Virology Chapter 2-3: General Features of Virus Replication Cycle Flashcards
What do viruses need from cells to replicate their genome and synthesize their proteins?
cellular ribosomes, ATP, tRNA, amino acids, etc.
depending on the particular virus, it may use cellular DNA and RNA polymerases, or it may have its own
Key Features of Virus Replication – Overview
- Virus particle attaches to host cell
- Genome enters host cell
- Genome is replicated and transcribed in the cytoplasm or nucleus (depends on the virus), and mRNA is translated on ribosomes in the cytoplasm
- Protein components self-assemble and associate with a copy of the replicated genome
- Virus particle leaves the cell by budding or lysis of the plasma membrane
Attachment to Host Cell – Overview
- Virus adsorbs to host cell
2. Specific binding of proteins on outside of virus particle, to host cell surface molecule
What causes attachment of virus to host cell?
random collisions between virus particles and host cells – does not require energy
reversible step
What is the host cell surface molecule (VIRUS RECEPTOR) that proteins on the outside of the virus particle binds to?
can be a protein, lipid, or carbohydrate portion of glycoprotein or glycolipid – involved in some normal function of the cell
What is the host range determined by?
- partly by whether cells express the virus receptor
- presence of complementary structure on virus surface (anti-receptor)
- whether host has proper intracellular factors (ie. polymerases) to allow replication and expression of the virus genome
What does HIV virus bind to?
CD4 protein – primarily found on helper T cells, and some macrophages
Susceptible vs. Permissive
susceptible: virus can infect the cell
permissive: virus can replicate in the cell
How might a cell become resistant to viral infection?
mutation in the virus receptor on host cell surface
however, viral receptors are often proteins that are essential for cell survival, and cannot easily be altered without harming the cell
What is a major strategy for preventing viral disease?
preventing virus attachment
How do vaccines prevent virus attachment to host cell?
vaccines induce production of neutralizing antibodies in the host
- antibodies bind to anti-receptor on virus surface and block binding of virus to viral receptor on host cell
What is the anti-receptor?
structure of the virus that binds to virus receptor on host cell surface
When would vaccination not be useful?
if viral anti-receptor mutates at a high rate (ie. influenza) – antibodies induced by vaccination would not be useful against this modified virus
What is an alternative method for preventing viral diseases?
block viral attachment with antibodies against the host cell’s virus receptors
however, an antibody against a host cell protein could alter the cell’s normal function, or disrupt important interactions with other cells
Does virus entry require energy?
yes
Do all viruses enter the host cell in the same way?
no – different mechanisms for a virus (or only its genome) to enter host cell
but for any given virus, the same method is always used
What are 4 examples of ways different viruses enter the genome?
- receptor-mediated endocytosis, followed by coating of the genome when the capsid breaks apart
- receptor-mediated endocytosis, followed by genome release by pore formation in endosome membrane
- receptor-mediated endocytosis, followed by fusion of endosome membrane and virus envelope
- fusion of virus envelope with plasma membrane
What are segmented genomes in some RNA viruses?
entire genome is contained in several molecules of RNA
What are the 2 functions of the viral genome that enters the host cell?
- used as template for synthesis of viral genomes for progeny virus
- used to synthesize viral mRNA so that viral proteins can be synthesized
What are the complementary strands of a double-stranded nucleic acid?
(+) strand
(-) strand
What type of strand is mRNA?
(+) strand
contains immediately translatable information
Are single-stranded RNA viruses (+) or (-) strand?
can be either – depends on whether RNA can be directly translated by ribosomes
What is a (+) strand RNA virus?
contains coding sequence that specifies amino acids of the protein
What is a (-) strand RNA virus?
cannot be used directly as the mRNA – must produce complementary (+) sequence, which will serve as the mRNA
What does the steps and enzymes involved in viral replication depend on?
type of nucleic acid the virus packs
What enzymes do DNA viruses use to replicate? Where do they obtain it?
DNA polymerase
some viruses use host cell DNA polymerase, some use their own (pre-made)
What enzymes do RNA viruses use to replicate? What does it do? Where do they obtain it?
RNA-dependent RNA polymerases (RDRP)
- synthesizes the complementary strand of RNA using virus RNA as a template
encoded by themselves – host cells do not have enzymes that can read RNA as a template
What enzymes do retroviruses use to replicate? What does it do?
reverse transcriptase (RT)
- synthesizes single strand of complementary DNA using viral RNA genome as template
- then synthesizes second strand of DNA
Do viruses often make their own amino acids and nucleotides during replication?
no
Do all viruses use the host cell’s ribosomes for protein synthesis?
yes
What does host cell RNA polymerase do?
reads DNA template and synthesizes RNA
Can DNA viruses that replicate in the cytoplasm of the cell use host cell DNA polymerase to replicate their DNA?
no
Can a virus with an RNA genome use host cell RNA polymerase to replicate its genome or synthesize its mRNA?
no
Can a cell be resistant to viral infection, yet be permissive to viral infection?
yes
cell may lack a structure for virus to bind to so that genome can then move into cell
if the genome can be introduced into the cell artificially, then the rest of the virus cycle can proceed
What are some of the limitations that a host cell presents to a virus with regards to its replication?
