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BIOL 2604 > Virology > Flashcards

Virology Flashcards

1
Q

What is the difference/similarity between a bacteriophage and a virus?

A

-Virus is the general class of organism.
-Phage is a subclass of virus that infects bacteria

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2
Q

How big is a typical bacteriophage or virus?

A

-MUCH smaller than cell it infects.
-Most are 30 to 300 nm (bacteria average 1000 nm in diameter)

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3
Q

What is the basic structure of a bacteriophage or virus?

A

-Nucleic acid surrounded by protein capsid

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4
Q

What types of nucleic acids are present in their genomes?

A

-All varieties, ssDNA, dsDNA, ssRNA, and dsRNA

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5
Q

What steps are involved in the reproductive cycle of a T4 lytic phage?

A

Eary-Takeover of host cell machinery
Middle-Replication of phage genome
Late-Capsomer production, Capsid assembly, Genome packaging, Host cell lysis

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6
Q

What is happening during the latent period of a phage lytic infection?

A

-No increase in the number of plaque-forming units=early and middle function
-PFU only increase during packaging

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7
Q

What is involved in the reproduction cycle of a lambda lysogenic phage?

A

-Most phage go into lytic cycle
-some go into lysogenic cycle where phage gene expression is silenced and the phage DNA is inserted into the host chromosome
-the phage DNA is replicated along with the host DNA during all “LYSOGEN” cell growth and division
-eventually the “PROPHAGE” can be induced, it exits the host chromosome and starts a new lytic cycle.

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8
Q

How can you measure the abundance of bacteriohages?

A

-Plaque assay
-Spread phage sample on plate along with host cells
-incubate to get bacterial lawn
-count the number of clear spots where cells were lysed=plaques
-each plaque derived from one phage particle

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9
Q

What is involved in the reproductive cycle of a retrovirus?

A

-ssRNA is used as template to produce dsDNA by REVERSE TRANSCRIPTION
-DNA inserts into host cell chromosome by INTEGRASE
-HIV genes are expressed from that PROVIRUS to produce mRNA, which is also the + strand RNA assembled into viral particles
-Translation produces polyprotein, which is cleaved into individual viral protein components by HIV protease

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10
Q

What is an enveloped virus and what types of molecules make up the envelope?

A

-A virus that has a membrane surrounding the nucleocapsid
-generally these infect animal cells
-the envelope contains lipids from the host cell cytoplasmic membrane plus viral “spike” protein that were inserted into the membrane during viral growth.

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11
Q

What is the difference between “RNA replicase” and “Reverse transcriptase”?

A

-RNA-direct RNA synthesis versus RNA-directed DNA synthesis

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12
Q

How do influenza viruses undergo antigenic shift?

A

-They acquire a significantly different gene encoding one of the two major antigens (H or N) when a single cell is infected by two different influenza virus strains
-this can happen only because the influenza genome is made up of 8 separate RNA molecules, each encoding a different protein

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13
Q

What is a viroid?

A

-is an infectious RNA molecule
-infects plants
-does not encode any protein

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14
Q

What is a prion?

A

-is an infectious protein molecule that is not produced from any infectious nucleic acid
-the gene is in the host chromosome
-protein is only infectious when it is improperly folded and able to catalyze the further misfolding of host-produce proteins

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15
Q

What are plus and minus strand RNA?

A

-(+) strand is mRNA
-(-) strand id the complement of mRNA which can be used as a template by RNA replicase to produce + strand RNA

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16
Q

Bacteriophages

A

-infect bacteria

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17
Q

Viruses

A

-NOT FREE LIVING
-obligate intracellular parasites
-not cellular
-infect eukaryotes or archaea
-need a host and their machines to make copies/reproduce
-no metabolism

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18
Q

Are viruses smaller or bigger than living cells? and do they have small or big genomes?

A

-smaller in size than living cells
-Small genomes

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19
Q

Baltimore Classification Scheme

A

-based on the nucleic acid metabolism of the virus
-7 classes
-Baltimore got a noble prize

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20
Q

Viral Class

A

-DNA viruses
-RNA viruses
-RNA - DNA viruses

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21
Q

Viral Genome

A

-DNA viruses = ssDNA and ds DNA
-RNA viruses = ssRNA and ds DNA
-RNA-DNA viruses = ssRNA (retroviruses) and dsDAN (hepadnarviruses)

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22
Q

Virus Structure

A

-Nucleocapsid
-Sometimes covered by an envelope (membrane)
-Sometimes carries specialized enzymes
-genome protected by protein coat
-Helical vs Icosahedron shapes

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23
Q

Nucleocapsid

A

-nucleic acid plus capsid
-composed of proteins
-naked virus

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24
Q

Enveloped viruses

A

-form of nucleocapsid
-composed of lipids, and brown balls - are proteins that code the outside and allow the virus to enter the host cell

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25
Q

What are the types of protein coats that protect genome?

