Viral Pathogens : Classification, Biology, Diseases - I Flashcards
What are the 4 types of viral genome?
β ssRNA
β dsRNA
β ssDNA
β dsDNA
What are the two ways that viral genomes can encode information?
β positive or negative
β 5β-3β or 3β5
What is the central dogma of molecular biology?
β DNA β RNA β Protein
Why does the central dogma fall apart?
β Viruses can go from protein β RNA β DNA using reverse transcriptase
What are the 7 groups that make up the baltimore classification?
β Group 1 - ds DNA (+/-)
β Group 2 - ssDNA (+)
β Group 3 - dsRNA (+/-)
β Group 4 - ssRNA (+) positive sense
β Group 5 - ssRNA (-)
β Group 6 ssRNA (+) reverse transcriptase
β Group 7 DNA (+/-) reverse transcriptase
What is the structure of HIV?
β A nucleic acid (two RNA strands)
β a protein capsid
β a lipid bilayer
β proteins on the top that mediate entry into the cell
What does the outer layer of HIV consist of?
β lipid bilayer with protruding Env spikes
What are Env spikes made from?
β SU3TM3
What is inside the envelope of HIV?
β Gag proteins
What forms the conical capsid in HIV?
β CA
What coats the viral RNA genome in HIV?
β Nucleocapsid
What does the HIV core contain?
β two genomic RNA strands (+ strand)
β tRNA lys53
β 50 copies of each viral enzyme : PR, RT and IN
What are the three proteins that retroviruses synthesize?
β Gag
β Pol
β Env
What does Gag code for?
β group specific antigen β viral core proteins β matrix β capsid β nucleocapsid
What does Pol code for?
β viral enzymes
β protease
β reverse transcriptase
β integrase
What does Env code for?
β Envelope glycoprotein : Gp120SU
βgp41 TM
What are the 6 accessory proteins to HIV?
β Tat β Rev β Vif β Nef β Vpu β Vpr
What is the function of Tat?
β potent activator of viral transcription
What is the function of Rev?
β mediates unspliced RNA nuclear export
What is the function of Vif?
β Critical regulator of virus infectivity
What is the function of Nef?
β Immune modulator, T cell activation, virus spread
What is the function of Vpu?
β immune modulator, virus release
What is the function of Vpr?
β Cell cycle, virus nuclear import
What proteins does the HIV envelope consist of?
β Trimer of gp41 and gp120 peptide subunit covered with glycans
What proteins does HIV-1 require for entry?
β CD4 and a chemokine receptor (CCR5/CXCR4)
What is the cellular receptor for HIV in humans?
β CD4
How does HIV enter the membrane?
β The envelope glycoprotein samples the membrane
β it sticks to CD4
β HIV specific CD4 receptors and co-receptors CCR5 and CXCR4 which also recognise CD4
β 6 helix bundle structure is formed
β the membrane fusion allows the virus to enter the cell
What is the 6 helix bundle ?
β The structure of the envelope meshing the viral membrane and the cellular plasma membrane
What is HIV tropic to?
β CD4 expressing cells such as T helper cells and macrophages
What happens if the body loses helper T cells and macrophages?
β AIDS
β immunodeficiency
What does the HIV do while it is travelling to the nuclear membrane?
β Replicates the genome
What gives the HIV directionality inside the cell and what is this called?
β moving down the microtubule
β intracellular trafficking
What does HIV use to get entry into the nucleus?
β NPC
β nuclear pore complex
What directs the HIV genome into the nucleus?
β At the NPC it interacts with Nup358 and Nup153
What is the protein composition of reverse transcriptase?
β heterodimers of p66 and p51
In what subunit are the catalytic properties of reverse transcriptase?
β p66
What is the function of p51?
β structural role and lacks RNAse H domain
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
What are the three basic steps of reverse transcription?
β RNA forms intrinsic structures which the enzyme recognises
β the RNA primer moves to the other end of the genome
β the HIV DNA genome (provirus) is integrated into the host chromosomes
How does HIV integrate its genome into the host?
β There are specific sequences called TTAAs at the end of the HIV genome
β the target sequences find each other
β the integrase protein recognises the target sequence and flips the integrated form of the genome into the host DNA
What is the function of the integrase?
β loops the viral DNA around the target DNA
β it brings the TTAA termus sequences together
β it breaks open the host DNA and anneals the viral DNA to the human DNA one strand at a time
What is the function of the LEDGF protein?
β it is bound by the virus and brings it through the nuclear membrane
β it allows the integrase protein to recognise target sequences
When does the HIV pick up LEDGF?
β it picks it up on the way to the nucleus
What does the HIV-1 promoter contain?
β binding sites for transcription factors present in T lymphocytes
What is transcription controlled by?
β the binding of transcription factors to the viral DNA
How does the HIV-1 provirus generate different mRNAS for the different viral proteins?
β splicing
What protein mediates nuclear export of viral RNA?
β HIV-1 Rev
What does the TAT-TAR association do?
β preferentially brings the RNA polymerase to the genome
What is HIV Rev essential for?
β nuclear export of intron containing viral mRNAs
What does the HIV Rev protein interact with?
β HIV-1 Rev protein interacts with Crm1 and RRE RNA
What is the mRNA for Gag and Gag-Pol proteins?
β unspliced HIV RNA
How are two genomes able to be packed in HIV?
βUnspliced HIV-1RNA is the mRNA for Gag and Gag-Pol proteins
βThere is an interaction of two RNA genomes (the Gag and Gag-Pol) surrounded by protein
βIn the viral RNA there are kissing loop complexes of RNA that can interact with each other
βIn the SL1 and SL4 domains the loop occurs
βDimerisation of the unspliced viral RNA allows packing of two genomes
How does HIV get different proteins from the same mRNA?
β the βslippery sequenceβ
β if you start at one end of the genomic RNA you get Gag
β if you βslipβ the ribosome and get it into a different reading frame you get the Pol protein
How do the proteins get to the plasma membrane?
β Myristoylation of glycines in the MA domain of Gag mediates association with the plasma membrane
What has to be added to the end of the protein so it can associate with the plasma membrane?
β Myristic acid
What is required for virus budding and what does it mediate?
β HIV-1 PT(S)AP
β mediates binding of the host Tsg101 protein
How does the capsid formation occur?
βP6 binds the Tsg101 protein
βThe ESCRT machinery is hijacked by HIV to exit the membrane
βDuring cell division cytokinesis uses the ESCRT machinery
βThe virus hijacks the ESCRT machinery
βProtease releases the individual proteins from Gag and Gag-Pol polyproteins
βThe polyproteins come together and form the capsid
