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SS- CMOD Block 2 > Microbiology > Flashcards

Microbiology Flashcards

1
Q

Virus

A

obligate intracellular parasite that replicates by self assembly of components

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2
Q

Segmented genome

A

effectively like several chromosomes in one virion

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3
Q

capsid

A

protein shell that virus genomes are packaged in

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4
Q

Types of capsids

A

helical
icosahedral (spherical)
complex

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5
Q

capsomeres

A

self assembles into a capsid
determines the shape of the capsid
lots of repeating units because of limited genome

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6
Q

nucleocapsid

A

genome + capsid

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7
Q

lipid envelope

A

derived from cellular membranes

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8
Q

Factors affecting stability of enveloped viruses

A

less stable than naked viruses

  • more susceptible to drying
    • can’t survive as fomites
  • sensitive to detergents and alcohols
  • cannot survive GI tract
    • reside in blood and respiratory tract
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9
Q

Virally-encoded glycoproteins

A

inserted into the cell membrane and serve as virus attachment proteins and membrane fusion proteins
(enveloped viruses)

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10
Q

Virion for naked virus

A

nucleocapsid

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11
Q

Virion for enveloped virus

A

nucleocapsid + membrane

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12
Q

Spread of enveloped viruses

A

spread in large droplets, secretions, organ transplants, and blood transfusions

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13
Q

concerted assembly

A

cover up genome with nucleocapsid as the genome is being made

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14
Q

procaspid

A

proteins sequential self assembly without the virus genome inside, then the genome gets stuffed in
favored by DNA virus

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15
Q

Benefits of enveloped virus

A
  • avoid immune system

- have same siliac acid and are partially camouflaged by host carbohydrates

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16
Q

viral entry into host cell: naked virus

A
  • endocytosis

- - pH dependent from endosomes into cytoplasm

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17
Q

viral entry into host cell: enveloped virus

A

membrane fusion

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18
Q

Major steps in viral replication

A
  1. attachment
  2. penetration
  3. uncoating
  4. early transcription
  5. genome replication
  6. late transcription
  7. assembly
  8. release
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19
Q

early transcription

RNA vs. DNA viruses

A

synthesis of nonstructural proteins
RNA: virally encoded RNA-dependent RNA pol
DNA: use host DNA-dependent RNA pol

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20
Q

location of genome replication

A

RNA: cytoplasm
DNA: nuclear (except poxvirus)

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21
Q

late transcription

A

synthesis of structural proteins

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22
Q

assembly location

A

RNA: cytoplasmic
DNA: nuclear (except poxvirus and hepadnavirus)

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23
Q

Release of virus particles

A
  • cell lysis

- budding (enveloped)

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24
Q

viral cytopathogenesis

A
  1. inhibition of cellular protein synthesis
  2. inhibition and degradation of cellular DNA
  3. alteration of cell membrane structure
  4. disruption of cytoskeleton
  5. formation of inclusion bodies
    - DNA: nucleus
    - RNA: cytoplasm
  6. toxicity of virion components
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25
Q

+RNA virus genome

A

Functions as mRNA and is immediately translated by cellular ribosomes

  1. translated as a polyprotein that must be cleaved into individual proteins
  2. makes RNA-dependent RNA pol protein
    - - transcribe -RNA from +RNA
    - - -RNA used as template to make lots of +RNA
  3. +RNA copies are used as mRNA
    - - make structural proteins
    - - encapsidated to produce nucleocapsids
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26
Q

-RNA virus genome

A

CanNOT be used as mRNA and is used as a template to transcribe +RNA (mRNA)

  1. carries RNA-dependent RNA pol
    - - transcribe -RNA to +RNA
  2. +RNA
    - - translated into individual proteins (including more RNA pol; does NOT make polyprotein)
    - - template for more -RNA
  3. new -RNA is encapsidated to produce nucleocapsids
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27
Q

Retrovirus

A
  1. carries RNA-dependent DNA pol (reverse transcriptase)
  2. +RNA is reverse transcribed into dsDNA and integrated into host genome
  3. host enzymes (DNA-dependent RNA pol) produce proteins and +RNA genome
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28
Q

Reverse transcriptase mechanism

A
  1. make a DNA strand (with the RNA strand)
  2. get rid of RNA strand
  3. make second DNA strand
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29
Q

DNA virus genome

A

transcribed by host DNA-dependent RNA pol

  1. many viruses have a host shut-off mechanism that degrades host mRNA
  2. many viruses use specific transcription factors that redirect host polymerases to viral genes and away from cellular genes
  3. replication dependent on DNA-dependent DNA pol
    - - large virus: virally encoded
    - - small virus: host encoded
  4. newly produced DNA genomes are encapsidated to produce nucleocapsids
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30
Q

Why do we have antivirals that can target herpes but not HPV?