A

-capsid
-capsomere (individual subunits that make up capsid)

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26
Q

Helical

A

-ex. Tobacco
-long and hollow
-capsids are in a spiral shape around the RNA

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27
Q

Icosahedron

A

-20 sides
-12 vertices
-sides are triangular shape
-2, 3, and 5 fold symmetry

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28
Q

What type of microscope are you able to viral structures under?

A

-Electron microscope

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29
Q

Parts of a bacteriophage T4 structure

A

-head (nuclide capsule)
-collar
-tail
-tail pins
-base plate
-tail fibers

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30
Q

What does bacteriophage T4 infect and what does it look like?

A

-E. coli
-moon lander

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31
Q

Steps of viral repliaction

A

-Attachment
-Penetration (punch it way through)
-Synthesis (make nucleic acid and viral proteins)
-Assembly and packaging
-Release (Outside!)

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32
Q

Can a virus infect if it doesn’t attach?

A

-No

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33
Q

Detail steps viral replication

A

-attachment (absorption of phage virion)
-Penetration of viral nucleic acid, viral DNA enters, and protein coat remains outside
-Synthesis of viral nucleic acid and proteins using cellular machinery and subunits
-Assembly and packaging of new viruses (make head like structure)
-cell lysis and release of new virions

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34
Q

Parts of a one-step growth curve for virus replication

A

-virus added -> latent period -> increase slope
-eclipse and maturation
-look at slides

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35
Q

Parts of the eclipse section on the graph

A

-early enzymes
-nucleic acid
-proteins coats

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36
Q

Parts of the maturation section on the graph

A

-assembly and release

37
Q

Blast Size

A

-number of virions released from an infected host cell during the lytic cycle of viral replication

38
Q

Quantification of Viruses: bacterial cells

A

-based on destruction of bacterial cells
-plaque assay for bacteriophage
-isolation of pure virus strain in a plaque
-confluent

39
Q

Quantification of Viruses: eukaryotic cells

A

-based on the destruction of eukaryotic cells
-plaque assay for animal viruses uses tissue culture cells
-confluent monolayer of tissue cells
-stain dyes all red

40
Q

Attachment and Penetration by Bacteriophage

A
  1. Tail compress to eject T4 to the peptidoglycan layer
41
Q

Does a hole punched through the peptidoglycan layer kill the cell?

A

-No, the hole has to go through the cytoplasmic membrane to kill the cell

42
Q

Synthesis of viral nucleic acids: DNA

A

-Class I
-Class II
-Class VII

43
Q

Class I

A

-dsDNA (+) virus
-classical semiconservative
-transcription of minus strand
-no rRNA

44
Q

Class II

A

-ssDNA (+) virus
-classical semiconservative
-discard (-) strand
-synthesis of other strand, ds DNA intermediate, transcription of minus strand

45
Q

Class VII

A

-dsDNA (+) virus
-transcription followed by reverse transcription
-transcription of minus strand
-has rRNA

46
Q

what does (+) mean?

A

-mRNA coding

47
Q

Synthesis of viral nucleic acids: RNA Viruses

A

-Class III
-Class IV
-Class V
-Class VI

48
Q

Class III

A

-dsRNA virus
-transcription of minus strand
-makes ssRNA (+) and transcribe from this to give ssRNA (-) genome

49
Q

Class IV

A

-ssRNA virus (+)
-used directly as mRNA
-makes ssRNA (-) and transcribe from this to give ssRNA (+) genome

50
Q

Class V

A

-ssRNA (-) virus
-transcription of minus strand
-make ssRNA (+) and transcribe from this to give ssRNA (-) genome

51
Q

Class VI

A

-ssRNA (+) retrovirus
-reverse transcription
-dsDNA intermediate
-transcription of minus strand
-integrate into chromosome
-make ssRNA (+) genome by transcription off of (-) strand of dsDNA

52
Q

Types of bacteriophage that infect bacterial cells

A

-RNA= ss MS2 and ds O6
-ssDNA = Ox174 and fd, M13
-dsDNA = T3, T7 (T odd) and Mu and Lambda and T2, T4 (T even)

53
Q

Lytic/Virulent phage: T4 phage

A

-early gene expression
-middle gene expression
-late gene expression

54
Q

Early gene expression

A

-takeover of cellular machinery
-T4 nucleases
-DNA polymerase
-new sigma factors

55
Q

Late gene expression

A

-phage head proteins
-tail, collar, base plate and tail fibers

56
Q

What happens in the lysis stage in T4?

A

-mature T4 virion
-T4 lysozyme production

57
Q

How long does Lytic phage take to mature?

A

-25 minutes

58
Q

What type of phage is Lambda phage?

A

-Lysogenic/temperate phage
-prophage when inserted into genome

59
Q

Lysogenic Pathway

A

-Attachment of the virus to the host cell
-injection of viral DNA
-Viral DNA is integrated into host DNA
-Viral DNA is replicated with host DNA at cell division

60
Q

Lytic Pathway

A

-Attachment of the virus to the host cell
-injection of viral DNA
-Lytic events are initiated
-Induction
-Phage components are synthesized and virions are assemble
-Lysis of the host cell and release of new phage virions

61
Q

Are lysogenized cells immune to reinfection from same phage?

