Retroviruses

Question 1

Retrovirus RNA structure

Answer 1

Dimeric ssRNA

Question 2

Retrovirus genes

Answer 2

LTR - PBS + packaging signal - gag - pol - env - polypurine tract -LTR

Question 3

Retrovirus life cycle

Answer 3

Fusion
core released into cytoplasm
RT reaction in cytoplasm
dsDNA goes to nucleus and integrated into host genome

Question 4

Function of LTRs

Answer 4

contain regulatory elements for gene expression

Question 5

Morphology and taxonomy of retroviruses

Answer 5

Enveloped viruses with surface spikes
spherical w diameter of 80-100nm
core is spherical or rod-shaped

Question 6

Origin of retroviruses

Answer 6

evolved from simpler RT elements

Question 7

Retrovirus general structure

Answer 7

Transmembrane + surface glycoproteins
Lipid envelope
Matrix proteins
Capsid proteins
Attached to RNA: Nucleocapsid proteins, RT, Integrase

Question 8

What does env encode?

Answer 8

Transmembrane and surface glycoproteins
Variable regions

Question 9

Retrovirus entry

Answer 9

SU binds to receptor
Causes conformational change in TM trimer
Fusion peptide activated and facilitates membrane fusion
Only viral core enters

Question 10

Common retroviral targets

Answer 10

Usually immune cells e.g. macrocytes - main reservoir

Question 11

Where does Reverse transcription occur

Answer 11

cytoplasm in virion core

Question 12

Steps of RT

Answer 12

7 steps

Question 13

In what direction does Rt synthesise DNA

Answer 13

3’-5’ direction

Question 14

What is the R region in retrovirus genome

Answer 14

LTR containing promoter and primer binding sites
encodes a polyadenylase

Question 15

Polypyrimidine tract

Answer 15

Acts as primer for second strand synthesis - immune to RNAseH activity

The purpose of the polypyrimidine tract in the retroviral genome is to act as a splicing signal for the viral RNA.

Question 16

Retrovirus integration

Answer 16

Controlled by Integrase (pol)
Makes staggered cuts
Only integrates in activitely transcribing areas of genome - can only fit here

Question 17

What do retroviruses use to regulate gene expression?

Answer 17

Motifs that bind transcription factors
Promoter and enhancer motifs

Question 18

HIV gene expression regulators

Answer 18

Tat and TAR

Question 19

Tat

Answer 19

Transactivator
Accessory protein that binds to TAR
Mediates phosphorylation of host polymerase to fully elongate RNA

Question 20

TAR

Answer 20

Region of viral mRNA which Tat binds to

Question 21

rev

Answer 21

controls export of RNA especially structural genes from nucleus
nuclear localisation signal

Question 22

How is complete splicing prevented in the nucleus?

Answer 22

1. Inefficient splicing w bad splicing
2. RNA secondary structure that bind to host proteins + help export
3. Viral protein produced e.g. HIV/ATLV rev

Question 23

How does rev work in HIV

Answer 23

early stages: rev produced by splicing, there’s none atm
RNA gets spliced - accesory proteins prodcued and no structural produced
rev produced and enters nucleus + binds to rre in RNA -> promotes export

Question 24

RRE

Answer 24

Rev Responsive Element
Looped secondary structure in HIV ssRNA

Question 25

How is Pol produced?

Answer 25

Translated as part of gag/pol polyprotein

20:1 gag:pol ratio –> need many more copies of gag

Question 26

Termination suppression

Answer 26

Looped secondary structure after UAG stop codon
1 out of 20 times it causes ribosome to misread the codon
Pol produced w gag
Gammaretroviruses

Question 27

Ribosomal frameshifting

Answer 27

The HIV genome contains a frameshift signal/slippery sequence in the gag-pol region, which directs the ribosome to shift the reading frame from the gag gene to the pol gene during translation. This results in the production of a Gag-Pol fusion protein, which is then cleaved into individual Gag and Pol proteins by the viral protease.

Question 28

Where is env processed

Answer 28

ER and golgi

Question 29

Particle formation