A

herpes: evolved to have own DNA pol giving unique targets
HPV: small and has to use host DNA pol; no unique targets

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31
Q

Viral RNA pol lacks efficient proof reading function, unlike DNA pol (host or viral). What are the consequences?

A

Can have antigenic variation

    • most mutations are detrimental
    • more drug resistance (need combo therapy)
    • RNA viruses keep the genome small to reduce lethal mutations to virus
    • DNA pol is more fit: can have a larger genome
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32
Q

plaque

A

hole in a confluent monolayer of cells due to viral lysis

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33
Q

lysate

A

suspension of virions in culture medium that results from unrestricted growth of the virus on a cell monolayer

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34
Q

particle-to-pfu ratio

A

number of physical particles compared to the number of infectious virions

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35
Q

plaque assay

A

measure the number of infectious virions in a given volume of lysate

    • titer = pfu/ml of lysate
    • determines infectivity
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36
Q

Multiplicity of infection (MOI)

A

ratio of the number of infectious particles to the number of target cells to be infected
– MOI = 5-10 for all cells to be infected

37
Q

eclipse period

A

post-penetration phase until virus can be detected intracellularly
– uncoating, early transcription, genome replication steps, ends at virus assembly

38
Q

latent period

A

post-penetration phase until virus can be detected extracellularly
includes eclipse period
– uncoating, early transcription, genome replication, virus assembly, and release

39
Q

Why do viral mutations occur at a relatively high frequency?

A
  1. large number of genome copies in every cell

2. polymerase errors

40
Q

complementation

A

*RNA and DNA
An exchange of proteins
– virus A has a lethal mutation in gene X and virus B in the same cell is WT
– virus A uses virus B proteins
Mutant genome can infect a second cell upon release, but will not be able to replicate.

41
Q

recombination

A

*DNA only
An exchange of genetic material on the same
segment of genome.
Genome with lethal mutation exchanges with WT genome.
Can replicate.
Occurs frequently in DNA viruses

42
Q

reassortment

A

*segmented genome
An exchange of genetic material on different segments of genome.
Two segmented viruses infect same cell.
Creates a novel strain of virus from both parents.
Influenza

43
Q

Routes of viral entry

A
  1. breaks in skin or mucosa

2. inhalation

44
Q

Localized spread of virus

A
  1. release of virus from infected cell and infection of surrounding cells
  2. syncytia formation
45
Q

syncytia formation

A

some enveloped viruses can fuse an infected cell with an uninfected cell

46
Q

secondary spread

A

spread from original site on infection by gaining access to the bloodstream or lymphatics
can access CNS through CSF or uptake by peripheral nerves

47
Q

viremia

A

virions in the blood

48
Q

incubation period

A

period post infection to onset of symptoms

can be infectious

49
Q

acute phase of infection

A

symptomatic phase

50
Q

3 forms of persistent infection

A
  1. chronic
  2. latent
  3. transforming
51
Q

chronic infection

A

virus is produce at low levels, but may not cause disease symptoms (HBV)

52
Q

latent infection

A

virus genome, remains in cells indefinitely, but virus particles are not produced until reactivation (herpes and HIV)

53
Q

transforming infection

A

viral genome integrates into cellular DNA or is otherwise maintained in the cell and immortalizes the cell, alters its growth properties
– oncogenic

54
Q

oncogenic viruses

A

RNA: retrovirus and HCV
DNA: HBV, papilloma, polyoma, adenovirus type 2, EBV, herpes-8, pox

55
Q

immune responses to viruses

A
  1. nonspecific
  2. antigen specific (several days post infection)
  3. evolved immune defense mechanisms
  4. viral immunopathogenesis
56
Q

Non-specific viral immune response

A
  1. PRRs (TLR and NOD) recognize PAMP
  2. induce alpha and beta IFNs
  3. IFNs bind uninfected cells and prevent viral replication
  4. PKR, 2-5A, and MX pathways
57
Q

viral PAMPs

A
  1. dsRNA
  2. unmethylated DNA
  3. 5’ modified ssRNA
58
Q

protein kinase (PKR) pathway

A

inactivates initiation factor elF-2 (inhibits viral protein translation)

59
Q

2-5A pathway

A

activates RNase L

60
Q

Mx pathway

A

GTPases that inhibit RNA pol

61
Q

antigen specific viral responses

A
  1. CD8+ T cells (lysis)

2. Ab (neutralize or facilitate lysis with complement)

62
Q

viral evolved immune defense mechanisms

A
  1. antigen variation (Ab)
  2. inhibition of antigen presentation (cellular)
  3. cytokine homologs that down regulate or block cellular response
  4. latent infection in neurons where there is no MHC class I
63
Q

viral immunopathogenesis

A
  1. flu like symptoms by IFN
  2. inflammation by T cells, PMNs and macrophages
  3. hemorrhagic disease (T cells, Ab, and complement)
  4. immune complex disease
  5. immunosupression
64
Q

types of vaccines

A
  1. live attenuated
  2. killed
  3. subunit (recombinant DNA)
65
Q

Why don’t we have vaccines for all viruses?

