virus replication L13

Question 1

what does entry to host cell by virus depend on

Answer 1

the interaction between viral surface proteins and host cell surface protein AKA virus receptors

Question 2

why are viruses referred to as parasites

Answer 2

they rely on host cell machinery (ribosomes, enzymes and precursors) for biosynthesis
- biosynthesis is genome replication + mRNA synthesis + translation

Question 3

what are the 4 stages of attachment

Answer 3

1. diffusion - through extracellular fluid to get to receptor
2. binds to low affinity receptor
   - increase concentration of virus on host so more likely to bind to primary receptor
3. binds to primary receptor
4. binds to co-receptor
   - like using multiple passwords or keys to enter cell, before virus structure changes to release the genome. Is critical that virus doesn’t release genome to early or into wrong (non-permissive cell type).

Question 4

give the example of HIV attaching

Answer 4

Attachment of HIV to a CD4+ cell. The outer domain of gp120 binds to the CD4 antigen. This leads to a conformational change in gp120 and a co-receptor binding site is exposed. This region of gp120 binds to the chemokine receptor. Binding to the chemokine receptor allows another conformational change to occur so that regions of the gp41 HIV protein interact to form a fusion domain that allows the viral and cell membrane to fuse. As a result the viral core enters the cytoplasm

Question 5

why cant we just target the host receptors to stop viruses from entering
- give examples

Answer 5

the receptors have functions vital to cell process
- if we target receptors, will not get same biological effect
- Acetylcholine receptor is a neuronal signal transducer but is hijacked by rabies
- Angiotensin-converting enzyme 2 (ACE2) important in vasoconstriction and blood pressure but is hijacked by COVID 19

Question 6

describe the two methods of internalisation

Answer 6

1. fusion
   - envelope viruses bind to receptors on plasma membrane
   - fuses with plasma membrane releasing genome wrapped in capsid into cytoplasm
2. receptor mediated endocytosis
   - enveloped virus bind to receptor
   - it is then endocysed forming vesicle
   - vesicle fuses with endosome lowering pH in vesicle
   - low pH induces viral membrane to fuse with vesicle membrane – releases nucleocapsid
   - for non-enveloped viruses, they are taken up the same but the low pH causes conformational change allowing it to form pores in the vesicle where nucleocapsid can escape from

Question 7

what happens to virus once it has entered

Answer 7

genome must be uncoated, replicated, transcribed to mRNA and translated to proteins
The mechanisms of genome replication and transcription vary depending upon the nature of the genome

Question 8

what features can viral genome be

Answer 8

• DNA or RNA
• single or double stranded
  If ss: +ve sense (coding) or –ve sense (complimentary to coding strand)
• linear or circular

Question 9

how do DNA viruses replicate and transcribe their genome

Answer 9

DNA genome can be replicated by host DNA polymerases
DNA genome can be transcribed by host RNA polymerases

Question 10

how do RNA viruses replicate and transcribe their genome

Answer 10

RNA virus genomes cannot be replicated and transcribed by host polymerases as host cell DNA and RNA polymerases can only use DNA as a template
RNA viruses MUST encode their own polymerases which can use RNA as a template

Question 11

what are polymerases that can use RNA as a template called

Answer 11

RNA dependant RNA polymerase
make DNA from RNA not DNA

Question 12

what enzyme to retroviruses contain to convert RNA to DNA

Answer 12

reverse transcriptase

Question 13

What is the function of the proteins encoded by the virus genome?

Answer 13

• replication of the genome
• package the genome into virus particles
• alter the metabolism of the infected cell

Question 14

what’s the difference between structural and non-structural proteins

Answer 14

structural form part of the virus particle whereas non-structural are not e.g enzymes involved in transcription

Question 15

how do viruses use host machinery to translate mRNA

Answer 15

Eukaryotic initiation factors (eIFs) bind to cap recruiting 40S ribosomal subunit
- translation starts at AUG

Question 16

how have viruses evolved to to ensure viral mRNA is translated more efficiently than host cell mRNA

Answer 16

Protein synthesis is often inhibited in virally infected cells
- done directly by virus or by the action of interferon
Some viral RNAs can be translated via cap-independent mechanism (internal ribosome entry site: IRES) to get round this issue
- Initiation complex is recruited directly to IRES

Question 17

what features of post translational modification do viral proteins go through

Answer 17

Viral proteins undergo the same range of post translational modifications as the host cell proteins eg. glycosylation, acylation, lipoylation.

Some virus genomes are translated to produce a single large viral polyprotein which must be post-translationally cleaved to release individual viral proteins

Question 18

describe the pathway of forming a virus P1

Answer 18

1. viral mRNA translated into GLYCOproteins at ER
2. viral glycoproteins inserted into ER
3. ER is pinched off with viral glycoproteins inside
4. vesicle goes to Golgi where is it glycosylated
5. vesicle is trafficked to cell surface where is fuses with plasma membrane so viral glycoproteins are displayed on the surface

Question 19

Describe the pathway of forming a virus P2

Answer 19

1. nucleocapsid forms in cytoplasm
2. it migrates to surface and interacts with proteins in plasma membrane in cytoplasmic domain
3. causes part of membrane with viral glycoproteins to wrap around it
4. buds off

Question 20

what are the 4 ways virus can be released from host cell

Answer 20

1. Release by cell lysis, eg poliovirus
2. Release by budding:
   from plasma membrane (eg influenza)
   into lumen of endoplasmic reticulum (eg rotavirus)
3. Virus can also spread from cell to cell
   via pores between cells (eg herpesvirus?)
   by inducing fusion of their membranes (eg RSV)
4. Release may be preceded by or followed by a maturation step

Question 21

where may viruses shed from

Answer 21

1. primary site of replication
2. secondary sites of replication
   - if virus is carried from primary to secondary via lymph or blood
   - secondary sites may be liver, bone marrow, spleen, blood vessel endothelium
3. target organs

Question 22

what are bacteriophages

Answer 22

viruses that infect bacteria
There is probably a phage for every type of bacterium

There are more phage on earth than all other organisms put together.

Question 23

what types of phage’s can you get and give examples

Answer 23

1. single stranded DNA
   - ΦX174 phage
   - M13 phage
2. ds DNA
   - most common
   - Caudovirales
3. SS or DSRNA

Question 24

Describe M13 filamentous bacteriophage

Answer 24

Circular ssDNA
Cloning and DNA-sequencing
Released without lysing host cell
(Wouldn’t see plaques in an assay)
‘budding’ makes own channel

Question 25

how do phage’s infect

Answer 25

bind to surface of host using tail fibres
base plate makes contact with membrane
lysosomes create holes in peptoglycan layer
DNA extruded into host

Question 26

describe the two cycles of bacteriophages

Answer 26

1. Lysogenic
   viral DNA enter host chromosomes and lies dormant
   just replicates along with host chromosome
   only becomes active when the cell or extracellular environment changes
2. lytic
   - viral DNA is translated to proteins
   - viral DNA and proteins are packaged to form bacteriophages that break out host

Question 27

why are bacteriophages important

Answer 27

1. Can turn bacteria virulent (phenotypic change)
   C. diptheriae
   S. typhimurium
   EPEC
2. Alternative to antibiotics – phage therapy
3. Great tool in the lab – recombinant DNA technology