Viral Structure Flashcards
are elegant assemblies of viral, and
occasionally cellular, macromolecules. (50-90% protein).
virion (virus particles)
virions are what percent protein
50-90 percent
come in many sizes and shapes and vary
enormously in the number and nature of the molecules
from which they are built.
virus particles
predicted that the only two ways in
which asymmetric subunits could be assembled to form
virus particles would generate structures with either cubic
or helical symmetry.
Watson and Crick
Watson and Crick predicted that the only two ways in
which asymmetric subunits could be assembled to form
virus particles would generate structures with either __ or __ symmetry
cubic
helical
virion function (2)
protection of the genome
delivery of the genome
Assembly of a stable protective protein shell.
Specific recognition and packaging of the nucleic acid genome .
Interaction with host cell membranes to form the envelope
what function of virion
protection of genome
Binding to external receptors of the host cell.
Transmission of signals that induce uncoating of the genome Induction of fusion with host cell membranes.
Interaction with internal components of the infected cell to direct transport of the genome to the appropriate site .
what function of virion
delivery of the genome
other functions of virion
Interactions with cellular components for transport to intracellular sites of assembly.
Interactions with cellular components to ensure an efficient infectious cycle.
single, folded polypeptide chain
subunit (protein subunit)
unit from which capsids or nucleocapsids are built; may comprise one protein or multiple, different protein subunits
structural unit
the protein shell surrounding the nucleic acid genome
capsid
nucleic acid protein assembly packaged within the virion; used when this is a discrete substructure of a particle
nucleocapsid
the host cell derived lipid bilayer carrying viral glycoproteins
envelope (viral membrane)
infectious virus particle
virion
main viral structrures and general morphology (6)
core nucleic acid types
capsid
envelope
envelope glycoprotein enzymes
non-genomic viral nucleic acid
cellular macromolecules
core nucleic acid type (4)
dsDNA
ssDNA
dsRNA
ssRNA
Code for viral proteins:
special enzyme,
inhibitory proteins,
structural proteins
core nucleic acid
subunit of a capsid
capsomeres
capsids are multiple copies of one ___
protein
a capsid and a nucleic acid makes up a
nucleocapsid
capsid is shaped
helical or icosahedral
envelope is made up of
lipids, proteins, and carbohydrates
Derived from
membrane of host cell
envelope
part of viral envelope that help virus attach
to cells prior during
infection
spikes
do all viruses have envelope?
no
the protein coat that encases and protects the
nucleic acid genome
capsid or nucleocapsid
most virus particles appear to be ___ shaped or ___under the
electron microscope.
rod, spherical
construction of capsids from a small number of subunits would
minimize the genetic cost of encoding structural proteins -Such is ____
genetic economy
viruses use a smart strategy to build their protective shells efficiently, using minimal genetic instructions
genetic economy
repetition of such inter-actions among a limited number of proteins
results in a regular structure, with symmetry that is determined by the
spatial patterns of the interactions. In fact, the protein coats of many
viruses do display what symmetry
helical or icosahedral
- protein coat surrounding and
protecting the viral genome
viral capsid
collection or assembly of protein
molecules making up a viral capsid
capsomere
structure that consists of lipid
containing layers
viral envelope
type of symmetry of capsomere
arrangement associated with spiral-shaped viruses
helical
roughly spherical geometric structure
with 20 triangular faces and the most efficient
arrangement of capsomeres in a viral capsid.
icosahedral
viruses can have a range of shape and symmetries (4)
helical capsid
icosahedral capsid
multiple helical capsid in a spherical viral envelope
complex capsid (icosahedral head, helical tail)
structure of baceriophage
icosahedral head
helical tail
nucleocapsids of some enveloped animal viruses, as well as plant viruses and bacteriophages are shaped ___ or ___ Structures with helical symmetry
rod-like
filamentous
described by the number of structural units per turn of the helix
nucleocapsid
any volume can be enclosed by varying the length of the helix vs icosahedral symmetry with a fixed ____ volume
internal
virus that comprises of one single molecule of strand RNA, about 6.4kb in length, enclosed within a helical protein coat
tobacco mosaic virus
repetitive intreactions among coat protein subunits form ___ in turn assemble as a long, rod-like, right handed helix
disks
repetitive intreactions among coat protein subunits form disks in turn assemble as a long, rod-like, ___handed helix
right
each coat protein binds ___ nucleotides of the RNA genome
three
made up of 20 triangular faces, five at the top, five at the
bottom and10 around the middle, with 12 vertices .
