Virus Structure and Function

Question 1

General Properties of Viruses

Answer 1

• Obligatory parasites; they need to hijack host metabolic machineries to replicate
• They are small
• Made of a nucleic acid genome surrounded by a protein coat (capsid) and a facultative lipid membrane (envelope)
• Viruses exist that can infect all living organisms

Question 2

Nucleic Acid Genome

Answer 2

• DNA; ss or ds
• RNA; ss (+/-) or ds
• usually between 2-20kb; (1.2Mb for megaviruses); minimal info required (hijacks host’s machineries); only specific genes
• ds > ss; DNA > RNA
• usually one molecule that can be fragmented

Question 3

Capsid

Answer 3

• made of proteins (one or more) called capsomers

- self assembly products; highly ordered

Question 4

Envelope

Answer 4

• made of a lipid bilayer with (glyco)proteins from host or virus-encoded
• allows entry into host cell (fusion/endocytosis)

Question 5

Bacteriophages

Answer 5

• Contain a mixture of icosahedral/filamentous structures (and others)

Question 6

Non-symmetrical Viruses

Answer 6

• Poxyviridae (small pox)

Question 7

Virus Classification

Answer 7

• Named after the disease they cause
• Named after the places where they were first reported
• Named after the host and signs of disease
• Named after their shape
• Named after their discoverer
• Named after their supposed transmission mechanism
• Named after a combination of the above-mentioned criteria

Question 8

The Baltimore Classification

Answer 8

• Group I, II and VII; DNA viruses

- Group III, IV, V and VI; RNA viruses

Question 9

Class I Genome Replication

Answer 9

• Classical semi-conservative

Question 10

Class II Genome Replication

Answer 10

• Classical semi-conservative

- Discard (-) strand

Question 11

Class VII Genome Replication

Answer 11

• Transcription followed by reverse transcription

Question 12

Class III Genome Replication

Answer 12

• Make ssRNA (+) and transcribe from this to give ssRNA (-) partner

Question 13

Class IV Genome Replication

Answer 13

• Make ssRNA (-) and transcribe from this to give ssRNA (+)

Question 14

Class V Genome Replication

Answer 14

• Make ssRNA (+) and transcribe from this to give ssRNA (-) genome

Question 15

Class VI Genome Replication

Answer 15

• Make ssRNA (+) genome by transcription of (-) strand of dsDNA

Question 16

Class I

Answer 16

• dsDNA
• Enveloped; Herpes virus (120-220kb) and Poxvirus (130-375kb)
• Non-enveloped; Adenovirus (3.0-4.2kb) and Papillomavirus (5.3-8.0kb)

Question 17

Class II

Answer 17

• ssDNA

- Adeno-associated virus (5kb); non-enveloped

Question 18

Class III

Answer 18

• dsRNA

- Reovirus (18-31kb); non-enveloped

Question 19

Class IV

Answer 19

• (+) ssRNA
• Enveloped; Togavirus (9.7-11.8kb), Hepatitis C virus (10.5kb)
• Non-enveloped; Poliovirus (7.4kb), Foot-and-mouth disease virus (7.5kb) and Hepatitis A virus (10.5kb)

Question 20

Class V

Answer 20

• (-) ssRNA

- Influenza virus (12-15kb); enveloped

Question 21

Class VI

Answer 21

• (reverse) RNA

- HIV (9.7kb); enveloped

Question 22

Class VII

Answer 22

• (reverse) DNA

- Hepatitis B virus (3.1kb); enveloped

Question 23

What are the 5 major steps of the life cycle of a virus?

Answer 23

1) Attachment
2) Genome injection
3) Production of nucleic acid and proteins
4) Maturation (assembly of viral particles)
5) Release

Question 24

Life Cycle of Bacteriophages

Answer 24

1) Attachment
2) Penetration (DNA injection)
3) Phage DNA circularises
Lytic Cycle
4) Phage DNA and proteins are synthesised and assembled into virions
5) Cell lyses, releasing phage virions
or
Lysogenic Cycle
4) Phage DNA integrates within the bacterial chromosome by recombination
5) Cell division - the prophage many excise from the bacterial chromosome initiating a lytic cycle

Question 25

Life Cycle of DNA Viruses (Group I, II and VII)

Answer 25

1) Attachment - virion attaches to host cell 2) Penetration - virion enters cell, DNA is uncoated 3) Biosynthesis - viral DNA is replicated, viral proteins are produced 4) Maturation - virions assemble 5) Release - virions are released

Question 26

Life Cycle of RNA Viruses (Group IV)

Answer 26

ssRNA (+) sense strand 1) Attachment 2) Penetration 3) Proteins made directly from ssRNA (+), genome made via ssRNA (-) 4) Maturation 5) Release

Question 27

Life Cycle of RNA Viruses (Group V)

Answer 27

ssRNA (-) antisense strand 1) Attachment 2) Penetration 3) ssRNA (+) is made first and is then used to produce proteins and ssRNA (-) genome 4) Maturation 5) Release

Question 28

Life Cycle of RNA Viruses (Group III)

Answer 28

dsRNA 1) Attachment 2) Penetration 3) ssRNA (+) is made and is then used to produce proteins and a ssRNA (-) genome 4) Maturation 5) Release

Question 29

Life Cycle of Retroviruses (Group VI)

Answer 29

ssRNA (+) 1) Retrovirus enters by fusion between attachment spikes and the host receptors 2) Viral RNA genome and 3 viral enzymes are released; reverse transcriptase, integrase and protease 3) Reverse transcriptase copies viral RNA to dsDNA 4) dsDNA is transported into the nucleus and integrated into the host genome by viral integrase - the provirus can replicate when the host cell replicates 5) Transcription of the provirus produces new genomes and RNA encoding capsid, enzymes and envelope proteins 6) Viral proteins are processed by viral proteases; some go to the plasma membrane 7) Mature retrovirus buds out of the host cell, acquiring an envelope and attachment spikes

Question 30

dsDNA Viruses

Answer 30

- encapsidation is coupled with maturation of the replicative genome

Question 31

ssRNA Viruses (including retroviruses)

Answer 31

- electrostatic interactions between basic capsid proteins and RNA genome (acidic) - promote cooperative assembly of capsomers

Question 32

Fragmented Genomes

Answer 32

Genomic fragments in complex with proteins are paired before encapsidation