Virology: Chapter 3

Question 1

where is the location of protein assembly

Answer 1

cytoplasm / nucleus
(some start in the nucleus and complete it in the cytoplasm)

Question 2

all components of virus particles must accumulate in …

Answer 2

1 location

Question 3

proteins must ….. with viral genome in order to be packaged

Answer 3

bind

Question 4

proteins have affinity for viral nucleic acids, this means…

Answer 4

they can interact with nucleic acids

Question 5

what is the trigger of assembly

Answer 5

when high concentration of viral genome + proteins accumulate exceeding a threshold
(they have high affinity)

Question 6

when does protein assembly happen

Answer 6

after genome replication

Question 7

assembly requires energy yes or no

Answer 7

yes it’s energetically favourable

Question 8

capsid is made out of subunits that spontaneously assemble, what are the 3 interactions?

Answer 8

folding into secondary / tertiary structures
hydrogen bonds
hydrophobic interactions

Question 9

what is the difference between simple and complex assembly

Answer 9

simple: only rely on capsin protein interactions and it’s affinity

complex: multi-step process that involves structural, non-structural and cellular proteins

Question 10

genome packaging in the capsid can be done both either early or later on

Answer 10

yes, true

Question 11

Helical capsid assembly

Answer 11

self-assemble around the genome (in cytoplasm)

Question 12

Icosahedral capsids

Answer 12

assemble by affinity around the genome (in cytoplasm)

Question 13

Complex capsids

Answer 13

use scaffolding proteins forming empty procapsids then genome is added after those proteins are removed (in cytoplasm)

Question 14

Assembly in the Nucleus (Nuclear Assembly), is usually for some DNA viruses, where their capsid proteins need….

Answer 14

nuclear localization signals

Question 15

for assembly in the nucleus, large icosahedral capsids need what protein

Answer 15

scaffolding protein

Question 16

Why are capsids made using subunit construction?

Answer 16

• use less genetic material since it’s a repeating unit.
  if you use 1 large protein, it might not cover the entire genome
  misfolding proteins is common so using subunits, we can avoid that
• subunits are more stable

Question 17

2 types of virus egress

Answer 17

cell lysis and budding

Question 18

cell lysis is only for…

Answer 18

naked virus / non-enveloped

Question 19

budding is only for…

Answer 19

enveloped virus

Question 20

process of cell lysis

Answer 20

cell breaks open, release virus, kills host cell, due to viruses release viroporins / lytic phospholipids to disrupt membrane

Question 21

why does budding not harm the cell?

Answer 21

because it maintains the integrity of the plasma membrane

Question 22

process of cell budding (starting with virus is fully assembled)

Answer 22

virus move towards host membrane
viral proteins trigger membrane to curve around virus particle
virus wraps itself in the curve membrane so it becomes the virus envelope
scission: membrane “pinches off” and virus released

Question 23

Why enveloped viruses bud?

Answer 23

because they need to have a membrane envelope to infect the next cell

Question 24

what is the function of the envelope

Answer 24

hide from the immune system and carries spike proteins so virus can attach to receptor

Question 25

Using eukaryotic cells as a host cell can have its limitations, one of which is the cell's DNA and RNA pol are in the nucleus, explain why is that a disadvantage towards RNA viruses that replicate in the cytoplasm

Answer 25

they can't use the DNA / RNA pol because its in the nucleus, so they bring their own enzymes, RDRP

Question 26

another disadvantage is that eukaryotic cells lack enzymes that synthesize viral mRNA from viral RNA, so what does the virus have to do

Answer 26

bring it's own enzyme

Question 27

viral mRNA don't have 5' cap or poly-3'-A tail like eukaryotic cell, why is that a limitation

Answer 27

the viral mRNA must out-compete the host mRNA for ribosomes to translate, or they must block host translation

Question 28

eukaryotic ribosomes only translate one gene per mRNA (monocistronic), why is that a limitation for virus

Answer 28

this means virus must make an mRNA for each gene OR make mRNA for all genes that can be translated into one polyprotein, then it will be cleaved into multiple proteins

Question 29

virus classification has 2 systems, which are..

Answer 29

classical system and baltimore system

Question 30

in the classical system, viruses are group into genera based on their

Answer 30

shared properties NOT diseases / properties of the cell they infect

Question 31

what are the 4 main properties of the classical system

Answer 31

1. Is Genome DNA/RNA? 2. Capsid Symmetry 3. Is there an envelope? 4. Dimension of virion + capsid

Question 32

Baltimore system is based on the genetic system of each virus, it describes the relationship between...

Answer 32

genome and the production of the virus mRNA

Question 33

what are the 3 main properties of the Baltimore system

Answer 33

1. Is Genome DNA/RNA 2. Is it (+) or (-) Sense 3. Does it use Reverse Transcriptase

Question 34

Virus maturation happens after it leaves OR is leaving the host cell, it's the...

Answer 34

cleavage of protein

Question 35

How are the virus genomes selected from all of the nucleic acid that might be present in an infected cell?

Answer 35

from specific protein---nucleic acid interactions (e.g: spliceosomes remove introns)

Question 36

Virus capsid doesn't package host cell's nucleic acid, but in SOME cases it may package...

Answer 36

tRNA that is used as a primer for RT (HIV)

Question 37

How would a mis-sense or non-sense mutation in a gene encoding a capsid protein result in the failure of a virus particles being produced during an infection?

Answer 37

mean that the virus could not assemble the components it needed for virus protein (i.e., no capsid protein or capsid proteins that don’t fit together. If the capsid cannot be assembled, the virus won’t be able to egress from the celll)

Question 38

What usually ends a productive infection cycle?

Answer 38

the release of infectious virus particle

Question 39

A new virus is able to infect a monkey cell but not a human cell when cultured in the laboratory. However, if the genome is extracted and then micro-injected into a human cell, a productive infection will occur. In other words, progeny viruses are produced. Is the human cell susceptible and/or permissive?

Answer 39

its permissive but not susceptible

Question 40

For a DNA virus that replicates in the cytoplasm of the host cell, what is the on enzyme it must have packaged in its capsid to ensure its replication in the host cell? What enzyme is also likely to be present

Answer 40

Bring it's own RNA Pol Sometimes DNA pol to speed up the process