General Features of the Virus Replication Cycle Flashcards
1
Q
What do viruses alternate between?
A
Viruses alternate between an extracellular stage that is inert and an intracellular stage in which new viruses are made.
The entire process from attachment to release from the cell is called the virus replication cycle.
2
Q
Why is it termed virus replication cycle and not virus reproduction cycle?
A
Since viruses are not able to reproduce without a host cell, the term replication is used instead of reproduction when describing the production of new virus particles.
3
Q
The entire virus replication cycle from attachment to progeny virus release can be completed within 8–24 hours for many animal viruses - describe what happens in this cycle.
A
- The virus particle must bind to a structure on the cell surface and the viral genome must enter into the cell.
- Once inside the cell, the viral genome is replicated, viral mRNA is synthesized, viral proteins are made, and new virus particles are assembled and released.
- Viruses use the cellular ribosomes, ATP, tRNA, amino acids, etc., to replicate their genome and synthesize their proteins.
- Depending on the particular virus example, it may use the cellular DNA and RNA polymerases, or it may have its own.
- The protein components self-assemble and associated with a copy of the replicated genome.
- The virus particle then egresses from the cell by budding or lysis the plasma membrane.
4
Q
What is the first step of viral attachment to the host cell?
A
The first step is the adsorption of the virus particle to the host cell; this is a reversible step that results from random collisions between the virus particles and the host cells.
It does not require energy from the host cell.
5
Q
What is the second step of viral attachment to a host cell?
A
The second step is the specific binding of proteins on the outside of the virus particle to a cell surface molecule of the host cell.
This structure may be a protein, a lipid or the carbohydrate portion of a glycoprotein or glycolipid involved in some normal function of the cell.
It is often called the “virus receptor” because it is a structure that is exploited by the virus for infecting a host cell
6
Q
What is the host range?
A
The cell types, and even which species a virus can infect
7
Q
What determines the host range?
A
Determined in part, by whether the cells express the virus receptor.
Host range is also determined by whether the host cell has proper intracellular factors (e.g., polymerases) to allow the replication and expression of the virus genome.
8
Q
Give an example of a virus with a restricted host range and contrast with a virus with a wider host range.
A
Some viruses have a restricted host range in which the virus receptor is found only on a few cell types.
For example, HIV binds to the CD4 protein that is primarily found on helper T cells and perhaps on some macrophages.
The normal role of CD4 is to function as a co-stimulatory molecule of T cells.
In contrast, most cells express the CD46 molecule, which is the receptor for the measles virus.
So whereas HIV can only infect certain cells in a human, the measles virus can infect most human cells.
9
Q
What is a susceptible cell?
A
Cell types that a virus can infect are called susceptible.
10
Q
What is a permissive cell?
A
Cells in which a virus can replicate are called permissive.
11
Q
Describe how SARS-CoV-2 coronavirus binds to a cell surface protein?
A
The SARS-CoV-2 coronavirus binds to the cell surface protein Angiotensin-Converting Enzyme 2 (ACE-2, a metallopeptidase) which is abundantly expresses on the epithelia of the lung and small intestine.
ACE-2 is referred to as the cell’s virus receptor.
The spike protein (S) on the virus, is the virus’ anti-receptor, a structure that is complementary to the cell’s virus receptor.
12
Q
What is a major strategy for preventing viral diseases?
Give an example.
Give an example where this strategy would not be useful.
A
Preventing virus attachment is a major strategy for preventing viral diseases.
For example, vaccines have been developed that induce the production of neutralizing antibodies in the host. The antibodies would bind to the “anti-receptor” on the virus surface (the structure of the virus that binds to host cell surface receptor) and block the binding of the virus to the viral receptor on the host’s cell. However, if the viral anti-receptor mutates at a high rate (e.g., Influenza virus) the antibodies that had been induced by vaccination would not be useful against this modified virus.
13
Q
There are many different mechanisms for a virus (or only its genome) to enter the host cell. For any given virus, the same method is always used. Give some examples of different viruses attaching to cells and the entry of the genome.
A
A) Receptor-mediated endocytosis of virus particle followed by coating of the genome when the capsid breaks apart.
B) Receptor-mediated endocytosis of virus particle followed by genome release by the formation of a pore in the endosome membrane.
