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Block 6 - week 4 > Viral classification, structure and replication - Aucoin > Flashcards

Viral classification, structure and replication - Aucoin Flashcards

1
Q

Describe some characteristics of viruses.

A
  1. can pass thru a filter
  2. are obligate intracellular parasites
  3. cannot make energy or proteins independently of a host cell
  4. genomes may be RNA or DNA but not both
  5. have a naked capsid or an envelope
  6. are not living
  7. must be infectious to endure in nature
  8. have been optimized by mutation and selection to infect humans
  9. virus genome must encode any required processes not provided by cell
    10 viral components must self assemble
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2
Q

What are the components of the basic virion?

A
  1. DNA or RNA
  2. structural proteins to protect genome
  3. possibly needs enzymes and nucleic acid binding proteins
    The above forms a nucleocapsid. This would be a naked capsid virus also called a non-enveloped virus.
    To form an enveloped virus the nucleocapsid is surrounded by glycoproteins and a membrane.
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3
Q

Give some examples of naked capsid viruses.

A
  1. papilloma virus
  2. adenovirus
  3. poliovirus
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4
Q

Give some examples of enveloped viruses.

A
  1. herpes virus

2. retroviruses

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5
Q

Are DNA or RNA viruses bigger?

A

DNA viruses tend to be bigger - up to 200 kb. RNA viruses are smaller - up to 30 kb with many under 10 kb.

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6
Q

Describe some means of classification and naming of viruses.

A
  1. structure, size, morphology and type of nucleic acid - i.e. picornavirus.
  2. biochemical characteristics - structure and mode of replication - ie retrovirus
  3. disease caused
  4. means of transmission
  5. tissue or organ that is the target (tropism) - ie adenovirus
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7
Q

What are the units of measurement used in describing viruses?

A

They are measured in nanometers. Pox viruses are the largest at 200 nm and are almost visible under a light microscope.

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8
Q

What is a virion?

A

An infectious viral particle consisting of nucleic acid genome packaged into a protein coat called a capsid or ribonucleocapsid. If it also has a membrane (host cell derived) then it is an enveloped virus.

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9
Q

What is the relationship between size of virus and genome?

A

The bigger the genome, the bigger the virus and also it will be a more complex virus.

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10
Q

Describe an enveloped virus.

A

These viruses have a host derived membrane surrounding their genome and capsid. In between the two is the tegument layer. This layer typically contains viral proteins.

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11
Q

What mediates the interaction of the virus with the target cell?

A

The viral attachment protein or VAP. This protein is located on the surface of the capsid or envelope.

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12
Q

What is the difference between a capsid and a ribonucleocapsid?

A

The capsid is formed of structural proteins surrounding the genome, ribonucleocapsid is formed by the structural proteins actually binding to the nucleic acid.

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13
Q

When antibodies can bind to VAP’s what are they called?

A

Neutralizing antibodies - they bind to VAP’s and block them from infecting cells.

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14
Q

Name some characteristics of naked capsid viruses.

A

The capsid is rigid and helps the virus resist drying, acid environments and detergents. They are hardy enough to be transmitted via the fecal-oral route.

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15
Q

Name some characteristics of enveloped viruses.

A

The viral envelope contains lipids, proteins and glycoproteins and is maintained only in aqueous solutions and so they are more vulnerable to drying out and are transmitted via bodily fluids.

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16
Q

What are the 2 shapes that capsids take?

A
  1. helical

2. icosahedral

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17
Q

Describe a helical capsid.

A

The helical capsid is rod shaped and self-assembles as a ribonucleocapsid on the RNA genome. Most negative-strand RNA viruses have helical capsids.

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18
Q

Describe icosahedral capsids.

A

Structural proteins come together to form a protomer and 5 protomers come together to form a capsomer.The capsomers come together symmetrically. The smallest of these capsids is made from 12 capsomers and for larger capsids structural proteins join the capsomers.

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19
Q

Describe a viral envelope.

A
  1. composed of lipids, proteins and glycoproteins formed from host membrane.
  2. most glycoproteins act as VAP’s that bind to target cells to initiate entry and are themselves antigens to the host’s immune system.
  3. in between the capsid and the envelope is the tegument layer which contains enzymes and other proteins that facilitate viral infection.
  4. all of the neg. strand RNA viruses are enveloped.
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20
Q

What are VAP’s that bind to red blood cells called?

A

Hemagglutinins, they bind to sialic acid receptors expressed on many different cells in many different hosts.

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21
Q

What do viruses need for replication?

A

They need host cell provided substrates, energy and some of the replication machiner.

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22
Q

What are the phases of viral replication?

A
  1. virus must recognize target cell, attach and penetrate the plasma membrane.
  2. the virus must uncoat its genome in the cytoplasm and in some cases deliver its genome to the nucleus.
  3. it must replicate its genome, form proteins and self assemble.
  4. the virus must release itself from the cell.
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23
Q

What is latency?

A

When extracellular infectious virus is not detected but viral genomes are still present and can be detected.

24
Q

Where do DNA viruses replicate?

A

In the host nucleus.

25
Q

Where do most RNA viruses replicate?

A

In the host cytoplasm.

26
Q

How do viruses get into cells?

A

Cells must have a receptor that can bind to viral attachment proteins. The most common way into the cell after attachment is via receptor mediated endocytosis. Enveloped viruses may get in by fusion of the envelope with host cell envelope.

27
Q

How do viruses get out of cells?

