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

Question

Opsithokonta characteristics

Answer 1

* animals * true fungi (yeast) * microsporidians

Answer 2

* amebas * slime molds * includes human & agricultural pathogens

Answer 3

* land plants - secondary endosymbiosis * red algae

Answer 4

* amebas with filamentous pseudopods * part of SAR supergroup

Answer 5

* protists with cortical alveoli * includes human & agricultural pathogens * part of SAR supergroup

Answer 6

* protists with hairy flagella * includes human & agricultural pathogens * brown algae * part of SAR supergroup

Answer 7

* protists with mitochondria with discoid cristae * part of excavata supergroup

Answer 8

* protists lacking mitochondria * part of excavata supergroup

Answer 9

* alveolata phylogeny group * organism: plasmodium (parasite)

Answer 10

* metamonada phylogeny group * organism: giardia

Answer 11

* euglenozoa (discoba) phylogeny group * organism: trypanosoma

Answer 12

* alveolata phylogeny group * organism: dinoflagellates

Answer 13

* heterokonta phylogeny group * organism: phytopthora

Answer 14

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

Answer 15

* primary producers * evolved from englufing phototrophs

Answer 16

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

Answer 17

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

Answer 18

* 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

Answer 19

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

Answer 20

* 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)

Answer 21

* 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

Answer 22

* 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)

Answer 23

* 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

Answer 24

* 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)

Answer 25

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

Answer 26

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

Answer 27

* **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

Answer 28

* LPS * OmpF * TolC * Flagellar motor * receptor specificity drives host range specificity and tissue topism

Answer 29

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

Answer 30

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)

Answer 31

* 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

Answer 32

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

Answer 33

* block binding/invasion * block RT * block integration * block capsid maturation

Answer 34

* azt binds to RT and blocks DNA synthesis * inhibit protease cleavage (necessary enzyme for capsid assembly)

Answer 35

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

Answer 36

- beam of electrons is shot at virus - allows us to see their 2D shape

Answer 37

- 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

Answer 38

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

Answer 39

- Barbara McClintock: Mobile DNA fragments within the genome

Answer 40

- contact transmission - vehicle transmission - vector transmission

Answer 41

- Direct contact - indirect contact by fomites - droplets

Answer 42

- Waterborne - Airborne, including dust particles - Foodborne

Answer 43

- Mechanical (on insect bodies) - Biological (microbes multiply inside of living vector body)

Answer 44

* 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.

Answer 45

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

Answer 46

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

Answer 47

* Contact transmission (direct contact, droplet, fomites)

Answer 48

- 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

Answer 49

* 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

Answer 50

- 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

Answer 51

- Pfizer (mRNA) - Moderna (mRNA) - J&J (adenovirus) - Novavax (protein) - Pfizer and moderna are most effective

Answer 52

* 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

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

(79 cards)