Chapter 12

Question 1

3 different names and grouped of viruses

Answer 1

• they are grouped into families (ended in -viridiae) ex: retroviridiae
• they are given a genus name (end in -virus) ex: lentivirus
• they are given a species name (usually in english) ex: Human immunodeficiency virus

Question 2

classificatin is based on 5 characteristics

Answer 2

1. nature of the host (animal, plant, bacteria) ex: bacteriophages infect bacteria
2. type of disease caused (pneumonia, enteric, leukemia..) ex: murine leukemia virus (MLV)
3. life cycle (pathways of nucleic acid replication and transcription)
4. naked or enveloped
5. type of nucleic acid and strandedness (+ strand: same as mRNA)

Question 3

baltimore classification scheme is based on what

Answer 3

• it is base on the type of genome. It is useful because the kind of genome will dictate the replication mechanism
  RNA genome:
  1. plus configuration: same strand than mRNA (can be translated directly)
  2. minus configuration: complementary to mRNA (needs to be tramscribed into plus strand before it can be translated)

Question 4

6 steps of life cycle of viruses

Answer 4

1. adsorption: attachment of the virus to specific receptors on the surface of the cell. Plant viruses are usually introduced into the host by insect vectors, or following mechanical damage
2. penetration: virus genome enters the cell
3. uncoating: removal of the enveloppe and/or the capsid by the host enzymes, sometimes within lysosomes (in eukaryotes)
4. replication of the nucleic acid, transcription and protein synthesis
5. maturation: assembly of virus components, nucleic acid, nucleocapsid and accessory proteins to form new virions. Usually, the assembly is spontanous (occur by itself)
6. release: mature virions exit the cell host by means of budding or by causing lysis of the cell. plant viruses exit and are transmitted by means of vectors

Question 5

3 different penetration

Answer 5

• in naked viruses, the capsid may be left at the surface
• in enveloppe viruses, the enveloppe may be left at the cell surface such that only the nucleopcapsid enters in the cell
• in envelopped and naked viruses, the complete virion may enter the cell: most envelopped viruses of eukaryotes use endocytosis (viropexis). everything gets in (in a second enveloppe). such viruses are then delivered to lysosomes which degrade the capsid and the nucleic acid is release into the cytoplasm

Question 6

steps of virus replication

Answer 6

1. latent period: eclipse + maturation
   - eclipse: time necessary for the host cell to replicate the viral genome and to synthesize the viral components
   - maturation: time needed for the different components to be assembled
2. release (rise period)
   - virions are detected outside the cell
   - lysis: virus-encoded proteins damage the cytoplasmic membrane. in bacteria, virus-encoded protein destroys the peptidoglycan layer
   - budding (envelopped virus)

• burst size: number of virions released (variez according to the virus, host cell..)

Question 7

time for replication of bacterial virus and animal virus

Answer 7

bacterial: 20-60 min
animal: 8-40h

Question 8

bacteriphages: best studied infect what + most phages contain what

Answer 8

• e.coli

- most contain dsDNA genomes. Most are naked, but some possess lipid enveloppes

Question 9

2 types of bacteriophages

Answer 9

1. virulent phages: infection of host cells always leads to replication resulting in host cell lysis (lytic pathway ex: T4
2. temperate phages have 2 options:
   - lytic pathway
   - lysogenic pathway: the genome become incorporated into the bacterial host genome ex: lamba

Question 10

3 steps bacteriophages T4 (adsorption through injection)

Answer 10

1. adsorption: T4 attaches to the core region of LPS by the tail fibers
2. following attachment, the tail sheat contracts, forcing the central core through the outer membrane. Tail lysozymes digest the peptidoglycan layer, forming a small pore
3. the phage DNA is then injected into the cytoplasm of the host cell

Question 11

what happen during latent period and rise period of the replication of bacteriphages T4

Answer 11

1. nuclease, DNA polymerase, newy sigma factors
2. phage DNA
3. phage head proteins
4. tail, collar, base plate and tail fiber proteins
5. mature phage particle
   in rise period, the cell lysis, there is the T4 lysozyme production

** environ 25-30 minutes long

Question 12

4 aspects of the bacteriophage lambda (result of the infection, what is prophage and lysogen, what can do the prophage sometimes)

