M13: Introduction to Viruses: Viral Growth and Replication Flashcards
Properties of viruses:
Viruses are (obligate / facultative) (intracellular / extracellular) parasites that use the machinery of the host to replicate.
The virus genome is composed either of _ or _ surrounded by a protein _: the capsid of some viruses is surrounded by an _
On its own, a virus may be considered as an inert biochemical complex since it cannot _ outside of a living cell.
Once it has invaded a cell it is able to direct the host cell machinery to _.
obligate
intracellular
DNA or RNA
capsid
envelope
replicate
synthesize new intact infectious virus particles (virions)
Properties of viruses:
Viruses attach to host cells by binding to receptors expressed on the host cell surface; the virus then enters host cells by _ or direct penetration of the host cell membrane.
Viruses lack the genetic information necessary for the generation of _ or for _.
Because viruses are _, they are entirely dependent on _ for chance movement and spread to infect other susceptible cells.
Can be acquired from other _ or from the _.
endocytosis
metabolic energy (ATP) protein synthesis (ribosomes)
non-motile
external physical factors
humans
environment
Properties of viruses:
Infection within the host is controlled primarily by _. Some viruses can escape elimination by the _ (latent or persistent viral infections).
Can be diagnosed by inoculation of , _ staining and identification of virus particles or antigens or by detection of viral nucleic acids ().
Viruses are rapidly and constantly evolving – they have high _ and _ rates. This allows them to evade host defenses and to develop antiviral drug resistance.
There are relatively few effective treatments for viruses.
cell-mediated immunity
immune system
cell cultures
immunocytochemical
PCR
replication
mutation
Virus Structure:
The genome of a virus is either a _ molecule or one or more molecules of _
- The viral genome is always enclosed within a protein shell called a _. Most exhibit one of two kinds of symmetry (2)
- Capsids may or not be composed of _, which are defined as morphologic subunits of the capsid discernible by electron microscopy.
- Capsids are formed by the specific _ of capsid proteins.
- Virus particles come in two forms:
- _ – composed of a viral genome enclosed within a capsid (_).
- _ – composed of a nucleocapsid surrounded by a lipid-containing envelope.
DNA
RNA
capsid
- Helical or rod shaped capsids
- Spherical capsid with icosahedral symmetry
capsomeres
clustering
- Nonenveloped (nucleocapsid).
- Enveloped
Definitions:
Virion - The _
Viral Genome – the viral _
Capsid – The protein _ surrounding the viral _
Capsomere - a clustering of _ discernible by electron microscopy.
Nucleocapsid - The viral _ + the _
Nonenveloped viruses - have only the viral _ and _ (naked nucleocapsids, Adenovirus).
Enveloped viruses – have a _ external to the _
intact, infectious viral particle
nucleic acid (either DNA or RNA)
shell, nucleic acid
capsid proteins
genome, capsid
genome, capsid
lipoprotein membrane, protein capsid
Importance of viral surface proteins:
- The proteins on the viral surface can determine viral _ (_)
- Neutralizing antibodies can recognize and bind to proteins on the viral surface and interfere with the ability of a virus to _, thus neutralizing the infectivity of a virus.
a. For nonenveloped viruses, neutralizing antibodies recognize the _ proteins.
b. For enveloped viruses, neutralizing antibodies recognize the _ proteins, typically _ that stick out from the lipoprotein membrane. - The envelope is an essential part of the infectious virion for _ viruses.
a. Without its envelope, the virus is _.
b. Enveloped viruses are in general (easier / harder) to destroy than nonenveloped viruses.
- tropism (what cell types the virus can infect)
- enter a cell
a. capsid
b. outer envelope, glycoproteins - enveloped
a. noninfectious
b. easier
Symmetry:
Virus capsids demonstrate one of two types of symmetry. (2)
Helical
Icosahedral
Symmetry:
Helical:
_ proteins are arranged in a helical coil.
One can visualize a helix by forming a two-dimensional lattice and rolling it into a cylindrical structure of a diameter that accommodates the viral _.
Animal viruses with helical nucleocapsids also possess _.
Capsid
nucleic acid
envelopes
Symmetry:
Icosahedral:
Capsid proteins are arranged in an icosahedron or _ structure.
