Lecture 3 - structure of viruses Flashcards
what are viruses?
Viruses infect all living things
More than 1031 virus particles on Earth!
107 per mL in coastal seawater.
There are ~1016 HIV-1 genomes on the planet today.
Many of the viruses that infect us have little or no impact on our health or well being.
An infectious, obligate intracellular entity comprising genetic material (DNA or RNA) surrounded by a protein coat ± membrane (envelope)
Viruses carry or transport genetic information from cell to cell: “extracellular organelles”
Infectious virus particle (“virion”) is a molecular machine that:
-package viral genome.
-escapes from infected cell.
-survives transfer from one cell to another cell.
-attaches, penetrates, initiates replication in a new host cell.
are viruses living entities or not?
-They contain nucleic acid/genetic material.
They can replicate and go through evolution.
but
They must have a host cell to replicate.
They exploit host cell processes such as the translational machinery
if they are not living or non living then what are they?
Are they an evolutionary bridge between non-living viruses and living organisms??
Genome contains 911 potential protein-coding genes.
ORFs showing stronghomologyto genes that encode aminoacyl-tRNA synthetases, translation initiation factors, metabolic pathways, DNA repair and protein folding
what size are viruses
Most viruses are ~10x smaller than bacteria
Some have less than 5 genes compared to 30,000 genes for humans
what are viral genomes?
Small genomes («_space;bacteria)
Some human virus examples
HIV-1 – 9.7kb (ssRNA)
Influenza – 13.5kb (ssRNA, segmented)
Ebola – 18.9kb (ssRNA)
Cytomegalovirus – (dsDNA, 236kbp)
what is a virion?
Allows the delivery of the virus genomes to sites of replication within the cell and allows infection of new cells.
what is the general structure of a virus?
Some viruses acquire a lipid bilayer “envelope” as they bud from the surface of cells.
Other enveloped viruses exist that acquire their membranes via the secretory pathway (poxviruses and flaviviruses).
Often envelope viruses contain proteins that are heavily glycosylated that are important for infecting other cells.
what is virus symmetry?
Virus capsids can lack global symmetry
Many virus possess capsids that posses symmetry
There are two primary shapes
Icosahedral - with two, three and five fold symmetry axis eg herpesvirus
Helical - possess a screw axis
Virus are extremely efficient in their coding capacity
Capsids can be made up several copies of one or a few subunits
Sometimes they are made of a single kind of subunit which takes up multiple confirmations
what are parvoviruses?
5 kb ssDNA genome
50 kDa molecular mass coat protein
Inner radius of shell: 80 A
= just enough volume to package a 5 kb genome, of which
about 1/3 dedicated to coding for coat protein
what are complex viruses?
A good example of a virus with complex structure is bacteriophage T4.
It has an icosahedral head.
A helical tail.
A number of tail fibres.
what is a virus genome?
All living things have genetic material made of DNA
Many viruses have DNA genomes.
Most viruses have genetic material made of RNA.
Some viruses have genetic material that swaps between RNA and DNA!
ie Retroviruses
what is Baltimore Classification based on genome?
all viruses need to produce mRNA for translation by host ribosomes
what are virus enzymes?
Sometimes virions contain enzymes that are important for the life cycle of the virus
e.g. some bacteriophage Tail-associated lysozyme ofbacteriophage needed for entry of their DNA
HIV-1 virions contain integrase allowing the DNA to integrate in the host-cell.
RNA viruses always have their own replicase.
For HIV-1, this is reverse transcriptase enzyme
Copies RNA into DNA
how do viruses replicate?
A virus absolutely requires a living host cell to make copies of its genetic material and the proteins and enzymes it needs to replicate
The virus takes over the host cell metabolism for its own ends
The one cellular process that ALL viruses require is protein translation on the ribosomes
what are the stages of virus replication?
Attachment
Entry
Synthesis
Assembly
Release (egress)
what is the attachment and entry stage in animal cells?
Viruses bind to a specific receptor on the cell surface
Viruses enter animal cells by
Membrane fusion
Endocytosis
The attachment process contributes to host cell specificity
Example : HIV-1 uses CD4 as a primary receptor and either CCR5 or CXCR4 as a co-receptor
how is viral nucleic acid produced?
The first steps in replication are:
Production of at least some virus proteins
This requires viral mRNA
Then the genome is replicated
how is the virus formed?
Some virus proteins form the virus coat
The virus coat forms around the nucleic acid
Virus capsids self assemble!
how are viruses released?
Viruses can get out of cells by budding through the cell membrane. This leads to the virus acquiring an envelope
Release into the environment following cell lysis
Release following cell death
what are sub viral entities?
Helper or defective viruses
e.g. bacteriophage P4 of E.coliP4 does not encode a capsid protein and relies on phage P2 to provide its capsid
e.g. adeno-associated virus (satellite virus)
AAV needs adenovirus (unrelated virus) to replicate
Hepatitis Delta virus (HDV)(satellite virus)
what is HDV?
an example of sub viral entities
Discovered 1977
Genome 1.7kb (smallest of any known animal virus)
Needs HBV infection (5% of persons with chronic HBV are infected with HDV)
Can lead to more rapid progression to cirrhosis and death
what are viroids?
they are another example of sub viral entities
Viroids are found in plants and cause disease – smallest known pathogens
eg. Apple scar skin viroid
They are small circular RNA molecules that do not have a protein coat
The special structure of viroid RNA makes it stable inside and outside cells
Viroids contain no protein-coding genes!
what are Subviral entities – Prions and Transmissible Spongiform Encephalopathies (TSEs)
Prions consist entirely of protein
No RNA or DNA but they are infectious