A

Not practical if

  1. large number of virus strains
  2. virus undergoes lots of antigenic variation due to high mutation rate
66
Q

Immune globulin

A

passive immunization

– used both pre and post exposure

67
Q

attenuated virus vaccine

A 
can cause subclinical infection
Advantages
1. cheap
2. strong, long lasting response (IgG, IgA, T cell)
Disadvantages
1. labile in transport
2. cannot give to immunocompromised
3. can revert to virulence in rare cases
68
Q

killed virus vaccine

A 
Cannot cause illness
Advantages
1. stable
2. rare side effects
3. cannot revert to illness
Disadvantages
1. more expensive
2. shorter term immunity (mostly IgG)
69
Q

Subunit viral vaccines

A

*HBV and HPV
Composed of single viral proteins that are exposed in yeast using recombinant DNA
Advantages
1. cannot cause disease
2. are not derived from blood (another HBV vaccine is)
Disadvantages
1. requires multiple injections

70
Q

Gene Therapy

A

treating disease based on modifying the expression of a person’s genes toward a therapeutic goal

71
Q

Somatic gene therapy

A

manipulation of gene expression in cells so as to be corrective for the patient, but this correction is not inherited by the next generation

72
Q

Germline gene therapy

A

genetic modification of germ cells that will pass the selected change on to the next generation
– limited to animal models

73
Q

Describe ex vivo, somatic cell gene therapy

A
  1. remove piece of patient’s liver
  2. treat with retrovirus carrying LDL receptor gene
  3. liver cells that incorporate the corrective gene are reimplanted into the patient’s liver
    - - can also be done with RBC
74
Q

Diseases being treated in gene therapy clinical trials

A
  1. genetic deficiencies
  2. viral infection
  3. autoimmunity
  4. cancer
  5. diseases in which several genes and the environment interact
75
Q

What do the majority of clinical trials involved in gene therapy treat?

A

cancer

Next: cardiovascular and monogenic diseases like OTC or ADA

76
Q

Genetic diseases being treated in gene therapy clinical trials

A
  1. ornithine transcarbamylase (OTC) deficiency
  2. Lipoprotein lipase (LPL) deficiency
  3. Phenylketonuria (PKU)
  4. hemophilia A and B (Factors VIII or IX)
  5. Leber congenital amaurosis
  6. sickle cell anemia
  7. adenosine deaminase deficiency (ADA)
  8. muscular dystrophy
  9. cystic fibrosis
77
Q

Viral infection being treated in gene therapy clinical trials

78
Q

Autoimmunity being treated in gene therapy clinical trials

A

rheumatoid arthritis

79
Q

Cancers being treated in gene therapy clinical trials

A
  1. head and neck tumors

2. prostate, breast, and colon cancer

80
Q

Diseases in which several genes and the environment being treated in gene therapy clinical trials

A
  1. diabetes

2. coronary artery disease

81
Q

Glybera

A

First commercial gene therapy product approved in Nov. 2012 in Europe
NONE are approved in the U.S.
AAV vector
Treats: Lipoprotein lipase deficiency

82
Q

Therapeutic gene therapy strategies

A

vector carries a gene that encodes a protein that is either defective or that is not present due to mutation in the patients’ endogenous genes
ex: adenovirus vector that has CF chloride channel

83
Q

Cytolytic gene therapy strategies

A

vector designed to destroy or eliminate a diseased cell or tissue
ex: virus with thymidine kinase gene from herpes simplex (TK converts gancyclovir to toxic product)

84
Q

adenovirus vector

A
  1. episomal
  2. high transduction efficiency
  3. infects replicating and non-replicating cells
  4. elicits an immune response
  5. insert capacity 8-36kb
85
Q

adeno-associated virus vector

A
  1. integrates genome into specific region on human chromosome 19
  2. low immunogenicity (no Ab/inflammation)
  3. no associated disease
  4. infects both dividing and non-dividing cells
  5. limited insert capacity (about 5kb)
86
Q

herpesvirus vector

A
  1. episomal
  2. large insert capacity
  3. broad host range
  4. . infects dividing and non-dividing cells
87
Q

Liposomes/Naked DNA vector

A
  1. no limit to the size of genes that can be delivered
  2. low immunogenicity
  3. poor levels of gene transfer
88
Q

retrovirus vector

A
  1. non-pathogenic in humans
  2. stably transduces dividing but not non-dividing cells
  3. inserts genome into host cell’s DNA
  4. long term expression
  5. insert capacity of 8kb
  6. inactivated by human complement
89
Q

lentivirus vector

A

type of retrovirus

– inserts into dividing and non-dividing cells

SS- CMOD Block 2 (16 decks)

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