A
  1. lysis
  2. budding
  3. receptor mediated exocytosis via the secretory pathway
28
Q

What determines if a cell will become infected?

A

It must have a receptor that can bind to the VAP on a virus. Viruses may bind to receptors on cell types of specific species only - they have a specific host range.

29
Q

What is tissue tropism?

A

It is defined as the susceptible target cell of the virus.

30
Q

How do most non enveloped viruses enter the cell?

A

By receptor mediated endocytosis.

31
Q

How do most enveloped viruses enter the cell?

A

Their membranes fuse with the cellular membranes to deliver the nucleocapsid or genome into the cytoplasm. Some enter via receptor mediated endocytosis and need the acidic conditions of the endosome.

32
Q

What happens to the capsid and or envelope of the virus.

A

The envelope and capsid must be removed. This may happen at the cell surface and/or in an endosome?

33
Q

Where do most DNA genomes go once they reach the cytoplasm?

A

They usually go to the nucleus.

34
Q

Where do most RNA genomes go once they reach the cytoplasm?

A

Most stay in the cytoplasm. Influenza virus is the only RNA virus where the genome is replicated in the nucleus.

35
Q

Describe how DNA viruses make proteins.

A

Once the DNA of a virus gets to the nucleus, the host cell’s DNA -dependent DNA polymerase and other enzymes are used to create mRNA. The mRNA must acquire a 3 prime poly A tail and a 5 prime methylated cap. The mRNA then is used to make proteins using the host cell machinery. Large DNA viruses often code for their own polymerase and transcription factors.

36
Q

Describe how RNA viruses make proteins.

A

There are negative sense RNA viruses and positive sense RNA viruses. RNA viruses replicate and produce mRNA in the cytoplasm. The neg. sense RNA virus must enter the host cell with RNA-dependent RNA polymerase in order to replicate then use the host cell machinery for translation. The pos. sense RNA can use the host machinery to produce RNA-dependent RNA polymerase which then forms neg sense RNA templates from which many copies of pos. sense RNA can be made. Then it will use host machinery to make proteins.

37
Q

Which type of virus can encode for their own transcription factors to regulate the expression of viral genes?

A

Complex DNA viruses.

38
Q

Where does viral DNA replication begin and what enzyme is needed?

A

Replication begins at the origin of replication and this is where viral replication factors such as DNA-dependent DNA polymerase binds.

39
Q

Can large DNA viruses encode their own DNA polymerase?

A

Yes, and viral DNA polymerase makes more errors leading to more mutations.

40
Q

Viral polymerases can be the target of what?

A

Antiviral nucleotide analogs used to treat viral infections.

41
Q

Do all of the genes of viruses with large genomes get transcribed at once?

A

No, first the immediate early genes which often encode transcription factors are transcribed. Then early genes are transcribed and replication occurs then late stage genes which code for structural proteins are transcribed.

42
Q

What must an RNA virus either bring with them into the cell or code for in their genome?

A

RNA dependent RNA polymerase. This type of polymerase is fast and has a high mutation rate.

43
Q

WHy can positive sense RNA alone initiate an infection?

A

Pos. sense RNA genomes act as mRNA, bind to ribosomes and direct protein synthesis.

44
Q

What structure on a viral mRNA allows it to bind to host ribosomes?

A

Viral mRNA may get modified by the addition of the 5 prime cap which binds to the ribosome or they may have another, internal structure that allows binding to the ribosome.

45
Q

What is a unique feature of viral protein production?

A

Ribosomes may bind to viral mRNA and may produce one large polyprotein which then needs to be cleaved by cellular or viral proteases.Sometimes viruses block cellular mRNA from leaving the nucleus so that viral mRNA is preferentially translated.

46
Q

What are some types of post-translational modifications that viral proteins undergo?

A
  1. phosphorylation

2. glycosylation

47
Q

Where are viral glycoproteins synthesized?

A

They are synthesized on membrane bound ribosomes. They have amino acid sequences to allow for insertion into the rough ER where they are used in N-linked glycosylation.

48
Q

When does viral assembly occur?

A

When the concentration of viral structural proteins is high enough then protein-protein, protein-nucleic acid and protein-membrane interactions occur.

49
Q

Describe viral budding.

A
  1. can occur after association of the nucleocapsid with the intracellular portion of viral glycoproteins.
  2. some viruses assemble at the plasma membrane and get their envelope by budding off.
  3. some viruses bud from the ER or golgi to get their envelopes.
50
Q

Where can enveloped viruses get their membranes?

A
  1. plasma membrane budding

2. by budding from the Golgi or the ER.

51
Q

How are viruses released?

A
  1. cell lysis - often occurs with naked capsid viruses.
  2. exocytosis
  3. budding from the plasma membrane - often occurs with enveloped viruses.
52
Q

What are wild type viruses?

A

These are non-mutated viruses.

53
Q

What are 3 outcomes of viral mutation?

A
  1. no change in phenotype
  2. lethal mutation - virus no longer infectious or the mutation is detrimental and virus becomes attenuated (less pathogenic)
  3. enhancement of infectious nature and resistance to drugs
54
Q

How can new virus strains be produced?

A

By intramolecular exchange (recombination) between viruses or between virus and host.

55
Q

What is reassortment?

A

If two different virus strains with segmented genomes (genome is in fragments instead in one piece) infect the same cell they can shuffle their segments. Influenza virus can do this.

Block 6 - week 4 (9 decks)

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