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Microbiology > 3- Viral pathogens: classification, biology, diseases - I > Flashcards

3- Viral pathogens: classification, biology, diseases - I Flashcards

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1
Q

Define what a virus is

A

➝An infective agent that typically consists of a nucleic acid molecule in a protein coat, is too small to be seen by light microscopy, and is able to multiply only within the living cells of a host- obligate cellular parasites.

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2
Q

What are the 4 types of viral genome?

A

➝ ssRNA
➝ dsRNA
➝ ssDNA
➝ dsDNA

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3
Q

What are the 2 types of DNA genome?

A

➝DNA genomes can be linear or circular.

➝Double-stranded genomes have complementary base pairing

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4
Q

What are the 2 types of RNA genome?

A

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

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5
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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6
Q

What is the central dogma of molecular biology?

A

Replication, Transcription, and Translation

➝ DNA ➝ RNA ➝ Protein

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7
Q

Why does the central dogma fall apart?

A

➝ Viruses can go from RNA ➝ DNA

➝using reverse transcriptase

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8
Q

How do viruses use the central dogma to their own advantage?

A

➝DNA viruses- replicate DNA via DNA polymerase
➝Produce RNA from DNA via RNA polymerase
➝RNA viruses replicate RNA via RNA dependent RNA polymerase
➝Retroviruses- produce DNA from RNA via reverse transcriptase

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9
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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10
Q

What is the structure of HIV?

A

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

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11
Q

What does the outer layer of HIV consist of?

A

➝ lipid bilayer with protruding Env spikes

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12
Q

What are Env spikes made from?

A

➝ heterotrimers of SU3TM3

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13
Q

What is inside the envelope of HIV?

A

➝ Gag proteins

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14
Q

How is the conical capsid formed?

A

➝ Matrix associates with the membrane capsid to form the conical capsid

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15
Q

What coats the viral RNA genome in HIV?

A

➝ Nucleocapsid

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16
Q

What does the HIV core contain?

A

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

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17
Q

What are the three polyproteins that retroviruses synthesize?

A

➝ Gag
➝ Pol
➝ Env

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18
Q

What does Gag code for?

A 
➝ group specific antigen
➝ viral core proteins
➝ matrix
➝ capsid
➝ nucleocapsid
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19
Q

What does Pol code for?

A

➝ viral enzymes
➝ protease
➝ reverse transcriptase
➝ integrase

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20
Q

What does Env code for?

A

➝ Envelope glycoprotein : Gp120 surface

➝gp41 transmembrane

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21
Q

What are the 6 accessory/ regulatory proteins to HIV?

A 
➝ Tat
➝ Rev
➝ Vif
➝ Nef
➝ Vpu
➝ Vpr
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22
Q

What is the function of Tat?

A

➝ potent activator of viral transcription

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23
Q

What is the function of Rev?

A

➝ mediates unspliced RNA nuclear export

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24
Q

What is the function of Vif?

A

➝ Critical regulator of virus infectivity

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25
What is the function of Nef?
➝ Immune modulator, T cell activation, virus spread
26
What is the function of Vpu?
➝ immune modulator, virus release
27
What is the function of Vpr?
➝ Cell cycle, virus nuclear import
28
What proteins does the HIV envelope consist of?
➝ Trimer of gp41 and gp120 peptide subunit covered with glycans
29
What proteins does HIV-1 require for entry?
➝ CD4 and a chemokine receptor (CCR5/CXCR4)
30
What is the cellular receptor for HIV in humans?
➝ CD4
31
How does HIV enter the membrane?
➝ 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
32
What is the 6 helix bundle ?
➝ The structure of the envelope meshing the viral membrane and the cellular plasma membrane
33
What is HIV tropic to?
➝ CD4 expressing cells such as T helper cells and macrophages
34
What happens if the body loses helper T cells and macrophages?
➝ AIDS | ➝ immunodeficiency
35
What does the HIV do while it is travelling to the nuclear membrane?
➝ Produces viral DNA via reverse transcription
36
What gives the HIV directionality inside the cell and what is this called?
➝ moving down the microtubule | ➝ intracellular trafficking
37
What does HIV use to get entry into the nucleus?
➝ NPC | ➝ nuclear pore complex
38
What directs the HIV genome into the nucleus?
➝ At the NPC it interacts with Nup358 and Nup153
39
What is the protein composition of reverse transcriptase?
➝ heterodimers of p66 and p51 subunits
40
In what subunit are the catalytic properties of reverse transcriptase?
➝ p66
41
What is the function of p51?
➝ structural role and lacks RNAse H domain
42
What are the three enzymatic activities of Reverse transcriptase?
1) RNA dependent DNA polymerase 2) RNAse H (cleaves RNA from RNA/DNA hybrid) 3) DNA dependent DNA polymerase
43
What are the three basic steps of reverse transcription?
➝ 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
44
How does HIV integrate its genome into the host?
➝ 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
45
What is the function of the integrase?
➝ 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
46
What does LEDGF/P75 bind to?
➝ binds HIV-1 integrase and facilitates targeting to chromatin
47
What is the function of the LEDGF protein?
➝ it is bound by the virus and brings it through the nuclear membrane ➝ it allows the integrase protein to recognise target sequences
48
When does the HIV pick up LEDGF?
➝ it picks it up on the way to the nucleus
49
What does the HIV-1 promoter contain?
➝ binding sites for transcription factors present in T lymphocytes
50
What is transcription controlled by? | What factors promote/ enhance transcription?
➝ the binding of transcription factors to the viral DNA | ➝ Lef and Nf-Kb - major ones
51
How does the HIV-1 provirus generate different mRNAS for the different viral proteins?
➝ splicing
52
What does TAR RNA bind to?
➝ The Tat protein
53
What does the TAT-TAR association/binding do?
➝ preferentially brings the RNA polymerase II to the genome | ➝ enhances elongation of RNA pol II
54
What protein mediates nuclear export of viral RNA?
➝ HIV-1 Rev
55
What does the HIV-1 Rev protein mediate?
➝ nuclear export of unspliced and singly spliced viral RNA
56
What is HIV Rev essential for?
➝ nuclear export of intron containing viral mRNAs
57
What does the HIV Rev protein interact with?
➝ HIV-1 Rev protein interacts with Crm1 and RRE RNA
58
What is the mRNA for Gag and Gag-Pol proteins?
➝ unspliced HIV-1 RNA
59
What allows packaging of two genomes in HIV?
➝ Dimerisation of the unspliced viral RNA
60
How are two genomes able to be packed in HIV?
➝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
61
How does HIV get different proteins from the same mRNA?
➝ 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
62
What generates Gag-pol protein?
➝-1 ribosomal frameshifting induced by a ‘slippery’ sequence ➝an RNA hairpin structure
63
How do the proteins get to the plasma membrane?
➝ Myristoylation of glycines in the MA domain of Gag mediates association with the plasma membrane
64
What has to be added to the end of the protein so it can associate with the plasma membrane?
➝ Myristic acid
65
What is required for virus budding and what does it mediate?
➝ HIV-1 PT(S)AP motif | ➝ mediates binding of the host Tsg101 protein
66
How does the capsid formation occur?
➝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

Microbiology (11 decks)

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