Retrovirus

Question 1

What are retroviruses

Answer 1

viruses that go from rna-dna-rna?

Question 2

are retrovirus +or- amd are they ss or diploid

Answer 2

+ and diploid

Question 3

which call are retrovirus in ba;timore

Answer 3

6

Question 4

what ais the hallmark of retrpviruses

Answer 4

is their replicative strategy, which includes reverse transcription of the viral RNA into linear dsDNA, which is the
reverse of the usual flow of genetic information

Question 5

true or false: groups 1-5 in retrovirus are non oncogenic

Answer 5

false they are

Question 6

what os the organization of the retroviral genome

Answer 6

-gag: directs the synthesis of structural proteins such as matrix, capsid and nucleoprotein
-pol: contains the information for the viral enzymes such as the RT and the integrases
-env: derived the surface transmembrane components such as the viral envelope glycoproteins

Question 7

what are the 2 main categories of retroviruses

Answer 7

-simple and complex

Question 8

what is in simple retrovirus

Answer 8

gag
pol
env

Question 9

what is in complex retrovirus

Answer 9

gag
pol
env
auxilary and regulatory proteins

Question 10

does hiv have glycoproteins

Answer 10

yeah

Question 11

retrovira; virion struicture

Answer 11

-Matrix (MA/p17) lines the inner surface of the viral envelope linking it to the viral core. MA also plays
important roles in transport and binding of Gag to the plasma membrane during virion assembly
-= Capsid (CA/p24) monomers dimerize to form the capsid core, which surrounds the viral genome in the
mature virus
-= Nucleocapsid (NC/p7) monomers are structurally associated to the two copies of retroviral ssRNA, and
package them tightly into the viral core

Question 12

what is the ma,e opf the p that makes up the hiv capsid

Answer 12

p24

Question 13

retroviral virion structure: virally encoded enzymes

Answer 13

-reverse transcriptase (RT) is a RNA-
dependent DNA polymerase.
= integrase (IN) is an enzyme that enables viral genomic
material to be integrated within the DNA of the cell.
- some retroviruses express proteases which are enzymes that cleave proteins. Although many
eukaryotes express their own proteases, viruses tend to encode their own which are specific to a restricted
set of substrates, e.g. HIV protease cleaves Gag into the components MA, CA, and NC in the mature virion

Question 14

true or false: hiv is kinda like transposons

Answer 14

true

Question 15

true or false: HIV only infects humans

Answer 15

false it infects monkeys and cats

Question 16

HIV Env codes for two glycoproteins

Answer 16

gp120 (extracellular surface)
gp41 (trans-membrane)
-The make-up of envelope glycoproteins depend on the retrovirus; it determines the tissue
and cell tropism of the virus, as this is what binds to cell-surface receptors.

Question 17

Detailed Steps of the Retrovirus Replication Cycle

Answer 17

1. Retroviruses enter the host cell through the attachment of their surface glycoproteins to specific plasma membrane receptors.
2. This leads to the fusion of virus and cell membranes and expulsion of the viral core into the cytoplasm.
3. In the cytoplasm, the viral RNA (still within the viral core) is transcribed into DNA by the enzyme reverse transcriptase.
4. The virus-derived dsDNA is translocated to the nucleus, where it is integrated into the host chromosomal DNA with the aid of
   the viral enzyme integrase, to form a stable provirus (i.e integrated HIV dsDNA).
5. Transcription of the provirus results in spliced and unspliced mRNAs (producing various viral products), as well as full-length
   progeny viral (v)RNA genomes (to be encapsidated in the mature virion).
6. The viral mRNAs are translated by cellular ribosomes.
7. The translation products together with the the full-length vRNA traffic to the plasma membrane and assemble into a viral
   particle (simplified version).
8. The viral particle buds from the plasma membrane, acquiring an envelope derived from the cellular plasma membrane.
9. Virus maturation is achieved during and following budding by proteolytic cleavage of the viral Gag and Gag/Pol polyproteins into its respective constituents.