C) Receptor-mediated endocytosis of virus particle followed by fusion of the endosome membrane and virus envelope.
D) Fusion of the virus envelope with the plasma membrane.
14
Q
When does virus entry occur?
A
Virus entry is an energy dependent process that occurs almost immediately after attachment.
The viral genome and any essential viral proteins must enter the cytoplasm of a cell in order for the virus to replicate.
15
Q
The nucleic acid of the viral genome can be DNA or RNA, and both types of nucleic acid are sometimes found inside the same virus particle.
True or false?
A
False
The nucleic acid of the viral genome can be either DNA or RNA, but both types of nucleic acid are never found inside the same virus particle.
Some RNA viruses have segmented genomes - that is, their entire genome is contained in several molecules of RNA.
16
Q
What are the two functions that the viral genome that enters the cell has?
A
- it is used as a template for the synthesis of viral genomes for the progeny virus, and
- it is used to synthesize viral mRNA so that viral proteins can be synthesized.
17
Q
What are the (+) and (-) strand designations?
A
A double-stranded nucleic acid has one strand designated as the plus (+) strand and the other as the minus (–) strand. The two strands are complementary.
When one of the strands is used as a template to synthesize a complementary strand, the new strand has the opposite sign.
By a molecular biology convention, mRNA is defined as a positive (+) strand because it contains immediately translatable information.
18
Q
Is mRNA a (+) or (-) strand?
A
By a molecular biology convention, mRNA is defined as a positive (+) strand because it contains immediately translatable information.
19
Q
Are single stranded RNA viruses (+) or (-) strand?
A
Single stranded RNA viruses are either (+) strand or (–) strand depending on whether or not the RNA can be directly translated by the ribosomes.
When virus RNA can be translated directly by the ribosome, it is designated as the (+) strand and contains the coding sequence that specifies the amino acids of the protein.
If the RNA sequence cannot be used directly as the mRNA it is designated as the (–) strand. The complementary sequence of the (–) strand must be made to serve as the mRNA.
20
Q
The process of transcription and translation are the same for DNA and RNA viruses.
True or false?
A
False.
The process of transcription and translation differs greatly between DNA and RNA viruses, and RNA viruses with opposite nucleic acid polarity.
The steps and the enzymes involved in viral replication depend on the type of nucleic acid the virus carries.
21
Q
How do DNA viruses replicate their DNA?
A
Using a DNA polymerase.
Some viruses will use the host cell DNA polymerase; other viruses will supply their own (pre-made) DNA polymerase.
22
Q
How do RNA viruses replicate their genome?
A
RNA viruses (except retroviruses) encode RNA-dependent RNA polymerases (RDRP).
The host cells do not have an enzyme that can read RNA as a template.
RDRP will synthesize the complementary strand of RNA using the virus RNA as a template.
23
Q
How do retroviruses replicate their genome?
A
Retroviruses are RNA viruses that use reverse transcriptase (RT) to synthesize a single strand of complementary DNA (cDNA) using the viral RNA genome as a template.
The RT enzyme then synthesizes the second strand of DNA.
24
Q
What are the five distinct stages of the virus replication cycle?
A
- attachment
- entry
- replication and synthesis of viral proteins
- assembly of new virions
- egress.
25
What does a virus' host range require?
A cell that is susceptible (allows virus entry) and permissive (allows virus replication).
26
What is (+) RNA?
(+) RNA is the equivalent of mRNA: ribosomes can directly translate mRNA or (+) RNA into protein.
27
What is (-) RNA?
(–) RNA cannot be translated by a ribosome, instead, it is complementary to (+) RNA and is used as a template to synthesize (+) RNA.
28
Viruses are capable of replication independent of host cells.
True or false?
False.
29
All viruses replicate their genomes in the nucleus of the host cell.
True or false?
False.
30
Viruses often make their own amino acids and nucleotides during replication.
True or false?
False.
31
All viruses use the host cell’s ribosomes for protein synthesis.
True or false?
True
32
"Translation" is the process of synthesizing messenger RNA (mRNA).
True or false?
False
33
Host cell RNA polymerase reads a DNA template and synthesizes RNA.
True or false?
True.
34
DNA viruses that replicate in the cytoplasm of the cell can still use the host cell DNA polymerase to replicate their DNA.
