Viral pathogens: classification, biology, diseases I Flashcards
What is a virus?
- 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
- Viruses aren’t alive - molecular machines that wish to replicate
State the differences between virus, bacteria and prions?
- Bacteria contain nucleic acid (DNA) covered in protein, have a polysaccharide cell wall (a coat of sugar molecules) and can replicate outside of the cell.
- Remember viruses can be found within bacteria
- Prions are proteins, do not contain nucleic acid and replicate inside the cell.
- Viruses are nucleic acid (DNA or RNA) covered by proteins, have no cell wall and may or may not have a lipid coat. Viruses must replicate in the cell; they are “obligate cellular parasites”
State the similarities between virus, bacteria and prions?
Similarity is that they all are infectious and too small to be seen under a microscope
Why are viruses described as obligate cellular parasites?
- OCP require a host cell to live and reproduce - they cannot reproduce outside their host cell. Same way viral proteins are formed and exist
- The reproduction of the virus is entriely reliant on intracellular resources of the host
What are the essential structural features of a virus? VD
- Different viruses have different structures - but retain similar organisation
- The structure dictates host range (organisms or place where virus is found) and tissue tropism (tissue where virus is found)
State the different types of configurations/structure of viral genomes? (PART 1)
- Single-stranded RNA (SSRNA)
- Double-stranded RNA (dsRNA)
- Single-stranded DNA (SSDNA)
- Double-stranded RNA (dsDNA)
- Double-stranded genomes have complementary base pairing
State the different types of configurations/structure of viral genomes? (PART 2)
- RNA genomes can be linear and segmented i.e. more than one RNA per capsid
- Segmented where the genome is fragmented into 2 or more nucleic acid molecules
- DNA genomes can be linear or circular.
- Genomes can be encode information (genes) in positive or negative sense; 5’-3’ or 3’-5’ respectively.
What is the central dogma?
The ‘Central Dogma’ is the process by which the instructions in DNA are converted into a functional product - protein
How do viruses use it?
- (-) sense RNA Is a template strand for mRNA - complementary to mRNA, but can’t be directly translated
- Is reverse complementary to both the positive-sense strand and the
RNA transcript. It is actually the antisense strand that is used as the template from which RNA polymerases construct the RNA transcript, - (+) sense RNA is produced from - sense RNA (complementary to tis) via
RdRp as its sequences signifies of a particular viral mRNA sequence, so can be directly translated into viral proteins - if its nucleotide sequence corresponds directly to the sequence of an RNA transcript which is translated or translatable into a sequence of amino acids
What is baltimore classification?
System used to classify viruses based on the structure of the genome and how this used is used to produce mRNA.
What are the essential features of virus replication?
- Entry into the cell - attachment/entry receptors - direct fusion or endocytosis.
- Genome movement within the cell - intracellular structures.
- Genome replication
- Genome packaging into protein shells - “Packaging” sequences in viral DNA or RNA.
- Exit from the cell - budding or lysis -> New virus is formed
Describe the molecular structure of HIV particle?
- Outer envelope + core
- Core: 2 (+) RNA strands, tRNA^Lys3, + ~50 copies of viral enzymes - protease, reverse transcriptase + integrase -> surrounded by nucleocapsid (coats viral RNA genome, capsid (conical capsid formation) + matrix associates with membrane (in order)
- OE -> Lipid bilayer + protuding Envelope spikes (surface OR transmembrane)
- Envelope -> shells of Gag proteins
State what polyproteins are synthesised by HIV retroviruses which go on to form the required proteins for HIV formation?
- Gag -> Group specific antigen -> Forms viral core proteins -> MA, CA + NC
- Pol -> viral enzymes -> PR, RT, IN
- Env -> Envelope glycoprotein -> gp120 SU OR gp41 TM spikes
State and describe the function of HIV-1 regulatory/accessory proteins in the HIV genome structure?
- 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 import (?)
What are the 2 elements found on HIV RNA and 1 on HIV DNA known as?
- HIV RNA - Trans-activation response element (5’ end) + Rev response element (3’ end)
- HIV DNA - Long terminal repeat
How do viral proteins enter the cell?
Entry: Viral envelope proteins with cellular receptor attaches to cell + fuse into cell cytoplasm
Describe the composition of HIV-1 Env + roles in HIV-1 entry?
- Trimer of gp41 (TM) + gp120 (SU) -> covered with glycans
- Tm - Mediates fusion of viral envelope
- SU -> Cell surface receptor recognition
What does HIV-1 entry require and what HIV tropic for - what can this lead to?
- 2 membrane proteins - CD4 + chemokine receptor (CCR5/CXCR4)
- Tropic for -> CD4 expressing cells (Th OR macrophages) - loss = immunodefiency (+ AIDS)
Describe the process of HIV-1 entry?
- Native trimer: looking for cell with CD4 receptor ->
- CD4 binding (T20 binding site exposure): CD4 binds - conformational changes - open trimer formation - uncovers TM subunit - interaction of lipid + TM ->
- CoR binding to membrane - fusion peptide inserted ->
- 6-helix bundle formation - membrane fusion
Describe the phases after entry of HIV-1 until into nucleus?
Viruses fuses + deposits core (containing viral genome) into cell ->
- Uncoats + undergoes Reverse transcriptase ->
- Microtubule network moves core towards nuclear membrane for replication
Describe reverse transcriptase in terms of subunits and its 3 enzymatic activities?
- Heterodimer of p66 (catalytic) + p55 subunit (structural + lacks RNAse H domain)
- EA -> RNA-dependent DNA polymerase, RNAase H (cleaves RNA from RNA/DNA hybrid), DNA-dependent DNA polymerase
Describe the basic steps of reverse transcriptase?
- RNA genome bound by RNA primer ->
- RT acts as polymerase ->
- Converts to dsDNA ->
- Inserted into viral genome + transported to nuclear membrane
Describe how nuclear entry of HIV-1 occurs + how it could be prevented?
- Nuclear pore -> requires nucleoporin Nup358 + Nup153 -> for optimal gene density -> mutation of capsid or impaired NP prevents entry
Retroviral replication cycle - integration
How is the viral RNA + integrase targeted to the chromatin?
Preintegration complex (containing LEDGF/P75) binds I -> facilitates targetting
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