Virus Genomes and Proteins

Question 1

What are the two ways viruses can encode their genetic information?

Answer 1

RNA

DNA

Question 2

What viruses are RNA + strand and non-enveloped?

Answer 2

Picornaviridae

Caliciviridae

Question 3

What viruses are RNA - strand and enveloped?

Answer 3

Togaviridae
Flaviviridae
Coronaviridae
Retroviridae

Question 4

What viruses are RNA - stranded and enveloped?

Answer 4

Filoviridae
Bunyaviridae
Rhaboviridae
Orthomyxoviridae
Paramyxoviridae
Arenaviridae

Question 5

What viruses are dsRNA and non-enveloped?

Answer 5

Reoviridae

Question 6

What are facts about RNA viruses?

Answer 6

small genomes 3-32Kb
polymerase error prone
mostly single-stranded

Question 7

Why do RNA viruses not follow the Central Dogma?

Answer 7

miss out the DNA step

Question 8

Facts about positive-sense RNA viruses?

Answer 8

• directly translated
• share structural features of mRNA - piggy back on host cell machinery
• often have 5’ cap and 3’ polyA tail

Question 9

why do eukaryotic mRNAs have the 5’ 7-methylguanoise Cap?

Answer 9

resistance to exonucleases

Recognition by translational machinery

longer half life

Question 10

What is the IRES?

Answer 10

genome folds to form RNA secondary structure using H-bonds

act as cap for translation

Question 11

What is the genome size of flaviviruses and examples?

Answer 11

11Kb
Yellow Fever Virus
West Nile Virus
Dengue Fever Virus

5’ cap and 3’ poly A tail

Question 12

What is the genome size of picornaviruses and examples?

Answer 12

7.5Kb
Poliovirus
Rhinovirus
Hepatits A virus

Question 13

What are features of the picornavirus genome?

Answer 13

5’ Vpg
IRES
Single ORF encodes 2200aa polyproteins
Poly(A) tract

Question 14

What is the genome size of alphaviruses and examples?

Answer 14

12Kb
Eastern equine encephalitis virus
Chikungunya virus

Question 15

What are features of the alphavirus genome?

Answer 15

5’ m7G cap
non-structural ORF1
structural ORF2
PolyA tract

Question 16

What is the genome size of coronaviruses and examples?

Answer 16

33Kb
SARS
MERS

Question 17

What are features of the coronavirus genome?

Answer 17

multiple ORFs
5’m7G cap
3’ PolyA tract
‘leader’ sequence

Question 18

What is the genome size of retroviruses and examples?

Answer 18

9-11Kb
Mo-MLV
HTLV
HIV

Question 19

What are features of the retrovirus genome?

Answer 19

5' cap 
3' polyA tail
LTR
Multiple overlapping ORF's 
replicate via duplex DNA copy

Question 20

What is the simplified retrovirus replication cycle

Answer 20

Reverse transcribed into RNA-DNA hybrid

DNA

integrated into the host genome

Question 21

What are features of negative sense RNA viruses?

Answer 21

genome is REVERSE COMPLEMENT of the coding strand

No cap or PolyA

Question 22

Which negative sense RNA viruses are non-segmented?

Answer 22

Rhabdoviruses
Paramyxoviruses
Filoviruses

Question 23

Which negative sense RNA viruses are segmented?

Answer 23

Orthomyxoviruses

Bunyaviruses

Question 24

What is the genome size of rhabdoviruses and examples?

Answer 24

6.4Kb
Rabies
VSV

Question 25

What are features of the rhabdovirus genome?

Answer 25

PolyU tracts terminator & promoter sequences replicated & transcribed into positive RNA molecule

Question 26

What is the genome size of filoviruses and examples?

Answer 26

19Kb Ebola Marburg

Question 27

What are features of the filovirus genome?

Answer 27

highly conserved transcriptional signals at 3' termination signals at 5' intragenic regions vary in length

Question 28

Orthomyxovirus examples?

Answer 28

Influenza

Question 29

What are features of the Influenza genome?

Answer 29

Negative RNA segmented 8 segments 890-2341 bases common 3' 5' termini

Question 30

What human dsDNA viruses are Non-enveloped?

Answer 30

Adenoviridae (L) | Papillomaviridae (C)

Question 31

What human dsDNA viruses are enveloped?

Answer 31

poxviridae (L) Herpesviridae (L) Hepadnaviridae (C)

Question 32

What human ssDNA viruses are nonenveloped?

Answer 32

parvoviridae (C)

Question 33

What are features of DNA Virus genomes?

Answer 33

- Origins of DNA replication - Promoters/enhancers - drive transcription of viral genes - DNA replication & transcription - temporally controlled - viral mRNAs spliced - overlapping genes

Question 34

What is the genome size of adenoviruses?

Answer 34

duplex DNA genomes up to 36Kb

Question 35

What are features of the adenovirus genome?

Answer 35

``` ITR 100-140bp Terminal protein (TP) linked to 5' ends (primer) ```

Question 36

What is the size of herpesvirus genome?

Answer 36

150Kb

Question 37

What are features of the herpesvirus genome?

Answer 37

4 isomers 3 origins of DNA replication 80 virus encoded proteins temporally controlled gene expression

Question 38

What is the genome size of papillomaviruses and examples?

Answer 38

8Kb | HPV

Question 39

What are features of the papillomavirus genome?

Answer 39

early & late expressing genes | Overlapping reading frames - transcribed at different stages

Question 40

What are virus structural proteins?

Answer 40

protect the nucleic acid genome co-ordinated assembly Mechanism for delivery of genome to new cell

Question 41

What are capsid proteins?

Answer 41

highly positively charged rich in arginine & lysine package nucleic acid self assemble - helical & icosahedral

Question 42

What are picornavirus capsid proteins?

Answer 42

- 4 proteins from building block of capsid - 60 form icosahedral capsid - negative charge of RNA counteracted by Na+/K+ ions

Question 43

What are Matrix proteins?

Answer 43

- only enveloped viruses | - interact with capsid & envelope proteins

Question 44

What are viral glycoproteins?

Answer 44

recognise specific receptors Mediate fusion between viral & cellular membranes protection from immune system

Question 45

How are glycoproteins synthesised?

Answer 45

Addition of N-acetylglucosamine to Asn-X-Ser/Thr Transport to Golgi Glycan processing Transport to plasma membrane Expression on cell surface

Question 46

How are viral glycoproteins matured?

Answer 46

Proteolytic cleavage by cellular enzyme e.g. Furin

Question 47

What are virus non-structural proteins?

Answer 47

- Produced within infected cell - replication of virus nucleic acids - assembly of virus particles - regulation of host cells

Question 48

What are viral polymerases?

Answer 48

Enzymes involved in genome replication encode own catalyse replication of viral genome tagets for anti-viral drugs

Question 49

What type of proteins are required for genome replication?

Answer 49

accessory proteins encode helicase enzymes unwind duplex DNA/RNA Requires energy requires NTPase activity

Question 50

What are viral proteases?

Answer 50

cleaves polypeptides chains - specific aa polyproteins sometimes need to be cleaved further polyprotein processing

Question 51

What way to viral proteases cleave in?

Answer 51

in cis and in trans

Question 52

What are regulatory proteins?

Answer 52

play a role in survival transforming proteins interfere with immune response interfere with host cell metabolism - help viral replication