True or false?
False
35
A virus with an RNA genome can use the host cell RNA polymerase to replicate its genome or synthesize its mRNA.
True or false?
False.
36
Some viruses do not have a DNA component in the replication cycle.
True or false?
True.
37
“Transcription” refers to the process of protein synthesis in a cell.
True or false?
False.
38
Untranslated regions (UTRs) are the 5’ and 3’ regions of an mRNA transcript that do not encode proteins.
True or false?
True.
39
Ribosomes can translate both (+) RNA and (–) RNA.
True or false?
False.
40
Viruses package ribosomes in their capsid to translate their mRNA when they are not in a host cell.
True or false?
False.
41
During translation on a ribosome, the (–) RNA is read in a 5’ to 3’ direction.
True or false?
False.
42
A nucleic acid strand that has the same sequence as mRNA is designated "plus" and a nucleic acid strand that has the sequence complementary to the mRNA is designated "minus."
True or false?
True.
43
A virus can infect any type of host cell once it has entered the body through the respiratory tract or gastrointestinal tract.
True or false?
False.
44
How do viral replication strategies differ among viruses?
Synthesis of viral mRNA
Synthesis of viral proteins
Replication of viral genome
45
What are the functions of structural capsid proteins?
1. Protection of the chemically labile virus genome:
1. from nucleases in the environment,
2. from agents that might damage the base of a nucleotide,
3. shearing of the viral genome from mechanical forces.
2. Attachment of the virion to a host cell and fusion of the virion envelope (if present) to a cellular membrane.
3. Delivery of the virus’ genome to the location within the cell where the genome can be replicated and expressed.
46
What is a virus receptor?
Host cell has a “virus receptor” – a normal cell structure that the virus exploits as a binding site.
Can be: protein, carbohydrate attached to protein
47
What is an anti-receptor?
Virus has an “anti-receptor” – a virus structure that binds to the host cell.
## Footnote
*A host cell is susceptible if it has the proper “virus receptor.”*
48
Are virus particles stable or unstable?
Virus particles are metastable structures – the capsid is stable enough to persist in the environment, but unstable enough to allow for the release of the genome.
49
What does the release of the viral genome require?
The release of the genome requires some triggering event and a succession of interactions.
If everything is in order, conformational changes in the virus particle result in the genome being released into the cell.
If not, the virus detaches from the cell and the process is repeated until the correct cell is found.
50
Compare susceptibility and permissiveness.
**Susceptibility** – ability of virus to get its genome into the host cell (cell surface structure).
**Permissiveness** – ability of the virus to replicate its genome in the host cell (presence of enzyme, expression is linked to the cell cycle).
*Viruses that persist in nature have been successful at encountering host cells that are both susceptible and permissive.*
51
What applies to both DNA and RNA polymerases?
All read a template in the 3’ to 5’ direction.
All synthesize a complementary (and anti-parallel) strand in the 5’ to 3’ direction.
52
Which direction do ribosomes read and synthesize?
All read a mRNA template in the 5’ to 3’ direction.
All synthesize the polypeptide in the N to C direction.
53
Why do some viruses package their own replicative enzymes in their capsids?
Two main reasons:
1. Some species of viruses replicate their genomes in the cytoplasm of the cell – can’t use the cellular DNA or RNA polymerases that are in the nucleus. *These viruses also have to encode the genes for their polymerases.*
2. For RNA viruses, the cell’s RNA polymerase does not read an RNA template (it reads a DNA template). *All RNA viruses must have in their genome, a gene that encodes a polymerase that can read RNA as a template and synthesize RNA or DNA, and some even have a functional copy of the enzyme inside the particle.*
54
What is viral RDRP?
RNA dependent RNA polymerase = Viral RDRP
55
What do RNA viruses (excluding retroviruses) need an enzyme for?
An enzyme that can read RNA as a template and make RNA for both their genomes and mRNA.
## Footnote
*The cell does not have a polymerase that can read RNA as a template.*
56
RNA viruses (excluding retroviruses) need an enzyme that can read RNA as a template and make RNA for both their genomes and mRNA. Can RNA viruses synthesize such an enzyme?
The virus must have a gene that encodes such an enzyme:
(+) sense RNA viruses can synthesize it after infecting the cell (–) sense RNA viruses must have some packaged within their capsid.
