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MIMG 101 > Bacteria, Archaea, Eukaryote, Virus Phylogeny Groups, SARS CoV-2, and Infectious Spread > Flashcards

Bacteria, Archaea, Eukaryote, Virus Phylogeny Groups, SARS CoV-2, and Infectious Spread Flashcards

1
Q

What are the 8 bacterial phylogeny groups?

A
  1. Cyanobacteria
  2. Gram (+)
  3. Deep branching thermophiles
  4. Deep branching gram (-)
  5. PVC
  6. Spirochetes
  7. Proteobacteria
  8. CPR (candidate phyla radiation)
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2
Q

Cyanobacteria characteristics

A
  • oxygenic photosynthesis
  • ancestors of chloroplasts
  • many also fix nitrogen
  • may be filamentous/multicellular
  • found in communities with other organisms
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3
Q

Gram (+) characteristics

A
  • Firmicutes & actninoycetes
  • tough skin
  • commonly form endospores
  • models for bacterial development
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4
Q

What are examples of gram (+) bacteria

A
  • bacillus subtilis
  • bacillus thuringiensis - insecticide
  • clostridim botulinum - botox
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5
Q

Proteobacteria/Gram (-) characteristics

A
  • largest and most diverse group in structure and metabolism
  • commonly endosymbionts
  • ancestors of mitochondrion
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6
Q

What are examples of proteobacteria/gram (-) bacteria

A
  • e.coli
  • rickettsia
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7
Q

Deep-branching gram (-) characteristics

A
  • gram -, but diverged early from proteobacteria
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8
Q

What are examples of deep-branching gram (-)

A
  • Fusobacteria - virulent pathogens, dental plaque
  • Chorobi - green sulfur bacteria, chlorosomes (efficient photosynthesis)
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9
Q

Spriochetes

A
  • spiral cell
  • endoflagellum
  • agent of lyme disease
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10
Q

PVC

A
  • compartmentalized cells
  • many have no peptidoglycan
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11
Q

What are examples of PVC bacteria

A
  • planctomycetes = internal double-membrane around DNA
  • verrucomicrobia
  • chlamydiae
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12
Q

Deep branching thermophiles

A
  • extreme environments
  • diverse and highly mosaic genomes - many share genes and traits with archaea
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13
Q

What are the 5 groups of Archaeal diversity?

A
  1. Euryarchaeota
  2. Crenarchaeota
  3. TACK (proteoarchaeota) - includes crenarchaeota
  4. Asgard
  5. DPANN
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14
Q

Asgard/Lokiarchaeota

A
  • have several genes previously through to be unique to eukaryotes
  • many models indicate that eukaryotes branch from lokiarchaeota
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15
Q

Euryarchaeota

A
  • includes methanogens
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16
Q

Crenarchaeota

A
  • includes many hyperthermophiles
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17
Q

TACK (proteoarchaeota)

A
  • includes crenarchaeota
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18
Q

DPANN

A
  • loss of many genes
  • typical of obligate symbionts
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19
Q

What is cultured bacteria and archaea versus not cultured

A
  • cultured - known about bacteria
  • not cultured - not known about organisms
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20
Q

What is metagenomics

A
  • the study of community genomes (recover organisms and DNA from environmental samples and then sequence the entire sample)
  • example: human microbiome, sargasso sea, deepwater horizon oil spill
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21
Q

Why use metagenomics

A
  • helps to discover new organisms, metabolic capabilities, and phylogenetic relationships
  • better awareness of microbial communities
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22
Q

What is FISH

A
  • Fluorescence In Situ Hybridization
  • Tag signature sequences on specific microbes (archaea, bacteria, or eukaryotes) with fluorescence - helps identify them in large mixed sample
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23
Q

What are 8 major clades of eukaryote diversity

A
  1. Opisthokonta
  2. Amoebozoa
  3. Plantae (Archaeplastida)
  4. Rhizaria
  5. Alveolata
  6. Stramenopiles (Heterokonta)
  7. Discoba
  8. Metamonada
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24
Q