A

-Yes

62
Q

RNA phage: MS2

A

-genome encodes only 4 proteins
-Overlapping genes
-“+” RNA in virion serves as mRNA template for - RNA
-“-“ RNA is replication intermediate and template for + RNA

63
Q

What are the 4 proteins that MS2 genome encode?

A

-Maturation protein (1 copy in viral particle)
-Coat protein (capsomere)
-Lysis protein
-RNA replicase

64
Q

How can genes overlap?

A

-they are set in different frame
-look at notes for viral multiplication

65
Q

Nonenveloped DNA viruses that infect Eukaryotic Host

A

-Parvovirus (ssDNA)
-Papovavirus (dsDNA)
-Adenovirus (dsDNA) = causes colds
-Iridovirus (dsDNA)

66
Q

Viruses that Infect Eukaryotic Host

A

-Infect plants and animals

67
Q

Enveloped DNA viruses that infect Eukaryotic Host

A

-Hepadnarvirus (partially dsDNA)
-Poxvirus (dsDNA)
-Herpesvirus (dsDNA) = causes cold sores and integrate into chromosome

68
Q

Nonenveloped RNA viruses that infect Eukaryotic Host

A

-Picronavirus (ssRNA) = small
-Reovirus (dsDNA)

69
Q

Enveloped RNA viruses that infect Eukaryotic Host

A

-all ssRNA
-Rhabdovirus
-Togavirus
-Orthomyxovirus
-Bunyavirus
-Coronavirus
-Arenavirus
-Retrovirus
-Paramyxovirus

70
Q

Eukaryotic viruses

A

-possible outcome of infection
-most viruses are lytic
-very few cause cancer

71
Q

What is the anti-cancer cell?

A

-P53

72
Q

What can come from a eukaryotic virus cell?

A

-transformation into a tumor/cancer cell
-lysis of infected cell and release of virus
-Persistent infection
-Latent infection
-cell fusion (2 nuclei)

73
Q

Persistent infection

A

-virus gets outside cell
-slow release of virus without cell death

74
Q

Latent infections

A

-Virus present but not replicating

75
Q

-Eukaryotic Viruses: Influenza

A

-RNA virus
-Genome is in eight segments of RNA
-Immunity is via antibodies against surface proteins
-various strains infect humans, pigs, birds and other animals

76
Q

What surface proteins are against influenza immunity?

A

-Neuraminidase
-Hemagglutinin

77
Q

How are new strains of influenza produced?

A

-Co-infection of one animal/cell by two strains of influenza can allow mixing of the segmented genome (Antigenic shift)
-this produces a new strand that human haven’t seen previously and no immunity against it

78
Q

Steps of Eukaryotic Viruses: Retroviruses

A

-Retrovirus virion containing two copies of ssRNA
1. Entrance
2. Uncoating
3. Reverse Transcription
4. Travel to nucleus and integration into host DNA
5. Transcription - viral mRNA and genomic RNA
6. Encapsidation - nucleocapsid
7. Binding - host cytoplasmic membrane
8. Release - progeny retrovirus virions

79
Q

Corona Viruses - COVID 19

A

-Spike protein binds to a receptor on the surface of susceptible cells
-receptor for COVID is the ACE-2 protein

80
Q

What is ACE-2 and where is it found?

A

-angiotensin converting enzyme 2
-is found on the surface of many types of cells, including respiratory and intestinal epithelia (diarrhea)

81
Q

Steps of corona virus

A
  1. Infection, ssRNA genome release
  2. Translation of replicase gene
  3. Synthesis of minus strand
  4. Synthesis of monocistronic mRNA and synthesis of genome copies
  5. Translation of yield viral proteins
  6. viral assembly
82
Q

Stages of HIV and AIDS

A

-eukaryotic retrovirus
-symptom free
-swollen lymph glands
-Subclinical immune dysfunction
-opportunistic infection
-systemic immune dysfunction

83
Q

Levels of T cells

A

-normal range
-significantly depressed
-severe T cell depletion

84
Q

Viroid

A

-infectious RNA molecules
-small circular ssRNA molecules that cause plant diseases
-no protein coat
use plant machinery to replicate
-replication of virion in plants causes disruption of normal function

85
Q

Prions

A

-Infectious proteins
-Normal protein is a normal component of nerve cells
-infectious form is improperly folded and catalyzes improper folding of native protein
-look at slides

86
Q

Prion virus in animals

A

-Scrapie = sheep
-Chronic wasting disease (deer)
-Mad cow disease = humans
-Creutzfeldt - Jakob disease
-Kuru = caused by cannibals

87
Q

Definition of Prions

A

-composed of proteins
-cause degenerative and fatal neurological disease
-protein misfolding

88
Q

What is the difference between “RNA replicase” and “Reverse transcriptase”?

A

-RNA-direct RNA synthesis versus RNA-directed DNA synthesis

BIOL 2604 (17 decks)

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