104 Questions
What is the purpose of staining cells in the plaque assay?
To visualize plaques, which appear clear
Why are dilutions done in virus counting?
To make it easier to count the number of viruses
What is the result of excess virus binding with red blood cells in a hemagglutination assay?
Agglutination (clumping) of red blood cells
What causes a clearing of the bacterial culture in the presence of bacteriophages?
Lysis of the bacterial cells
What method is used to visualize virus particles?
Transmission electron microscopy
How are virus replication cycles studied?
Using the MOI (Multiplicity of Infection)
What is the initial drop in infectious titer attributed to?
Defective particles and uncoating inside the host cell
How are viruses classified based on the system developed by David Baltimore?
Seven groups
What are capsids composed of?
Many copies of identical subunits
What defines the symmetry of helical capsids?
The number of subunits per turn and the displacement along the helical axis between subunits
What type of symmetry do identical subunits in capsids have?
Tetrahedral, cubic, or icosahedral
What is used to study detailed pathways of virus replication?
Analysis of viral macromolecules
What is the method for ensuring each cell receives at least one infectious particle during virus replication cycle studies?
Infecting with an excess of virus using MOI
What is the basis for the classification of viruses into seven groups by David Baltimore's system?
Viral genome replication strategy
What is the role of identical subunits in capsids?
Providing genetic economy and self-assembly
What is the method for visualizing virus particles as light images against a dark background?
Negative staining in electron microscopy
What is the basis for grouping virus species into genera?
Shared genome organization and size
How are virus families grouped according to the International Committee on Taxonomy of Viruses (ICTV)?
Overall genome organization, virion structure, and replication mechanisms
What distinguishes most viruses with dsDNA genomes?
Segmented genome and capsids with icosahedral symmetry
What is a characteristic of viruses with reverse transcriptase (RT) in their replication cycle?
RT enzyme is packaged in the virion
What is a distinguishing feature of '' RNA viruses that infect vertebrates?
They are enveloped
What is a characteristic of dsRNA viruses that contributes to their broad host range?
They have their own RNA replication machinery
What is a distinguishing feature of satellite viruses?
They only encode their own capsid proteins
How do satellite nucleic acids replicate in the presence of a helper virus?
Their genomes are encapsidated by the helper virus capsid
What distinguishes viroids from other viruses?
They do not encode for proteins
What is a unique characteristic of dsRNA viruses' mechanism of transcription?
Capsids act as tiny intracellular machines for mRNA transcription
What is the process of developing viral envelopes at the cell membrane called?
Budding
What reflects the composition of the membrane from which the viral lipid bilayer was derived?
The lipid content of the lipid bilayer
Where can viral glycoproteins be inserted during the budding process?
Both a and b
What interacts directly with cytoplasmic tails of envelope proteins during budding?
Some nucleocapsids
What do some viruses use to interact with both viral spikes and nucleocapsids during budding?
Matrix (M) protein
What is inserted into the lipid membrane to form the viral envelope?
Glycoproteins (spikes)
What is the nature of viral envelopes in terms of symmetry?
Not always symmetrical
Aside from lipid analyses, what other method can be used to determine where a virus budded from?
Electron analysis
What is the process of developing viral envelopes at internal membranes called?
Budding
What is wrapped in a membrane into which viral glycoproteins have been inserted?
Nucleocapsid
Where are envelope proteins synthesized?
On ribosomes in the ER
What prevents dehydration of virus particles' external surfaces?
Glycosylation in the ER/Golgi
What directs the specificity for incorporation of viral genomes into virions?
Packaging signals
What neutralizes the negative charges on DNA and condenses the viral DNA for optimal packaging?
Core proteins
What drives the formation of viral envelopes by budding?
Interactions between viral proteins
What can some viruses generate during budding?
Empty envelopes
How is the release of the viral genome from virions achieved?
Proteolytic cleavage of capsid proteins
What are virions energetically?
Metastable
What is virus classification based on?
Molecular architecture, genetic relatedness, and host organism
What can capsid assembly depend on?
Size, shape, and complexity of the capsid
What is the process of developing viral envelopes at the cell membrane called?
Budding
What reflects the composition of the membrane from which the viral lipid bilayer was derived?
Lipid content
Where are viral glycoproteins inserted during the budding process?
Cell membrane
What interacts directly with cytoplasmic tails of envelope proteins (viral spike) during budding?
Nucleocapsid
What is the nature of viral envelopes in terms of symmetry?
Can be symmetrical or asymmetrical
What drives the formation of viral envelopes by budding?
