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26 Cards in this Set

  • Front
  • Back
Vocab: subunit, capsid, nucleocapsid, envelope, virion
Subunit (protein subunit)
-Single, properly folded polypeptide involved in virus structure
Capsid (coat)
-Protein shell surrounding the nucleic acid genome
Nucleocapsid (core)
-Nucleic acid-protein assembly packaged into virion
Envelope
-Lipid bilayer carrying viral glycoproteins
Virion
-Complete infectious viral particle
Comparison of viruses and cells
Viruses:
-DNA or RNA but not both
-Few proteins
-No ribosomes
-No mitochondria
-Exponential replication
Basic structure of all viruses
1. Nucleic Acid
a. either RNA or DNA
b. single- or double stranded
c. linear or circular

2. Protective coat
a. Capsid - either icosahedral or helical protein structure enclosing nucleic acid. Helical capsid is composed of single repeating subunit
b. Lipid membrane envelope. Derived from host cell membrane. Viral “spike proteins” project from the surface
Icosahedral capsid

Helical capsid
Like a "golf ball" with RNA wrapped inside

Pleomorphic bag with "slinky" inside
Functions for the Viral Coat
1. Protects genome from degradation.

2. Serves as viral attachment protein to bind to host cell

3. Is often a major site for binding of neutralizing antibodies.
What is the simplest virus?
Minimal: Viral Genome and Coat Protein encoded in Genome

But virus needs a polymerase to reproduce copies of viral genome.

In the “minimal” virus, polymerase would have to be contributed by host cell.

Variations on origin of polymerase for virus growth:
-Virus can encode its own polymerase – RNA viruses
-Can rely on host polymerases
-Can use a combination of host and viral polymerases.

Polymerase can be DNA-dependent DNA polymerase for DNA viruses or an RNA-dependent RNA polymerase for RNA viruses.
Two Classes of Viral Proteins: Structural and Non-structural
1. Structural Proteins will be a part of the Progeny Virus that is released from the cell.
2. Non-structural Proteins are not contained in released virus particles.


Example:
-Capsid proteins are Structural (Architecture)
-Polymerase proteins that replicate the genome are
-Non-structural (Catalytic).

Viruses have evolved mechanisms to regulate the levels of Structural (lots) and Non-structural proteins (very little) that are made during an infection.
Classification of viruses
1. Type of nucleic acid, (e.g., RNA vs DNA, ss vs. ds)

2. Presence of lipid envelope?

3. Replication Strategy

4. Serological methods – Antibodies to viral components.

5. Virion morphology
Assays for Viruses and Viral Infections
1. Molecular Biology Techniques – e.g. PCR

2. Cytopathic effect – e.g., “Cell rounding”; multinucleated cells (syncytia) and inclusion bodies

3. Viral enzyme activity – e.g., retrovirus reverse transcriptase

4. Antibody reactivity – e.g., western blotting, immunostaining
Syncytia
Cytopathic effect

Multinucleated cells

Formed by viruses inside cells which deposit F (fusion) protein on the cell surface. Cells then fuse with uninfected cells, forming sycytial cell.
Viral Inclusion Bodies in Infected Cells
Cytopathic effect

So much capsid protein made that it falls out of solution and forms aggregate in cytoplasm.

Common with Herpes virus, Cytomegalovirus, Paramyxovirus,
Rabies virus (Negri bodies)
Hemagglutination Inhibition (HAI) Assay
Must have hemagglutination properties
-bind RBC

Lack of agglutination = red dot
Antibodies prevent agglutination

Clinical Assay for Antibody Titer Against Influenza Virus
-Titer is dilution at which you have inhibition
Virus attachment
Attachment receptor on host cell doesn't always have to be a protein
Receptor doesn't account entirely for tropism (just because it attaches, it doesn't mean the cell will be infected)
Viruses have evolved to take over and use receptors
Penetration of Virus Particles Across
the Plasma Membrane
1. Direct fusion of viral envelope with cell membrane (e.g., paramyxoviruses)

