Viruses I/II Flashcards by Alex Maxted

Why is viral DNA larger and more complex than viral RNA?

The DNA pol can proofread, but RNA is not proofread; the RNA will contain many errors and therefore be nonfunctional if it is too large

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What is a segmented genome?

RNA virus genome may be broken into pieces, which function like chromosomes

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Function of a capsid?

Protect the vulnerable genetic material

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3 basic morphological structures of viruses.

Complex, helical, Icosahedral

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What makes the Icosahedral structure so stable?

Triangular pieces form the best ratio of volume to surface area without additional support

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What’s remarkable about the proteins in a helical virus?

During synthesis, the proteins self assemble onto the helical protein surrounding the nucleic acid (so it is rarely exposed)

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Why does RNA require more “protection” than DNA?

More readily degraded

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How will additional nucleic acid length affect self assembling capsomeres?

They will continue to add no matter the length

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What is a capsomere?

Individual component of capsid structure

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How does the construction of the icosahedron capsid structure progress?

Via self assembly of capsomeres, which join into pentomer units

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What is a procapsid?

Shell without nucleic acid

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What is sequential assembly?

Capsid synthesized separately from nucleic acid.

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What happens if too much DNA is put into a capsid?

Increased turgor pressure; places too much pressure onto interior of capsid, resulting in “blowing up”

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Headful packaging

The right amount of DNA in a capsid

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Concerted assembly is for _____ viruses (type of viral structure)

Helical

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Sequential assembly is for _____ viruses (type of viral structure)

Headful packaging

Icosahedral?

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Nucleocapsid

Genome + capsid

Virion for naked viruses

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Enveloped viruses

Nucleocapsid + membrane

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What is the function of virally encoded glycoproteins?

Attach and penetrate cells

2. target immune response

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Where is viral membrane derived from?

Host

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Why do viruses use repeating subunits to build capsids?

More efficient than building various specialized proteins (like animal cells) due to limited genome

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What are the consequences of having an envelope (versus a virus not having an envelope)?

Less stable than naked virus, need aqueous environment

-more susceptible to drying
-sensitive to detergents and etoh
-can’t survive in GI tract (acid)

**limited spread

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T/F: Enveloped viruses may spread fecally and orally.

F: can’t survive acid of GI tract

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Why is it important to determine receptors utilized by viruses?

By blocking these receptors, viruses ability to enter cell is blocked.

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Describe the methods of viral endocytosis

Takes advantage of the cells normal processes: virus attaches, enters cell within vesicle, pinches into endosome allowing nucleocapsid to be released into cell

T/F: Endocytosis is limited to enveloped viruses

F: enveloped and nonenveloped

Fusion proteins.

Proteins that disrupt vesicle or cause merging of envelope/vesicle, releasing nucleocapsid.

The role of pH in membrane fusion.

Fusion proteins are activated in low pH, and undergo a conformational change.

This type of virus fuses directly with the plasma membrane.

Enveloped

pH independent penetration

plasma membrane fusion

pH dependent penetration

endocytosis

Proteins contained within the envelope of viruses that undergo plasma membrane fusion

Fusion and attachment proteins

Proteins contained within the envelope of viruses that undergo plasma membrane fusion

Two ways that antivirals affect viral penetrance.

1) can't release itself from the endosome | 2) changes ridgity of the cell membrane in order to block envelope fusion

What happens to the capsid during uncoating?

Complete disassembly

What occurs after early transcription?

genome replication

Early transcription yields...

Proteins/enzymes necessary for replication

When is RNA dependent RNA pol transcribed?

Early transcription

What is the downside to replicating so many genomes so quickly?

Introduction of many errors (even more if it is RNA)

What is created during late transcription?

Structural proteins

RNA viruses replicate/assemble within the _____ of cells

cytoplasm

DNA viruses replicate/assemble in the _____ of cells

nucleus

Lysis

release of naked virus from host

Budding

release of enveloped virus (does not kill cell)

Release of enveloped virus

Budding

Release of naked virus from host

Lysis

The original glycoproteins on the enveloped virus

are reacquired when the virus buds from the host.

Naked genome is likely what shape?

Icosahedral, because the nucleic acid isn't being shielded as it is synthesized.

(+/-) RNA viruses look like messenger RNA

Internal Ribosomal Entry Site

Viral substitue for our 5' cap structure; provides a site for ribosome binding

Location where ribosomes bind on (+) RNA

internal ribosomal entry site

What is the function of protease in RNA synthesis?

Cuts long polyprotein synthesized into the appropriate pieces

What is necessary to synthesized the 3' to 5' strand during (+) RNA virus replication?

RNA dependent RNA polymerase

encoded by virus to create RNA from an RNA template

Complement strand synthesized by (+) RNA makes

Templates (more + strand RNA for progeny) or translates into capsid proteins (this will be in 3' to 5')

When should RNA dependent RNA polymerase be made in (+) RNA?

