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Introductory Microbiology > Taxonomy of viruses > Flashcards

Taxonomy of viruses Flashcards

1
Q

What does -viridae ending mean

A

When viruses are grouped into families

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2
Q

What does -virus ending mean

A

When viruses are given a genus name

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3
Q

What name is given in English to viruses

A

Species names

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4
Q

On what characteristics (5) classification is based

A
  • Nature of the host (animal,plant, bacteria,etc.
  • Type of disease caused (enteric, leukemia,pneumonia)
  • Life cycle(pathways of nucleic acid replication and transcription)
  • Type of nucleic acids and strandedness (+strand: same as mRNA)
  • Naked or enveloped
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5
Q

The Baltimore classification scheme is based on ____. It is useful because ____

A

-Based on the type of genome. Useful becasue the kind of genome will dictate the replication mechanism

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6
Q

What is plus RNA configuration and minus RNA configuration

A
  • Plus configuration: same strand that mRNA( can be translated directly)
  • Minus configuration: complementary to mRNA ( needs to be transcribed into plus strand before transcribed)
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7
Q

6 stages of life cycle of viruses

A
  • Absorption
  • Penetration
  • Uncoating
  • Replication
  • Maturation
  • Release
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8
Q

Describe absorption as a stage in life cycle and how plant viruses get in

A

Attachment of the virus to specific receptors on the surface of the cell. Plant viruses are usually introduced into the host by insect vectors, or following mechanical damage

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9
Q

Describe penetration as a stage in life cycle and what happens with different viruses when diffusing

A

Virus genome enters the cell

  • In enveloped and naked viruses, the complete virion may enter the cell.
  • In enveloped viruses, the envelope may be left at the cell surface such that only the nucleocapsid enters the cell
  • In naked viruses, the capsid may be left at the surface
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10
Q

Describe uncoating as a stage in life cycle

A

Removal of the envelope and/or the capsid by host enzymes, sometimes within lysosomes (in eukaryotes)

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11
Q

Most envelope viruses of eukarytes use ___ to get in. Such viruses are then delivered to ___ where

A

endocytoses or viropexis, where everything gets in

They are delivered to lysosomes which degrade the capsid and the nucleic acid is release into the cytoplasm

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12
Q

Describe replication as a stage in life cycle

A

Replication of nucleic acid, transcription and protein synthesize

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13
Q

Describe maturation as a stage in life cycle

A

Assembly of virus components, nucleic acid, nucleocapsid and accessory proteins to form new virons. Usually, the assembly is spontaneous (occurs by itself)

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14
Q

Describe release as a stage in life cycle

A

Mature virions exit the host cell by means of budding or by causeing lysis of the cell. Plant viruses exit and are transmitted by means of vectors

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15
Q

Two periods of virus replication

A
  • Latent period

- Rise period

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16
Q

What is included in latent period and rise period

A

Latent period: eclipse and maturation

Rise period: release

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17
Q

Explain eclipse

A

Time necessary for the host cells to replicate the viral genome and synthesize the viral components

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18
Q

Explain maturation

A

Time needed for the different components to be assembled

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19
Q

Explain rise period

A

Virions are detected outside the cell
two things can happen why the virus are detected outside:
-Lysis: virus-encoded proteins damage the cytoplasmic membrane. In bacteria, a virus-encoded protein destroys the peptidoglycan layer.
-Budding (enveloped virus)

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20
Q

What is burst size

A

Number of virions released (varies according to the virus, host cell, etc.)

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21
Q

What is the usual time for virus replication cycle in bacterial and animal viruses

A

Bacterial: 20-60 min
Animal: 8-40 h

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22
Q

Best-studied bacteriphages infect ___

A

E.coli (gram-negative)

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23
Q

Most phages contain ___ genomes. Most are ___, nut some have ___

A

dsDNA genomes

Most are naked, but some have lipid envelopes

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24
Q

Two types of bacteriophages

A
  • Virulent phages

- Temperate phages

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25
Q

Explain what is virulent phage and give examples

A

Infection of host cells always leads to replication resulting in host cell lysis (lytic pathway)

Example: T4

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26
Q

Explain what is temperate phage and give examples

A

Have two options:
1) lytic pathway
2)Lysogenic pathway- the genome becomes incorporated into the bacterial host genome.
Ex.: Lambda

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27
Q

Lambda was discovered by

A

Ester Lederberg

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28
Q

T4 virus looks like

A

Usual complex virus, spider

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29
Q

How does T4 gets absorbed

A

T4 attaches to the core region of LPS by the tail fibers

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30
Q

What is the genome of T4

A

ds DNA, linear

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31
Q

What happens after T4 gets attached

A

The tail sheath contracts, forcing the central core through the outer membrane. Tail lysozymes digest the peptidoglycan layer, forming a small pore

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32
Q

What happens after the formation of the pore in peptidoglucan by T4

A

The phage DNA is then injected onto the cytoplasm of the host cell

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33
Q

Steps of T4 inside of bacteria

A

Nucelases, DNA polymerases, New sigma factors help in translation of phage DNA-> phage head proteins, tail, etc.-> mature phage particle-> T4 lysozyme prodiction->lysis

