Viral Pathogens :Classification ,Biology -Diseases 1

Question 1

What are the different types of viruses?

Answer 1

Tobacco mosaic virus
Adenovirus
Influenza virus
Bacteriophage T4

Question 2

How do we classify viruses?

Answer 2

Not by structure but rather through genomes :
Single-stranded RNA (ssRNA)
Double stranded RNA (dsRNA)
Single stranded DNA (ssDNA )
Double stranded RNA (dsDNA)

Double stranded genomes contain 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

They can be linear /circular

It can have one genome or segmented

Genomes can encode information(genes ) in positive or negative sense

Question 3

What is the central DOGMA

Answer 3

This is the process through which proteins can be created from DNA bouble strand .

Question 4

How can viruses use the central dogma ?

Answer 4

There are DNA viruses which replicate DNA , RNA virus which create RNA or retroviruses which can create both.

All produce proteins

Question 5

Outline the baltimore classification

Answer 5

This is how viruses are grouped .
It contains information of genome types and how they are replicated .
Produce RNA which produces proteins

Question 6

What does HIV look like ?

Answer 6

Nucleic acid surrounded by protein

Two copies of RNA , covered by protein and then membrane.
Glycoproteins stick out of the membrane (envelope proteins )

Enzymes found in HIV :
Protease
Integrase
Reverse transcriptase

Question 7

Outline the structure of a mature HIV-1 particle

Answer 7

Outer envelope of HIV consists of a lipid bilayer with protruding ENV spikes (heterodimers of SU3TM3)

Inside the envelope lie shells of Gag proteins.
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)
tRNA and aprox 50 copies of d IN)

Question 8

Outline the genome organisation of Retroviruses

Answer 8

HIV has the same genome structure ,long stranded R NA from which we can produce different polyproteins through alternative splicing , transcriptional frame shift

To make the proteins three polyproteins are required:

Synthesise 3 polyproteins

Gag which produces (group specific antigen );viral core proteins ; MA (matrix) , Ca(Capsid) and NC (nucleocapsid)
NC (Nucleocapsid)

Pol: Viral enzymes
protease (PR), reverse transcreiptase (RT) and integrase (IN)

Env; envelope glycoprotein
gp120 SU (surface );gp41 TM (Transmembrane)

Question 9

Outline retroviral entrance into the cell

Answer 9

This entrance requires the engagement of the viral envelope proteins with cellular receptors which allows the virus to attach and fuse into the cell cytoplasm.

Question 10

Describe and outline HIVs envelope proteins

Answer 10

HIV envelope (spike proteins) consists of trimer of transmembrane subunits (gp10 peptide subunits & gp120 peptide subunits) and is covered with glycans.

Glycans are a post-translational modification.

Question 11

What are glycans ?

Answer 11

Sugar-based polymers that coat cells and decorate most proteins, forming glycoproteins.

Question 12

What is the mechanism of HIV-1 entry into the cell ?

Answer 12

It requires two membrane proteins : CD4 and a chemokine receptor (CCR5/CXR4)

Native trimer
These are the native trimers of the virus searching for cell surface receptor.
The gp120 is tucked into conformation called native.

.CD4 binding site exposure
CD4 recognises a sequence /structure within surface subunit of HIV ( gp120) of envelope.

Fusion peptide insertion
Following the surface subunit engages with CD4 this causes a conformational change in the envelope protein and becomes a open conformation

The open conformation will uncover the transmembrane subunits

HIV will also recognise a co receptor. The interaction between surface subunit with co-receptor stimulates the transmembrane region to go into cell membrane.

Insert transmembrane domain and surface subunit into lipid bilayer and this will form 6-Helix Bundle Formation
Membrane fusion.

Envelope trimers are three copies of transmembrane.

HIV is tropic for CD4 expressing cells such as helper T cells and macrophages; the loss of which results in immunodeficiency (& AIDS)

Question 13

Outline the early phases of HIV-1 infection

Answer 13

Following fusion:

The virus enters the cell and needs to move to site of replication.
This is the area which the replication genome will most favour.
The HIV virus wants to replicate in the nucleus mostly.