Viral glycoproteins
What is a distinguishing feature of dsRNA viruses' mechanism of transcription?
Unidirectional transcription
What is the method for visualizing virus particles as light images against a dark background?
Dark-field microscopy
What is the basis for grouping virus species into genera?
Genomic organization
What is wrapped in a membrane into which viral glycoproteins have been inserted?
Nucleocapsid
What is a distinguishing feature of most '' RNA genomes less than 10kb?
They do not have envelopes
What is a characteristic of dsRNA viruses that contributes to their broad host range?
They have their own RNA replication machinery
What is a unique characteristic of dsRNA viruses' mechanism of transcription?
Capsids act as tiny intracellular machines
What is a distinguishing feature of satellite viruses?
They only encode their own capsid proteins
What is the basis for grouping virus species into genera?
Genome organization and size
What is a characteristic of viruses with reverse transcriptase (RT) in their replication cycle?
They can have RNA or DNA genomes
What is a distinguishing feature of most viruses with dsDNA genomes?
They include some of the largest known viruses
What is a distinguishing feature of viroids?
They do not encode for proteins
What is a distinguishing feature of satellite nucleic acids?
Their genomes are encapsidated by the helper virus capsid
What is a characteristic of viruses with ssDNA genomes?
They tend to be small and have few genes
Which organelle is involved in the glycosylation process of viral proteins?
Golgi apparatus
What drives the formation of viral envelopes by budding?
Interactions between envelope glycoproteins
What is the role of packaging signals in virion assembly?
Direct the specificity for incorporation of viral genomes into virions
What is the basis for virus classification according to David Baltimore's system?
All of the above
What is the function of core proteins in viral assembly?
Neutralize the negative charges on DNA and condense the viral DNA
What can some viruses generate during budding?
Empty envelopes
What is the characteristic of virions in terms of stability?
Energetically metastable
What is the function of scaffolding proteins in capsid assembly?
Assist in procapsid formation
What type of integral membrane proteins are involved in viral assembly?
Type I and Type II
Where are envelope proteins synthesized?
Endoplasmic reticulum
What is the process of developing viral envelopes at the cell membrane called?
Budding
Where can viral envelopes be derived from?
Endoplasmic reticulum
What do some nucleocapsids interact directly with during budding?
Cytoplasmic tails of envelope proteins (viral spikes)
What reflects the composition of the membrane from which the viral lipid bilayer was derived?
Lipid content of the lipid bilayer
Where are envelope glycoproteins synthesized?
Ribosomes in the ER
What is the role of glycosylation in viral proteins?
Preventing dehydration of virus particles' external surfaces
What directs the specificity for incorporation of viral genomes into virions?
Packaging signals
What neutralizes the negative charges on viral DNA and condenses it for optimal packaging?
Core proteins
What drives the formation of viral envelopes by budding?
Membrane curvature
What is the basis for virus classification?
Nucleic acid genome type
What can some viruses generate during budding?
Empty envelopes
What is the basis for grouping virus species into genera?
Genome organization and size
What can cause the release of the viral genome?
All of the above
What is a distinguishing feature of most viruses with dsDNA genomes?
Enveloped structure
What are virions energetically?
Metastable
What is a unique characteristic of dsRNA viruses' mechanism of transcription?
Assembly of capsids from translated mRNAs
What are the two types of integral membrane proteins involved in viral assembly?
Type I and Type II
What is a characteristic of viruses with reverse transcriptase (RT) in their replication cycle?
Inclusion of RT enzyme in the virion
What can depend on the size, shape, and complexity of the capsid in viral assembly?
Capsid assembly
What is a distinguishing feature of satellite nucleic acids?
Replicate independently of helper virus
Where does the glycosylation process of viral proteins occur?
ER/Golgi
What is a distinguishing feature of satellite viruses?
Include their own capsid proteins
What is a distinguishing feature of viroids?
Replicate independently of other viruses
What is a characteristic of viruses with ssDNA genomes?
Lack of an envelope
What is a distinguishing feature of dsRNA viruses' mechanism of transcription?
Assembly of capsids from translated mRNAs
What is a distinguishing feature of satellite nucleic acids' replication?
Replicate in the absence of a helper virus
What is a distinguishing feature of satellite viruses' replication?
Replicate in the absence of a helper virus
What is a distinguishing feature of viroids' replication?