First, so additional RNA can be created

First event for (+) RNA

Translation of RNA dependent RNA polymerase

First event for (-) RNA

Transcription of (+) strand RNA (5' to 3')

What is the biggest difference between (+) and (-) RNA?

(-) must package and bring RNA dependent RNA polymerase with it into the cell

Translates individual proteins

(-) RNA

What components of (-) RNA continue on to infect the next cell?

RNA polymerase,

Retrovirus are (+/-) RNA

How does a retrovirus affect cells?

It integrates into host DNA

What enzyme does a DNA virus use to transcribe viral genes?

RNA pol III

How do small DNA viruses signal transcription enzymes?

Encode viral gene promoters to redirect host RNA pol II

What enzyme does a large DNA virus use to replicate viral genes?

its own DNA pol (target for antiviral drugs)

What enzyme does a small DNA virus use to replicate viral genes?

host DNA pol

"Hole" in a confluent monolayer of cells left after cell lysis

Plaque

"Hole" in a confluent monolayer of cells left after cell lysis

Lysate

Suspension of virions in culture medium that results from unrestricted growth of the virus on a monolayer of cells

Lysate

Biological assay of infectivity, measured in pfu/mL lysate

Plaque Assay

What is determined by a plaque assay?

Number of infectious viruses in a suspension

Particle to pfu ratio

Number of particles compared to the number of INFECTIOUS virions (assumes that not all viruses are capable of infection)

Multiplicity of Infection

ratio of infectious particles to number of target cells to be infected

What does a low particle to pfu ratio demonstrate?

Most of the cells are capable of infection

What does an MOI of 5-10 signify?

All cells are infected

2 reasons that viruses have high mutation frequencies:

1) Large number of genome copies | 2) High error rate among RNA polymerases

Complementation

Protein sharing among viruses (such as sharing a functional protein with a virus lacking that functional protein)

One way to repair a defective DNA virus.

Recombination

Reassortment

In segmented RNA viruses, segments of RNA can exchange (AABB + aabb --> AaBb + aAbB)

Common example of reassortment

Especially virulent strands of the flu virus

How does reassortment affect viral immunity?

The virus may have different epitopes, unfamiliar to immune system

When you infect cells at an MOI of 0.1, no lysate is obtained; when you infect at an MOI of 10, a lysate is obtained. Why?

Coinfection (such as complementation) is necessary to produce progeny (virus cannot leave cell if 1 defective virus infects the cell)

Most common route for viral infection

respiratory

Two ways for localized spread

1) Release of progeny and infection of surrounding cell | 2) Syncytia

Synctia

Fusion of infected cell and uninfected cells, forming a large multinucleated cell; does not require release and reentry

Viremia

Viruses within bloodstream

Viruses spread in the body via:

bloodstream and lymphatics

Methods for viruses gaining access to CNS:

1) circumventing the BBB 2) CSF 3) direct uptake in peripheral nerves (polio)

Acute phase

symptomatic phase

Viral genome remains in cell indefinitely, but virus particles are not produced unless activated

Latent viral infection

Virus is produced at low levels throughout persistent infection

Chronic viral infection

Viral genome integrates into cellular DNA and changes cells, i.e. cancer

Transforming (oncogenic) viral infection

First immune defense against viruses

NK cells and IFN

Induced by viral PAMPS binding to Toll-like receptors and PRRs

IFN

Three pathways induced by IFN

PKR, 2-5A system, Mx pathway

Inactivates/phosphorylates translation initiation factor eIF-2, which inhibits viral AND cellular protein translation

Protein kinase pathway

Activates RNase L, which cleaves RNA and destroys the genome or inhibits viral transcription

2-5A System

PKR

Inactivates/phosphorylates translation initiation factor eIF-2, which inhibits viral protein translation

2-5A System

Activates RNase L, which cleaves RNA and destroys the genome or inhibits viral transcription

Mx Pathway

GTPase proteins inhibit RNA polymerase activity

Mx Pathway

Antigen specific imune responses:

CD8+ cytotoxic cells and Neutralizing antibodies

What activates PKR pathway?

dsRNA

Immune Mechanisms of viruses:

Infection of neural cells (no MHC I), cytokine homologs, inhibition of antigen presention, antigen variation

When may a vaccine be impractical?

1) If many disease-causing strains exist | 2) Variation exhibited in dominant antigen structure (epitope)

Antibody responses from live vaccine.

IgG and IgA

Vaccine form that does not require injection

Live

Vaccine form with a single dosing that results in long term immunity

Live

Non-heat labile vaccine form

Inactivated

Benefit of IgA antibodies against a virus.

The virus is inactivated in the gut, so it is not shed/spread to others

Form of vaccine that may revert to virulence

Live

Derived from only ONE viral protein expressed in yeast so it cannot cause disease (but requires multiple injections)

Subunit vaccine (HBV and HPV)