57
Only one of the cell’s DNA strand is transcribed to make mRNA.
Remember that the mRNA is complementary and anti-parallel to this strand.
Which strand is transcribed?
The mRNA is always (+).
Therefore the template has to be complementary or the (–) strand.
58
Only one of the cell’s DNA strand is transcribed to make mRNA.
Remember that the mRNA is complementary and anti-parallel to this strand.
This strand is also called:
**The coding strand** has the information that is equivalent to mRNA (here we would have to substitute the T’s with U’s).
59
What is the alternative approach of a retrovirus?
* Transcribe the ssRNA to dsDNA first.
* dsDNA is transcribed to make more of the ssRNA viral genome.
* Need an enzyme that reads RNA and synthesizes DNA *(Reverse transcriptase = RT).*
60
What are the 3 distinct enzyme activities of reverse transcriptase?
* The first is RNA dependent DNA polymerase. This results in a DNA-RNA hybrid molecule.
* The second is Rnase H – an enyzme that removes the RNA in DNA-RNA hybrids.
* The third is a DNA dependent DNA polymerase to make the complementary DNA strand so that the ssDNA becomes a dsDNA molecule.
61
What type of virus use the host cell's DNA polymerase?
DNA viruses that replicate their genomes in the cell’s nucleus can use the cell’s DNA polymerase.
DNA viruses can then use the cell’s RNA polymerase to transcribe their DNA.
All DNA viruses that replicate in the cytoplasm and all RNA viruses (excluding retroviruses) must encode their own RNA polymerase.
They must package or be able to synthesize the enzyme once in the cell.
62
What must all DNA viruses that replicate in the cytoplasm and all RNA viruses (excluding retroviruses) do?
Encode their own RNA polymerase.
They must package or be able to synthesize the enzyme once in the cell.
63
What sequence do eukaryotic ribosomes like to translate?
mRNA with 5’ cap, start codon, a single ORF, stop codon, polyA tail at 3’ end.
64
Why is translation of mRNAs a challenge for some viruses?
Viral mRNA monocistronic or polycistronic.
Eukaryotic ribosomes are not good at translating polycistronic mRNA with a sequence like: +/– 5’ cap, start codon, ORF, stop codon, start codon, ORF, stop codon, start codon, ORF, stop codon, polyA tail at 3’ end.
The simple strategy that viruses have evolved involves translating the entire mRNA into a polyprotein, the cutting up the polyprotein into the individual proteins
(e.g., capsid, RDRP and protease).
65
All of the components of the virus particle must accumulate at a particular location in the cell.
True or false?
True
66
Give an example of a protein that needs to be packaged inside a virus particle.
Proteins that need to be packaged inside a virus particle (e.g., RNA dependent RNA polymerase) bind to the viral genome.
These proteins have an affinity for the viral nucleic acid which ensures they are packed with up with the viral genome.
67
Where do viruses assemble?
Some viruses assemble in the nucleus of the host cell, others assemble in the cytoplasm – it depends on the site of replication of the viral genome in the cell.
Some viruses will start the assembly process in the nucleus of the cell then complete the assembly in the cytoplasm of the cell.
68
How may the process of viral assembly be triggered?
The process of viral assembly may be triggered when the concentration of viral genomes and viral proteins exceeds some threshold concentration.
This usually occurs relatively late in the virus replication cycle after the genome has been replicated.
Self-assembly occurs when there are high concentrations of proteins.
The viral proteins have high affinity for each other.
69
What does the process of capsid assembly rely on?
The process of capsid assembly relies on the inherent protein affinities and the fact that capsids are stable and ensure low free energy.
*It is therefore an energetically favourable process.*
70
Is virus assembly simple?
For some viruses, the assembly process is a relatively simple process involving the affinity and interaction of the proteins that make up the capsid.
For other viruses, it is a complex multi-step process involving viral proteins (both structural and non-structural proteins) and cellular proteins. The non-structural viral proteins and cellular proteins help capsid assembly occur in a certain way.
71
When is the genome packaged inside the capsid?
Depending on the virus, the genome is packaged inside the capsid early in the assembly process or later when the capsid is almost completely assembled.
Most viruses capsid spontaneously self-assembles around the viral genome in the cytoplasm, thus linking the assembly and packaging process.
