Viral Pathogens : Classification, Biology, Diseases - I

Question 1

What are the 4 types of viral genome?

Answer 1

➝ ssRNA
➝ dsRNA
➝ ssDNA
➝ dsDNA

Question 2

What are the two ways that viral genomes can encode information?

Answer 2

➝ positive or negative

➝ 5’-3’ or 3’5

Question 3

What is the central dogma of molecular biology?

Answer 3

➝ DNA ➝ RNA ➝ Protein

Question 4

Why does the central dogma fall apart?

Answer 4

➝ Viruses can go from protein ➝ RNA ➝ DNA using reverse transcriptase

Question 5

What are the 7 groups that make up the baltimore classification?

Answer 5

➝ Group 1 - ds DNA (+/-)
➝ Group 2 - ssDNA (+)
➝ Group 3 - dsRNA (+/-)
➝ Group 4 - ssRNA (+) positive sense
➝ Group 5 - ssRNA (-)
➝ Group 6 ssRNA (+) reverse transcriptase
➝ Group 7 DNA (+/-) reverse transcriptase

Question 6

What is the structure of HIV?

Answer 6

➝ A nucleic acid (two RNA strands)
➝ a protein capsid
➝ a lipid bilayer
➝ proteins on the top that mediate entry into the cell

Question 7

What does the outer layer of HIV consist of?

Answer 7

➝ lipid bilayer with protruding Env spikes

Question 8

What are Env spikes made from?

Answer 8

➝ SU3TM3

Question 9

What is inside the envelope of HIV?

Answer 9

➝ Gag proteins

Question 10

What forms the conical capsid in HIV?

Answer 10

➝ CA

Question 11

What coats the viral RNA genome in HIV?

Answer 11

➝ Nucleocapsid

Question 12

What does the HIV core contain?

Answer 12

➝ two genomic RNA strands (+ strand)
➝ tRNA lys53
➝ 50 copies of each viral enzyme : PR, RT and IN

Question 13

What are the three proteins that retroviruses synthesize?

Answer 13

➝ Gag
➝ Pol
➝ Env

Question 14

What does Gag code for?

Answer 14

➝ group specific antigen
➝ viral core proteins
➝ matrix 
➝ capsid
➝ nucleocapsid

Question 15

What does Pol code for?

Answer 15

➝ viral enzymes
➝ protease
➝ reverse transcriptase
➝ integrase

Question 16

What does Env code for?

Answer 16

➝ Envelope glycoprotein : Gp120SU

➝gp41 TM

Question 17

What are the 6 accessory proteins to HIV?

Answer 17

➝ Tat
➝ Rev
➝ Vif
➝ Nef
➝ Vpu
➝ Vpr

Question 18

What is the function of Tat?

Answer 18

➝ potent activator of viral transcription

Question 19

What is the function of Rev?

Answer 19

➝ mediates unspliced RNA nuclear export

Question 20

What is the function of Vif?

Answer 20

➝ Critical regulator of virus infectivity

Question 21

What is the function of Nef?

Answer 21

➝ Immune modulator, T cell activation, virus spread

Question 22

What is the function of Vpu?

Answer 22

➝ immune modulator, virus release

Question 23

What is the function of Vpr?

Answer 23

➝ Cell cycle, virus nuclear import

Question 24

What proteins does the HIV envelope consist of?

Answer 24

➝ Trimer of gp41 and gp120 peptide subunit covered with glycans

Question 25

What proteins does HIV-1 require for entry?

Answer 25

➝ CD4 and a chemokine receptor (CCR5/CXCR4)

Question 26

What is the cellular receptor for HIV in humans?

Answer 26

➝ CD4

Question 27

How does HIV enter the membrane?

Answer 27

➝ The envelope glycoprotein samples the membrane ➝ it sticks to CD4 ➝ HIV specific CD4 receptors and co-receptors CCR5 and CXCR4 which also recognise CD4 ➝ 6 helix bundle structure is formed ➝ the membrane fusion allows the virus to enter the cell

Question 28

What is the 6 helix bundle ?

Answer 28

➝ The structure of the envelope meshing the viral membrane and the cellular plasma membrane

Question 29

What is HIV tropic to?

Answer 29

➝ CD4 expressing cells such as T helper cells and macrophages

Question 30

What happens if the body loses helper T cells and macrophages?

Answer 30

➝ AIDS | ➝ immunodeficiency

Question 31

What does the HIV do while it is travelling to the nuclear membrane?