What are 2 supergroups of eukaryote diversity

A
  1. SAR (supergroup) - includes rhizaria, alveolata, stramenopiles
  2. Excavata (supergroup) - includes discoba and metamonada
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25
Q

Opsithokonta characteristics

A
  • animals
  • true fungi (yeast)
  • microsporidians
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26
Q

Amoebozoa characteristics

A
  • amebas
  • slime molds
  • includes human & agricultural pathogens
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27
Q

Plantae (archaeplastida) characteristics

A
  • land plants - secondary endosymbiosis
  • red algae
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28
Q

Rhizaria characteristics

A
  • amebas with filamentous pseudopods
  • part of SAR supergroup
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29
Q

Alveolata characteristics

A
  • protists with cortical alveoli
  • includes human & agricultural pathogens
  • part of SAR supergroup
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30
Q

Stramenopiles (heterokonta) characteristics

A
  • protists with hairy flagella
  • includes human & agricultural pathogens
  • brown algae
  • part of SAR supergroup
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31
Q

Discoba characteristics

A
  • protists with mitochondria with discoid cristae
  • part of excavata supergroup
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32
Q

Metamonada characteristics

A
  • protists lacking mitochondria
  • part of excavata supergroup
33
Q

What is the cause of malaria

A
  • alveolata phylogeny group
  • organism: plasmodium (parasite)
34
Q

What is the cause of epidemic diarrhea

A
  • metamonada phylogeny group
  • organism: giardia
35
Q

What is the cause of sleeping sickness

A
  • euglenozoa (discoba) phylogeny group
  • organism: trypanosoma
36
Q

What is the cause of red tides

A
  • alveolata phylogeny group
  • organism: dinoflagellates
37
Q

What is the cause of the great irish potato famine

A
  • heterokonta phylogeny group
  • organism: phytopthora
38
Q

Fungi characteristics

A
  • very close to animals
  • multicellular and unicellular (yeast) forms
  • mycelia = networks of filaments (hypahae) for nutrient absorption and communication
39
Q

Algae characteristics

A
  • primary producers
  • evolved from englufing phototrophs
40
Q

Excavata supergroup characteristics

A
  • many devastating human pathogens: giardia (diarrhea), t.brucei(sleeping sickness)
  • no introns
  • polysistronic gene expression
  • two nuclei
41
Q

What are the 7 virus classifications (Baltimore Classification)?

A
  1. dsDNA
  2. ssDNA
  3. dsRNA
  4. (+) sense ssRNA
  5. (-) sense ssRNA
  6. Retrovirus
  7. ParaRetrovirus
42
Q

Characteristics of dsDNA and examples

A
  • must enter host nucleus before replication
  • host cell polymerases replicate DNA, transcribe into + sense mRNA for ribosome to read
  • phage lambda: bacteriphage lambda (e.coli), chloroviruses (algae), herpeseviruses (chickenpox), human papillomavirus
43
Q

Characteristics of ssDNA and examples

A
  • (+) ssDNA
  • complimentary - strand DNA is synthesized, allows for transcription of + mRNA
  • Geminivirus: bacteriophage M13 (e.coli), parvovirus (cat, dog, animals)
44
Q

Characteristics of dsRNA and examples

A
  • needs RNA dependent RNA polymerase and doesn’t require host machinery for duplication
  • RdRP duplicates existing dsRNA and + sense mRNA is transcribed
  • Rotavirus: birnavirus (fish) cystovirus (bacteria), reoviruse (infants)
45
Q

Characteristics of + sense ssRNA and examples

A
  • need RNA dependent RNA polymerase
  • RdRp encodes - sense strand so + sense strand can continue replication
  • ribosome can directy access the mRNA and turn into protein
  • rhinovirus: coronavirus, flaviviruse (zika fever, yellow fever, hepatitis C), poliovirus, tobacco mosaic virus
46
Q

Characteristics of - ssRNA and examples

A
  • need RNA dependent RNA polymerase
  • RdRp transcribes - sense RNA into + sense mRNA for ribosomes to read
  • Rabies: filovirus (ebola), orthomyxoviruse (influenza), paramyxoviruses (measels and mumps), rhabdovirus (rabies)
47
Q