72
How do helical capsids assemble?
Helical capsids assembly around the nucleic acid and rely on self and nucleic acid interactions to assemble.
73
How do icosahedral capsids assemble?
Icosahedral capsids usually assemble by affinity around the viral genome.
74
How do complex capsids assemble?
Complex capsids need the help of scaffolding proteins to assemble into empty procapsids.
The scaffolding proteins are removed from the empty capsid before the genome is packaged.
75
Describe :
Virus Capsid Assembly and Packaging in the Nucleus.
A subset of nuclear replicating viruses assemble their capsid into the nucleus (top of diagram).
This implies that all capsid component are targeted to the nucleus through nuclear localization signals.
The large icosahedral capsids require scaffolding proteins for assembly.
76
What is virus egress?
Virus Egress (Release)
The newly formed virus particles egress from the cell by one of two methods: cell lysis or budding.
77
How do most non-enveloped viruses egress?
Most non-enveloped viruses egress by cell lysis.
It simply involves the breaking open of the cell and the release of the virus progeny.
Lysis results in the death of the host cell
78
How do most enveloped viruses egress?
Most enveloped viruses egress by budding from the host cell.
The virus acquires its lipid envelope as it extrudes out of the nucleus, or into an intracellular vesicle (i.e., from the Golgi) or at the plasma membrane.
Depending on the particular virus, budding is sometimes, but not always, harmful to the host cell.
Some cells can release enveloped viruses for a long time before the cell is killed.
79
How do enveloped viruses modify the lipid envelope?
All enveloped viruses will modify the lipid envelope by inserting viral-encoded proteins – these proteins are then used for attachment to the host cell for the next round of infection.
## Footnote
*Some viruses need to enzymatically cleave structures on the cell membrane to free themselves from the host cell (e.g.,Influenza virus).*
80
How does the Influenza Virus free itself from the host cell?
Some viruses need to enzymatically cleave structures on the cell membrane to free themselves from the host cell (e.g.,Influenza virus).
81
Describe:
Virus Egress After Assembly.
Most naked viruses and a few enveloped virus require cell lysis in order to release the new virus particles from the host cell.
Lysis is actively induced by many viruses and consists of the disruption of cellular membranes and the release of cytoplasmic in the extracellular space.
This results in the death of the host cell.
Some viruses encode viroporins or lytic phospholipids to disrupt the cell membrane.
Budding enables viruses to exit the host cell and is mostly used by enveloped viruses which must acquire a host-derived membrane enriched in virus proteins to form their external envelope.
Viruses can bud at every stage in the ER-Golgi-cell membrane pathway.
Nucleocapsids assembled or in the process of being built induce formation of a membrane curvature in the host cell membrane and wrap up in the forming bud which is eventually pinched off by membrane scission to release the enveloped particle.
82
What constraints does organization of the eukaryotic cell places on the replication of the viral genome and the synthesis of viral mRNA?
The cell’s DNA and RNA polymerases are localized in the nucleus of the cell. For viruses that replicate in the cytoplasm, these enzymes are not available. Furthermore, the cell lacks enzymes to synthesize a viral mRNA using the viral RNA as a template.
Eukaryotic mRNAs are modified by the addition of a methylated guanine cap at the 5’ end, which is involved in the binding of the mRNA to the ribosomes. Eukaryotic mRNAs are also modified by the addition of a poly-A tail at the 3’ end. Many viral mRNAs lack these structures and must out-compete the cellular mRNA for translation by the ribosomes. The virus does this by giving the viral mRNA a competitive advantage or by inhibiting cellular mRNA synthesis or translation altogether.
Eukaryotic ribosomes translate monocistronic mRNA (i.e., mRNA containing the coding information for one gene only) and they usually will not recognize internal initiation sites within mRNAs. Therefore, the virus must synthesize an mRNA for each gene or it must synthesize an mRNA for all genes that can be translated on a ribosome to synthesize a polyprotein. A polyprotein is a large precursor protein which is enzymatically cleaved into smaller proteins.
83
What are eukaryotic mRNAs modified by?
Addition of a methylated guanine cap at the 5’ end, which is involved in the binding of the mRNA to the ribosomes.
Eukaryotic mRNAs are also modified by the addition of a poly-A tail at the 3’ end.