-To use the cells machinery to multiply

Following fusion , it utilises the cell microtubule network to carry the core containing the genome to the nuclear membrane.

Question 14

What are some different methods of nuclear entry pathways of HIV genome core

Answer 14

Typically , the Viral core containing the viral RNA genome has capsid modifications

Question 15

What happens once the virus reaches the nucleus ?

Answer 15

Reverse transcriptase is used for reverse transcription.
RNA to DNA

RNA is in the capsid , reverse transcriptase enzyme will mediate the production of DNA

Question 16

Outline the structure of RT

Answer 16

RT is a heterodimer of p56 and p51 subunits
Catalytic properties are in the p66 subunit ,p51 serves structural roles and lacks RNAase H domain

RT displays three distinct enzymatic activities:
RNA-dependent DNA polymerase
2.RNAse H (cleaves RNA from RNA /DNA hybrid)
3.Dna-dependent DNA polymerase

Question 17

Outline the integration of the HIV DNA genome (provirus) into host chromosomes)

Answer 17

RNA is made from cellular DNA which is a template for making RNA,this is used by the virus.
Instead of making a new mechanism ,the Virus will use these cellular factors;

Using viral integrase enzyme it will integrate its viral DNA into cellular DNA.

Question 18

Outline the integration of the HIV DNA genome (provirus) into host chromosomes)

Answer 18

RNA is made from cellular DNA which is a template for making RNA,this is used by the virus.
Instead of making a new mechanism ,the Virus will use these cellular factors;

Using viral integrase enzyme it will integrate its viral DNA into cellular DNA.

There is a viral linear DNA and on either termini there are specific sequences which are recognised by the integrase enzyme which then binds.

It also binds to the cellular DNA, then cuts the cellular DNA and pastes the viral DNA into the cellular DNA. This requires folding the two ends of the linear ends of viral DNA and bends it to bring it into close proximity.

Question 19

What are some Viral cell proteins ?

Answer 19

Cellular proteins such as LEDGF/P75 complex and TRN-SR2.This is called the pre-integration complex which recognises the cellular DNA and guides the viral DNA to it.

Question 20

How does HIV produce its RNA ?

Answer 20

HIV will use existing cellular processes

It recruits to the viral genome cellular proteins which are used for mRNA transcription.

Two major transcription factors are upstream enhancer region and core enhancer which the virus will attract.

Question 21

How does the virus ensure there is transcription from the viral genome ?

Answer 21

First thing produced from viral genome is the Tat protein which is a RNA binding protein. Binds to viral RNA and enhances the production of RNA.This happens in a positive feedback mechanism.
There is a process which priorities viral RNA over cellular RNA.

Question 22

What is Rev?

Answer 22

The Rev protein which is produced comes back into the nucleus and binds to the genomic DNA specifically through the RRE.This promotes the movement of viral RNA out of the nucleus. The nuclear export of the viral RNA is favoured.

Question 23

How can we make new viruses?

Answer 23

The virus is made up of two strands of viral RNA covered by capsid and lipid bilayer which contains envelope proteins.
HIV will co-ordinate the production of all of these structures in one place which is near the cell surface.

There is the production of viral proteins -polyprotein or splicing
Export of viral genomic DNA
Production of viral envelope glycoproteins -golgi apparatus

Production of mature virions which can infect cell

Question 24

How does HIV produce virions ?

Answer 24

These are entire virus particles consisting of an outer protein shell called a capsid.
Produce a viral genomic RNA-unspliced

The dimerization of two copies of viral RNA will promote its movement to the plasma membrane.

RRE and TAT are used here
Stem-loop structures

Question 25

What proteins does the viral RNA interact with in the cytoplasm ?

Answer 25

The viral RNA is encapsulated in new cores.

Question 26

Outline what myristylation i

Answer 26

This is a process of myristylation of Glycines which is the addition of Myristic acid to the proteins . Post-translational modification.It promotes association with the plasma membrane.This is through cellular proteins called TSG101 with our protein.