a2.3 (viruses)

Question 1

viruses share relatively few features, suggesting they have what?

Answer 1

multiple evolutionary origins

Question 2

viruses may vary in ____ x7

Answer 2

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

Question 3

most viruses are in what size range?

Answer 3

0.02–0.2 μm

Question 4

features common to viruses x7

Answer 4

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

Question 5

2 components to classifying viruses

Answer 5

the type of genetic material they contain: DNA or RNA

whether the genetic material is linear or circular

Question 6

positive-sense RNA vs negative-sense RNA vs

Answer 6

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

Question 7

what is the purpose of retrovirus RNA?

Answer 7

Retroviruses have RNA that is first “reverse transcribed” to make DNA. The DNA is then transcribed and translated to make virus proteins

Question 8

3 things a virus is working to do as it hijacks the cellular machinery of a cell

Answer 8

make more virus nucleic acid (DNA or RNA)

make more virus proteins

assemble new virus molecules

Question 9

virus capsids are predominantly one of two shapes (and occasionally complex architectures), what are the two common ones?

Answer 9

helical or icosahedral

Question 10

where are viral envelopes are acquired from?

Answer 10

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)

Question 11

why is cell lysis is the most common exit mode from the host cell for non-enveloped viruses? resistancy to what? x4

Answer 11

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

Question 12

most viruses that infect bacteria and plants are _______

Answer 12

non-enveloped

Question 13

enveloped viruses tend to be more sensitive to what? x4

Answer 13

extreme pH, heat, dryness, and simple disinfectants

Question 14

LOOK OVER EXAMPLES (SLIDES 20-23)

Question 15

what are the obligate intracellular viruses that specifically infect bacteria?

Answer 15

bacteriophage (phage)

Question 16

lambda is a phage that infects E. coli bacteria.

lambda can alternate between two approaches of infection: what are they? state and explain

Answer 16

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

Question 17

is the lytic cycle specific to bacteriophages?

Answer 17

no, many viruses use it

Question 18

step 1 to the lytic/lysogenic cycle: phage attachment to host cell

x3 points to know

Answer 18

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.

Question 19

step 2 to the lytic/lysogenic cycle: phage RNA/DNA entry into host cell

x1 point to know

Answer 19

injection of the phage’s genetic material into the host cell is coordinated by the phage tail.

Question 20

phage tail structure

Answer 20

phage tails vary widely through nature, but many have a tube for delivering genetic material surrounded by a sheath of contractile proteins

Question 21

step 3 to the lytic cycle: phage RNA/DNA replication

x3 points to know

Answer 21

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.

Question 22

step 4 to the lytic cycle: phage protein synthesis

x2 points to know

Answer 22

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

Question 23

step 5 to the lytic cycle: assembly of new phage viruses

x3 points to know

Answer 23

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.

Question 24

step 6 to the lytic cycle: lysis

x2 points to know (one is avg # of phage progeny that are released)

Answer 24

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

Question 25

step 7 to the lytic cycle: spread

x1 point to know

Answer 25

the new virus particles are now able to infect other cells.

Question 26

when actively infecting and damaging host cells, viruses are said to be what?

Answer 26

“virulent”

Question 27

steps in the lysogenic cycle x5

Answer 27

phage attachment to host cell

phage DNA entry into host cell

phage DNA is integrated into host genome

DNA replication

cell division

Question 28

step 3 to the lysogenic cycle: phage DNA integration

x3 points to know

Answer 28

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.

Question 29

step 4 to the lysogenic cycle: DNA replication

x2 points to know

Answer 29

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.

Question 30

step 5 to the lysogenic cycle: cell division

x1 point to know

Answer 30

the host cell divides, creating two daughter cells which each contain the prophage

Question 31

when the virus is a prophage, it is “temperate”, what does this mean?

Answer 31

meaning it is in a dormant state. it does not kill its host and does not actively infect other cells.

Question 32

how is the lytic cycle entered from the lysogenic cycle? what is this process called?

Answer 32

If a bacterium containing prophage is exposed to stressors, such as UV light, low nutrient conditions, or chemicals

this process is called induction

Question 33

1 hypothesis on the origin of viruses that is NOT supported by current evidence

Answer 33

the virus-first hypothesis states that viruses predate or coevolved with their current cellular hosts.

Question 34

2 hypotheses on the origin of viruses that IS supported by current evidence

Answer 34

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.

Question 35

components of the virus-first hypothesis x2

Answer 35

could self-replicate

existed in a pre-cellular world

Question 36

2 pieces of evidence either for/against the virus-first hypothesis

Answer 36

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

Question 37

Nasir and Caetano-Anolles (2015)’s evolutionary family trees shows what about virus proteins? what conclusion can be drawn?

Answer 37

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.

Question 38

according to Nasir and Caetano-Anolles, when did viruses evolve?

Answer 38

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)

Question 39

broad to specific is called

Answer 39

deduction

Question 40

specific to broad is called

Answer 40

induction

Question 41

example evidence for 2 hypotheses on the origin of viruses that IS supported by current evidence

Answer 41

progressive hypothesis: retroviruses
regressive hypothesis: mimivirus (other large viruses)

Question 42

what happens in convergent evolution?

Answer 42

different lineages evolve similar features because of selection for function rather than inheritance from a common ancestor

Question 43

define generation time

Answer 43

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

Question 44

why do viruses evolve so quickly? x5

Answer 44

very short generation time

each viron produces many offspring viruses

high rates of mutations

large population sizes

easy adaptation to host environment

Question 45

what is the eclipse period? how long does it last (range)?

Answer 45

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

Question 46

define viron

Answer 46

a single virus particle

Question 47

the burst size is defined as what?

Answer 47

the expected number of virions produced by one infected cell over its life-time

Question 48

why does high rate of mutations in viruses increase evolution?

Answer 48

with each new mutation, there is a new variation upon which natural selection can act

Question 49

ideal conditions for more mutations in viruses x2

Answer 49

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)

Question 50

define mutation rate

Answer 50

the average number of mutations per nucleotide in the genome per replication cycle (mutation/nucleotide/cycle)

Question 51

examples of mutations that benefit viruses

Answer 51

may enable the viron to bind to a new type of host cell

evade immune defense

escape recognition by immune cells

Question 52

define antigenic drift

Answer 52

a process consisting of small mutations that can lead to changes in the surface proteins of the virus

Question 53

define antigenic shift

Answer 53

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

Question 54

when an antigenic shift occurs, most people have _____________________

Answer 54

little or no immunity against the new virus