icosahedral symmetry
how many axes in icosahedral symmetry
three axes by two-,three-,five fold axes
Each of 20 faces of an icosahedron is an ___
triangle, and five such triangles interact at each of the 12
vertices
equilateral
a ____of a single viral protein (the subunit)
corresponds to each triangular face of the icosahedron
trimer
As an icosahedron has ___faces, ____identical subunits (3
per face 20 faces) is the minimal number needed to
build a capsid with icosahedral symmetry.
20
60
accommodation of viral genomes
necessitates a high degree of
condensation and compaction.
packaging the nucleic acid genome
binding of viral nucleic acids to capsid
proteins appears to provide sufficient
___ ___required to achieve
packaging
energy force
how many mechanisms for condensing and
organizing nucleic acid molecules within
capsids can be distinguished
three
three packaging of nucleic acid genome
direct contact with a protein shell
packaging by specialized viral protein
packaging by cellular proteins
nucleic acid makes direct contact with the protein(s) that
forms the protective shell of the virus particle
*advantageous arrangement for viruses with small
genomes
what packaging
direct contact of the genome with a protein shell
*nucleocapsid proteins ; important function of such
proteins is to condense and protect viral genomes
what type of packaging
packaging by specialized viral protein
circular, double-stranded DNA genomes of these
viruses are organized into nucle-osomes that contain
the four core histones, H2A, H2B, H3, and H4 -like a
minichromosome
what kind of packaging
packaging by cellular proteins
envelope formed by a viral protein-containing
membrane that is derived from the host cell,
but they vary considerably in size,
morphology, and complexity.
viral envelope
viral envelope vary in
lipid composition
number of protein
location
phospholipids in viral envelope have different names such as
phosphatidylcholine
phosphatidylethanolamine
phosphatidylserine
form the outermost layer of enveloped animal
viruses, but in bacteriophages and archaeal
viruses of the PRD1 family the membrane lies
beneath an icosahedral capsid
viral envelope
viral envelope form the outermost layer of enveloped animal
viruses, but in bacteriophages and archaeal
viruses of the PRD1 family the membrane lies
beneath an ___ ____
icosahedral capsid
integral membrane proteins firmly embedded in the lipid bilayer by a short membrane-spanning domain
viral glycoproteins
binding sites for cell surface virus receptors, major antigenic determinants, and sequences that mediate fusion of viral with cellular membranes during entry
external domains
separate large external domains with oligosaccharides from smaller internal segments
hydrophobic a-helix
hydrophobic a-helix separate large external domains with ___ from smaller internal segments
oligosaccharides
make contact with other components of the virion, are often essential for virus assembly
internal domains
Viral envelopes mainly consist of
envelope proteins (E)
membrane proteins (M)
spike proteins (S)
involved in viral host binding and
subsequent virus-host membrane
fusion to establish the pathogenesis
of the virus.
viral fusion proteins
SARS Coronavirus possess a ___
glycoprotein, which itself performs
the membrane fusion for the entry of
the virion and its fusion with host cell
spike glycoprotein
three modes of interaction between the internal domains of viral glycoproteins and viral capisd or nucleocapsids
direct protein-protein interactions
scaffolding proteins
lipid rafts and membrane microdomains
Viral glycoproteins can directly interact with capsid or nucleocapsid proteins through specific binding sites.
what modes of interaction between the internal domains of viral glycoprotein and viral capsids
direct protein-protein interaction
what modes of interaction between the internal domains of viral glycoprotein and viral capsids
Some viruses use ___proteins to mediate interactions between glycoproteins and capsid or nucleocapsid proteins.
