Viral Pathogens: Classification, Biology, Disease 1

Question 1

How are viruses classified?

Answer 1

Based on their structural viral genomes

Baltimore classification

Question 2

List the possible structure of viral genomes

Answer 2

Single-stranded RNA (ssRNA)

Double stranded RNA (dsRNA)

Single stranded DNA (ssDNA)

double stranded DNA (dsDNA)

DNA genomes can be linear or circular

Question 3

What is the central dogma of viral biology?

Answer 3

The production of proteins

1. Reverse transcription can occur to convert RNA to DNA
2. (-) sense RNA can be converted to (+) sense RNA

Question 4

Describe the structure of HIV

Answer 4

dsRNA

Capsid

Lipid bilayer

Envelope protein or spikes

Protease integrase

Reverse transcriptase

Gag protein inside shell

Matrix

Question 5

Describe the genome organisation of HIV

Answer 5

Mainly 3 polyproteins

Gag: group scientific antigen: viral core proteins; matrix, capsid

Pol; viral enzymes: protease, reverse transcriptase and integrase

Env: envelope glycoprotein

Question 6

What two proteins are required for HIV-1 to enter a host cell?

Answer 6

CD4

Chemokine receptor (CCR5/CXCR4)

Question 7

How does HIV-1 enter a host cell?

Answer 7

1. Naive Trimer
2. CD4 binding - T20 binding site exposure
3. CoR binding - Fusion peptide insertion
4. 6-helix bundle formation - Membrane fusion

Question 8

How is HIV-1 tropic?

Answer 8

Topic for CD4 expressing cells such as T cells and macrophages

Question 9

Describe what occurs during the early stages of HIV-1 infection

Answer 9

1. Virgin fuses with membrane
2. Uncoating of viron and reverse transcription
3. Incorporation of cellular proteins during intracellular trafficking
4. Nuclear entry

Question 10

What is reverse transcriptase?

Answer 10

A heterodimer of p66 and p51 subunits

Catalytic properties are in p66

P51 serves structural role

Question 11

What are the 3 next activities of reverse transcriptase?

Answer 11

RNA-dependent RNA polymerase

RNAse H (cleaves RNA from RNA/DNA hybrid)

DNA dependent DNA polymerase

Question 12

What occurs once the viral genome has entered the nucleus of the host cell?

Answer 12

Reverse transcription

HIV DNA genome is integrated into the host DNA via viral intagrase enzyme

Question 13

What occurs during reverse transcription?

Answer 13

Reverse transcriptase converts viral RNA into DNA

Question 14

What happens during retroviral integration?

Answer 14

1. Retroviral DNA and host cell DNA get bent until both terminals are in close proximity
2. Host DNA is cut by viral integrase enzyme
3. Host DNA then binds to viral DNA
4. Repair process occurs, making sure the cuts are resolved

Question 15

What is the role of LEDGF/P75 in Reverse transcription?

Answer 15

Binds to HIV-1 integrase and facilitates targeting to chromatin

Question 16

How does HIV DNA bind to host DNA?

Answer 16

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

Eg. Transcription factors Lef and Nf-kb

Question 17

How do viruses ensure that they’re RNA are given preferential treatment?

Answer 17

Viral TAT protein will bind specifically to viral RNA and enhance the production of RNA

POSITIVE FEEDBACK MECHANISM

Question 18

How is unspliced viral RNA exported out of the nucleus?

Answer 18

Rev protien mediates the export of spliced and unspliced viral RNA

1. Rev is produced by the transcription and translation of the genome
2. Rev re enters the nucleus and binds to RRE and interacts with CRM1
3. This promotes the movement of viral RNA out of the nucleus and splicing of into-containing viral mRNAs

Question 19

Describe what happens after translation occurrs for HIV

Answer 19

Genomic RNA enters the cytoplasm

Genomic RNA forms a kissing loop complex when two sequences in the RNA recognise each-other

Dimerisation of of the unspliced viral RNA allows packing of two genomes

Question 20

What the two ways in which viral protein can be made from mRNA?

Answer 20

Gag-pol protein is generated by -1 ribosomal frame shifting induced by a “slippery” sequence and a RNA hairpin structure

Question 21

How does Gag associate with the plasma membrane mediated?

Answer 21

Myristolaytion of glycines in the MA domain of Gag

Question 22

How is Gag traffic towards the plasma membrane?

Answer 22

Using the association of Tsg101

Question 23

How are the viral proteins organised at the plasma membrane in preparation for budding off?

Answer 23

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

Abscission is the organisation of all proteins and RNA together in a new capsid.

New capsids are pushed out of plasma membrane

Question 24

How are proteins released from Gag or Gag-pol polyproteins?

Answer 24

Proteases cut the protiens at specific location to release smaller proteins

Question 25

What’s the structural differences between a immature and a mature capsid?

Answer 25

Immature contains proteases - Polyprotiens are yet to be cleaved