84
What structures do viral mRNAs lack?
How do viral mRNAs out-compete cellular mRNA in spite of this?
Methylated guanine cap at the 5’ end, and poly-A tail at the 3’ end.
*Many viral mRNAs lack these structures and must out-compete the cellular mRNA for translation by the ribosomes.*
The virus does this by giving the viral mRNA a competitive advantage or by inhibiting cellular mRNA synthesis or translation altogether.
85
Eukaryotic ribosomes translate monocistronic mRNA, and they will usually recognize internal initiation sites within mRNAs.
True or false?
False.
Eukaryotic ribosomes translate monocistronic mRNA (i.e., mRNA containing the coding information for one gene only) and they usually will not recognize internal initiation sites within mRNAs.
Therefore, the virus must synthesize an mRNA for each gene or it must synthesize an mRNA for all genes that can be translated on a ribosome to synthesize a polyprotein.
86
What are the four characteristics to be used in the classification of all viruses in the classical system?
1. Nature of the nucleic acid in the virion (i.e., DNA or RNA).
2. Symmetry of the capsid.
3. Presence or absence of an envelope.
4. Dimensions of the virion and the capsid.
87
What is the Baltimore classification system?
This system describes the formation of viral mRNA by different classes of viruses after the virus has infected the cell.
The polarity of their genomes [i.e., (+) or (–) designations] is based on the molecular biologist’s conventions, with (+) RNA being considered as the equivalent of mRNA.
88
The classical and the Baltimore classification systems are mutually exclusive and do not complement each other.
True or false?
False
The classical and the Baltimore classification systems are not mutually exclusive and actually complement each other.
89
What are capsids assembled from?
Capsids are assembled from virus encoded protein subunits (capsomeres).
90
What do capsomeres interact with during virus particle assembly and packaging?
Capsomeres may also interact with the virus nucleic acid during virus particle assembly and packaging.
91
How is cell lysis triggered?
Cell lysis is triggered by the virus and results in the death of the host cell and the release of the virus particles in the extracellular environment.
92
What does budding form?
Budding results in the formation of an envelope for the virus, but does not necessarily kill the infected host cell.
93
What does the Baltimore system describe?
The Baltimore system is one way of classifying viruses.
It is based on the genetic system of the virus (RNA or DNA, single stranded or double stranded) and describes how the genome and production of viral mRNA occurs.
94
All viruses replicate their genomes in the nucleus of the host cell.
True or false?
False
95
All viruses have a lipid envelope.
True or false?
False.
96
All viruses use the host cell’s ribosomes for protein synthesis.
True or false?
True.
97
Most enveloped viruses bud through the plasma membrane of the host cell.
True or false?
True.
98
The genomes of virus can be single stranded or double stranded nucleic acids.
True or false?
True.
99
The first stage of viral replication is the synthesis of virus proteins.
True or false?
False.
100
A nucleic acid strand that has the same sequence as mRNA is designated (+), and a nucleic acid strand that has the sequence complementary to the mRNA is designated (–).
True or false?
True.
101
A virus with an RNA genome can use the host cell RNA polymerase to replicate its genome or synthesize its mRNA.
True or false?
False
102
Some viruses do not have a DNA component in the replication cycle.
True or false?
True
103
Viral envelopes are derived in part from lipids synthesized using viral enzymes.
True or false?
False.
104
All viruses cause the lysis of cells when the virus particles are released.
True or false?
False.
105
Ribosomes can translate both (+) RNA and (–) RNA.
True or false?
False.
106
Viruses package ribosomes in their capsid to translate their mRNA when they are not in a host cell.
True or false?
False.
107
All icosahedral viruses are enveloped.
True or false?
False.
108
All viruses integrate their nucleic acid into that of their host cell.
True or false?
False.
109
The replication cycles of ALL viruses have 5 key steps.
Which steps exhibit variation amongst viruses?
1. Virus adsorption and attachment to susceptible host cell - chance
2. Genome (and any needed proteins) enters the cell
3. Synthesis of viral mRNA
4. Synthesis of viral proteins
5. Replication of viral genome
6. Assembly of virus from parts Release from host cell
110
What do all viruses contain?
All viruses contain protein and nucleic acid.