Answer 12

• infection by temperate results in a prolonged, latent state of infection (lysogeny). The phage is carry on the chromosome
• prophage: phase genome within the host cell chromosome
• lysogen: bacteriums that contains a prophage
• sometimes, the prophage can exit the chromosome (a process call excision) and continue along the lytic pathway, resulting in the production of new virus particles and host cell lysis

Question 13

3 characteristics of the genome of lambda

Answer 13

• phage lambda genome is linear dsDNA with cohesive ends, a region of single-stranded complementary DNA
• the cohesive ends join, forming a circular molecure of dsDNA
• the lambda genome is integrated at a specific site in the bacterial chromosome: the att(pi) site. The att region in the phage genome is homologous to the att(pi) site. The enzyme lambda integrases catalyzes integration of the phage genome at this site. the lambda integrase is encoded on the phase genome

Question 14

steps for formation of single-stranded DNA phage (5)

Answer 14

** Phage X174 is a + stramd DNA phage (same strand as mRNA). The minus strand must be synthesize first to produce a dsDNA genome, the replicative form.

1. replicatve form DNA is nicked by gene A protein
2. New + strand begin synthesis
3. continued extensions of orginial + strand with synthesis of new strand
4. one revolution complete and one progeny virus made
5. one X174 genome of + strand ssDNA

Question 15

2 steps for the viral genome

Answer 15

1. the genome is first used as a mRNA and directs the synthesis of an RNA replicase (RNA-dependent RNA polymerase, this function is not performed by the host) and other viral proteins.
2. the RNA synthesize a minus strand RNA that is used to produce additionnal mRNA and additional copies of the genome (plus strand) for the production of new virions

Question 16

animal viruses: where is the replication of viral DNA and RNA

Answer 16

• in eukaryotic cells, DNA replication is in the nucleus
• the genome of DNA viruses will usually be replicated in the nucleus of the cell
• the genome of RNA viruses will usually be replicated in the cytoplasm of the cell

Question 17

DNA genome: every steps of the replication of the viruses in the host cell

Answer 17

• examples: herpesvirus, papovavirus (human papilomavirus)
  1. penetration: fusion of the cell cytoplasmic membrane with the virus enveloppe. Nucleocapsid is transported to the nucleus where viral DNA is uncoated
  2. host transcription/translation apparatus synthesizes:
• immediate early proteins (transcription factors and in some cases, virus-specific RNA polymerase)
• delayed early proteins (viral-specific DNA polymerase, and other viral proteins necessary for replication)
• late proteins: nucleocapsid
  3. assembly occurs in the nucleus, enveloppe is added via budding process through the inner membrane of the nucleus. The complete virions are then secreted out of the cell by the ER-golgi complex.

** if ssDNA genome: first converted to a dsDNA replicative form

Question 18

3 characteristics of the plus-strand RNA (examples..)

Answer 18

ex: poliovirus, hepatitis A virus
- the genome can be translated directly
- in poliovirus, the plus-strand RNA serves as a template for synthesis of a larger polyprotein that is cleaved into proteins

Question 19

5 characteristics of poliomyelitis

Answer 19

• usually through faecal-oral route
• little to no symptoms at 99% of cases
• paralytic polio in 0,5-1% cases (usually in the legs)
• skeletal deformities post-paralytic polio
• no cure, but safe and effective vaccine

Question 20

examples of minus-strand RNA + steps

Answer 20

ex: measles, rabies (rhabdovirus), influenza (orthomixovirus)
* * the genome cant be translated directly. The RNA genome (minus-strand) is first transcried into a plus-strand RNA by an RNA-dependent RNA polymerase carried inside the virions.

1. • strand: transcription by viral RNA polymerase. Result: mRNAs (+ sense)
2. translation using host enzymes. Result: + strand RNA to - Strand RNA genome
3. assembly of - strand RNA genome, virions bud through the host cytoplasmic membrane
4. viral enveloppe proteins added as virions bud through the host cytoplasmic membrane

Question 21

1 example of dsRNA + characteristics

Answer 21

ex: rotavirus (reovirus)
- can’t be translated at is
1. plus-strand RNA must be synthesized by a viral-encoded RNA-dependent RNA polymerase using the minus strand as a template
2. the plus strand is then translate into proteins and used it as a template to synthesize a minus strand to yield dsRNA genomes