The most economical way to build a spherical shell of maximal internal volume is to arrange (symmetric / nonsymmetric) proteins with icosahedral symmetry.
An icosahedron comprises 20 triangular faces organized with characteristic _, _, and _-fold axis of rotational symmetry.
spherical
nonsymmetric
2-, 3-, and 5-fold
Classification of Viruses:
Baltimore Classification System – Six classes based on the nature of the viral genome.
DNA
- dsDNA
- ssDNA
RNA
- dsRNA
- ssRNA
- -> plus strand –> retroviruses
- -> minus strand
DNA Viruses:
- Two classes of DNA viruses – _ and _
- Seven families (7)
- The initials of DNA virus families spells (HHAPPPI)
- All DNA viruses except _ are dsDNA
- All are linear except _ and _ (circular).
- All have icosahedral capsid except _
- All replicate in the nucleus except _
- Enveloped (4)
- Naked (noneveloped) (3)
dsDNA and ssDNA
hepadna, herpes, adeno, pox, papova, parvo, irido
parvoviruses
papovaviruses and hepadnaviruses
pox
pox
hepadna, pox, herpes, irido
parvo, adeno, papova
DNA Viruses:
ssDNA
–> nonenveloped (1)
dsDNA
- -> linear
- -> –> icosahedral capsid, replicate in nucleus
- -> –> –> enveloped (2)
- -> –> –> nonenveloped (1)
- -> –> nonicosahedral capsid, doesn’t replicate in nucleus, enveloped (1)
- -> circular
- -> –> enveloped (1)
- -> –> nonenveloped (1)
PARVOviridae
HERPESviridae
IRIDOviridae
ADENOviridae
POXviridae
HEPADNAviridae
PAPOVAviridae
RNA Viruses:
Four classes of RNA viruses containing thirteen medically relevant families.
- ss(+)RNA - (#) families
- ss(-)RNA - (#) families
- segmented ss(-)RNA - (#) families
- segmented dsRNA – _
six
three
three
reoviruses
RNA Viruses:
dsRNA
–> nonenveloped (1)
ssRNA(-)
–> enveloped (6)
ssRNA(+)
- -> enveloped (4)
- -> nonenveloped (2)
- segmented genomes
REOviridae*
ARENAviridae* BUNYAviridae* FILOviridae ORTHOMYXOviridae* PARAMYXOviridae RHABDOviridae
TOGAviridae
CORONAviridae
FLAVIviridae
RETROviridae
PICORNAviridae
CALCIviridae
RNA Viruses:
Mnemonic
Courageous - corona Bunyan - bunya* Fighter - filo Pilots - picorna Can - calici Fly - flavi Over - orthomyxo* Paraguay - paramyxo And - arena* Rhapidly - rhabdo* Return - retro To - toga Reo - reo*
The Life cycle of Viruses: Initiation Phase (3)
Attachment
Penetration
Uncoating
The Life cycle of Viruses:
Initiation Phase:
Attachment:
Attachment of the viral particle to the cell occurs via binding of a protein on the virion _ to a cell-surface protein that acts as the viral _.
The influenza virus _ protein binds to sialic acid, found as antennary sugars on most complex oligosaccharides found on cell surface proteins and lipids. Both _ and entry are mediated by this binding.
Penetration:
Movement of the complete _ or the _ through the cell plasma membrane
- _ between the viral lipid envelope and the cell plasma membrane - this can occur for (enveloped / unenveloped) viruses only.
- Receptor-mediated _ – enveloped or unenveloped viruses.
- Some viruses enter cells by poorly understood mechanisms.
Uncoating:
_ of the viral genome from the viral capsid.
surface
receptor
Hemagglutinin (HA)
attachment
viral particle
nucleocapsid
- Fusion, enveloped
- endocytosis
Release
The Life cycle of Viruses: Replication Phase (2)
Gene expression
Genome Replication
The Life cycle of Viruses:
Replication Phase:
Gene expression - synthesis of _.
Genome Replication - synthesis of _. Hundreds to thousands of copies of the viral genome are produced.
NOTE: Some viruses (e.g. _ viruses) have early and late gene expression phases
viral proteins
viral nucleic acid
DNA
The Life cycle of Viruses: Release Phase (2)
Assembly
Release/Egress
The Life cycle of Viruses:
Release Phase:
Assembly - viral particles are assembled = the viral _ + the viral _ + other virion-associated _.
