Hale - Intro

Question 1

What are the 7 functions of viral proteins?

Answer 1

1. Protect the genome
2. Deliver genome into cells (e.g. binding/fusion)
3. Facilitate genome replication
4. Facilitate mRNA production
5. Facilitate virus particle assembly
6. Reprogramme cellular functions
7. Protect against host immunity

Question 2

Why are these definitions of viruses starting to get challenged?

Answer 2

Existence of giant viruses, that contain unusual proteins involved in proofreading, metabolism, ribosomal proteins and tRNAs.

Question 3

What difference does an envelope make for a virus?

Answer 3

Non-enveloped virus are usually more resistant to temperature, pH, dessication and detergents, which makes it more easy to spread (infectivity remains in tough conditions, e.g. intestinal tract.)

Question 4

What is the preferred mode of transmission of enveloped viruses and why?

Answer 4

Usually spreads in fluids - humidity aids infection as envelope is stable there.

Question 5

Which are the two roles of the viral envelope?

Answer 5

Protection and a vehicle for the genome.

Question 6

Which are the four morphologies for viruses?

Answer 6

Spheres
Bullets -Rhabdo
Rods - Baczki
Threads

Question 7

Which are the genome options for RNA viruses?

Answer 7

ssRNA or dsRNA
Linear or Circular
Segmented or Not
Positive or Negative

Question 8

Which are the genome types for DNA viruses?

Answer 8

ssDNA or dsDNA

Linear or Circular

Question 9

On what is the Baltimore Classification based on?

Answer 9

On the pathways involved to go from genome to mRNA for each viruses.

Question 10

What basic rules do DNA virus replication follows?

Answer 10

Requires a template and base pairing
Semi conservative
Begins and ends at specific sites
5' -> 3'
Requires a primer with free 3’OH (RNA, protein, DNA structure)

Question 11

Which DNA genome replication mechanism always uses an RNA primer? Cite 3 viruses using such a mechanism.

Answer 11

Replication Fork, used by HPV, Polyoma, HSV.

Question 12

Which DNA genome replication mechanism never uses an RNA primer? Cite 3 viruses using such a mechanism.

Answer 12

Strand Displacement mechanism, used by Adeno, Parvo and Poxviruses.

Question 13

There is an issue stemming at the ends of the genome for DNA-replicating viruses. How can the virus solve the problem?

Answer 13

• Using Hairpins as primers (AdV2)
• Circularising its genome (SV40)
• Using protein primers (AdV5)

Question 14

What virus-induced cellular structure is universal in DNA virus replication?

Answer 14

Replication factories: developping near the nucleus, they concentrate host and viral factors and substrate to increase efficiency.

Question 15

What’s the three strategies developed by DNA viruses in regard of the Cell Cycle?

Answer 15

• Bring Your Own: the virus codes for a bunch of DNA-synthesis related enzymes (Helicases, Polymerases etc) and doesn’t care about the cell cycle much.
• Push into S phase: these viruses code for proteins interfering with Cell Cycle regulation, pushing it in DNA synthesis phase and hijacking host enzymes: HPV, AdV.
• Replication by mitosis: these viruses integrate their genome into the cell (latency) or keep it as an episome (EBV), and get replicated when the cell divides.

Question 16

What’s the difference between + and - RNA virus?

Answer 16

Positive RNA are directly infectious, their genome can serve as mRNA to make proteins. This is not the case for negative RNAs that need to make a positive intermediary before starting protein synthesis.

Question 17

Do RNA viruses necessarily need to bring their RdRp with them in the particle?

Answer 17

Nope: only the (-)RNA viruses as they need it to make the positive-stranded RNA genome first.

Question 18

Structurally, what’s different between (-) and (+) RNA viruses?

Answer 18

(+): no RdRp packaged in. Naked genome. Secondary RNA structures.
(-): must bring RdRp. Genome + NP = RNP, serving as template for the RdRp.

Question 19

How does the transcription from a DNA template work for viruses?

Answer 19

dsDNA is the template: if the genome itself is not dsDNA; it must be created. For that, some viruses use DNA repair mechanisms, DNA synthesis or RT + integration (HIV) to achieve the dsDNA template.

Question 20

How can DNA-based viruses regulate transcription?

Answer 20

Either doing cis-regulation using enhancer sequences (e.g. the famous SV40 present in many vectors) or using enhancer proteins (Tat from HIV).
Note that those enhancer proteins can be of use to regulate early/late transcription modes.

Question 21

Where does problems arise from for a transcription from an RNA genome?

Answer 21

Since these viruses need a RdRp, this same enzyme is used for both mechanisms so it’s tough to balance both. Positive viruses don’t care too much as genomes = mRNA. A strategy to go about this is to induce NP-gradients to switch from transcription to replication.

Question 22

What strategies are used by RNA viruses to cap their mRNAs?

Answer 22

• Bring their own capping enzymes (paramyxo et rona)
• Use a viral protein as a cap.
• Have an IRES (HepC).
• cap Snatching
• polyU tracts to stutter the RdRp.

Question 23

Can viruses translate proteins on their own ?

Answer 23

Nope, no exceptions.

Question 24

Reminder: eukaryiotic translation process:

Answer 24

Binding to cap
Scanning for AUG 
Initiation 
Elongation R
elease at PolyA
Disassembly of Ribosome.

Question 25

Give a few examples of how viruses make the most of their genomes for translation (alternative ORFs)

Answer 25

Polyproteins,
Leaky Scanning,
FS
Reinitiation

Question 26

How are polyproteins regulated?

Answer 26

Concentration of linked enzymes

Cellular localisation

Question 27

How’s a leaky scanning working?

Answer 27

Essentially the initiation codon is either weak or in a weak context: therefore tRNAs will miss it sometimes, therefore impacting secondary protein amounts.