Viral Pathogens: Classification, Biology, Diseases - I

Question 1

The structure of viral genomes

Answer 1

`Configuration of viral genomes;

Single-stranded RNA (ssRNA)

Double-stranded RNA (dsRNA)

Single-stranded DNA (ssDNA)

Double-stranded RNA (dsDNA)

Double-stranded genomes have complementary base pairing

RNA genomes can be linear and segmented i.e. more than one RNA per capsid

DNA genomes can be linear or circular.

Question 2

Describe encoding of genome

Answer 2

Genomes can encode information (genes) in positive or negative sense; 5’-3’ or 3’-5’ respectively.

Question 3

HIV structure

Answer 3

SU = surface
TM
Protease
Matrix
Nucleocapsid
Capsid
RT
\+ strand mRNA
Integrase
Lipid bilayer

Question 4

Describe outer envelope of HIV

Answer 4

The outer envelope of HIV consists of a lipid bilayer with protruding Env spikes (heterotrimers of SU3TM3).

Question 5

Describe inside envelope of HIV

Answer 5

Inside the envelope lie shells of Gag proteins. In the immature particle, Gag itself forms a single shell.

Question 6

Describe coating of viral genome in HIV

Answer 6

MA associates with the membrane CA forms the conical capsid

NC coats the viral RNA genome.

Question 7

Describe the core of HIV

Answer 7

The core contains two genomic 
RNA strands (plus strand), tRNALys3, and ~50 copies of each viral enzyme (PR, RT, and IN).

Question 8

Retroviruses synthesise 3 polyproteins:- List and give examples

Answer 8

Retroviruses synthesise 3 polyproteins:-
Gag; group specific antigen; viral core proteins; MA (matrix), CA (capsid), NC (nucleocapsid)

Pol; viral enzymes; protease (PR), reverse transcriptase (RT) and integrase (IN)

Env; envelope glycoprotein; gp120 SU (surface); gp41 TM (transmembrane)

Question 9

HIV-1 Regulatory / Accessory Proteins - list 6 and describe function

Answer 9

Tat - potent activator of viral transcription
Rev - mediates unspliced RNA nuclear export
Vif - critical regulator of virus infectivity
Nef - immune modulator, T-cell activation, virus spread (?)
Vpu - immune modulator, virus release
Vpr - cell cycle, virus nuclear import (?)

Question 10

Entry at HIV cell surface is triggered by

Answer 10

Entry at cell surface that is triggered by conformation changes driven by Env/receptor interactions contrasts with the pH-dependent entry of adenovirus, influenza virus, etc

Question 11

Describe membrane fusion of HIV

Answer 11

Native trimer is present,
CD4 binds + T20 binding site exposed
CoR binds, fusion peptide insertion
6-helix bundle formation = membrane fusion

Question 12

HIV-1 entry requires two membrane proteins:

Answer 12

HIV-1 entry requires two membrane proteins: CD4 and a chemokine receptor (CCR5/CXCR4)

Question 13

Describe RT and significance of its subunits

Answer 13

RT is a heterodimer of p66 and p51 subunits.

Catalytic properties are in p66 subunit, p51 serves structural role and lacks RNAse H domain

Question 14

RT displays three distinct enzymatic activities:

Answer 14

RT displays three distinct enzymatic activities:

1. RNA-dependent DNA polymerase
2. RNAse H (cleaves RNA from RNA/DNA hybrid)
3. DNA-dependent DNA polymerase

Question 15

The HIV-1 promoter contains binding sites for

Answer 15

The HIV-1 promoter contains binding sites for transcription factors that are present in T-lymphocytes

Question 16

The HIV DNA genome (provirus) is integrated into what

Answer 16

The HIV DNA genome (provirus) is integrated into the host chromosomes

The viral integrase enzyme binds both host and viral DNA

Question 17

LEDGF/P75 binds what and describe its function

Answer 17

LEDGF/P75 binds HIV-1 integrase and facilitates targeting to chromatin

Question 18

The HIV-1 Rev protein functions

Answer 18

The HIV-1 Rev protein mediates nuclear export of unspliced and singly spliced viral RNA

HIV Rev is essential for the nuclear export of intron-containing viral mRNAs

The HIV-1 Rev protein interacts with Crm1 and the RRE RNA

Question 19

The unspliced HIV-1 RNA use

Answer 19

The unspliced HIV-1 RNA is the mRNA for Gag and Gag-Pol proteins

Question 20

Dimerisation of the unspliced viral RNA allows

Answer 20

Dimerisation of the unspliced viral RNA allows packing of two genomes

Question 21

Gag and Gag-Pol proteins function

Answer 21

Gag and Gag-Pol proteins assemble viral particles

Question 22

Gag-pol protein is generated by

Answer 22

Gag-pol protein is generated by -1 ribosomal frameshifting induced by a ‘slippery’ sequence and an RNA hairpin structure

Question 23

Myristoylation of Glycines function

Answer 23

Myristoylation of Glycines in the MA domain of Gag mediates association with the plasma membrane

Question 24

Myristoylation define

Answer 24

lipidation modification where a myristoyl group, derived from myristic acid, is covalently attached by an amide bond to the alpha-amino group of an N-terminal glycine residue.

Question 25

The HIV-1 PT(S)AP motif is required

Answer 25

The HIV-1 PT(S)AP motif is required for virus budding

and mediates binding of the host Tsg101 protein

Question 26

The ESCRT machinery relation to HIV

Answer 26

The ESCRT machinery is hijacked by HIV to perform membrane abscission during viral release

Question 27

Protease releases what in membrane interactions of HIV

Answer 27

Protease releases the individual proteins from

Gag and Gag-Pol polyproteins

Question 28

Gag processing generates what

Answer 28

Gag processing generates mature virions