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π“œπ‘’π’Ήπ’Ύπ’Έπ’Άπ“ π“œπ’Ύπ’Έπ“‡π‘œπ’·π’Ύπ‘œπ“π‘œπ‘”π“Ž > Viral Pathogens : Classification, Biology, Diseases - I > Flashcards

Viral Pathogens : Classification, Biology, Diseases - I Flashcards

1
Q

What are the 4 types of viral genome?

A

➝ ssRNA
➝ dsRNA
➝ ssDNA
➝ dsDNA

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2
Q

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

A

➝ positive or negative

➝ 5’-3’ or 3’5

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3
Q

What is the central dogma of molecular biology?

A

➝ DNA ➝ RNA ➝ Protein

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4
Q

Why does the central dogma fall apart?

A

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

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5
Q

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

A

➝ 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

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6
Q

What is the structure of HIV?

A

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

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7
Q

What does the outer layer of HIV consist of?

A

➝ lipid bilayer with protruding Env spikes

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8
Q

What are Env spikes made from?

A

➝ SU3TM3

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9
Q

What is inside the envelope of HIV?

A

➝ Gag proteins

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10
Q

What forms the conical capsid in HIV?

A

➝ CA

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11
Q

What coats the viral RNA genome in HIV?

A

➝ Nucleocapsid

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12
Q

What does the HIV core contain?

A

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

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13
Q

What are the three proteins that retroviruses synthesize?

A

➝ Gag
➝ Pol
➝ Env

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14
Q

What does Gag code for?

A 
➝ group specific antigen
➝ viral core proteins
➝ matrix 
➝ capsid
➝ nucleocapsid
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15
Q

What does Pol code for?

A

➝ viral enzymes
➝ protease
➝ reverse transcriptase
➝ integrase

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16
Q

What does Env code for?

A

➝ Envelope glycoprotein : Gp120SU

➝gp41 TM

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17
Q

What are the 6 accessory proteins to HIV?

A 
➝ Tat
➝ Rev
➝ Vif
➝ Nef
➝ Vpu
➝ Vpr
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18
Q

What is the function of Tat?

A

➝ potent activator of viral transcription

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19
Q

What is the function of Rev?

A

➝ mediates unspliced RNA nuclear export

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20
Q

What is the function of Vif?

A

➝ Critical regulator of virus infectivity

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21
Q

What is the function of Nef?

A

➝ Immune modulator, T cell activation, virus spread

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22
Q

What is the function of Vpu?

A

➝ immune modulator, virus release

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23
Q

What is the function of Vpr?

A

➝ Cell cycle, virus nuclear import

24
Q

What proteins does the HIV envelope consist of?

A

➝ Trimer of gp41 and gp120 peptide subunit covered with glycans

25
Q

What proteins does HIV-1 require for entry?

A

➝ CD4 and a chemokine receptor (CCR5/CXCR4)

26
Q

What is the cellular receptor for HIV in humans?

A

➝ CD4

27
Q

How does HIV enter the membrane?

A

➝ 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

28
Q

What is the 6 helix bundle ?

A

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

29
Q

What is HIV tropic to?

A

➝ CD4 expressing cells such as T helper cells and macrophages

30
Q

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

A

➝ AIDS

➝ immunodeficiency

31
Q

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

A

➝ Replicates the genome

32
Q

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

A

➝ moving down the microtubule

➝ intracellular trafficking

33
Q

What does HIV use to get entry into the nucleus?

A

➝ NPC

➝ nuclear pore complex

34
Q

What directs the HIV genome into the nucleus?

A

➝ At the NPC it interacts with Nup358 and Nup153

35
Q

What is the protein composition of reverse transcriptase?

A

➝ heterodimers of p66 and p51

36
Q

In what subunit are the catalytic properties of reverse transcriptase?

A

➝ p66

37
Q

What is the function of p51?

A

➝ structural role and lacks RNAse H domain

38
Q

What are the three enzymatic activities of Reverse transcriptase?

A

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

39
Q

What are the three basic steps of reverse transcription?

A

➝ 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

40
Q

How does HIV integrate its genome into the host?

A

➝ 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

41
Q

What is the function of the integrase?

A

➝ 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

42
Q

What is the function of the LEDGF protein?

A

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

43
Q

When does the HIV pick up LEDGF?

A

➝ it picks it up on the way to the nucleus

44
Q

What does the HIV-1 promoter contain?

A

➝ binding sites for transcription factors present in T lymphocytes

45
Q

What is transcription controlled by?

A

➝ the binding of transcription factors to the viral DNA

46
Q

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

A

➝ splicing

47
Q

What protein mediates nuclear export of viral RNA?

A

➝ HIV-1 Rev

48
Q

What does the TAT-TAR association do?

A

➝ preferentially brings the RNA polymerase to the genome

49
Q

What is HIV Rev essential for?

A

➝ nuclear export of intron containing viral mRNAs

50
Q

What does the HIV Rev protein interact with?

A

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

51
Q

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

A

➝ unspliced HIV RNA

52
Q

How are two genomes able to be packed in HIV?

A

➝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

53
Q

How does HIV get different proteins from the same mRNA?

A

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

54
Q

How do the proteins get to the plasma membrane?

A

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

55
Q

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

A

➝ Myristic acid

56
Q

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

A

➝ HIV-1 PT(S)AP

➝ mediates binding of the host Tsg101 protein

57
Q

How does the capsid formation occur?

A

➝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

π“œπ‘’π’Ήπ’Ύπ’Έπ’Άπ“ π“œπ’Ύπ’Έπ“‡π‘œπ’·π’Ύπ‘œπ“π‘œπ‘”π“Ž (17 decks)

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