Virology - reverse transciption etc.

Question 1

what were retro viruses called in the earlier 20th centrury?

Answer 1

tumor viruses

cause they caused tumors

Question 2

type of genome in baltimore class VI viruses?

Answer 2

have a positive sense, single-stranded RNA genome, but replicate through a DNA intermediate.

Question 3

what type of viral genome integrates into the host genome?

Answer 3

specifically RNA retro viruses

there are DNA viruses that contain reverse transcriptase in their replication cycle (e.g. hepatitis B) but they don’t integrate

Question 4

what is RT?

Answer 4

reverse transciptase is an enzyme that has the ability to ‘reverse the flow of genetic info’.
normal flow would be RNA to DNA but in this case, its DNA to RNA to proteins

RT is primer dependent, can be either DNA or RNA primer
the template can also be either one

note: also Bacteria, Archaea, eukaryotes have RT activity in the cells

Question 5

retro viruses can be broadly divided into?

Answer 5

simple & complex genomes retroviruses

simple like E.g. Avian leucosis virus
complex like HIV

Question 6

what is unique about the retrovirus genome?

Answer 6

Retroviruses are the only viruses with a diploid genome.
This means that two copies of the viral RNA genome are packaged into the virion.

Question 7

what is a provirus?

Answer 7

A provirus is an inactive virus genome that is integrated into the DNA of a host cell.

Question 8

mRNA is the same as?

Answer 8

positive sense RNA

Question 9

what is a kissing loop complex?

Answer 9

RNA kissing interactions, also called loop-loop pseudoknots, occur when the unpaired nucleotides in one hairpin loop, base pair with the unpaired nucleotides in another hairpin loop.

When the hairpin loops are located on separate RNA molecules, their intermolecular interaction is called a kissing complex.

Question 10

pbs ?

Answer 10

primer binding site

Question 11

what is the function of an RNA dimer?

Answer 11

The genome of the retroviruses is a dimer composed by two homologous copies of genomic RNA (gRNA) molecules of positive polarity.

Its believed to contribute to RT viruses resistence to UV light and ionizing radiation.

Another theory is that when mutation occurs in one strand recombination with the other, originally identical, strand would allow the genome to return to nonmutated.

Question 12

what is “copy-choice” in regard to retroviral replication?

Answer 12

Copy-choice recombination by reverse transcriptases is a mechanism where the new dna molecule comes about by replicating selected parts of each parental dna molecule and by alternating between the two.

two templates could build one functional genome

Question 13

ppt

Answer 13

polypurine tract

is a primer for plus-strand DNA synthesis during reverse transcription.

Question 14

LTR

Answer 14

long terminal repeat

is a pair of identical sequences of DNA, several hundred base pairs long, which occur in pseudogenes that form a endogenous retrovirus or a retroviral provirus.

Question 15

RNase H

Answer 15

an endonuclease enzyme used in retroviral replication

Cleaves RNA only when in duplex form. RNA can be in RNA:RNA or RNA:DNA duplexes.

Question 15

RNase H

Answer 15

an endonuclease enzyme used in retroviral replication

Cleaves RNA only when in duplex form. RNA can be in RNA:RNA or RNA:DNA duplexes.

Question 16

what are retroviral elements?

Answer 16

Ancient and modern retroelements in cell genomes (yes, ours too!).
Retroelement is a sequence that moves around in the genome via RT.

ERVs are endogenous viral elements in genomes that closely resemble and can be derived from retroviruses.
They are abundant in the genomes of jawed vertebrates, and they comprise up to 5–8% of the human genome (lower estimates of ~1%).

Question 17

endogenization

Answer 17

retroviruses infect thegermline (sperm and ova) via endogenization
= endogenous retroviruses (ERVs)

retroelements are typically not infectious (except in mice)

Question 18

What is unique about hepadnaviruses?

Answer 18

e.g. hepatitis B

are DNA viruses that encode reverse transcriptase.
contain partially gapped double-stranded DNA and replicat via an RNA intermediate.

Question 19

Sequential assembly

Answer 19

type of virion assembly method

genome is pumped into a preformed empty shell
e.g. Picornaviruses, Herpesviruses

Question 20

concerted assembly

Answer 20

type of virion assembly method

a protein shell is built around the genome
e.g. influenza virus

Question 21

what are cellular chaperones in relation to viral assembly?

Answer 21

are cellular proteins that assist in folding reactions

Question 22

what are the 2 methods of virus assembly called?

Answer 22

sequential and concerted assembly

Question 23

Budding can be driven by 4 factors:

Answer 23

1. viral envelope and capsid proteins can drive budding.
2. internal matrix proteins can drive budding.
3. envelope proteins can drive budding.
4. matrix proteins with additional components needed for efficiency or accuracy.

Question 24

what are 3 methods of release of new virions from a host cell?

Answer 24

Lysis – host cell bursts

Exocytosis – usees cell’s export pathways
E.g. Coronavirus, Herpesvirus

Budding – buds off from the plasma membrane
E.g. Influenza virus, Retrovirus

Question 25

Two options for release of of non-enveloped viruses:

Answer 25

lytic and non lytic which are further divided

lytic: apoptotic, viroporins, inhibition of membrane protein synthesis

non lytic: double-membraned vesicles or exosome use