Answer 31

➝ Replicates the genome

Question 32

What gives the HIV directionality inside the cell and what is this called?

Answer 32

➝ moving down the microtubule | ➝ intracellular trafficking

Question 33

What does HIV use to get entry into the nucleus?

Answer 33

➝ NPC | ➝ nuclear pore complex

Question 34

What directs the HIV genome into the nucleus?

Answer 34

➝ At the NPC it interacts with Nup358 and Nup153

Question 35

What is the protein composition of reverse transcriptase?

Answer 35

➝ heterodimers of p66 and p51

Question 36

In what subunit are the catalytic properties of reverse transcriptase?

Answer 36

➝ p66

Question 37

What is the function of p51?

Answer 37

➝ structural role and lacks RNAse H domain

Question 38

What are the three enzymatic activities of Reverse transcriptase?

Answer 38

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

Question 39

What are the three basic steps of reverse transcription?

Answer 39

➝ RNA forms intrinsic structures which the enzyme recognises ➝ the RNA primer moves to the other end of the genome ➝ the HIV DNA genome (provirus) is integrated into the host chromosomes

Question 40

How does HIV integrate its genome into the host?

Answer 40

➝ There are specific sequences called TTAAs at the end of the HIV genome ➝ the target sequences find each other ➝ the integrase protein recognises the target sequence and flips the integrated form of the genome into the host DNA

Question 41

What is the function of the integrase?

Answer 41

➝ loops the viral DNA around the target DNA ➝ it brings the TTAA termus sequences together ➝ it breaks open the host DNA and anneals the viral DNA to the human DNA one strand at a time

Question 42

What is the function of the LEDGF protein?

Answer 42

➝ it is bound by the virus and brings it through the nuclear membrane ➝ it allows the integrase protein to recognise target sequences

Question 43

When does the HIV pick up LEDGF?

Answer 43

➝ it picks it up on the way to the nucleus

Question 44

What does the HIV-1 promoter contain?

Answer 44

➝ binding sites for transcription factors present in T lymphocytes

Question 45

What is transcription controlled by?

Answer 45

➝ the binding of transcription factors to the viral DNA

Question 46

How does the HIV-1 provirus generate different mRNAS for the different viral proteins?

Answer 46

➝ splicing

Question 47

What protein mediates nuclear export of viral RNA?

Answer 47

➝ HIV-1 Rev

Question 48

What does the TAT-TAR association do?

Answer 48

➝ preferentially brings the RNA polymerase to the genome

Question 49

What is HIV Rev essential for?

Answer 49

➝ nuclear export of intron containing viral mRNAs

Question 50

What does the HIV Rev protein interact with?

Answer 50

➝ HIV-1 Rev protein interacts with Crm1 and RRE RNA

Question 51

What is the mRNA for Gag and Gag-Pol proteins?

Answer 51

➝ unspliced HIV RNA

Question 52

How are two genomes able to be packed in HIV?

Answer 52

➝Unspliced HIV-1RNA is the mRNA for Gag and Gag-Pol proteins ➝There is an interaction of two RNA genomes (the Gag and Gag-Pol) surrounded by protein ➝In the viral RNA there are kissing loop complexes of RNA that can interact with each other ➝In the SL1 and SL4 domains the loop occurs ➝Dimerisation of the unspliced viral RNA allows packing of two genomes

Question 53

How does HIV get different proteins from the same mRNA?

Answer 53

➝ the 'slippery sequence' ➝ if you start at one end of the genomic RNA you get Gag ➝ if you 'slip' the ribosome and get it into a different reading frame you get the Pol protein

Question 54

How do the proteins get to the plasma membrane?

Answer 54

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

Question 55

What has to be added to the end of the protein so it can associate with the plasma membrane?

Answer 55

➝ Myristic acid

Question 56

What is required for virus budding and what does it mediate?

Answer 56

➝ HIV-1 PT(S)AP | ➝ mediates binding of the host Tsg101 protein

Question 57

How does the capsid formation occur?

Answer 57

➝P6 binds the Tsg101 protein ➝The ESCRT machinery is hijacked by HIV to exit the membrane ➝During cell division cytokinesis uses the ESCRT machinery ➝The virus hijacks the ESCRT machinery ➝Protease releases the individual proteins from Gag and Gag-Pol polyproteins ➝The polyproteins come together and form the capsid