a2.3 (viruses) Flashcards
viruses share relatively few features, suggesting they have what?
multiple evolutionary origins
viruses may vary in ____ x7
range of size
range of shape
DNA or RNA as the genetic material
genome presentation (single or double stranded, circular or linear, range of size)
which genes are present
proteins in and shape of the capsid
presence of a lipid envelope
most viruses are in what size range?
0.02–0.2 μm
features common to viruses x7
all are intracellular parasites
all are small
all are fixed in size, no growth or development
all use nucleic acid as the genetic material
all have a capsid/outer coating made of protein
none have cytoplasm
all have no (or very few) enzymes
2 components to classifying viruses
the type of genetic material they contain: DNA or RNA
whether the genetic material is linear or circular
positive-sense RNA vs negative-sense RNA vs
positive-sense RNA viruses have viral mRNA, which can be directly translated into virus proteins
negative-sense RNA viruses have RNA that must first be transcribed before being translated into virus proteins
what is the purpose of retrovirus RNA?
Retroviruses have RNA that is first “reverse transcribed” to make DNA. The DNA is then transcribed and translated to make virus proteins
3 things a virus is working to do as it hijacks the cellular machinery of a cell
make more virus nucleic acid (DNA or RNA)
make more virus proteins
assemble new virus molecules
virus capsids are predominantly one of two shapes (and occasionally complex architectures), what are the two common ones?
helical or icosahedral
where are viral envelopes are acquired from?
host cell membranes during the maturation of the virus by the process known as “budding.” (is enveloped as the virus leaves the inside of the host cell)
why is cell lysis is the most common exit mode from the host cell for non-enveloped viruses? resistancy to what? x4
during lysis, the cell membrane is ruptured, causing cell death and significant tissue damage to the host organism. non-enveloped viruses are more resistant to the following:
extreme pH
heat
dryness
simple disinfectants
most viruses that infect bacteria and plants are _______
non-enveloped
enveloped viruses tend to be more sensitive to what? x4
extreme pH, heat, dryness, and simple disinfectants
LOOK OVER EXAMPLES (SLIDES 20-23)
what are the obligate intracellular viruses that specifically infect bacteria?
bacteriophage (phage)
lambda is a phage that infects E. coli bacteria.
lambda can alternate between two approaches of infection: what are they? state and explain
lysogenic cycle - the virus assimilates its genome within the host cell’s genome to achieve replication without killing the host
lytic cycle - the virus reproduces and bursts out of the host cell, kill it
is the lytic cycle specific to bacteriophages?
no, many viruses use it
step 1 to the lytic/lysogenic cycle: phage attachment to host cell
x3 points to know
the phage must first attach itself to a receptor protein within the bacterial cell membrane.
initial contact between phage and bacterium often happens through random collisions.
not all bacteria-phage combinations have compatible receptors, so this is a selective process.
step 2 to the lytic/lysogenic cycle: phage RNA/DNA entry into host cell
x1 point to know
injection of the phage’s genetic material into the host cell is coordinated by the phage tail.
phage tail structure
phage tails vary widely through nature, but many have a tube for delivering genetic material surrounded by a sheath of contractile proteins
step 3 to the lytic cycle: phage RNA/DNA replication
x3 points to know
within the bacteria, the ends of the linear phage DNA join to form a circle
then, exact copies of the phage DNA are produced using rolling-circle replication, in which one strand is nicked and replication enzymes are used to extend the free 3’ end
as a complementary strand (A1.2.8) is synthesized around the circular DNA, the 5’ end is peeled off, leading to a displaced strand that continues to grow in length.
step 4 to the lytic cycle: phage protein synthesis
x2 points to know
the host cell’s RNA polymerase is used to transcribe phage DNA into phage RNA
the host cell’s ribosomes are used used to translate phage RNA into phage proteins
step 5 to the lytic cycle: assembly of new phage viruses
x3 points to know
capsid proteins assemble to form empty heads into which condensed phage DNA is packed.
the tail parts assemble independently of the head structure
the last step in synthesis is joining the filled heads to the tails to form progeny phage.
step 6 to the lytic cycle: lysis
x2 points to know (one is avg # of phage progeny that are released)
enzymes produced by the phage gradually weaken the bacterial cell wall and are then released
on average 100-200 phage progeny are released into the surrounding environment
step 7 to the lytic cycle: spread
x1 point to know
the new virus particles are now able to infect other cells.
when actively infecting and damaging host cells, viruses are said to be what?
