Virus Genomes and Proteins Flashcards
What are the two ways viruses can encode their genetic information?
RNA
DNA
What viruses are RNA + strand and non-enveloped?
Picornaviridae
Caliciviridae
What viruses are RNA - strand and enveloped?
Togaviridae
Flaviviridae
Coronaviridae
Retroviridae
What viruses are RNA - stranded and enveloped?
Filoviridae Bunyaviridae Rhaboviridae Orthomyxoviridae Paramyxoviridae Arenaviridae
What viruses are dsRNA and non-enveloped?
Reoviridae
What are facts about RNA viruses?
small genomes 3-32Kb
polymerase error prone
mostly single-stranded
Why do RNA viruses not follow the Central Dogma?
miss out the DNA step
Facts about positive-sense RNA viruses?
- directly translated
- share structural features of mRNA - piggy back on host cell machinery
- often have 5’ cap and 3’ polyA tail
why do eukaryotic mRNAs have the 5’ 7-methylguanoise Cap?
resistance to exonucleases
Recognition by translational machinery
longer half life
What is the IRES?
genome folds to form RNA secondary structure using H-bonds
act as cap for translation
What is the genome size of flaviviruses and examples?
11Kb
Yellow Fever Virus
West Nile Virus
Dengue Fever Virus
5’ cap and 3’ poly A tail
What is the genome size of picornaviruses and examples?
7.5Kb
Poliovirus
Rhinovirus
Hepatits A virus
What are features of the picornavirus genome?
5’ Vpg
IRES
Single ORF encodes 2200aa polyproteins
Poly(A) tract
What is the genome size of alphaviruses and examples?
12Kb
Eastern equine encephalitis virus
Chikungunya virus
What are features of the alphavirus genome?
5’ m7G cap
non-structural ORF1
structural ORF2
PolyA tract
What is the genome size of coronaviruses and examples?
33Kb
SARS
MERS
What are features of the coronavirus genome?
multiple ORFs
5’m7G cap
3’ PolyA tract
‘leader’ sequence
What is the genome size of retroviruses and examples?
9-11Kb
Mo-MLV
HTLV
HIV
What are features of the retrovirus genome?
5' cap 3' polyA tail LTR Multiple overlapping ORF's replicate via duplex DNA copy
What is the simplified retrovirus replication cycle
Reverse transcribed into RNA-DNA hybrid
DNA
integrated into the host genome
What are features of negative sense RNA viruses?
genome is REVERSE COMPLEMENT of the coding strand
No cap or PolyA
Which negative sense RNA viruses are non-segmented?
Rhabdoviruses
Paramyxoviruses
Filoviruses
Which negative sense RNA viruses are segmented?
Orthomyxoviruses
Bunyaviruses
What is the genome size of rhabdoviruses and examples?
6.4Kb
Rabies
VSV
What are features of the rhabdovirus genome?
PolyU tracts
terminator & promoter sequences
replicated & transcribed into positive RNA molecule
What is the genome size of filoviruses and examples?
19Kb
Ebola
Marburg
What are features of the filovirus genome?
highly conserved transcriptional signals at 3’
termination signals at 5’
intragenic regions vary in length
Orthomyxovirus examples?
Influenza
What are features of the Influenza genome?
Negative RNA segmented
8 segments
890-2341 bases
common 3’ 5’ termini
What human dsDNA viruses are Non-enveloped?
Adenoviridae (L)
Papillomaviridae (C)
What human dsDNA viruses are enveloped?
poxviridae (L)
Herpesviridae (L)
Hepadnaviridae (C)
What human ssDNA viruses are nonenveloped?
parvoviridae (C)
What are features of DNA Virus genomes?
- Origins of DNA replication
- Promoters/enhancers - drive transcription of viral genes
- DNA replication & transcription - temporally controlled
- viral mRNAs spliced
- overlapping genes
What is the genome size of adenoviruses?
duplex DNA genomes up to 36Kb
What are features of the adenovirus genome?
ITR 100-140bp Terminal protein (TP) linked to 5' ends (primer)
What is the size of herpesvirus genome?
150Kb
What are features of the herpesvirus genome?
4 isomers
3 origins of DNA replication
80 virus encoded proteins
temporally controlled gene expression
What is the genome size of papillomaviruses and examples?
8Kb
HPV
What are features of the papillomavirus genome?
early & late expressing genes
Overlapping reading frames - transcribed at different stages
What are virus structural proteins?
protect the nucleic acid genome
co-ordinated assembly
Mechanism for delivery of genome to new cell
What are capsid proteins?
highly positively charged
rich in arginine & lysine
package nucleic acid
self assemble - helical & icosahedral
What are picornavirus capsid proteins?
- 4 proteins from building block of capsid
- 60 form icosahedral capsid
- negative charge of RNA counteracted by Na+/K+ ions
What are Matrix proteins?
- only enveloped viruses
- interact with capsid & envelope proteins
What are viral glycoproteins?
recognise specific receptors
Mediate fusion between viral & cellular membranes
protection from immune system
How are glycoproteins synthesised?
Addition of N-acetylglucosamine to Asn-X-Ser/Thr
Transport to Golgi
Glycan processing
Transport to plasma membrane
Expression on cell surface
How are viral glycoproteins matured?
Proteolytic cleavage by cellular enzyme e.g. Furin
What are virus non-structural proteins?
- Produced within infected cell
- replication of virus nucleic acids
- assembly of virus particles
- regulation of host cells
What are viral polymerases?
Enzymes involved in genome replication
encode own
catalyse replication of viral genome
tagets for anti-viral drugs
What type of proteins are required for genome replication?
accessory proteins
encode helicase enzymes
unwind duplex DNA/RNA
Requires energy
requires NTPase activity
What are viral proteases?
cleaves polypeptides chains - specific aa
polyproteins sometimes need to be cleaved further
polyprotein processing
What way to viral proteases cleave in?
in cis and in trans
What are regulatory proteins?
play a role in survival
transforming proteins
interfere with immune response
interfere with host cell metabolism - help viral replication
