Lec 7: Assembly & Exit

Question 1

Nucleocapsid assembly: (4)

Answer 1

1. ) Helical viruses
2. ) Icosahedral viruses
3. ) Genome packaging
4. ) Assembly mechanisms

Question 2

Helical viruses:

Answer 2

A few copies of a protein species bind to a helical ssRNA molecule, then more copies bind until the RNA is completely coated.

Question 3

Icosahedral viruses:

Answer 3

• Procapsid (prohead) — empty protein shell (with hole)
• Filled with a copy of genome (through hole)
• Modification to form mature capsid (close hole by the use of protein conformational change)
  - Needs chaperones from host cell

Question 4

procapsid =

Answer 4

Empty shell w/ hole

Question 5

capsid =

Answer 5

Filled shell w/ no hole

Question 6

How does the virus tell which DNA or RNA to fill procapsid?

Answer 6

• Signal sequences on genome is recognized by procapsid hole proteins

Question 7

(Genome Packaging)
How are virus genomes selected from all the cell and virus nucleic acids? (3)
- \_\_\_\_\_ \_\_\_\_ =
- The intermediate molecules...
- Some host nucleic acids are still...

Answer 7

• Packaging signal = a specific sequence of viral genome recognized by virial proteins.
• The intermediate molecules (template DNAs and RNAs) are not packed, the signals are masked by proteins.
• Some host nucleic acids are still packed into virions, in terms of retreoviruses, some host tRNAs are important

Question 8

Assembly mechanisms: (2)

Answer 8

1. ) Simple viruses (ex: TMV) = can assemble by themselves in test tubes under the right condition (ex: pH, ions, etc.)
2. ) Complex viruses (ex: herpes viruses and tailed phage) = need the environment of host cells — (directed assembly)

Question 9

In vitro = outside of cells

In vivo = inside of cells

Answer 9

= outside of cells

= inside of cells

Question 10

(Differences???)
Simple viruses:
Complex viruses:

Answer 10

can assemble spontaneously

needs host cells to assemble

Question 11

Formation of virion membranes: (2)

Answer 11

1. ) Budding through cell membranes

2. ) De novo synthesis of viral membranes

Question 12

Host cells display…

- exit is…

Answer 12

…surface proteins

- …STILL part of assembly step

Question 13

(De novo viral membrane synthesis)
Minority of viruses can…
- Some cases: the membrane forms…
- Other cases: the membrane forms…

Answer 13

…direct the synthesis of lipid membrane late in the replication cycle.

• …virion envelope
• …layer below the surface of the capsid

Question 14

(Virion Exit from the infected cell)
Many viruses initiate:
- Many phages produce…
- Other phages synthesize…

Answer 14

cell burst (lysis)

• …enzymes (lysins, such as lysozymes) that break bonds in the peptidoglycan of the host bacterial cell walls
• …proteins that inhibit host enzymes with roles in cell wall synthesis (leads to weakening of the cell wall and ultimately to lysis)

Question 15

Average yields of infectious virions per cell…

Answer 15

vary considerably

Question 16

Many viruses do not…

Answer 16

lyse their host cells; instead, progeny virions are released from the cells over a period of time.

Question 17

(+) ssRNA genome viruses has…

Retroviruses have…

Answer 17

…less steps

…more steps

Question 18

Outcomes of infection for the host: (2)

Answer 18

1. ) Productive
2. ) Non productive
   - Become latent = virus genome stays with the cells perhaps for the lifetime, and even in the daughter cells.
   - Infection is abortive = neither productive or latent, due to virus genome mutations.

Question 19

Productive infection =

Answer 19

= release of infective progeny virions from an infected cell.

Question 20

Non productive infection can become

Answer 20

latent or abortive

Question 21

latent (non productive) infection =

Answer 21

virus genome stays with the cells perhaps for the lifetime, and even in the daughter cells.

Question 22

abortive (non productive) infection =

Answer 22

= neither productive or latent, due to virus genome mutations.

Question 23

Factors affecting outcomes of infection: (4)

Answer 23

1. ) Innate immunity in vertebrates
2. ) Adaptive immunity in vertebrates
3. ) RNA silencing
4. ) Programmed cell death

Question 24

Interferons =
& function =
& are part of…

Answer 24

= proteins synthesized and secreted by cells in response to virus infection.

= to protect adjacent cells from infection and to activate T cell-mediated immunity

…part of innate immunity

Question 25

A potent trigger for interferon production is

Answer 25

dsRNA (produced by dsRNA viruses & ssRNA viruses as they replicate)

Question 26

After secretion, the interferon molecules...

Answer 26

...diffuse to nearby cells, where they can trigger various anti-viral activities by binding to interferon receptors.