Question 22

8 steps of the retrovirus (ex: HIV, causing cancer: rous sarcoma virus)

Answer 22

1. entrance of the retrovirus containing two copies of the plus-strand ssRNA
2. uncoating
3. reverse transcription: the reverse transcriptase is and RNA-dependent RNA polymerase that reverses transcribe the RNA genome into DNA
4. the DNA genome travel to nucleus and integration into host DNA
5. transcription (viral mRNA and genomic RNA): LTR (long terminal repeats) contain promoters for transcription and participate in the integration process
6. encapsidation
7. budding
8. release

Question 23

what is provirus

Answer 23

integrated viral DNA. contrary to the lambda prophage, it can not excise from the host genome

Question 24

5 different consequences of viral infection in animal cells

Answer 24

1. transformation into tumor cells, then tumor cell division
2. death of cell (lysis) and release of the virus
3. slow release of virus without the death of the cell
4. virus present but not replicating (but may revert to lytic infection)
5. cell fusion

Question 25

2 characteristics of cell fusion

Answer 25

• envelopped virus that fuse with host cytoplasmic membrane carries viral proteins that fuse biological membranes
• cell fusion results in hybrid cells that have chromosomal aberrations, and are usually short-lived

Question 26

oncogenic/tumor-producing viruses , 2 characteristics

Answer 26

• some viral infection are implicated in the conversion of normal cell to tumor cell, a cell that has acquired immortality, characterized by uncontrolled replication. this process is called transformation
• both DNA and RNA viruses are known to cause tumor in animal and in humans. in most cases, other factors are involve. viruses are not the only cause of cancer

Question 27

4 different mechanisms for tumor-producing viruses

Answer 27

1. transduction
2. insertion of a strong promoter
3. inactivation of a tumor suppressor gene
4. expression of a viral protein that induces transformation (DNA virus)

Question 28

estimated that 15-20% of human cancers are associated with 5 viruses:

Answer 28

1. epstein-barr virus (DNA)
2. hepatitis C virus (DNA)
3. human T-lymphotrophic virus type 1 (retrovirus)
4. hepatitis B virus (RNA)
5. human papillomavirus (DNA)

Question 29

what is transduction (+ one ex)

Answer 29

ex: RNA virus
- ex: Rous sarcome virus (avian)
- the virus carries one or many oncogenes (tumor-causing genes), called v-oncogenes (for virus-encoded oncogenes). The v-oncogene was acquired from the host. This process is called transduction
- oncogenes are similar to normal genes found in eukaryotes., known as proto-oncogenes or c-oncogenes. Proto-oncogenes is usually involved in the regulation of the cell cycle or in safety mechanisms that prevent transformation
- high expression of the oncogenes affects the regulation of replication and/or cell death and cause transformation

Question 30

what is Src and how is expression worked

Answer 30

• it is an adaptor protein that orchestrates signal transduction in animal cells
• expression of v-Src is locked in ON mode. When expressed in a cell, v-Src activates numerous pathways that should not be active, resulting in transformation of the cell

Question 31

2 characteristics of the insertion of the promoter

Answer 31

• retrovirus
• the virus does not encode an oncogene
• insertion of a strong promoter of the provirus next to a proto-oncogene (c-onc). The proto-oncogene is then expressed at high levels and results in misregulation of the pathway that prevents transformation. the site of integration of the provirus is very important and transformation will occur only if a proto-oncogene is affected.

Question 32

2 characteristics of inactivation of a tumor suppressor gene

Answer 32

• retrovirus
• the virus does not encode an oncogene
• insertion of a provirus in a gene involved in the regulation of proto-oncogene expression. Insertion causes inactivation of the gene and uncontrolled expression of the proto-oncogene, resulting in transformation

Question 33

1 example and 3 characteristics of expression of a viral protein

Answer 33

ex: Human papilloma virus (HPV)
- retrovirus
- viral protein does not have a cell counterpart
- integration of the viral genome into the host genome may occur (such as in the case of adenovirus, dsDNA) or the viral genomemay persist in the cell as an extrachromosomal episome
- some DNA viruses that cause tumors do so because they have infected a nonpermissive host, in which they cannot complete their infection cycle. the cell is infected and undergoes uncontrolled replication. because the virus cannot complete is replication, the cell will never die