Viral Pathogens

Question 1

What are the different viral structures?

Answer 1

→helical
→icosahedral
→complex virus
→enveloped virus

Question 2

What are the 4 structures of viral genome?

Answer 2

→Single-stranded RNA (ssRNA) →Double-stranded RNA (dsRNA) →Single-stranded DNA (ssDNA)
→Double-stranded RNA (dsDNA)

Question 3

In what sense, can viral genomes be encoded?

Answer 3

→both 5’3’ and 3’5’

Question 4

What is the Baltimore classification?

Answer 4

→classification system that places viruses into one of seven groups depending on a combination of their nucleic acid (DNA or RNA), strandedness (single-stranded or double-stranded), Sense, and method of replication

Question 5

What is group 1 of the BCS?

Answer 5

→dsDNA

→+and -

Question 6

What is group 2 of the BCS?

Answer 6

→ssDNA viruses (+)sense DNA

Question 7

What is group 3 of the BCS?

Answer 7

→dsRNA viruses

Question 8

What is group 4 of the BCS?

Answer 8

→(+)ssRNA viruses (+)sense RNA

Question 9

What is group 5 of the BCS?

Answer 9

→(−)ssRNA viruses (−)sense RNA

Question 10

What is group 6 of BCS?

Answer 10

→ssRNA-RT viruses (+)sense RNA with DNA intermediate in life-cycle

Question 11

What is group 7 of BCS?

Answer 11

→dsDNA-RT viruses

Question 12

What does the outer envelope of HIV consist of?

Answer 12

→lipid bilayer with protruding Env spikes (heterotrimers of SU3TM3)

Question 13

What lies in the envelope of HIV?

Answer 13

→Gag proteins

Question 14

What coats the RNA genome?

Answer 14

→nucleocapsid

Question 15

What does the core of the HIV virus contain?

Answer 15

→two genomic RNA strands (plus strand),

→tRNALys3,
→~50 copies of each viral enzyme: protease, integrase and reverse transcriptase

Question 16

What are the three polyproteins retroviruses synthesise?

Answer 16

→Gag
→Pol
→Env

Question 17

What are Gag polyproteins?

Answer 17

→group specific antigen

→viral core proteins

Question 18

What are Pol polyproteins?

Answer 18

→viral enzymes

→RT, IN,PR

Question 19

What are Env polyproteins?

Answer 19

→envelope glycoprotein

Question 20

What are the HIV-1 regulatory accessory proteins?

Answer 20

→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 impor

Question 21

What are the components of HIV RNA?

Answer 21

→Trans-activation response element
→Rev responsive element  
→5 and 3 UTR
→Repeat
→Long Terminal repeat

Question 22

What does the Env polyprotein in HIV-1 consist of?

Answer 22

→a trimer of gp41 and gp120 peptide subunits

→covered with glycans

Question 23

What are glycans?

Answer 23

→post translational modification eg carbohydrates

Question 24

What does HIV-1 entry require?

Answer 24

→CD4

→a chemokine receptor (CCR5/CXCR4)

Question 25

What is HIV-1 tropic for?

Answer 25

→for CD4 expressing cells such as helper T cells and macrophages

Question 26

What does loss of CD4 result in?

Answer 26

→immunodeficiency (AIDS).

Question 27

Why does HIV-1 replicate in the nucleus?

Answer 27

→nucleic acid present

Question 28

How does HIV-1 gain entry into the nucleus after fusion?

Answer 28

→uses microtubule network

Question 29

What allows the core to be deposited into the nucleus?

Answer 29

→Viral core has capsid modifications

Question 30

What are the components of RT?

Answer 30

→heterodimer of p66 and p51 subunits

Question 31

What are the roles of p66 and p51?

Answer 31

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

Question 32

What are the three enzymatic activities of RT?

Answer 32

→RNA-dependent DNA polymerase →RNAse H (cleaves RNA from RNA/DNA hybrid) →DNA-dependent DNA polymerase

Question 33

How does the viral genome integrate into host genome?

Answer 33

→integrase enzymes →recognise flanking sequences →bends host DNA →brings together host and viral DNA

Question 34

What is the function of LEDGF/P57 in viral integration?

Answer 34

→binds HIV-1 integrase and facilitates targeting to chromatin

Question 35

How doe ensure we get preferential transcription?

Answer 35

→Viral Tat protein- binds specifically to viral RNA and enhance RNA pol II

Question 36

What produces different mRNAs for viral proteins?

Answer 36

→HIV-1provirus

Question 37

What protein mediates nuclear export of unspliced RNA?

Answer 37

→ HIV-1 Rev →binds to RRE region Promotes viral export over cellular RNA export →has specificity

Question 38

What does HIV-1 Rev protein interact with?

Answer 38

→Crm1 and the RRE RNA

Question 39

What is the purpose of unspliced HIV-1 mRNA?

Answer 39

→for Gag and Gag-Pol proteins

Question 40

Why does unspliced viral RNA dimerise?

Answer 40

→allows packing of two genomes | →kissing loop complex

Question 41

What is Gag-pol protein generated by?

Answer 41

→1 ribosomal frameshifting induced by a ‘slippery’ sequence →an RNA hairpin structure

Question 42

What allows viral genome to be associated with the plasma membrane?

Answer 42

→Myristoylation of Glycines in the MA domain of Gag

Question 43

What is required for virus budding?

Answer 43

→HIV-1 PT(S)AP motif

Question 44

What is abscission?

Answer 44

→organisation of all the proteins that pushes viral protein into cytoplasm

Question 45

What allows abscission of viral release?

Answer 45

→The ESCRT machinery is hijacked by HIV

Question 46

What are the components of the ESCRT machinery?

Answer 46

→Gag →Tsg101 →Alix →ESCRT-II CHMP4A

Question 47

What causes the release of proteins from Gag and Gag-Pol polyproteins?

Answer 47

→Protease | →viral proteins are cut up into individual proteins allowing them to reorganise