Question 18

how can retrovirus cause cancer

Answer 18

1 –
Viral genes encodes proteins that drive the cell into continuous, uncontrolled proliferation (“foot on the accelerator” model) e.g., src and RSV
2 –
Viral genome can integrate adjacent to cellular proto-oncogenes, and the viral LTR can stimulate aberrant expression of the oncogene (“insertional mutagenesis”), e.g., lymphoid leukemia
and MMTV
3 –
Viral gene encodes a protein that binds and transactivates host cellular genes to
dysregulate the cell cycle and genomic
integrity, e.g., Tax and HTLV-1

Question 19

what was the first oncogene discovered

Answer 19

src gene in rsv

Question 20

Retrovirus and insertional mutagenesis

Answer 20

Some retroviruses like the mouse mammary tumor virus (MMTV) produce tumors by
inserting their genomes into the critical sites near or within a proto-oncogene, which
is then converted into an active oncogene by active transcription of the provirus .

Question 21

what does HTLV 1 cause

Answer 21

an aggressive form of leukemia calles adult T cell leukemia

Question 22

what does the gene TAX of HTL1 do?

Answer 22

-The gene Tax of HTLV-1 is responsible
for activating transcription of viral
HTLV-1 proteins from the integrated
provirus.
-However, it also has the capacity to
regulate human genes, generally
those involved in cell cycle regulation
and the maintenance of genomic
integrity.
-Tax is what contributes to the onset
of ATL in HTLV-1-infected individuals

Question 23

Endogenous retroviruses

Answer 23

-Endogenous retroviruses (ERVs) are genetic elements found ubiquitously in eukaryotic DNA, including humans (HERVs).
-They have the ability to amplify themselves to an RNA intermediate (1) and with the help of intrinsically-encoded RT and integrase enzymes,
copy-paste themselves elsewhere in the
genome, in a random fashion (2)

Question 24

Retroviruses in the biotech industry

Answer 24

-RT is used to make cDNA from an RNA
template for reverse transcription-PCR
-Lentiviruses used as vectors for targeted gene therapy ex vivo
-lentivirus to send the protein acs9

Question 25

what is in gag proteins

Answer 25

Ma(p17): membrane associated or matric
-CA: capsid
-NC: nucleocapsid
-p6 and 2 spacer peptides
between each genes there is a site for the viral protease so cut

Question 26

assembly of retroviruses

Answer 26

matrix:
-in virions, MA forms a membrane bound layer
-the N terminal mysisyl group is required for membrane binding
-the MA domain of GAG targets the protein to the membrane

Capsid: role in particle assembly
-ca forms the conical core

Question 27

Nucleocapsid of HIV

Answer 27

-highly basic n terminus and zinc fingers bind hiv rna
-binding of gag to hiv rna may promote gag-gag interactions
-nc unwinds the trna primer and also helps to place it onto the PBS
-nc facilitates processing DNA synthesis
-nc also interracts with vpr, which is involved in the pre-initiation complex

Question 28

why do we have a dimer of genomic rna in each virion of hiv

Answer 28

• function for NC in this process
• ensure replicative advantage
• core can fit 2 RNA genomes
• It is likely that the presence of
  two genomes in one virion is
  advantageous for survival, providing
  an extra template that can be used
  when one RNA molecule is
  damaged and giving genetic
  variety to the progeny

Question 29

how does hiv get out of the cell

Answer 29

it buds outtt using the escrt proteins and some stuff is cleaved so that it is a mature infectious particle

Question 30

where does reverse transcription happens

Answer 30

in the cytoplasm

Question 31

what is the 2 activities of RT

Answer 31

-polymerase: p66, can use either rna or DNA as a template
-nuclease: p51: RNAseh1

Question 32

steps in RT

Answer 32

-RT needs two things to start
transcription: a template (aka the
vRNA) and a primer (in the case
of retroviruses, a host cell tRNA)
-RT starts at the 3’ end of the tRNA and copies The RNA template until the 5’ end into DNA with its RNA-dependent DNA polymerase activity
-Following the creation of cDNA, RT destroys the complementary RNA (before PBS) with its nuclease activity.
-The newly synthesized DNA is then transferred to the 3’ end of the viral RNA to begin minus-strand (3’ – 5’) DNA synthesis
-As DNA synthesis proceeds
so does RNAseH degradationAs soon as RT synthesizes the complementary PBS sequence targets the tRNA for RNAaseH degradation
-Removal of the tRNA
causes translocation of the new + strand
to bind to the – strand via the PBS
-Reverse transcription of RNA creates long terminal repeats, which are identical in sequence, at both end of the dsDNA: 5’ LTR and 3’ LTR. These are crucial as this is how retroviruses
integrate into the host genome!