scaffolding proteins
what modes of interaction between the internal domains of viral glycoprotein and viral capsids
In enveloped viruses, glycoproteins are often localized in this interactions where specialized regions of the host cell membrane facilitate the interaction between glycoproteins and capsid or nucleocapsid proteins during viral assembly and budding. This mechanism is particularly important for viruses like HIV and influenza
lipid rafts and membrane microdomains
DNA will need to bring its own DNA polymerase when it needs to replicate in the ___
cytoplasm
virus particles contain ___ necessary for synthesis of viral nucleic acid
enzymes
catalyze reactions unique to virus-infected cells
enzymes
enzymes catalyze reactions unique to virus-infected cells such as
synthesis of viral mRNA from RNA template or of viral DNA from RNA template
necessary because transcription of viral double stranded DNA genome takes place in the cytoplasm of infected cells vs cellular DNA-dependent RNA polymerases and RNA processing restricted to the nucleus
enzyme
other type of enzyme found in virus particles include
integrase
cap-dependent endonuclease
proteases
is a crucial enzyme produced by retroviruses, such as HIV, that enables the integration of viral DNA into the host cell’s chromosomal DNA
integrase
is an enzyme involved in the “cap-snatching” mechanism used by certain viruses, such as influenza, to initiate the transcription of their mRNA. This process allows the virus to hijack the host cell’s machinery for its own replication.
cap-dependent endonuclease
also known as peptidases or proteinases, are enzymes that catalyze the breakdown of proteins by cleaving peptide bonds between amino acids.
proteases
enzyme in human adenovirus that produces infectious particles
L3 23K
protein in Herpes simpelx virus that function in capsid maturation for genome encapsidation
VP24
protein enzyme for protein kinase in herpes simplex virus type 1
UL3
protein enzyme that act as RNase
herpes simplex virus type 1
protein that is an RNA-dependent RNA polymerase; synthesis of viral mRNA and vRNA; cap-dependent endonuclease in influenza A virus
P proteins
protein enzyme in vaccinia virus that is used to synthesize viral mRNA
DNA dependent RNA polymerase
protein enzyme in vaccinia virus that is used to synthesize poly (A) on viral mRNA
poly (A) polymerase
protein enzyme in vaccinia virus that is used to add 5’ caps to viral pre-mRNA
capping enzyme
protein enzyme in vaccinia virus that is used to sequence specific nicking of viral DNA
DNA topoisomerase
protein enzyme in vaccinia virus that is used in virus particle morphogenesis
proteases 1 and 2
more complex particles may contain additional viral proteins that are ___ but are important for an efficient infectious cycle
enzymes
viral proteins used for viral genome replication
protein primers
___ proteins of herpesviruses such as the VP16 protein is used to activate transcription of viral immediate-early genes to initiate the viral program of gene expression
tegument
which virus contain viral mRNAs
adenovirus
herpesvirus
retrovirus particles
A limited set of viral mRNAs, as well as some cellular
and artificial reporter mRNAs, are packaged into
particles of human ____, a
betaherpesvirus that is an important human pathogen
cytomegalovirus
viral mRNAs are translated soon after delivery to the
____ cell
host cell
difficult to exclude the possibility that their pres-ence
is a functionally irrelevant and secondary
consequence of nonspecific nucleic acid binding by
viral structural pro-teins.
non genomic viral nucleic acid
viral particles contain cellular macromolecules such as ___ that condense and organize polyomaviral and papillomaviral DNAs
histones
because of ___, envelope viruses can readily incorporate cellular proteins and other macromolecules
budding
as bud enlarges and pinches off during virus assembly, internal ___ components may be trapped within it
cellular
primer for initiation of synthesis of the neg strand DNA during reverse transcription in retroviral genomes is a specific ___
tRNA
is incorporated into virus particles by virtue of its binding to a specific sequence in the RNA genome and to reverse transcriptase
tRNA
unusual properties of HIV type 1 is the presence of ____, a chaperone that assist or catalyzes protein folding
cellular cyclophilin A
cellular membrane proteins such as ___ and ___ can also be incorporated in the viral enveloped and can contribute to attachment and entry of retroviral particles
Icam-1 and Lfa1
