Module 1 – Viruses: Types, Structures & Life Cycles

Question 1

Virus

Answer 1

when inside the cell

Question 2

Virion

Answer 2

when outside the cell

Question 3

Two types of viruses

Answer 3

1. naked - no envelope
2. enveloped - lipoprotein membrane around the nucleocapsid.
   - typically infect animal cells and use proteins on envelope for attachment
   (not all animal viruses are enveloped)

Question 4

What is a nucleocapsid?

Answer 4

capsid and nucleic acid

Question 5

capsid structure

Answer 5

made of individual units called capsomeres

Question 6

what are capsomeres?

Answer 6

• arranged in a repetitive pattern around nucleic acid
• made of single or multiple proteins
• can be self assembled
• sometimes self assembly requires help from chaperone proteins

Question 7

what are the two types of virus symmetry?

Answer 7

-1. rod shaped (helical)
2. spherical
(icosahedral symmetry meaning triangular faces)
-multiples of 60 capsomere units

(some viruses have both virus symmetries i.e. phage)

Question 8

genomes

Answer 8

DNA (ssDNA & dsDNA)
RNA (ssRNA & dsRNA)
- DNA & RNA
- DNA (dsDNA) : hepadnaviruses
- RNA (ssRNA) : retroviruses

Question 9

genome

Answer 9

if RNA genome is single stranded than it can be two things:
1. plus sense - same sequence as mRNA
2. minus sense - complementary sequence to mRNA

Question 10

viral life cycle

Answer 10

1. attachment (adsorption) of virion to a susceptible host cell
2. entry (penetration) of virus or its nucleic acid
3. synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus
4. assembly of capsids and packaging of viral genomes into new virions (maturation)
5. release of mature virions from host cell

• when prokaryotic cells (bacteria and archaea) are infected by viruses, only nucleic acid enters the host
• when plant and animal cells are infected, the entire virion is taken up by host cell

Question 11

length of viral replication cycle

Answer 11

bacteriophages: 20-60 minutes
animal viruses: 8-40 hours

Question 12

permissive (host)

Answer 12

when host cell supports complete replication of virus

Question 13

burst size

Answer 13

number of virions released per host cell

Question 14

what is the growth curve for viruses

Answer 14

growth curve for viruses is one-step growth curve

Question 15

eclipse phase

Answer 15

• first few minutes after infection when genome replication and and some translation occurs
• virion can no longer infect another cell

Question 15

maturation phase

Answer 15

• at the start new viral particles are assembled but can’t be detected in medium yet
• at the end new virions are released through lysis or budding

Question 16

what is a latent period?

Answer 16

latent period = eclipse + part of maturation period
- (no new virions released into media)

Question 17

viral life cycle (attachment)

Answer 17

• major determinant of host specificity for virus
• virion has protein on the surface that interacts with the receptor of the host
• receptors have normal metabolic in host cell but have been exploited by virus for infection

Question 18

viral life cycle (penetration)

Answer 18

phage:
- genome of phage enters bacterial host cell
- special proteins may enter too

animal & plant viruses:
- animal/plant viruses have nuclei where viral genome will be replicated
- entire virion needs to enter host cell
- for animal cells virus receptors are surface proteins that mediate cell-to-cell contact or intracellular communication
- in multicellular organisms (humans) receptors can be found in some tissues
- penetration of animal virus can occur through endocytosis or fusion with cytoplasmic membrane

Question 19

animal and plant viruses:
what is uncoating?

Answer 19

release of viral genome from capsid; must occur so genome can be replicated in nucleus of host cell
- can occur at membrane or cytoplasm

Question 19

What is the virus that causes the common cold called?

Answer 19

rhonavirus

Question 20

in what applications can viruses be used as vectors?

Answer 20

gene therapy, enzyme delivery, vaccination

Question 21

virus-based pesticides could combat

Answer 21

resistance to chemical pesticides in plants

Question 22

what would an enveloped virus have that a naked virus wouldn’t?

Answer 22

spike proteins

Question 23

capsid assembly requires many accessory proteins to help

Answer 23

false

Question 24

the genome of a plus sense RNA virus can be directly translated to give proteins

Answer 24

true

Question 25

which group of organisms has the highest diversity of viruses that can infect

Answer 25

animals

Question 26

Replication of Viral Genomes

Answer 26

- viruses can have different genome structures, there are several modes of genome replication - For viruses with ss (+) strand genomes and ssDNA viruses, a replicative form – a ds DNA version of the genome must be made after infection; Will be used for replication and transcription. - The mechanism of replication and transcription depends on genome structure.