At least 50%, and in some cases up to 90% of the mass of the virus particle is protein.
111
Why are capsids made using subunit construction?
1. **Genetic economy** - Less genetic material is required if the protein unit is used as a repeated unit.
2. **Economy** - There is no repair mechanism for misfolded proteins; thus, if a protein subunit is misfolded and used in the construction of the capsid, it affects only a small part of the virus particle’s structure.
3. **Stability of the structure** - As the proteins are asymmetrical, arrange the subunits symmetrically for minimal free energy
112
All virus particles complete a common set of assembly reactions
True or false?
True
113
What are the general features of the virus replication cycle, and which are common to all viruses?
1. Formation of individual structural units of the protein shell from one or several viral proteins
2. Assembly of the protein shell by appropriate and sometimes variable interactions among structural units
3. Selective packaging of the nucleic acid genome and other essential virion components
4. **Acquisition of an envelope**
5. Release from the host cell
6. **Virion maturation**
Bold = only common to some viruses
All others = common to all viruses
114
What structure do many ssRNA viruses have?
Helical symmetry
115
For which viruses are assembly and packaging of the genome linked?
ssRNA viruses that have capsids with helical symmetery
116
Define: ribonucleocapsid
Helical capsid assembly: The RNA is coiled in the form of α helix, and many copies of the same protein are arranged around the RNA forming the **ribonucleocapsid**.
For many viruses, the RNA is within the coil, but for some, it is outside of the coil.
The process of the assembly of a helical capsid appears to be similar for all helical capsids.
117
How are proteins arranged in a capsid with helical symmetry?
Proteins are aligned in a helix around the nucleic acid
118
In a capsid with helical symmetry, describe the appearance of the capsid, as well as its rigidity.
These capsids are elongated and have a rodlike appearance.
The capsid can be rigid or flexible depending on the properties of the capsid proteins.
119
How does capsid assembly begin for virus particles with icosahedral symmetry?
For virus particles with icosahedral symmetry, the process starts by the construction of a protein shell known as a procapsid.
The procapsid is filled with the virus genome during or after construction, (i.e., assembly and packaging of the genome may or may not be linked)
120
What are the smallest of icosahedral capsids built using?
The smallest of icosahedral capsids are built using 60 identical subunits.
## Footnote
*Most virus capsids are built with more than 60 subunits (but in multimers of 60).*
121
The proteins of a capsid with icosahedral symmetry may appear roughly spherical, and will have less contact with the genome than a helical capsid.
True or false?
True!
Some capsids are roughly icosahedral in shape (some may appear roughly spherical).
The proteins of the capsid have less contact with the genome than a helical capsid
122
Describe the structure of an icosahedron capsid.
An icosahedron is composed of 20 facets (each being an equilateral triangle); 5 at the top, 5 at the bottom and 10 in the middle.
There are 12 vertices, each formed where the vertices of the five triangles meet.
There are 30 edges where the sides of two triangles meet.
Some viruses have structures attached at the vertices - projections, fibers or knobs.
123
Do viruses package cellular nucleic acid?
Some viruses actually do package cellular nucleic acid; these may play a role in the initiation of the genome replication when the next host cell is infected (i.e., tRNA as a primer for the reverse transcriptase process in HIV).
However, most cell nucleic acids are not included in the virus particle.
124
How are the virus genomes selected from all of the nucleic acid that might be present in an infected cell?
The specific packaging of virus genome is achieved through the recognition:
* by a virus protein of a specific virus nucleic acid sequence (ss or ds genomes), and/or
* the presence of secondary structures in the genome (ss genomes).
125
For viruses with ss genomes, the virus has to identify the correct strand to package [i.e., either the (–) sense or the (+) strand].
If an RNA virus was supposed to package the (+) strand and it accidently packaged the (–) strand, what would happen?
Nothing!
The (–) strand cannot be translated directly.
126
How do the packaging mechanisms overcome the repulsion of the negatively charged phosphate groups in the nucleic acid?
It's a tight fit inside the capsid!
The repulsion of the negative charges can be overcome by packaging the genome with basic proteins that are positively charged.
The virus may encode these proteins in its genome, while others may use the cell’s histones to coat their genomes.
Some viruses will also package polyamines and cations with the genome.