Characteristics of retroviruses and examples

A
  • needs reverse transcriptase
  • + sense RNA is converted by RT into DNA -> DNA is incorperated into host genome -> makes + mRNA
  • Human immunodeficiency virus: HIV (AIDS), FeLV, RSV, ALV
  • difficult to treat since viral DNA is embedded in host DNA and you must kill the cell in order to kill the virus
48
Q

Characteristics of pararetrovirus and examples

A
  • needs reverse transcriptase
  • dsDNA is transcribed into + sense mRNA
  • RT turns mRNA into DNA and used to make more DNA by RT
  • Caulimorvirus: hepadanvirus (hepatitis B)
49
Q

What are the three bacteriophage cycles?

A
  1. Lytic cycle - progeny phage are packaged in capsids and release by cell lyses
  2. Lysogenic Cycle - phage integrates with host genome and bacteria duplicates
  3. Slow release: phages assemble without capsid and exit host cell without lysis -> cell continues to reproduce slowly
50
Q

Explain the lytic and lysogenic cycle how do they relate

A
  1. Lytic: bacteriophage insert DNA -> host cell creates capsids and replicates DNA -> host cell packages progeny phages -> cell lyses to release phages
  2. Lysogenic cycle: bacteriophage insert DNA -> DNA integrates with host genome by site specific recombination -> bacteria reproduces with host and viral DNA
  3. Lysogenic can switch into lytic if there is environmental stress: viral DNA is excised out of host genome
51
Q

How do animal viruses attach and enter the cell?

A
  • membrane fusion by viral RNA with membrane: attaches to host cell receptor proteins, viral membrane fuses with host membrane, and coated RNA enters cytoplasm.
  • Endocytosis by viral RNA: attached to receptor proteins and is endocytosed with host cell membrane (endosome), lysosome fuses and acidifies endosome, releasing uncoated RNA into cytoplasm
  • Endocytosis by viral DNA: attached to receptor proteins and is endocytosed with host cell membrane (endosome), endosome docks onto nuclear membrane and releases uncoated dsDNA into nucleus
52
Q

Four types of receptor proteins for viruses to attach to

A
  • LPS
  • OmpF
  • TolC
  • Flagellar motor
  • receptor specificity drives host range specificity and tissue topism
53
Q

How do you monitor virus growth?

A

Batch culture: culture medium + host cells + virons → count # free virons at different points in time

54
Q

How to count viral particles?

A

Plaque assay
* bacteriophage: add free virons into solution to make phage stock → add e.coli in rich browth culture → add phage-infected bacteria into liquid agar and pour mixture onto agar plate → incubate overnight
* animal cells: Animal cells: grow monolayer of animal cells first → on top add liquid medium with virus mixed in → after infection, removing viral medium → add gelatin medium and identify plaques
* Results:
- if there are plaques (zones of clearance in an other wise smooth bacteria lawn = sign of viral infection) → count number of plaques ($10^6$ phages per one bacteria)
- if the plaques are far apart → low MOI (multiplicity of infection)

55
Q

Cyopathic Effects (CPE)

A
  • Structural changes to animal cells by viral infection
  • culture human cells on plate → infect with poliobirus → imaged by phase conrast microscopy at different times post infection → compare to uninfected control culture
  • Results: Uninfected cells have an oblong shape and are attached → after infection, circular and detached → after lysing, dead cells cump together and plaques form
56
Q

How to visualize viral infection of animal cells?

A
  • Cyopathic Effects (CPE)
  • GFP - tagged viral capsid protein: infect lawn of host cells → visualize by fluorescence microscoppy
57
Q

Bacteriophage Growth Curve

A
58
Q

Animal Virus Growth Curve

A
59
Q

What are specific virus steps antiviral can target?

A
  • block binding/invasion
  • block RT
  • block integration
  • block capsid maturation
60
Q

AZT (azidothymidine) - what mechanisms does it inhibit as an anti-retroviral?