NOTE: _ are cellular structures or “factories” where viral replication and assembly takes place (can be nuclear or cytoplasmic, depending on the virus).
Release/Egress – movement to the _ and release of _.
- _ of the infected cell may or may not occur.
- Enveloped viruses exit from the infected cell either by
• _ through the plasma membrane
• _ of secretory vesicles containing virus particles with the plasma membrane. - All enveloped viruses derive their envelopes from the _ (e.g. _, or _).
- Nonenveloped viruses usually exit by _ of the cell, but can also exit by unknown mechanisms that do not cause cell _.
Once the progeny virions have been released, they can initiate _. Hundreds to thousands of infectious virions are produced in each infected cell.
capsid
genome
proteins
Inclusion bodies
cell surface
infectious virus particles
- Death
- budding, fusion
- cellular membrane, (plasma or nuclear membranes)
- lysis, lysis
a new round of infection and virus replication in new cells
Replication Strategies of Viruses:
Although all viruses need _ in order to synthesize viral proteins, most viruses _ to replicate the viral genome (viral _).
EXCEPTION: _ (the only single-stranded DNA viruses) use the host-cell DNA polymerase to replicate their DNA.
host cell enzymes
encode their own enzymes
polymerases
parvoviruses
Replication Strategies of Viruses:
Sites of replication:
- Most DNA viruses replicate their nucleic acid and assemble into nucleocapsid complexes in the _.
EXCEPTION: poxviruses are DNA viruses that replicate entirely in the _; they encode their own _, their own _ for transcription of mRNA, as well as enzymes for RNA _ and _.
- Most RNA viruses replicate and assemble entirely in the _.
EXCEPTION: Influenza viruses are unusual segmented negative-sense RNA virus that replicate their RNA genomes and make mRNAs in the _.
- nucleus
cytoplasm DNA polymerase RNA polymerase capping polyadenylation
- cytoplasm
nucleus
Replication Strategies of Viruses:
Viral replication is associated with a (high / low) mutation rate. This is an important mechanism of _ and anti-viral _.
Viral polymerases are _ – especially the RNA-dependent RNA polymerases (RNA viruses) which lack _ ability.
high
immune evasion
drug resistance
error-prone
proofreading
Central Dogma of Molecular Biology:
Information flow in cells goes from:
DNA TO DNA ()
DNA TO RNA ()
RNA TO PROTEIN (_)
REPLICATION
TRANSCRIPTION
TRANSLATION
Replication Strategies of Viruses:
Central Dogma for virus infected cells:
Information flow during viral replication goes from:
DNA TO DNA - _ dependent _ polymerase - _ and _
RNA to RNA - _ dependent _ polymerase - _
RNA to DNA - _ dependent _ polymerase - _
DNA TO RNA - _ dependent _ polymerase - _
RNA TO PROTEIN (_)
DNA
DNA
(DdDp)
DNA Viruses and Cells
RNA
RNA
(RdRp)
RNA Viruses
RNA
DNA
(RdDp)
Retroviruses
DNA
RNA
(DdRp)
Cells
TRANSLATION
Replication Strategies of Viruses:
Once inside cells the viral genomes primary function is to _.
However, viral genomes do not encode the machinery to carry out protein synthesis so they must produce _ that can be read by host cells mRNA translation system.
make viral proteins
messenger RNAs (mRNAs)
Replication Strategies of Viruses:
Important conventions: plus (+) and minus (-) strands:
mRNA is defined as the (positive / negative) strand, because it contains _ information.
A strand of DNA of equivalent polarity is also designated as a (+ / -) strand: i.e., if it were RNA it would be translated into _.
The RNA and DNA complement of this strand is the (+ / -) stand.
This strand cannot be _; it must first be copied to the other strand.
The (+) strand has (5’-3’ / 3’-5’) polarity and the (-) stand (5’-3’ / 3’-5’) polarity.
positive (+)
immediately translatable
(+)
protein
(-)
translated
5’-3’
3’-5’
DNA Viral Genome Replication:
- Encode their own viral _ (exception: _, the only single stranded DNA viruses).