Question 27

Phage T4 – dsDNA virus: Replication

Answer 27

-T4 phage encodes its own DNA Polymerase, some primases and helicases -genome replicated through semi-conservative replication -‘single-genome’ units produced and then several units recombine to form a concatamer -during maturation, headful packaging occurs: endonuclease cuts one DNA length just long enough to fill one head

Question 28

Phage T4 – dsDNA virus: Transcription & Translation

Answer 28

host cell replication, transcription and translation shut down quickly -transcription produces both monocistronic and polycistronic transcripts -three sets of genes: early, middle and late -translation follows order of transcription early proteins include an anti-sigma factor: binds to host RNA Pol (and its σ); Prevents transcription of host genes which results in transcription of viral early genes -middle protein includes factors that direct host RNA Pol to viral middle gene promoters -late proteins include new T4 sigma that directs host RNA Pol to late gene promoters -also, late proteins include phage components necessary for packaging

Question 29

Phage ΦX174 – circular ssDNA ‘+’ Strand: Replication

Answer 29

-after infection, host enzymes convert circular ssDNA for into circular dsDNA which is replicative form -first more several copies of replicative form of genome are made by semi-conservative replication of a circular genome (Genetics course) -purpose of this is to create a template for transcription then many copies of ‘+’ strand are made; These are copies of genome for packaging -occurs through rolling circle replication

Question 30

Phage ΦX174 – circular ssDNA ‘+’ Strand: Transcription & Translation

Answer 30

-genome is about 5.4 kb and has overlapping genes -transcription occurs using ‘-’ DNA strand as template -some parts of genome read more than once -for overlapping genes, transcription is reinitiated to produce transcripts with distinct reading frames -also, one protein A* made by another initiation of translation at a later start codon in same frame as A i.e. A* is shorter version of A

Question 31

Consequences of Animal Infection by Viruses

Answer 31

When animal cell infected by virus there are at least four possible consequences i) virulent infection (lysis of host) -most common ii) latent infection – viral DNA maintained in host but new virions not produced and no lysis iii) budding – release of new virions from host cell is slow and host cell may not be killed -host cell continues to produce virions over time; persistent infection -in some cases, host cells carrying viral genome can continue to divide iii) transformation – virus converts normal animal cell into tumour cell

Question 32

Coronaviruses

Answer 32

cause about 15% of common colds, SARS (SARS-CoV), and Middle East respiratory syndrome (MERS-CoV) -attacks respiratory system

Question 33

Coronaviruses: Transcription & Translation

Answer 33

‘+’ strand is polycistronic mRNA in part -ribosomal frame shifting also occurs to get different proteins from same sequence in genome. -polyprotein made and cleaved by proteases to give individual proteins including replicase -replicase – makes RNA using RNA as a template (i.e. RNA-dependent RNA polymerase or RdRp) -Virus must make replicase because no cellular protein has RdRp activity -replicase does two things: 1. makes copies of RNA genome for packaging 2. transcribes some mRNAs for translation

Question 34

Coronaviruses: Ribosomal frame shifting:

Answer 34

-One mRNA molecule is present and translation starts at the same start codon for both ORFs. During translation the ribosome Pauses. Pause causes shift upstream or downstream (-1 in case of corona virus) in certain percentage of cases (< 100%) -amino acids put in with ‘shift’ will differ compared to no shift i.e. different C-terminal portions of proteins produced

Question 35

Retroviruses – ssRNA ‘+’ Strand that use DNA Intermediates

Answer 35

-includes HIV, human T-cell leukemia virus (HTLV) -retroviruses have two copies of RNA genome that dimerize

Question 36

Retroviruses – ssRNA ‘+’ Strand that use DNA Intermediates: Transcription & Translation

Answer 36

-the enzyme reverse transcriptase (RT) is packaged into mature virions so present from the start with new infection -RT has 3 activities: i) reverse transcription- makes DNA using RNA template ii) ribonuclease – in this case degrades RNA in RNA:DNA hybrid iii) polymerase – makes DNA using DNA template