127
Many animal viruses have an external lipid bilayer called an envelope that surrounds the capsid (helical, icosahedral, or other shapes, e.g., conical).
How do the viruses acquire their envelopes?
By budding through a cellular membrane (usually cell membrane, but some use the membrane of the Golgi or even the nuclear membrane).
Associated with the envelopes are integral proteins that were encoded by the virus’ genome.
128
Describe the structure and role of virus envelope proteins.
Most of the envelope proteins have a relatively large glycosylated external domain, a hydrophobic trans-membrane anchor of about 20 amino acids, and a short cytoplasmic tail.
The glycosylation of the external domain ensures that the external surface of the virus particle is hydrated.
Some of the glycoproteins are involved in attachment of the virus to the host cell or fusion of the envelope and membrane.
129
# Fill in the blank!
[...] can adopt a variety of shapes.
[...] direct incorporation of viral genomes into virus particles.
Formation of viral envelopes by budding is driven by [...].
**Envelopes** can adopt a variety of shapes.
**Specific packaging signals** direct incorporation of viral genomes into virus particles.
Formation of viral envelopes by budding is driven by **interactions between viral proteins.**
130
What is the role of a matrix proteins in some enveloped viruses?
Some enveloped viruses will have protein layer (matrix) between the envelope and the nucleocapsid(s).
The matrix proteins are usually not glycosylated.
Matrix proteins link the nucleocapids to the envelope by transmembrane anchor domains or by protein-protein interactions with the envelope glycoproteins.
131
Many viruses encode in their genomes genes for non-structural proteins. Give examples.
* RNA dependent RNA polymerase,
* Reverse transcriptase
* Proteases
* Protein-type primers for genome replication
* Ion channel proteins
* Proteins that interfere with the host immune response
132
Some viruses will package non-structural proteins with the genome in the capsid structure - what does this depend on?
* the virus’ genome,
* when its needed during replication (start the process, damage host).
133
What is a common outcome of viral infection, and what does it consist of?
Cell lysis is a common outcome of viral infection.
It consists of a disruption of cellular membranes, leading to cell death and the release of cytoplasmic compounds in the extracellular space.
134
What is a viroporin?
Some viruses encode “viroporins” in their genomes to actively induce lysis by disrupting the cell membrane.
Viruses do this because cells seldom trigger lysis on their own (they tend do undergo apoptosis).
135
What viruses require cell lysis?
Most non-enveloped virus, and few enveloped virus require cell lysis in order to release new virus particles from the infected cell.
136
What is cell lysis associated with?
Necrosis – this triggers an inflammatory response (release of cell contents called DAMPs – damage associated molecular patterns – recognized by TLRs.
137
What is a DAMP?
Damage Associated Molecular Pattern – recognized by toll-like receptors
138
How does do enveloped icosahedral viruses egress by budding from the plasma membrane?
Enveloped icosahedral viruses that assembled in the cytoplasm approach the plasma membrane and bind to the cytoplasmic tails of the viral envelope proteins.
Progressive formation of contacts between the surface of the capsid and the cytoplasmic tails of the viral glycoproteins drives pinching-off of the bilayer by fusion.
139
How do enveloped viruses with helical nucleocapsids drive the budding process?
Many enveloped viruses with helical nucleocapsids have an internal matrix protein that mediates the association between viral glycoproteins inserted into the plasma membrane and the nucleocapsids in the cytoplasm, and helps to drive the budding process.
140
Describe capsid maturation.
The capsid may undergo modification after the packaging of the genome to form the mature virus particle which may involve cleavage of one or several of the virus proteins.
The maturation process may result in:
* the change of shape of the capsid,
* sealing of the genome in the capsid,
* release of proteins needed for the next infectious cycle.
141
Explain why the central dogma of molecular biology does not always apply to viruses.
142
Describe the Baltimore classification system for viruses.
Viruses need to make protein as part of their structures.
To make protein, they need to make mRNA.
Viruses are grouped by the process of how they make their mRNA.
This is related to the nature of their genomes – the type of nucleic acid, signal or double stranded, and the sense (+ or –) if single stranded.
The classical classification system is based on the virus’ physical properties.
143
Give an example of a virus with a (-) sense RNA genome.
Influenza
144
Give an example of a virus with a (+) sense RNA genome.
Poliovirus
HIV
