor-binding sites
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12
Q

What information is contained in the viral genome?

A
  • Replication
  • Assembly and packaging
  • Regulation of the replication cycle
  • Modulation of host defense
  • Spread
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13
Q

What information is NOT contained in the Viral Genome?

A
  • Complete protein synthesis
  • Membrane synthesis
  • Energy production
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14
Q

What is a capsid?

A
  • The protein shell surrounding the nucleic acid genome
  • Self-assembled into a “minimum structure, maximal space” to stably package the genome
  • 2 Main types of capsid structures
    • Symmetrical
      • icosahedral and helical
    • Complex
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15
Q

What do Symmetrical Capsids look like?

A
  • Icosahedral
    • EX: Parvoviruses
      • 20 equilateral triangles
      • Made up of 60 identical copies of the capsid protein
  • Helical:
    • Cylindrical structure
    • Capsomeres arranged in a spiral staircase with a central pole as the axis
    • EX: Rhabovirus (Rabies)
      • Coiled helical nucleocapsid with a bullet shaped virion morphology
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16
Q

What does a complex capsid look like?

A
  • Not helical or icosahedral
  • Possess no symmetry
  • EX:
    • Filoviridae
    • Poxviridae
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17
Q

What is the function of the Capsid?

A
  • Genome Packaging
  • Host cell attachment and entry- (non-enveloped viruses)
  • Un-packaging of the genome and release into cells
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18
Q

What is a Nucleocapsid?

A
  • The complete protein-nucleic acid complex that is the packaged from of the genome in a virus particle
    *
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19
Q

What is the structure of Nucleocapsids?

A
  • Helical capsids
    *
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20
Q

What Families of Viruses have Helical capsids and (-)ssRNA genomes

A
  • Paramyxoviridae (bovine parainfluenza virus 3)
  • Rhabdoviridae (rabies)
  • Orthomyxoviridae (Influenze A)
  • Filoviridae (Marburg and Ebola)
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21
Q

What are the contents of Enveloped Viruses?

A
  • Lipid Envelope
  • Capsid
  • Genome
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22
Q

What are the contents of Non-enveloped Viruses?

23
Q

How is a viral envelope created?

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A
  • Lipid bilayer is derived or “stolen” from the host cell membrane because the viral genome does not have the machinery to encode a lipid bilayer
  • Stolen from:
    • Nuclear membrane
    • Endoplasmic reticulum (ER)
    • Golgi
    • Plasma membrane
24
Q

What are the functions of the Viral envelope?

