L13 - G Smith - Nature of Viruses Flashcards
give 6 charateristics of viruses
- small size (20-2300 nm)
- obligate intracellular parasites: need a host cell for replication
- simple composition: can be only protein and nucleic acid
- unique mode of replication (not binary fission)
- great diversity: infect all cellular organisms, cause devastating plagues or asymptomatic infections
- numerous: estimated 1031 virions in biosphere
are the largest viruses smaller than the smallest bacteria?
no.
describe a virus structure
simplest virus particle (virion) is essentially a nucleic acid (genome) surrounded by a protein shell (capsid) that protects the genome from the environment and delivers the virus genome from one susceptible cell to another.
describe the symetry in viral capsids?
capsids are composed of repeating protein subunits (capsomers) that are arranged in a symmetrical array.
Symmetry is, in nearly all cases, helical or icosahedral.
The protein coat (capsid) can be composed of…
many identical subunits of a single polypeptide (i.e., the product of a single gene forms the capsid). Some plant viruses are like this
animal viruses are often more complicated - each subunit may be composed of several polypeptides and there may be more than one type of subunit.
do some viruses contain lipids too?
yep - lipid envelope
describe the viral lipid envelope?
Lipid envelope: some viruses have a lipid envelope surrounding capsid: derived from host cell, often by budding of nucleocapsid through cell membrane
how may carbohydrate be incoroprated into a virions structure
lipid envelope embedded with virus proteins, which may be glycosylated
terms for al of these?
Virus particle
Viral nucleic acid
Protein coat
Capsid proteins
Capsid + genome
Viral membrane
Envelope proteins
Structural proteins
Non-structural protein
label
fill in table
are viral genomes DNA or RNA?
can be both!
Virus genomes are either DNA or RNA, which may be….. (strucutre wise)
- linear
- circular,
- monopartite or
- segmented, and
- double stranded (ds) or
- single stranded (ss).
what is a ds virion?
double stranded
two classes of ssRNA?
If the RNA is messenger RNA (mRNA) sense (i.e. can be translated into protein) it is a positive-strand RNA genome.
If the genome is complementary to mRNA (i.e. mRNA is obtained by transcribing the virus genome as template), it is a negative- strand RNA genome.
monoparticulate genomes vs segmented
Usually, the genome is a single nucleic acid molecule (monopartite), but a few viruses contain several nucleic acid molecules (segmented); example, influenza virus and rotavirus.
some exmaples to peruse
what limits the size of RNA genomes?
The size of RNA genomes is limited by the error prone nature of RNA polymerases.
If the genome is too big (> ~20 kb) replication creates too many mutations, which are lethal.
l. Most RNA virus genomes are < __ kb.
l. Most RNA virus genomes are < 15 kb.
The largest RNA virus genomes are > 30 kb,
how do they avoid mistakes?
The largest RNA virus genomes are > 30 kb, and here the replication machinery has associated proof reading activity
largest viral genomes are…
The largest genomes are with dsDNA viruses (mimiviruses: up to 1500 kb).
function of protein nsp14 in coronovirus?
proof reading activity
gneral info on the protein capacity of different sized genome
How do viruses code for proteins efficiently?
- Densely packed genes
- Small intergenic spaces with few non-coding spaces
- Overlapping reading frames, use of a same nucleic acid to code for > 1 protein
- RNA splicing
Viruses are grouped into families (_____), subfamilies (______), genera, species and strains.
Viruses are grouped into families (viridae), subfamilies (virinae), genera, species and strains.
The arboviruses are a large group of viruses that are transmitted by …
4 The arboviruses are a large group of viruses that are transmitted by biting insects (arthropod
borne viruses).
virus Classification is based now on what?
Classification is based now on genetic relatedness and structural characteristics. The families are arranged into larger groups based on the type of nucleic acid genome. This is useful because it groups viruses with similar replication strategies.
6 wyas we can measure / observe viruses?
how do we use EM to see viruses?