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34
Q

Explain lambda structure

A

Has no tail fibers

Has only one tail

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35
Q

Explain Lambda replication

A

As a temperate phage it can be integrated into the host genome and remain silent and under certain conditions it can exit the chromosome and continue the lytic pathway

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36
Q

The exit of the prophage from the choromosome is called

A

Excision

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37
Q

What is lysogeny

A

Latent sate of infection when phage is carried on the chromosome

38
Q

What is prophage

A

Phage genome within the host cell chromosome

39
Q

What is lysogen

A

Batcerum that contains a prophage

40
Q

Phage Lambda’s genome is ___

A

Linear dsDNA with cohesive ends, a region of single stranded complimentary DNA

41
Q

What is happening with cohesive ends

A

They join, forming a circular molecule of dsDNA

42
Q

Explain how Lambda genome is incorporated into bacterial genome

A

It is incorporated into specific site: at attlamba site of bacterial chromosome. The at region in the phage genome is homologous to the attlambda site. The enzyme lambda intergrase(site-specific nucleases) catalyzes integration of the phage genome at this site. The lambda integrase is encoded on the phage genome

43
Q

Phage фX174 is ___ genome

A

plus strand DNA (same strand as mRNA)

44
Q

What Phage фX174 should do first

A

The minus strand must be synthesized first to produce a dsDNA genome, the replicative form

45
Q

Step by step replicaton of ssDNA strand in Phage фX174

A

-Formation of negative DNA strand inside circle plus strand.
-Cutting of the plus strand is accomplished by the A
protein
-Continued rotation of the circle leads to the
synthesis of a linear fX174 genome(counterclock wise)
-When the growing viral strand reaches unit length , the A protein cleaves it and then ligates the two
ends of the newly synthesized single strand to give a singlestranded
DNA circle

46
Q

The result of one replication cycle in fX174),

A

One relication form ( two circles)

One ssDNA positive form

47
Q

What is MS2 (genome)

A

Plus strand RNA phage (same strand as mRNA). For replication minus strand should be synthesized

48
Q

Explain how the replication of MS2 occurs

A

The genome first used as an mRNA and directs the synthesis of an RNA replicase (RNA-dependent RNA polymerase, this functin is not performed by th ehost) and other viral proteins.
Then the RNA replicase synthesizes a minus strand RNA that is used to produce additional mRNA and additional copies of the genome (plus strand) for the production of new virions

49
Q

Where the replication of the viral genome will occur (animal viruses)

A

DNA viruses-> in the nucleus

RNA viruses->cytoplasm

50
Q

Examples of animal viruses with DNA genome

A

Herpesvirus

Papovavirus (human papilomavirus)

51
Q

How the penetration of Herpesvirus ,Papovavirus occurs

A

Fusion of the cell cytoplasmic membrane with the virus envelope. Nucleocapsid is transported to the nucleus where viral DNA is uncoated

52
Q

How the transcription/ translation of Herpesvirus

Papovavirus genome occurs

A
  • Immediate early proteins (transcription factors and, in some cases, virus specific RNA polymerase)
  • Delayed early proteins (viral-specific DNA polymerase, and other viral proteins necessary for replication)
  • Late proteins:nucleocapsid
53
Q

How the replication of DNA virus occurs

A

Through rolling circle replication

54
Q

How does assembly of DNA virus occurs

A

Assembly occurs in the nucleus, envelope is added via budding process through the inner membrane of the nucleus. The complete virions are then secreted out of the cell by the ER-Golgi pathway

55
Q

If ssDNA genome comes into the cell , what happens first

A

It is converted to a dsDNA replicative form

56
Q

Example of plus RNA genome viruses (animal)

A

Poliovirus

Hepatitis A

57
Q

The genome of plus RNA viruses can be ___

A

Translated directly

58
Q

In poliovirus, what happens to proteins

A

The plus-strand RNA serves as a template for synthesis of a large polyprotein that is cleaved into proteins

59
Q

Poliomyelitis is transferred through

A

Faecal-oral route

60
Q

explain polimyelitia as a disease and if it is treated

A

Little to no symptoms in 99% cases
Paralytic poli in 0.5-1% cases( usually in legs)
-Skeletal deformities post-paralytic polio
-No cure, but safe and effective vaccine

61
Q

Example od minus strand RNA viruses

A

Measles, Rabies (rhabdovirus), Influenza (orthomyxovirus)

62
Q

How the genome of minus strand RNA replicated

A

Cannot be translated directly. It is first transcribed into a plus-strand RNA by an RNA-dependent RNA polymerase carried inside the virions

63
Q

Did we get rid of of measles

A

Yes

64
Q

What are severe complications of measles

A

Pneumonia
Encephalitis(deafness, intellectual disability)
Death

65
Q

What are long term complications of measles

A

-Subacute sclerosing panencephalitis(SSPE): progressive fatal neurodegenerative disease

66
Q

What can be done to prevent measles

A

Safe and effective vaccine

67
Q

The example of dsRNA virus

A

Rotavirus (reovirus)