Study These Flashcards
A
  • Membrane glycoproteins - Antigenic sites, attachment, fusion
  • Protects the nucleocapsid - the capsid with the viral nucleotides
  • Facilitates direct transmission of virions to adjacent cells (cell-to-cell spread)
  • Camouflage- (surrounded by host cell material)
25
Are Enveloped viruses stable?
* Enveloped viruses are often more **unstable** than non-enveloped viruses
26
What is E protein?
* Major structural protein on the surface of mature flavivirus virion * Each E monomer consists of: * Domain 1 (red) * Domain II (yellow) * Domain III (blue)
27
Are viruses alive?
* Viruses are NOT alive * Do Not reproduce * Do Not evolve * Do Not metabolize….. * Without first infecting a cell
28
What is a Virion?
The entire virus particle
29
What is a virus particle?
A structure that has evolved to transfer nucleic acid from one cell to another
30
How are Viruses classified?
* Viral genome characteristics and nucleotide sequence * Capsid symmetry * Enveloped and non-enveloped
31
What are the types of viral genomes?
* **Composition**: RNA, DNA * **From**: single or double stranded * **Polarity**: for ssRNA - Positive or Negative * Presence of **Reverse transcriptase** (RT)
32
What is the Viral envelope made of?
* Lipid bilayer from the host cell * Has Viral envelope Glycoproteins * “spikes” * Specific to the virus
33
How many different viral genomes are there?
* Double stranded (dsDNA) * Single stranded (ssDNA) * Double stranded (dsRNA) * single stranded positive (ss+RNA) * single stranded negative RNA (ss-RNA) * single stranded positive RNA with a DNA step
34
What are the requirements of the virus?
* Attachment to the host cell * Penetration * Uncoating of the viral genome * Replication of the viral genome * Assembly of a new virion * Exit the host cell * Transmission to another host or cell
35
What are the steps for viral replication?
1. Receptor mediated 2. Attachment and Entry 3. Uncoating 4. Genome replications 5. RNA and Protein synthesis 6. Assembly of nucleocapsid and maturation 7. Release from the cell
36
What is Reverse Transcriptase?
RNA-dependent DNA Polymerase
37
What types of cells can a virus enter and replicate in?
* **Susceptible:** has a receptor for a virus * **Resistant:** does not have the receptor for a virus * **Permissive:** can replicate the virus * **Susceptible & Permissive:** the virus can enter the cell and replicate
38
What are the Steps for attachment and entry in Viral Replication?
* Virions have to diffuse across the plasma membrane and then release the genome * Step: * **Adhere to the cell surface** * Not specific, happens by chance * **Attach to a receptor** * specific receptors on the cell * Made for proteins that the cell normally needs * **Genome is then transferred into the cell**
39
What are the mechanisms of virus entry?
* Macropinocytosis * Cavsolin/lipid raft * Phagocytosis * IL-2 * Clathrin-mediated endocytosis
40
What is Viral Fusion?
* Endosome and Envelop Protein bind * Change from a Dimer to a Trimer * Allows the nucleic acid to come out of the virus and is released into the cytoplasm
41
What is uncoating?
* Acidic condition in the endosome triggers changes in viral structural proteins resulting in uncoating and release of the viral genome
42
What information does the viral genome contain?
* Replication * Assembly and packaging * Regulation of the replication cycle * Modulation of host defense * Spread
43
How are viral genes transcripted?
* DNA genome viruses: * Host or virus DNA-dependent RNA polymerase generates viral mRNA * mRNA is translated into viral proteins using cellular machinery * RNA genome viruses: * Require a **viral-encoded RNA-dependent RNA polymerase (RdRp)** to make mRNA (and genomic RNA) * Virus must possess of synthesize RdRp
44
How is viral mRNA translated to viral proteins?
* Translate the mRNA into proteins * protein synthesis * Compare to cell mRNA * 5' cap UTR AUG ORF Stopp UTR AAAAAA 3' * Ribosomes are needed for Transltion * tRNA also needed to add the correct the AA * Translation also needs: * Initiation proteins * Elongation proteins * Termination proteins
45
How are viral proteins named?
* Named based on timing of synthesis * Early translation products * “immediate early” or “early” * mostly _nonstructural proteins_ (polymerases, regulatory proteins) * Late translation products * “late proteins” * _Structural proteins_ (capsid proteins, envelope glycoproteins)
46
What is Post translational modification of proteins?
* Further processing of viral proteins * RNA viruses frequently synthesize polyproteins that are cleaved by viral proteases * The first cleavage is an autocleavage to release a protease, which cleaves other proteins
47
What happens during assembly of nucleocapsids and virus maturation?
* **Self assembly of the capsid** * Many viral proteins assemble on their own * **Assisted assembly:** * Some need scaffolds and chaperones from the cell to form the viral structure * **All Viruses need to:** * Form the protein shell from one or many viral proteins * Assemble the protein shell * Release the virion from the host cell * **Some**: * Acquire an envelope * Go through virion maturation
48
How can viruses exit the cell?
* **Budding** - Acquires membrane * **Lysis** - break the cell open and release the virion * **Release virus without lysis** (poliovirus) * **Move from cell to cell without cell lysis**
49
How do dsDNA viruses replicate?
* Replicate in the nucleus * **Protein vhs** - cuts up the host cell mRNA which blocks host cell defenses (cell cannot make protein from mRNA) * **Protein VP16** - facilitates the transcription of herpesvirus RNA
50
What types of mRNA are produced by dsDNA viruses?
* 3 types: * a - immediate early * B - early * y - late
51
What types of proteins are produced by dsDNA virus?
* 3 types of proteins: * Immediate early * Early * Late
52
How are +RNA viruses (ie coronavirus) replicated?
* Replicates in the cytoplasm (NOT the host cell nucleus) * Buds in the ER/golgi * Only makes 8 viral proteins
53
How are Retroviruses replicated?
* Have a provirus step * Replicate in the nucleus for the DNA step * When the host cell divides the virus divides with it because of the provirus
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