- cellular enzymes (ie. polymerases) are designed to work with cellular nucleic acids – cell lacks enzyme to synthesize viral mRNA using viral RNA as template
- cellular ribosomes are designed to translate mRNA that has 5’ methylated guanine cap (binds mRNA to ribosomes) and polyA tail – not all viral mRNAs have this, and must outcompete cellular mRNA for translation by ribosomes
- some viruses replicate their genomes in cytoplasm of the cell, but cellular DNA and RNA polymerases are located in the nucleus
- eukaryotic ribosomes translate monocistronic mRNA and usually will not recognize internal initiation sites within mRNAs – virus must synthesize mRNA for each gene, or an mRNA for all genes that can be translated on a ribosome to synthesize polyprotein, which is then enzymatically cleaved into smaller proteins
What do cellular DNA and RNA polymerases both work on?
double-stranded DNA
What may be post-translationally modified in some virus proteins?
- cleavage into smaller polypeptides
- glycosylation (common in proteins that are part of virus’ envelope)
- additional modifications to virus particles may result after virus leaves host cell
Virus Particle Assembly – Overview
- All components of the virus particle accumulate at a particular location in the cell
- Proteins that need to be packaged inside a virus particle (ie. RDRP) bind to viral genome – have affinity for the viral nucleic acid, which ensures they are packed
Where does virus particle assembly occur?
nucleus of host cell, or cytoplasm – depends on site of replication of viral genome in the cell
some viruses start assembly process in nucleus, and complete it in the cytoplasm
When does the process of viral assembly begin?
triggered when concentration of viral genomes and viral proteins exceeds threshold concentration
usually occurs relatively late in virus replication cycle after genome has been replicated
When does self-assembly occur?
when there are high concentrations of proteins
Do viral proteins have high affinity for each other?
yes
What does the process of capsid assembly rely on?
- inherent protein affinities
- the fact that capsids are stable and ensure low free energy
Is capsid assembly an energetically favourable process?
yes
Describe the simple assembly process?
involves affinity and interaction of proteins that make up the capsid
Describe the complex assembly process.
complex multi-step process that involves viral proteins (structural and non-structural) and cellular proteins
non-structural viral proteins and cellular proteins help capsid assembly occur in a certain way
When is the genome packaged in the capsid?
early in the process, or later in the process (when capsid is almost completely assembled) – depends on the virus
How is the assembly and packaging process linked?
most virus’ capsid spontaneously self-assemble around the viral genome in the cytoplasm
How do helical capsids assemble?
assemble around the nucleic acid, and rely on self and nucleic acid interactions to assemble
How do icosahedral capsids assemble?
assemble by affinity around the viral genome
How do complex capsids assemble?
need scaffolding proteins to help assemble into empty procapsids
scaffolding proteins are removed from empty capsids before genome is pacakaged
In the nucleus, how are capsid components targeted to the nucleus for assembly?
through nuclear localization signals
What are the 2 methods for virus release from host cell?
- cell lysis
- budding
What viruses egress by cell lysis?
most non-enveloped viruses
Egression by Cell Lysis – Process
- Cell membrane is disrupted
- some viruses encode viroporins or lytic phospholipids to disrupt the membrane - Virus progeny is released
- Lysis results in death of host cell
What viruses egress by budding?
most enveloped viruses
Egression by Budding – Process
- Virus acquires its lipid envelope as it extrudes out of the nucleus, or into an intracellular vesicle (ie. from Golgi), or at plasma membrane
- Nucleocapsids assembled, or in the process of being assembled, induce formation of membrane curvature in host cell membrane
- Bud is formed, and is pinched off by membrane scission to release the enveloped particle
When can viruses bud?
at every stage in the ER-Golgi-cell membrane pathway
Does budding harm the host cell?
sometimes – depends on virus
some cells can release enveloped viruses for a long time before the cell is killed
How do all enveloped viruses modify the lipid envelope?
insert viral-encoded proteins that are then used for attachment to host cell in the next round of infection
What do some viruses need to do to free themselves from the host cell?
enzymatically cleave structures on the cell membrane (ie. influenza)
How does the virus outcompete cellular mRNA for translation by ribosomes?
- give viral mRNA a competitive advantage
- inhibit cellular mRNA synthesis or translation
What is the classical system of virus classification?
viruses are grouped (into genera and species) by their shared properties
(rather than properties of the cells or organisms they infect)
What are the 4 characteristics to be used in the classification of all viruses in the classical system?
- nature of nucleic acid in virion (DNA or RNA)
- symmetry of capsid
- presence or absence of envelope
- dimensions of virion and capsid
What is the Baltimore system of virus classification?
based on genetic system of each virus, and describes relationship between genome and production of virus mRNA
Are the virus classification systems for viruses (classifcal and Baltimore) distinct from one another?
classical and the Baltimore classification systems are not mutually exclusive, and actually complement each other
How stable must a capsid be?
has to be stable enough to survive transmission between host cells (which may include the environment outside of a host body), but unstable enough to
release the genome to initiate a replication cycle