68
Q

How dsRNA replicates

A

The dsRNA can not be translated as it is. First, a plus strand RNA must be synthesized by a viral-encoded RNA dependent RNA polymerase using minus strand as a template.
The plus-strand is then translated into proteins and is used as a template to synthesize a minus strand to yield ds RNA genomes

69
Q

Example of retrovirus

A

HIV

Rous sarcoma virus(causing cancer)

70
Q

Genome of retrovirus

A

The virons carries two identical copies of the genome( plus,strand ssRNA), reverse transcriptase , intergrase and proteases

71
Q

Explain the replication of the genome in retro viruses

A

Th reverse transcriptase is an RNA-dependent DNA polymerase that reverse trasnscribes the RNA genome into DNA
The DNA genome travel to the nucleus and is integrated into the host DNA

72
Q

What LTR and what is their function

A

Long terminal repeats.

Contain promoters for trasncription and participate in the integration process

73
Q

What is provirus

A

ingrated viral DNA. Contrary to the lambda, the provirus cannot excise from the host genome

74
Q

What are the consequnces of viral infection in animal cells

A
  • Tumor cell-> tumor cell division
  • Lysis( release of virus and death of cell)
  • Persitent infection (slow release of virus without the death of the cell)
  • Latent infection(virus present , but not replicating)
  • Cell fusion
75
Q

How does cell fusion happens with virus

A

Enveloped viruses that fuse with the host cell cytoplasmic membrane carries viral proteins that fuse biological membranes
cells fusion result in hybrid cells that have chromosomal aberrations, and are short lived

76
Q

What is transformation

A

Conversion of a normal cell into a tumor, a cell has acquired immortality and unconrolled replication. Can be caused by a viral infection. The cell can be already predisposed to it and the virus just pushes

77
Q

Both __ viruses are known to cause tumors in animals and in humans

A

DNA and RNA viruses

78
Q

Four different mechanisms how viruses can make the cell oncogenic

A
  1. Transduction
  2. Insertion of a strong promoter
  3. Inactivation of a tumor suppresor gene
  4. Expression of a viral protein that induces transformation (DNA virus)
79
Q

What viruses are associated with human cancer

A

-Epstein -Barr virus (DNA)
-Hepatitis C Virus (RNA)
-Human T-lymphotropic virus type 1 (retrovirus)
Hepatitis B virus (RNA)
Human papillomavirus (DNA)

80
Q

How does transduction scenario occurs with cancer and by what type of viruses

A

By RNA viruses (Rous Sarcoma Virus)
The virus carries one or many oncogenes, called v-oncogenes (for virus-encoded oncogene). The v-oncogene was acquired from the host, This process is called transduction. Oncogenes are similar to normal genes found in eukaryotes, known as proto-oncogenes or c-oncogenes. High expression of the oncogene affects the regulation of replication and/or cell death and causes transformation

81
Q

What is the purpose of proto-oncogene

A

The proto-oncogene is usually involved int he regulation of the cell cycle or in safety mechanisms that prevent transformation

82
Q

What is src

A

an adaptor protein in viral genome that orchestartes signal transduction in animal cells. Expression of v-Src is locked in an “ON”mode. When expressed in a cell, v-Src activates numerous pathways that should not be active, resulting in transformation of the cell

83
Q

Explain the mechanism of cancer development through promoter

A

The virus does not encode an oncogene.
insertion of a strong promoter of the provirus next to a proto-oncogene, he proto-oncogene is then expressed at high levels and results in misregulation of the pathway that prevents transformation. the site of integration of the provirus is very important and transformation will occur only if a proto-oncogene is affected

84
Q

Who usually does cancer development through a promoter

A

Retrovirus

85
Q

Who usually does cancer development through an inactivation of a tumor suppressor gene

A

retrovirus

86
Q

how does cancer development through an inactivation of a tumor suppressor gene occur

A

The virus does not have an oncogene
Insertion of the provirus in a gene involved in the regulation of proto-oncogene expression. Insertion causes inactivation of the tumor suppressor gene and uncontrolled expression of the proto-oncogene, resulting in transformation

87
Q

Who usually does cancer development through expression of a viral protein

A

DNA virus

88
Q

How does cancer development through expression of a viral protein occur

A

The viral protein does not have a cell counterpart.
Integration of the viral genome into the host genome may occur (such as int he case of adenovirus,dsDNA) or the viral genome may persist in the cell as an extrachromosomal episome.
Some DNA viruses that cause tumor do so because they have infected a nonpermissive host, in which they cannot complete their infection cycle. The cell is infected and undergoes uncontrolled replication. Because the virus cannot complete its replication, the cells will never die

89
Q

Example of viruses that make cancer through viral protein

A

Human papilloma virus(HPV)

Gene E6 and E7 induce transformation

90
Q

How HPV work

A

Infects epidermal or mucosal epithelial cells that are still able to proliferate( basal layer cells)
Basal layer:viral gene expression is largely suppressed, but limited expression of specific “early” viral genes (E5,E6 and E7)->enhanced proliferation infected cells and their lateral expansion

Introductory Microbiology (21 decks)

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