2. Endocytosis followed by fusion with endosomal membrane (e.g., influenza virus) or
disruption of vesicles (non-enveloped viruses)
Three types of virus uncoating
1. Uncoating at the plasma membrane
2. Uncoating within endosome
3. Uncoating at the nuclear membrane
Virus gene expression and genome replication overview
1. DNA Viruses
a. immediate early genes - regulatory
b. early - enzymes and regulatory
c. late - structural protein

2. RNA viruses
a. Positive strand genome - translation first
b. Negative strand genome - transcription first

3. Transcription - synthesis of mRNA

4. Replication - synthesis of progeny genomes
Virus assembly and release
1. Form units of protein shell
2. Assemble protein shell
3. Selectively package nucleic acid and other components
4. Acquire an envelope (some viruses)
5. Relase from cell
-lysis by non-enveloped viruses
-budding by enveloped viruses
--spike proteins go from golgi to cell membrane, nucleocapsid goes to cell membrane and fuses with spike proteins via matrix protein, reverse of fusion
6. Virion maturation (some viruses)
Example of Antiviral Targeting the Virus Attachment Step
Antibodies Inhibit Influenza Virus Hemaggluntinin
Attachment Protein
Example of Antiviral Targeting the Virus Uncoating Step
Amantadine Inhibits Influenza Virus M2 Protein (ion channel, which helps to acidify)
Examples of Antivirals Targeting the Virus
Genome Replication Steps
DNA Replication
(polymerase)
- Nucleoside analogs (AZT)
Nucleoside biosynthesis
-Ribaviron
Nucleoside scavenging
-nucleoside analogs (gancyclovir)
Example of Antiviral Targeting the Virus Release Step
Oseltamivir (Tamiflu) Inhibits Influenza Virus Neuraminidase

Neuraminidase normally cleaves receptor on host cell when virus leaves so that it doesn't reinfect same cell
Factors that can Influence Whether a Cell or Tissue Can Be Infected (Tropism) and the Outcome of Infection
1. Presence of cellular receptor - e.g., HIV.

2. Presence of cellular enzymes - e.g., proteases for influenza virus.

3. Presence of cellular transcription factors - DNA viruses.

4. Type and level of cellular antiviral responses – e.g., interferon.

5. Environment of virus-host interaction - pH, temperature
Three Phases of Gene Expression for DNA Viruses
Alpha - intermediate early: mRNA leaves nucleus, translated into regulatory proteins that re-enter nucleus and turn beta mRNA transcription on
Beta - Early:
mRNA leaves nucleus and is translated into enzymes that promote DNA replication and turn on gamma
Gamma - late:
mRNA to structural proteins that reenter nucleus and assemble with progeny DNA to make virions

DNA replication (R)
separates
early and late phases
Replication Scheme for Retroviruses – e.g. HIV
1.Reverse transcriptase converts parental retroviral RNA to Linear retroviral DNA
2. Integrase adds retroviral DNA to host cell DNA
3. Cellular polymerase either makes progeny viral + RNA which can form progeny virions or viral proteins OR it makes viral mRNA which makes viral proteins
Polarity of Viral RNA Can Be (+) or (-)
1. + sense RNA = mRNA sense = codes directly for protein
2. - sense RNA = compliment of mRNA sense = doesn't code for protein (needs another transcription step to produce + mRNA)
Replication of + strand RNA viruses
In cytoplasm of infected cell

1. First step is translation by ribosomes to produce a large polyprotein.
2. The viral polyprotein is cleaved by cellular and viral proteases (good antiviral target, self cleaves out of polyprotein) to produce mature proteins (e.g., capsid proteins) needed for growth.
3. One of these proteolytic products is viral polymerase which replicates the viral +ve sense RNA to the –ve sense intermediate and to progeny genomes.