Replicate in the presence of a helper virus
Study Notes
Virus Replication and Structure Overview
- Not all virus particles are infectious, as disrupted or defective virions, empty capsids, and cellular anti-viral defenses can interfere with virus replication
- Electron microscopy is used to visualize virus particles, which appear as light images against a dark background due to negative staining
- Virus replication cycles are studied using the MOI (Multiplicity of Infection) by infecting 10^3-10^6 cells with an excess of virus to ensure each cell receives at least one infectious particle
- The initial drop in infectious titer is due to defective particles and uncoating inside the host cell
- Analysis of viral macromolecules can reveal detailed pathways of virus replication, which vary greatly depending on host cell, viral genome, and virus complexity
- Virus replication cycles involve attachment to a host cell, entry into the host cell, genome replication and gene expression, assembly and morphogenesis, and release/exit
- Viruses can be divided into seven groups based on the system developed by David Baltimore
- Virions have evolved structures to efficiently transmit RNA or DNA genomes, with a rigid, symmetrical capsid and enclosed viral genome
- Capsids are composed of many copies of identical subunits, providing genetic economy and self-assembly
- Identical subunits can have tetrahedral, cubic, or icosahedral symmetry, with helical nucleocapsids accommodating variable genome lengths
- Helical capsids' symmetry is defined by the number of subunits per turn and the displacement along the helical axis between subunits
- For negative strand RNA viruses, the genome winds along a groove that follows a helical path of protein subunits, with each protein subunit binding a fixed number of nucleotides
Viral Structure and Assembly Overview
- Envelope glycoproteins have a large glycosylated external domain, a hydrophobic transmembrane anchor domain, and a short internal tail.
- Envelope proteins are synthesized on ribosomes in the ER and inserted into the plasma membrane via standard export pathways for cell surface proteins.
- There are two types of integral membrane proteins, Type I and Type II, with different orientations and signal sequences for membrane insertion.
- The glycosylation process of viral proteins occurs in the ER/Golgi and prevents dehydration of virus particles' external surfaces.
- Capsid assembly can depend on the size, shape, and complexity of the capsid, and some viruses require scaffolding proteins for procapsid formation.
- Packaging signals direct the specificity for incorporation of viral genomes into virions by interacting with capsid proteins.
- Core proteins neutralize the negative charges on DNA and condense the viral DNA for optimal packaging, resembling chromatin.
- Interactions between viral proteins drive the formation of viral envelopes by budding, involving membrane curvature and different mechanisms.
- Budding can be driven by interactions between envelope glycoproteins, matrix, or nucleocapsids, and some viruses can generate empty envelopes during budding.
- The release of the viral genome can occur by proteolytic cleavage of capsid proteins, unspooling of the genome, or interaction with cytoplasmic components.
- Virions are energetically metastable and can easily dissociate with the right trigger, and assembly and disassembly are not a simple reversal of the processes.
- Virus classification is based on molecular architecture, genetic relatedness, and host organism, using criteria such as nucleic acid genome type, capsid symmetry, and presence of an envelope.
Viral Structure and Assembly Overview
- Envelope glycoproteins have a large glycosylated external domain, a hydrophobic transmembrane anchor domain, and a short internal tail.
- Envelope proteins are synthesized on ribosomes in the ER and inserted into the plasma membrane via standard export pathways for cell surface proteins.
- There are two types of integral membrane proteins, Type I and Type II, with different orientations and signal sequences for membrane insertion.
- The glycosylation process of viral proteins occurs in the ER/Golgi and prevents dehydration of virus particles' external surfaces.
- Capsid assembly can depend on the size, shape, and complexity of the capsid, and some viruses require scaffolding proteins for procapsid formation.
- Packaging signals direct the specificity for incorporation of viral genomes into virions by interacting with capsid proteins.
- Core proteins neutralize the negative charges on DNA and condense the viral DNA for optimal packaging, resembling chromatin.
- Interactions between viral proteins drive the formation of viral envelopes by budding, involving membrane curvature and different mechanisms.
- Budding can be driven by interactions between envelope glycoproteins, matrix, or nucleocapsids, and some viruses can generate empty envelopes during budding.
- The release of the viral genome can occur by proteolytic cleavage of capsid proteins, unspooling of the genome, or interaction with cytoplasmic components.
- Virions are energetically metastable and can easily dissociate with the right trigger, and assembly and disassembly are not a simple reversal of the processes.
- Virus classification is based on molecular architecture, genetic relatedness, and host organism, using criteria such as nucleic acid genome type, capsid symmetry, and presence of an envelope.
Test your knowledge of virus replication and structure with this quiz. Explore topics such as electron microscopy, virus replication cycles, viral macromolecules, viral classification, and virion structures. Understand the intricate pathways of virus replication and the evolution of virions' structures to transmit RNA or DNA genomes efficiently.
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