Question 27

- Interferons released from virus-infected cells bind to... | - If the cells become infected,

Answer 27

- interferon receptors on other cells | - either block virus replication or kill the infected cells

Question 28

Anti-viral activities triggered by α- and β-interferons include: (3)

Answer 28

1. ) Activation of genes that encode antiviral proteins 2. ) Activation of NK cells (Innate/natural immunity) 3. ) Induction of apoptosis

Question 29

Natural killer aka

Answer 29

"(NK) cells"

Question 30

NK cells are present where

Answer 30

throughout the body, but mainly in the blood.

Question 31

NK cells function (2)

Answer 31

They recognize changes in the surface molecules of virus-infected cells as a result of infection, then bind to them and kill them. They also release γ-interferon, which activates macrophage

Question 32

Adaptive immunity (2)

Answer 32

antibodies | T cells

Question 33

Antibodies are

Answer 33

antigen-specific antibodies synthesized by plasma cells, which develop from a B cell after it has been stimulated by the antigen.

Question 34

B cell --> Plasma cell process requires

Answer 34

gene reorganization

Question 35

``` (Consequences of antibody binding) The antibody can coat... - Allowing... - Activate... - Neutralize... ```

Answer 35

...can coat both virions and virus-infected cells, and this may lead to their destruction by a variety of mechanisms. - Allowing certain type of cells in immune system to attach to antibody-coated virions and cells to phagocytose them or kill them. - Activate complement proteins, inactivate viruses. - Neutralize virus infectivity.

Question 36

What are produced several days after antigenic stimulation?

Answer 36

effector T cells

Question 37

2 types of T cells & function:

Answer 37

1. ) Helper T cells: trigger immune responses, e.g. trigger the production of B cells and cytotoxic T cells. 2. ) Cytotoxic T cells: kill virus-infected cells.

Question 38

B cells -->

Answer 38

plasma cells --> antibodies

Question 39

T cells --> (2)

Answer 39

--> helper T cells --> T cells or B cells or --> cytotoxic T cells

Question 40

Plasma cells, helper T cells, and cytotoxic T cells can

Answer 40

remain in reserve | - next infection = quick immune response

Question 41

Some B cells and T cells can survive as

Answer 41

memory cells long after the first or subsequent encounters with the viruses.

Question 42

Memory cells =

Answer 42

returned to a resting state, (can be reactivated if they encounter the same antigen again)

Question 43

- The outcome of infection of a vertebrate animal with a virus may depend on... - If immunological memory is present, then...

Answer 43

- whether or not the host has immunological memory of the virus antigens. - signs and symptoms of disease are likely to be less severe, or totally absent.

Question 44

RISC function:

Answer 44

(part of RNA silencing) cleaves target mRNA - Completely stops RNA synthesis (self-defense mechanism) - Our DNA is safe from this mechanism

Question 45

RISC only works if

Answer 45

VIRUS HAS dsRNA @ ANY POINT

Question 46

Once a lymphocyte has recognized a foreign antigen, it...

Answer 46

expands to eliminate the infection

Question 47

(Latent infections) | 2 Occurrences:

Answer 47

1. ) Virus DNA is integrated into a cell chromosome. After infection of the cell the virus genome is integrated into the genome of the host cell (ex: retroviruses) 2. ) Virus DNA present as multiple copies of circular molecules.

Question 48

(Latent infections) | Temperate phage can be

Answer 48

both lytic and lysogenic (latent) infection

Question 49

Latent phage genome aka

Answer 49

"prophage"

Question 50

Latent phage genome (prophage) can be

Answer 50

either integrated into bacteria genome or non-integrated circular DNA

Question 51

Some virulent factors of bacteria are coded by

Answer 51

the temperate phage, | e.g. Shiga toxin

Question 52

(Latent infections) | When to enter productive stage? (4)

Answer 52

1. ) A eukaryotic host cell moves into another phase of the cell cycle. 2. ) The host cell is irradiated with ultra-violet light. 3. ) A host organism becomes immunocompromised. 4. ) The host cell becomes infected with a second virus that provides a function that the first virus lacks. satellite virus and helper virus, respectively.

Question 53

Satellite virus =

Answer 53

A defective virus that depends on a helper virus to provide one or more functions.

Question 54

Helper virus =

Answer 54

A virus that can provide function(s) missing from a defective virus, thereby enabling the satellite virus to complete its replication cycle.

Question 55

The satellite viruses are like

Answer 55

"parasites of the helper virus. "

Question 56

Co-infection with a satellite virus can

Answer 56

increase the severity of the infection than just a helper virus alone.

Question 57

Reasons for Abortive infections: (3)

Answer 57

- concerning the cell, - the environmental conditions - and/or the virus.

Question 58

A virus may initiate... | ...and...

Answer 58

productive infections in some cell types (permissive cells)… | ...and abortive infections in other cell types (non-permissive cells)

Question 59

Productive infections = | & can cause...

Answer 59

Spread of infections within multicellular hosts | ...& can cause disease

Question 60

Virus infections result in: (3)

Answer 60

No disease Disease Death