A
  • azt binds to RT and blocks DNA synthesis
  • inhibit protease cleavage (necessary enzyme for capsid assembly)
61
Q

Cryo Electron Microscopy

A
  • Virus is preserved at cold temp and then frozen
  • allows us to see the viruses 3D space as well as the native structure
62
Q

Transmission Electron Microscopy

A
  • beam of electrons is shot at virus
  • allows us to see their 2D shape
63
Q

Mechanism of transformation: Gram (+) bacteria

A
  • transforming double strand DNA binds to Transformasome (DNA binding protein and pore) → DNA is cut into a single strand DNA and taken in by competence specific sssDNA binding proteins → RecA protein recombines DNA into bacterial plasmid
64
Q

Mechanism of transformation: Gram (-) bacteria

A

pilus binds to dsDNA and retracts → dsDNA unwinds and becomes ssDNA when entering cytoplasm → RecA integrates ssDNA to homologous site

65
Q

Transposable elements

A
  • Barbara McClintock: Mobile DNA fragments within the genome
66
Q

Modes of disease transmission

A
  • contact transmission
  • vehicle transmission
  • vector transmission
67
Q

Contact transmission

A
  • Direct contact
  • indirect contact by fomites
  • droplets
68
Q

Vehicle Transmission

A
  • Waterborne
  • Airborne, including dust particles
  • Foodborne
69
Q

Vector Transmission

A
  • Mechanical (on insect bodies)
  • Biological (microbes multiply inside of living vector body)
70
Q

What are the stages of infection?

A
  • incubation: time between acquisition of the pathogen and onset of symptoms (can still be contagious here)
  • prodome stage: nonspecific symptoms (fever or tiredness)
  • period of invasion: disease-specific symptoms increase and height of viral load
  • convalescent: ultimate recovery and symtoms disappear, usually take 10 days.
71
Q

Signs versus Symptoms

A
  • Sign: objective markers (classic signs of inflammation: redness, warmth, loss of function, swelling)
  • Symptoms: subjective indicator (experienced by the person)
72
Q

SARS CoV-2 Characteristics

A
  • enveloped, (+) ss RNA virus
  • E, S, and M
  • S-protein is how they attach to host cells and are potential antigens for therapies
73
Q

SARS CoV-2 Transmission

A
  • Contact transmission (direct contact, droplet, fomites)
74
Q

SARS CoV-2 Viral Cycle

A
  • SARS-CoV-2 uses spike proteins to attach to ACE2 (angiotensen converting enzyme 2) on host membrane and enters
  • Genome is released and ribosome translates + sense RNA
  • RdRp also transcribes the negative sense strand
  • replicated + sense RNA is then assembled and released
75
Q

SARS CoV-2 Viral Load and Antibodies

A
76
Q

SARS CoV-2 Diagnostic Tests

A
  • PCR - amplifies and detects RNA from host secretion sample
  • Antigen test - newer test that detects for viral proteins
  • Antibody tests - determines if individual has had past infection
77
Q

SARS CoV-2 Therapeutic Strategies

A
  • dexamethasone: inhibits inflammatory cytokines and neutrophil infiltration
  • chloroquine or hydroxychloroquin: prevents virus from entry and encoding
  • remdesivir, ribavarin, or favipiravir: inhibits RdRp (most success)
  • monoclonal antibody: neutralizes the virus
78
Q

SARS CoV-2 Vaccines Strategies

A
  • Pfizer (mRNA)
  • Moderna (mRNA)
  • J&J (adenovirus)
  • Novavax (protein)
  • Pfizer and moderna are most effective
79
Q

Differences between Archaea, Eukarya, and Bacteria

A
  • Cell membrane: Archaea have an entirely different cell membrane structure (ether linkage) than bacteria and eukarya (ester linkage). Archaea also have monolayer or bilayer membranes.
  • Inhibitors that affect translation: Archaea sensitivity to inhibitors is more similar to eukaryotes
  • RNA polyemerase: SDS page shows that archaea RNA polymerase is a mixture of bacteria and eukaryote RNA polymerase

MIMG 101 (12 decks)

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