VIROLOGY 2 - VIRUS STRUCTURE, GENOMES AND CLASSIFICATION

Question 1

what are structures present on a virus?

Answer 1

capsid: protein coat surrounding nucleic acid, composed of protein subunits called capsomeres
nucleocapsid: nucleic acid+capsid
envelope: combination of lipids and proteins (host derived), may possess viral glycoproteins (spikes) that recognise receptors and bing to hosts
most bacterial are plant viruses are naked, and most animal viruses are enveloped

Question 2

what are the functions of the capsid?

Answer 2

protection of the genome:
packaging of the nucleic acid genome
delivery of the genome (non-eneveloped viruses):
capsid binds host cell receptors, and the genome is delivered by two methods:
1. direct penetration, genome alone enters the cell
2. endocytosis: the host cell endocytosis the entire virus, then the capsid is uncoated and the genome is released

Question 3

what are some general morphologies of capsids?

Answer 3

helical viruses: hollow, cylindrical capsid
icosahedral viruses: many sided
complex viruses: complicated structures

Question 4

characteristics of helical capsid viruses?

Answer 4

• spiral or rod shaped
• length determined by the length of the nucleic acid
• width determined by the size and packaging of capsomeres
• helical capsids can only package ssRNA because of the rigidity of double stranded nucleic acids
• example: tobacco mosaic virus or ebola

Question 5

characteristics of icosahedral capsid viruses?

Answer 5

• spherical and rigid
• possess a closed shell enclosing the nucleic acid inside
• used to package ssRNA, dsRNA or DNA
• identical triangular faces, edges, vertices, 5,3 or 2 identical segments
• proteins of the icosahedral capsid can be assembled as pentamers and/or hexamers
• most efficient arrangement of subunits requires fewest capsomeres
• most animal viruses have this icosahedral capsid
• example: adenovirus, poliovirus,HPV

Question 6

characteristics of complex viruses?

Answer 6

• capsid symmetry is neither icosahedral or helical
• particularly bacterial viruses, bacteriophages
  capsid is polyhedral and then the tail sheath is helical
• poxvirus: overall shape is like a brick
  doesn’t contain clearly identifiable capsids but there are several coats around the nucleic acid

Question 7

what are enveloped virions and some characteritics?

Answer 7

• acquired from host cell during viral replication or release (budding)
• envelope proteins and glycoproteins play role in host recognition
• envelope gives protection to virus from the immune system

Question 8

why are enveloped viruses more fragile than naked viruses?

Answer 8

lipid bilayer of the envelope is sensitive to changes in the environment (pH, temperature)
easily disrupted by physical and chemical agents and can dry out easily

Question 9

how is the genome delivered from enveloped virions?

Answer 9

1. attachment of the virus to the host via receptors
2. endocytosis: engulfing of cirus by host cell
   or 2. membrane fusion: viral envelope and host membrane fuses, capsid into cell cytoplasm is released
3. uncoating of the capsid to release the genome

Question 10

what is the relationship between structure of genome and whether virus is enveloped?

Answer 10

there is no correlation between the two

Question 11

why are virions metastable?

Answer 11

why they are stable: must protect genome
why unstable: must come apart quickly upon infection, undergo structural changes to release viral genome into infected cell

Question 12

how is metastability achieved?

Answer 12

stable structure: symmetrical arrangement of many identical proteins to have maximal contact
unstable: not permanently boned, can be taken apart and loosened

Question 13

what are the two classic experiments that provided breakthroughs in virology?

Answer 13

hershey chase experiment with phage T2:
DNA virus infects bacteria
fraenkel conrat and singer with TMV:
RNA virus that infects tobacco leaves

Question 14

what was the hershey chase experiment and their findings?

Answer 14

• showed proof that DNA is the genetic material of bacteriophage T2
• virus grown in radioactive 35S had radiolabelled proteins (S is in proteins but not in DNA)
• virus grown in radioactive 32P had radiolabelled DNA (P is in DNA but not in proteins)
• phage labelled with 35S –> no radioactivity entered the bacteria cell –> protein is not inherited
• phage labelled with 32P –> radioactivity enters cell –> DNA is inherited

Question 15

what was the Fraenkel-Conrat-Singer experiment?

Answer 15

• proof that RNA is the genetic material of TMV
• based on the creation of hybrid viruses
• RNA from TMV A + protein from TMV B –> TMV A
• RNA protein TMV B + protein from TMV A –> TMV B

Question 16

what is the composition of viral genomes?

Answer 16

viruses are called DNA or RNA viruses based on the genomes
- dsDNA or ssDNA
- dsRNA or ssRNA
ss viral genome can be (+) sense or (-) sense

Question 17

what are the shapes of viral genomes?

Answer 17

• linear
• circular
• segmented

Question 18

what are the coding capacities of viral genomes?

Answer 18

• usually contain only a few genes, 4 to hundreds

Question 19

what is (+) and (-) sense RNA and DNA?

Answer 19

mRNA (ribosome ready) is always the (+) sense strand
RNA and DNA complements of the (+) strand are the (-) strands
(-) RNA cannot be translated
not all (+) RNA is mRNA, as not all are translated

Question 20

characteristic of eukaryotic DNA viruses?

Answer 20

mostly dsDNA genomes, different structure than host cell chromosome
DNA replication takes place in nucleus (except poxviruses that do it in the cytoplasm)

Question 21

characteristic of eukaryotic RNA viruses?

Answer 21

mostly ssRNA genomes
RNA replication takes place in the cytoplasm with some exceptions like retroviruses that need an intra nuclear step

Question 22

how do RNA viruses challenge the central dogma of biology?

Answer 22

central dogma:
DNA rep. by DNA polymerase
DNA transcr. by RNA polymerase
RNA transl. by ribosomes

RNA viruses encode or carry enzymes that can make RNA into DNA using RT
make RNA from RNA template using RNA dependent RNA polymerase (RdRP)
all RNA viruses except retroviruses required RdRP for replication

Question 23

what do DNA and RNA polymerases do?

Answer 23

DNA pol:
make DNA with
DNA template: DNA dependent DNA pol.
RNA template: RNA dependent DNA pol. (example reverse transcriptase)
RNA pol:
make RNA with
DNA template: DNA dependent RNA pol.
RNA template: RNA dependent RNA pol.
polymerases make complementary strands

Question 24

how do RNA viruses replicate their genomes?

Answer 24

all RNA viruses (except retroviruses) require RdRP to replicate their genomes and make viral mRNA
RNA virus genomes encode RdRP since mammalian hosts do not have it
RdRP= RNA transcriptase= RNA replicase

Question 25

which attributes are used to classify viruses?

Answer 25

• nature of nucleic acid in the virion
• symmetry of protein shell
• presence or absence of envelope
• host range

Question 26

what is ICTV classification?

Answer 26

international committee on taxonomy of viruses
based on classical hierarchical system:
order names ends in virales
family names end in viridae
genus names end in virus
species:
descriptive common names are used, subspecies are designated by number or letter

Question 27

what is baltimore’s system of virus classification?

Answer 27

viruses of same genome class show greater evidence of share ancestry w/ each other than viruses of different genome class
devised by baltimore to classify animal viruses
based on 3 criteria:
1. nucleic acid composition of viral genome
2. the way that it is replicated
3. the way the virus makes mRNA for expression of viral proteins
all cells and viruses need to make mRNA