Microbiology Flashcards
1
Q
Virus
A
obligate intracellular parasite that replicates by self assembly of components
2
Q
Segmented genome
A
effectively like several chromosomes in one virion
3
Q
capsid
A
protein shell that virus genomes are packaged in
4
Q
Types of capsids
A
helical
icosahedral (spherical)
complex
5
Q
capsomeres
A
self assembles into a capsid
determines the shape of the capsid
lots of repeating units because of limited genome
6
Q
nucleocapsid
A
genome + capsid
7
Q
lipid envelope
A
derived from cellular membranes
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
9
Q
Virally-encoded glycoproteins
A
inserted into the cell membrane and serve as virus attachment proteins and membrane fusion proteins
(enveloped viruses)
10
Q
Virion for naked virus
A
nucleocapsid
11
Q
Virion for enveloped virus
A
nucleocapsid + membrane
12
Q
Spread of enveloped viruses
A
spread in large droplets, secretions, organ transplants, and blood transfusions
13
Q
concerted assembly
A
cover up genome with nucleocapsid as the genome is being made
14
Q
procaspid
A
proteins sequential self assembly without the virus genome inside, then the genome gets stuffed in
favored by DNA virus
15
Q
Benefits of enveloped virus
A
- avoid immune system
- have same siliac acid and are partially camouflaged by host carbohydrates
16
Q
viral entry into host cell: naked virus
A
- endocytosis
- - pH dependent from endosomes into cytoplasm
17
Q
viral entry into host cell: enveloped virus
A
membrane fusion
18
Q
Major steps in viral replication
A
- attachment
- penetration
- uncoating
- early transcription
- genome replication
- late transcription
- assembly
- release
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
20
Q
location of genome replication
A
RNA: cytoplasm
DNA: nuclear (except poxvirus)
21
Q
late transcription
A
synthesis of structural proteins
22
Q
assembly location
A
RNA: cytoplasmic
DNA: nuclear (except poxvirus and hepadnavirus)
23
Q
Release of virus particles
A
- cell lysis
- budding (enveloped)
24
Q
viral cytopathogenesis
A
- inhibition of cellular protein synthesis
- inhibition and degradation of cellular DNA
- alteration of cell membrane structure
- disruption of cytoskeleton
- formation of inclusion bodies
- DNA: nucleus
- RNA: cytoplasm - toxicity of virion components
25
+RNA virus genome
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
26
-RNA virus genome
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
27
Retrovirus
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
28
Reverse transcriptase mechanism
1. make a DNA strand (with the RNA strand)
2. get rid of RNA strand
3. make second DNA strand
29
DNA virus genome
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
30
Why do we have antivirals that can target herpes but not HPV?
herpes: evolved to have own DNA pol giving unique targets
HPV: small and has to use host DNA pol; no unique targets
31
Viral RNA pol lacks efficient proof reading function, unlike DNA pol (host or viral). What are the consequences?
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
32
plaque
hole in a confluent monolayer of cells due to viral lysis
33
lysate
suspension of virions in culture medium that results from unrestricted growth of the virus on a cell monolayer
34
particle-to-pfu ratio
number of physical particles compared to the number of infectious virions
35
plaque assay
measure the number of infectious virions in a given volume of lysate
- - titer = pfu/ml of lysate
- - determines infectivity
36
Multiplicity of infection (MOI)
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
eclipse period
post-penetration phase until virus can be detected intracellularly
-- uncoating, early transcription, genome replication steps, ends at virus assembly
38
latent period
post-penetration phase until virus can be detected extracellularly
includes eclipse period
-- uncoating, early transcription, genome replication, virus assembly, and release
39
Why do viral mutations occur at a relatively high frequency?