- The (host / viral) DNA polymerase is more efficient than (host / viral) DNA pol at replicating viral DNA.
- Viral _ are important targets of antiviral therapy.
- Only the viral DNA _ is “required” for infectivity. The cellular machinery can make all the necessary proteins from the DNA (including viral polymerase).
- Early viral proteins are made (before / after) DNA replication and are important for altering the _ and for viral genome _ (e.g. viral polymerase).
- Late viral proteins are made (before / after) DNA replication and are important for virus _ and _ (e.g. nucleocapsid structural proteins).
- (Small / Large) DNA viruses like the herpesviruses, exhibit a more complex pattern of gene expression that is temporally divided into three classes (3)
Expression of the immediate early proteins is required for expression of _ and _ genes. The early genes encode proteins required for viral DNA _ and late genes encode _ proteins.
- DNA polymerase, parvoviruses
- viral, host
- polymerases
- genome
- before, host cell, replication
- after, structure, assembly
- Large, immediate early, early, and late.
early and late
replication
structural
RNA Viruses:
The genomes of RNA viruses come in a number of conformations:
- _ stranded of _ or _ polarity
- _ stranded
- _ or _
These structurally diverse viral RNA genomes share a common requirement: they must make _ for assembly into virions and make _ for the synthesis of viral proteins. Require viral _.
The genomes of all RNA viruses except _ encode an RNA-dependent RNA polymerase to catalyze the synthesis of new genomes and mRNA.
- single, (+) or (–)
- double
- unimolecular, segmented
copies of themselves
mRNA
polymerase
retroviruses
Replication Strategy of Positive Sense RNA Viruses:
- Viral RNA genome brought in with the virus can function as _ to encode viral proteins using host cell translation machinery.
- Viral RNA polymerase made in step 1 used to make _ copies of the viral genome – some of the new genomes are used for _ of viral proteins (capsid, envelope, polymerase).
- Some of the Viral (+) RNA is _.
- mRNA
- complementary, translation
- packaged into new virus particles to generate new infectious virus
Replication Strategy of Negative Sense RNA Viruses:
- Negative Strand Viruses Require a packaged _. (+ / -) RNA is converted to (+ / -) RNA using RNA polymerase brought into the cell as part of the virus particle.
- Viral (+ / -)RNA are translated by the host cell machinery
- make (4) - RNA polymerase makes (+ / -) RNA which is packaged into virus particles along RNA polymerase to generate _.
RNA polymerase
(-)
(+)
(+)
capsid, envelope, RNA polymerase plus other viral proteins
(-)
new infectious virus
Segmented Negative Sense RNA Viruses:
- _ like other negative sense RNA viruses
- Can swap _ (reassortment)
- Example: _
- Replicate
- RNA segments
- Influenza viruses
Replication Strategy of Retroviruses:
- +RNA is converted to dsDNA using _ brought into the cell as part of the virus particle
- Integration of the viral dsDNA genome into host cell DNA to generate the _
- _ brought into the cell as part of the virus particle carries out this step. - Viral _ are made from the provirus genome using the host cell machinery.
- Viral mRNAs are _ by the host cell machinery
- make (6) - Some of the viral RNA made in step 3 is packaged into new virus particles along with _, _, and _ to generate new infectious virus.
- reverse transcriptase (RT)
- provirus
- integrase - mRNAs
- translated
- capsid, envelope, RT, protease and integrase plus other viral proteins - RT, integrase and protease
Hepatitis B Virus Replication (Hepadnavirus):
Hepadnavirus family
(Completely / Incompletely) (single / double) stranded DNA virus
Unique DNA virus that uses _ for replication
Gapped DNA repaired in the _ – covalently closed circle
Viral mRNA and Pregenomic RNA are made using _.
Pregenomic RNA is exported to the _ where it serves as template for RT to form _ within newly formed viral particles.
- If enough envelope proteins available the particle is _.
- If not enough envelope proteins, the particle is _.
Incompletely
double
reverse transcriptase
nucleus
host cell machinery
cytoplasm
dsDNA
- released from the cell
- directed back to the nucleus
Properties of viruses:
Direct contact routes (2)
Environmental routes (3)
sexual contact
vertical transmission
respiratory (aerosols)
gastrointestinal (fecal-oral contamination)
transcutaneous (inoculation)
