Viruses Flashcards
Viral properties
Virus definition:
o Entities with genomes of nucleic acid
o Replicate inside living cells using the cellular synthetic machinery
o Cause the synthesis of specialized element that transfer viral genome to other cells
o Replication can result in damage manifested as disease
Properties:
• Obligate intracellular parasites
• No capacity for independent protein synthesis (no ribosomes)
• No capacity to generate energy (can’t make own ATP)
• No cell wall or nucleus
• Genomes either DNA or RNA (viruses do not have both)
o Exception: human cytomegalovirus (has DNA genome, packages 4 specific mRNAs into viral particles)
• Reproduce by subunit assembly not growth and division
Describe the major characteristics used in classifying virus families.
Nature of genome: RNA or DNA
Structure of genome: single- or double-stranded; segmented or non-segmented
Envelope: present or absent
Capsid symmetry: helical or cubic (icosahedral)
Define the terms virion, capsid, nucleocapsid, and envelope.
Virion: virus particle
o If naked/non-enveloped = nucleic acid + capsid
o If enveloped = nucleic acid + capsid + envelope
Capsid: Protein shell
Nucleocapsid: capsid + nucleic acid
Envelope: lipid bilayer made by host cell; contain glycoproteins
Describe the primary functions of the capsid for naked and enveloped viruses.
Helical symmetry:
• Capsid wraps around central axis
• Forms tube with nucleic acid inside
• 1 axis of symmetry
Cubic symmetry
• Capsid forms 20-sided polygon (icosahedron)
• 3 axes of symmetry
• For non-enveloped viruses: structures needed for attachment and entry located on vertices (12 vertices/virion)
Function:
• Protects viral genome from damage
• In naked viruses = contain attachment structures
Describe the primary functions of the envelope for enveloped viruses.
Attachment mediators:
• Single protein (ex: hemagglutinin of influenza virus)
• Attachment complex (ex: herpes simplex virus)
Explain why viruses disappear and infectious virus cannot be found shortly after infecting a cell. Why is this different from any other microbial pathogen?
- Seen in One Step Growth Curves (all cells infected synchronously)
- Titer drops because viruses fall apart to deliver genome once they enter cell
- Eclipse period = time from start of infection to when titer begins to increase (intracellular)
- Latent period = time from start of infection to when virus is released from cells (extracellular)
List the steps during the process of virus replication in a cell.
- Attachment
- Entry
- Uncoating
- Expression of early viral genes (regulation and replication)
- Replication of viral genome
- Expression of late genes (structural proteins to make viral particle)
- Assembly
- Release
Describe the importance of receptors for resistance, pathogenesis, and viral effects on specific tissues or organs.
Attachment requires:
o Virion attachment protein or complex
o Cellular receptors and co-receptors: 1) Proteins • CD4 and CCR5/CXCR4 in HIV 2) Carbohydrates • Heparin sulfate in HSV • Sialic acid in influenza 3) Glycolipids
Result: attachment like typical ligand-receptor interaction o Saturable o Specific o Major difference = multivalent • Additional binding interactions occur • Reaction becomes irreversible
Absence or presence of receptors regulates host range and tropism
Host range = ability to infect a given host
• Ex: hepatitis is very host-specific
Tropism = cell, tissue, or organ that can be infected
• Different serotypes can have different tropisms
• Ex: adenoviruses: affect different parts of body
Describe the two basic ways viruses use to enter cells.
Two basic methods:
1) Fusion at plasma membrane
• Only with enveloped viruses
• Ex: HIV
2) Receptor mediated endocytosis and formation of clathrin-coated pit
• Invagination and endosome formation
• Combine with lysosomes → phagolysosome
• Acidification or acid proteases expose fusion peptides
• Both enveloped and non-enveloped viruses
Note: some viruses able to use both methods
o Ex: Herpes simplex and Poxviruses
Process → conformational change → exposes hydrophobic region (fusion peptide) = inserts into target membrane
Uncoating
o Trigger for influenza = low pH
o For HIV = binds receptor and co-receptro at neutral pH
o Other viruses = use acid-activated proteases
Describe a generic growth cycle (genome replication) for a DNA virus
Genome must enter nucleus
• Exception: Poxviruses (replicate in cytoplasm)
Larger viruses:
• Ex: Adenovirus and Herpes viruses
2 parts early phase:
• Immediate early: genes are regulatory
• Delayed early: genes involved in DNA replication (most current antivirals target DNA replication)
Late phase: genes are structural proteins
• Encode own polymerase and replication factors (targets for antiviral drugs)
Smaller viruses:
• Use host cell polymerases
• Encode early proteins = direct host cell factors to viral genome
o Require host enzymes to make mRNA
• Exception: Poxviruses = encode all proteins to make viral mRNA and for DNA replication
Describe a generic growth cycle (genome replication) for an RNA virus
Must encode genes for RNA-dependent RNA polymerases (because host cells have no way of using RNA genomes)
Types:
1) Positive strand: genome acts as mRNA
• 1st step after entry: synthesis of viral proteins (ex: polymerase) from genome RNA
2) Negative strand: genome must be copied to positive strand first
• Must bring own polymerase with them (part of structural component of virus)
• 1st step: synthesis of mRNA for viral proteins by the polymerase
Describe a generic growth cycle (genome replication) for a retrovirus.
o Positive strand genomes
o Can’t be translated directly
o 1st copied into ssDNA via reverse transcriptase (viral polymerase that’s a structural component of the viral particle)
• Important antiviral drug target
o ssDNA used as template for RT to make a dsDNA
o dsDNA circularizes
o Enters nucleus
Integrates into host genome via integrase → “Provirus”
• Another structural protein
• Also a drug target
• Can cause mutations in host genes
Genome transcribed into mRNA
• Long terminal repeat (LTR) acts as promoter at 5’ end
Genes include: gag (capsid proteins), pol (polymerase and integrase); env (envelope)
Translation into viral proteins
Briefly describe how viruses solve the problem of monocistronic mRNA translation in eukaryotic cells to generate individual viral proteins and the significance of internal ribosome entry site (IRES) elements.
Problem: host cells only translate 1st open reading frame in mRNA
Viral solutions:
Use separate promoters for each gene
• Rabies virus
Use mRNA splicing
• DNA viruses like Adenovirus
Translate RNA into one large polyprotein that is then cleaved into individual proteins
• Rhinovirus, poliovirus
Segment the genome so each protein is on a separate RNA
Ribosomal frame shifting-individual bases are skipped changing reading frame
• “Pseudoknots” = cause ribosome to skip 1-2 bases
• HIV to make RT
Internal Ribosme Entry Sites (IRES) elements = force ribosome to initiate internally
• Picornaviruses
Most viruses use multiple methods depending on the protein
Briefly describe the basic strategies used by icosahedral and helical symmetry viruses for assembly of nucleocapsids
Helical:
o Genomic RNA or DNA like string of necklace
o Capsid proteins like beads= attach to string and bind to each other in helical manner
o Form tube
Cubic: o Capsid proteins form sub-structures o Attach to scaffold proteins o Scaffold removed by proteases o Nucleic acid inserted into shell o Conformational change = seals nucleocapsid
Describe briefly the mechanisms used by viruses for release from cells.
Cell lysis
Trigger apoptosis
o Enhances release
o Cells fall apart without inducing inflammation
o Ex: Adenovirus “death protein”
Enveloped viruses = released during envelope-budding from cell