1. large number of genome copies in every cell
| 2. polymerase errors
40
complementation
*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
recombination
*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
reassortment
*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
Routes of viral entry
1. breaks in skin or mucosa
| 2. inhalation
44
Localized spread of virus
1. release of virus from infected cell and infection of surrounding cells
2. syncytia formation
45
syncytia formation
some enveloped viruses can fuse an infected cell with an uninfected cell
46
secondary spread
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
viremia
virions in the blood
48
incubation period
period post infection to onset of symptoms
| can be infectious
49
acute phase of infection
symptomatic phase
50
3 forms of persistent infection
1. chronic
2. latent
3. transforming
51
chronic infection
virus is produce at low levels, but may not cause disease symptoms (HBV)
52
latent infection
virus genome, remains in cells indefinitely, but virus particles are not produced until reactivation (herpes and HIV)
53
transforming infection
viral genome integrates into cellular DNA or is otherwise maintained in the cell and immortalizes the cell, alters its growth properties
-- oncogenic
54
oncogenic viruses
RNA: retrovirus and HCV
DNA: HBV, papilloma, polyoma, adenovirus type 2, EBV, herpes-8, pox
55
immune responses to viruses
1. nonspecific
2. antigen specific (several days post infection)
3. evolved immune defense mechanisms
4. viral immunopathogenesis
56
Non-specific viral immune response
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
viral PAMPs
1. dsRNA
2. unmethylated DNA
3. 5' modified ssRNA
58
protein kinase (PKR) pathway
inactivates initiation factor elF-2 (inhibits viral protein translation)
59
2-5A pathway
activates RNase L
60
Mx pathway
GTPases that inhibit RNA pol
61
antigen specific viral responses
1. CD8+ T cells (lysis)
| 2. Ab (neutralize or facilitate lysis with complement)
62
viral evolved immune defense mechanisms
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
viral immunopathogenesis
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
types of vaccines
1. live attenuated
2. killed
3. subunit (recombinant DNA)
65
Why don't we have vaccines for all viruses?
Not practical if
1. large number of virus strains
2. virus undergoes lots of antigenic variation due to high mutation rate
66
Immune globulin
passive immunization
| -- used both pre and post exposure
67
attenuated virus vaccine
```
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
killed virus vaccine
```
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
Subunit viral vaccines
*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
Gene Therapy
treating disease based on modifying the expression of a person's genes toward a therapeutic goal
71
Somatic gene therapy
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
Germline gene therapy
genetic modification of germ cells that will pass the selected change on to the next generation
-- limited to animal models
73
Describe ex vivo, somatic cell gene therapy
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
Diseases being treated in gene therapy clinical trials
1. genetic deficiencies
2. viral infection
3. autoimmunity
4. cancer
5. diseases in which several genes and the environment interact
75
What do the majority of clinical trials involved in gene therapy treat?
cancer
| Next: cardiovascular and monogenic diseases like OTC or ADA
76
Genetic diseases being treated in gene therapy clinical trials
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
Viral infection being treated in gene therapy clinical trials
HIV
78
Autoimmunity being treated in gene therapy clinical trials
rheumatoid arthritis
79
Cancers being treated in gene therapy clinical trials
1. head and neck tumors
| 2. prostate, breast, and colon cancer
80
Diseases in which several genes and the environment being treated in gene therapy clinical trials
1. diabetes
| 2. coronary artery disease
81
Glybera
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
Therapeutic gene therapy strategies
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
Cytolytic gene therapy strategies
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
adenovirus vector
1. episomal
2. high transduction efficiency
3. infects replicating and non-replicating cells
4. elicits an immune response
5. insert capacity 8-36kb
85
adeno-associated virus vector
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
6. limited insert capacity (about 5kb)
86
herpesvirus vector
1. episomal
2. large insert capacity
3. broad host range
4. . infects dividing and non-dividing cells
87
Liposomes/Naked DNA vector
1. no limit to the size of genes that can be delivered
2. low immunogenicity
3. poor levels of gene transfer
88
retrovirus vector
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
lentivirus vector
type of retrovirus
| -- inserts into dividing and non-dividing cells