“virulent”
steps in the lysogenic cycle x5
phage attachment to host cell
phage DNA entry into host cell
phage DNA is integrated into host genome
DNA replication
cell division
step 3 to the lysogenic cycle: phage DNA integration
x3 points to know
within the bacteria, the ends of the linear phage DNA join to form a circle.
the phage DNA is inserted at a specific position into the bacterial DNA. viral enzyme integrase catalyzes the integration of the DNA into the host cell DNA
after integration, the virus only exists as a length of DNA within a bacterial genome. in this stage, the virus is called a prophage.
step 4 to the lysogenic cycle: DNA replication
x2 points to know
the prophage genome is then replicated passively along with the host genome during DNA replication
as the phage genome is generally comparatively small, the bacterial hosts are normally relatively unharmed by this process.
step 5 to the lysogenic cycle: cell division
x1 point to know
the host cell divides, creating two daughter cells which each contain the prophage
when the virus is a prophage, it is “temperate”, what does this mean?
meaning it is in a dormant state. it does not kill its host and does not actively infect other cells.
how is the lytic cycle entered from the lysogenic cycle? what is this process called?
If a bacterium containing prophage is exposed to stressors, such as UV light, low nutrient conditions, or chemicals
this process is called induction
1 hypothesis on the origin of viruses that is NOT supported by current evidence
the virus-first hypothesis states that viruses predate or coevolved with their current cellular hosts.
2 hypotheses on the origin of viruses that IS supported by current evidence
the progressive hypothesis states that states that viruses arose by taking and modifying cell components. (“escape hypothesis”)
the regressive hypothesis asserts that viruses arose by loss of cellular components.
components of the virus-first hypothesis x2
could self-replicate
existed in a pre-cellular world
2 pieces of evidence either for/against the virus-first hypothesis
all viruses are intracellular parasites, requiring a cell to replicate. because the virus-first hypothesis proposes that virus could replicate without a cell, it is disregarded by many scientists.
viruses use the same genetic code as all cells. the virus-first hypothesis would require that a single ancestral virus used this code and then evolved to become the first cell or that there was independent evolution of cells using the same genetic code. there is no evidence for either scenario
Nasir and Caetano-Anolles (2015)’s evolutionary family trees shows what about virus proteins? what conclusion can be drawn?
they found that 442 protein folds were shared between cells and viruses, and only 66 folds were unique to viruses.
if viruses had existed prior to the first cells, one would expect viruses to have more unique protein folds and share fewer with cells.
according to Nasir and Caetano-Anolles, when did viruses evolve?
the analysis of proteins suggests that viruses and cells share a common ancestor – a fully functioning, self-replicating cell that lived around 3.4 billion years ago, shortly after life first emerged on the planet
(in between origin of cells and LUCA)
broad to specific is called
deduction
specific to broad is called
induction
example evidence for 2 hypotheses on the origin of viruses that IS supported by current evidence
progressive hypothesis: retroviruses
regressive hypothesis: mimivirus (other large viruses)
what happens in convergent evolution?
different lineages evolve similar features because of selection for function rather than inheritance from a common ancestor
define generation time
the average time between two consecutive generations in the lineages of a population.
in human populations, generation time typically ranges from 20 to 30 years
why do viruses evolve so quickly? x5
very short generation time
each viron produces many offspring viruses
high rates of mutations
large population sizes
easy adaptation to host environment
what is the eclipse period? how long does it last (range)?
the time period between the entry of the virus genetic material into the host and the the appearance of new mature virus in the host cell. (it is essentially the generation time of a virus)
ranges from 8 to 72 hours
define viron
a single virus particle
the burst size is defined as what?
the expected number of virions produced by one infected cell over its life-time
why does high rate of mutations in viruses increase evolution?
with each new mutation, there is a new variation upon which natural selection can act
ideal conditions for more mutations in viruses x2
viruses with smaller genomes mutating faster than viruses with larger genomes
RNA viruses having a higher mutation rate than DNA viruses (this is because RNA polymerases all lack the proofreading capabilities present in DNA polymerases)
define mutation rate
the average number of mutations per nucleotide in the genome per replication cycle (mutation/nucleotide/cycle)
examples of mutations that benefit viruses
may enable the viron to bind to a new type of host cell
evade immune defense
escape recognition by immune cells
define antigenic drift
a process consisting of small mutations that can lead to changes in the surface proteins of the virus
define antigenic shift
is an abrupt, major change in a flu virus. shift can happen if a flu virus from an animal population gains the ability to infect humans
when an antigenic shift occurs, most people have _____________________
little or no immunity against the new virus
