Classification, Biology and Disease Flashcards
What are viruses?
Viruses are essentially nucleic acids surrounded by protein Come in many different structures RNA viruses e.g. TMC DNA viruses e.g. adenovirus Covered by a protein coat Covered by a membrane e.g. influenza
What are the different configurations of viral genomes?
Single-stranded RNA (ssRNA)
Double-stranded RNA (dsRNA)
Single-stranded DNA (ssDNA)
Double-stranded DNA (dsDNA)
Double-stranded genomes have complementary base pairing
RNA genomes can be linear and segmented i.e. more than one RNA per capsid 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 of molecular biology?
You have a genome from which you can produce viral proteins which are required for replication
Protein production follows the central dogma of molecular biology
- DNA polymerase replicated DNA
- RNA Polymerase transcribes RNA from DNA
- Ribosome produces protein from RNA template
How do viruses use the central dogma?
You can have DNA viruses that replicate DNA
RNA viruses replicate RNA in the positive and negative sense
Retroviruses replicate both
What features does the HIV virus have for replication?
We have the genome as two copies of RNA covered by a layer of protein covered by a lipid bilayer membrane
Sticking out of the membrane HIV has an envelope glycoprotein
Within the virus, there is not only the viral genome but also a number of different viral enzymes:
- Protease
- Integrase
- Reverse transcriptase
What is the structure of the mature HIV-1 particle like?
The outer envelope of HIV consists of a lipid bilayer with protruding Envelope spikes (heterotrimers of SU3TM3).
Inside the envelope lie shells of Gag proteins, composed of three different proteins:
- Matrix (MA)
- Capsid (CA)
- Nucleocapsid (NC)
In the immature particle, Gag itself forms a single shell.
MA associates with the membrane CA forms the conical capsid
NC coats the viral RNA genome.
The core contains two genomic RNA strands (plus strand), tRNALys3, and ~50 copies of each viral enzyme (PR, RT, and IN).
What 3 polyproteins do retroviruses like HIV synthesise?
Gag; group specific antigen; viral core proteins; MA (matrix), CA (capsid), NC (nucleocapsid)
Pol; viral enzymes; protease (PR), reverse transcriptase (RT) and integrase (IN)
Env; envelope glycoprotein; composed from gp120 SU (surface); gp41 TM (transmembrane)
What are some HIV-1 regulatory, accessory proteins?
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 (?)
How does HIV-1 enter a cell?
HIV-1 entry requires two membrane proteins: CD4 and a chemokine receptor (CCR5/CXCR4)
CD4 recognises the cell surface receptor that recognises gp120 of the HIV envelope tucked in its native confirmation
Once the surface subunit engages CD4 it causes a profound conformational change in the envelope; the surface comes to an open conformation
This leads to potentially fusion peptide insertion, where the open confirmation uncovers the trans membranes subunits
(So we essentially have two different functions within the envelope glycoprotein:
- Surface- which recognises the cell surface receptor
- The transmembrane subunits- mediating the fusion of the viral lipid bilayer)
During this process, HIV also recognises a core receptor and the interaction between the core receptor and surface subunits stimulates the transmembrane region to go into the cell membrane
This causes a 6-helix bundle formation, a membrane fusion, where we have these envelope trimers (three copies of the transmembrane which goes into the lipid bilayer
This pushes the membrane apart
HIV-1 is therefore tropic for CD4 expressing cells such as helper T cells and macrophages; the loss of which results in immunodeficiency (& AIDS).
How does HIV move to the nucleus of the cell?
HIV needs to replicate in the cell nucleus as this is where we find DNA replication so it can utilise all those factors to replicate its own genome
Once the virus is fused and has deposited the core containing the viral genome into the cell, it utilises the cellular microtubule network to move the core containing the genome to the nuclear membrane
What happens to the HIV once it gets to the nucleus of the cell?
It utilises reverse transcriptase
Reverse transcription is the process from RNA to DNA
RT is a heterodimer of p66 and p51 subunits.
Catalytic properties are in p66 subunit, p51 serves structural role and lacks RNAse H domain
RT displays three distinct enzymatic activities:
1. RNA-dependent DNA polymerase
2. RNAase H (cleaves RNA from RNA/DNA hybrid)
3. DNA-dependent DNA polymerase
What happens during reverse transcription?
Our viral RNA in our capsid
The reverse transcriptase enzyme mediates the production of DNA from RNA
RNA genome bound by an RNA primer and the reverse transcriptase acts as a polymerase making new copies of RNA from RNA template of RNA genome
RT converts RNA templates to DNA templates
DNA templates become dsDNA
How does the HIV integrate its genome into the host chromosome?
At the ends of that viral linear DNA are specific sequences
The integrase enzyme recognises these sequences and bind the viral DNA and the cellular DNA
It cuts the cellular DNA and repairs the cut ends
It then ‘sticks and pastes’ the viral DNA into the cut it has made in the cellular DNA by bending the viral DNA (because dsDNA is a helical shape) and bringing in in close proximity to the cellular DNA
The integrase mediates or promotes a repair process
How does HIV make its RNA?
The HIV-1 promoter contains binding sites for transcription factors that are present in T-lymphocytes
It recruits to the viral genome cellular proteins required for mRNA transcription using its promoter and enhancer regions
Lef and Nf-kh are two major transcriptional factors that the virus promotes the binding of the its own promoter enhancer region
These then enhance and promote transcription from the viral genome
How does HIV ensure that its genome gets preferential treatment?
The first thing that gets produced from the viral genome is the viral Tat protein
The TAR RNA binds the Tat protein
This RNA binding protein will bind specifically to viral RNA and enhance the production of RNA
This occurs via a positive feedback mechanism
(Binding of Tat protein to TAR RNA enhances elongation of RNA pol II)