The e.m. enabled the structure of virus particles to be seen.
This was useful for diagnosis and quantification. E.g. by mixing a virus preparation with a suspension of small beads of known concentration and counting both virions and beads under the e.m., the concentration of virions may be deduced. Note this measures total virus particles, not how many are infectious.
how do we use the PCR to measure viruses?
The genome sequences of very many viruses are known, so specific primers can be used in a PCR to identify and quantify virus genomes. This is specific and very sensitive and useful for diagnosis. But, like e.m., this does not measure virus infectivity.
describe how we use haemagluttination in viruses?
Some viruses bind to red blood cells (rbc) and cause their agglutination (clumping), haemagglutination.
So a crude measure of virus concentration can be made by mixing virus dilutions with a standard number of rbc and determining the maximum dilution of virus that can agglutinate the rbc.
Note, this is not measuring virus infectivity. Practical class.
describe a plaque assay?
- Measures virus infectivity.
- A series of virus dilutions is applied to lawns of susceptible cells.
- Where a virus binds to and enters a cell, it replicates and releases new virions.
- These infect and replicate in adjacent cells.
- Eventually, a visible area of cells is destroyed by the virus.
- this is a plaque.
- Each plaque derives from one infectious virus particle, so the titre of infectious virus particles can be calculated
can all viruses be titrated by plaque assay?
nope-
eg HBV cannot
Infectious virus titres are expressed as…..
Infectious virus titres are expressed as plaque-forming units (pfu) / mL and can reach extremely high levels (109 or 1010 pfu/mL).
Infected cells look sick: they have …….(morphology?)
Infected cells look sick: they have cytopathic effect, cpe.
bacterial or mammalian cells replicate by dividing 1 to 2, 2 to 4, 4 to 8 - do viruses do this?
no
3 phases of virus replicatio
adsorption and penetration
eclipse phase
assembly and release
label
what is T4 - infects ecoli - previous card
bacteriophage
what is the mean burst sizE?
he average yield of virus particles / cell (mean burst size) reflects the specific virus - host cell combination, and is influenced by the cell metabolic activity. For the above examples, the burst size is ~50.
label
describe the binding process
give 4 examples
between virus proteins and cell receptors
Examples:
- HIV gp120 : CD4
- Influenza virus haemagglutinin (HA) : sialic acid
- SARS-CoV-2 spike protein: angiotensin converting enzyme II (ACE-2)
- Antibodies to virus attachment proteins, block virus infection and are called neutralising antibodies
describe viral penetration
Penetration may occur at the cell surface (fusion), or the virus may be taken into vesicles by endocytosis or macropinocytosis and enter the cytoplasm after disruption of the vesicle membrane.
describe penetration via fusion:
fusion between virus and cell membranes
(can also occur in the intraceullar vesicles)
- HIV and measles virus at cell surface
- Influenza virus with acidified intracellular vesicles
describe influenza fusion
With enveloped viruses penetration occurs by fusion of the virus envelope and a cell membrane at either the cell surface (plasma membrane, ______ pH) or after endocytosis with the endosomal membrane (at _____ pH).
plasma membrane, neutral pH) or after endocytosis with the endosomal membrane (at low pH).
describe whats special about influenzas virus induced haemagglutinin
Influenza virus-induced ‘haemagglutinin’ is an ‘in vitro’ phenomenon that is useful for titrating influenza virus, but has no in vivo significance.
For non-enveloped viruses the process of membrane penetration is less defined, but there are 3 stages:
what are they>
- Binding of virus to receptor
- Conformational change causing disruption of host membrane enabling
- Transfer of virus nucleic acid or entire capsid into cell
examples of penetration by non enveloped viruses?
picornaviruses such as foot and mouth disease virus (FMDV) and polio virus. Bacteriophage T4 injects its DNA into E. coli by contraction of a syringe-like sheath
whats the eclipse phase?
fat
mamba
