week 10 lecture 1 and 2 Flashcards
What does virus phylogeny rely on?
genomic-sequencing
what characteristics of viruses can they be classified by?
- nucleic acid types
- presence or absence of an envelope
- capsid symmetry
- dimensions of virion and capsid
how do we classify viruses into groups of viruses?
- by the manner of their mRNA synthesis using the Baltimore classification system
- classifies viruses into seven groups based on their genome structure and how they replicate
ss? ds?
+ ? -?
single and double-stranded
- positive is the coding strand, sense strand, and positive strand
- negative: template
what is Group 1 of the Baltimore system? Genetic material processing? disease
Double-stranded DNA
dsDNA-> mRNA
small pox
What is Group 2 of the Baltimore system? Genetic material processing? disease
HPV
single-stranded DNA
+ssDNA -> dsDNA -> mRNA
What is Group 3 of the Baltimore system? Genetic material processing? Disease
ds RNA
dsRNA ->mRNA
rotavirus
disease? What is Group 4 of the Baltimore system? Genetic material processing?
covid
+ssRNA
+ssRNA -> -ssRNA -> mRNA
disease?What is Group 5 of the Baltimore system? Genetic material processing?
measles
-ssRNA
- ssRN -> mRNA
disease? What is Group 6 of the Baltimore system? Genetic material processing?
- HIV
+ssRNA-RT(single-stranded RNA with reverse transcriptase)
+ssRNA-> dsRNA–(RT)–> dsDNA0> mRNA
Disease? What is Group 7 of the Baltimore system? Genetic material processing?
Hepatitis B
double-stranded DNA with reverse transcriptase
(dsDNA-RT)
dsDNA-RT -> +ssRNA-> dsRNA –(RT)–> dsDNA ->mRNA
What is a double-stranded DNA virus?
- the largest group of known viruses and most bacteriophages and archeal viruses
- rely on host DNA/RNA pol
- examples: T4 lambdaa
how do T4 viruses inject their DNA into the host ? example of ?
- land and inject, and after 22 minutes virus will escape
- attachment begins when a long fiber contacts LPS outer membrane E. Coli proteins
- how ds DNA virus infect
how can escherichia virus lambda enter?
- lytic or lysogenic cycle upon infection, will attach to the host and release genome into cytoplasm
- specialized transduction
What determines if a lysogenic or lytic cycle is performed?
- regulatory proteins which function as a repressor of activator
cll
activator
cl
repressor
clll
proteasa inhibitor that promotes latency
integrase
catalyse integration of lambda genome into host chromosome
cro repressor
inhibits transcription of clll and cl gene
cro activator
Increase transcription of itself and regulatory protein Q
Latent infection means that
- laying formant using lysogenic cycle
- if cll/clll increase to high levels, then the lysogenic cycle will occur
- will not show symptoms right away unless trigger to lytic occurs
how does a lytic infection work in relation to Cl? UV radiation?
- cll/clll does not acculmate to high levels, and the cl repressor will not be made, CRO will accumulate, lytic will occur
- UV radiation - clll repressor cleavage, Cro, and other lytic genes are transcribed
- could show symptoms right away as cell will die
What do single-stranded DNA viruses use as an intermediate?
- ds is important for making a stable template for creating mRNA and lets virus replicate its genome efficiently
What is the process of using ss DNA for viruses?
- circular ssDNA will enter the cell and convert it into dsDNA intermediate
- converted to ds replicative form by bacterial DNA pol
- the dsDNA will be transcribed and translated to proteins to be assembled into viral structures
- direct synthesis of more RF copies and plus-strand DNA by rolling circle replication
- RCR turns dsDNA back into +DNA to be stored in the capsid
What are ds-RNA viruses dependent on?
- uses RNA-dependent RNA polymerase to complete life cycles - replicates and transcriptase activities
- Rotavirus
What is the kind of virus that is translated upon entry? example virus?
- plus-strand RNA virus
- corona virus
What is the first protein synthesized for the +RNA virus?
RNA-dependent RNA polymerase - synthesizes negative strand RNA
What are the steps of positive-RNA virus replication?
- enters and +RNA acts as mRNA and is translated to make proteins and RNA pol
- RNA pol makes -RNA (template) to make more +RNA
- second translation - more +RNA are translated to make proteins
- assemble to make positive-strand RNA virus
What is the issue with negative-strand RNA viruses?
- cannot serve as mRNA to form viral proteins - the viral genome is a template for mRNA synthesis
- must bring one RNA-dependent RNA pol to synthesize + strand RNA
- Ebola
What can HIV cause? characteristics of HIV?
- AIDS
- envloped virus, has reverse transcriptase and integrase
What are the 4 roles of reverse transcriptase in retroviruses?
- RNA-dependent DNA polymerase
- DNA-dependent DNA polymerase
- ribonuclease - pushes back on host response to protect the operation
- error-prone, has no proofreading capability
what are the characteristics of archeal viruses?
- extremophiles
- cell membranes - monolayer
- thermoplastic - lacks cell walls (pleomorphic) and plasma membrane has polysaccharides and glycoproteins for stability
- specialized solute regulation (salt in approach - prefers high salt concentration)
what are the three categories of archeal viruses?
- crenarchetota (use sulfur compounds as electron donors or acceptors)
- eurarachaeota
- korarcheota (found only in hypothermal environment)
recently discovered nanoarcheototaa - hyperthermophilic, nanosized archaea
What are most archaeal viruses considered?
microbial dark matter - never gorn in lab culture
what are two metabolic adaptions of archea?
- sulfur - extremely thermophilic and can anaerobically reduce sulfur into sulfide
- methanogenesis - make methane
What are the three examples of crenarchaetota?
- thermophiles - thermoacidophiles (thrive at high temperature 55-85C) and low pH (1-4)
- mesophiles
- psychrophiles
What are two types of euryarchaeotota?
- methanogens - make methane
halophiles
what are methanotrophs?
- some microbes/archea can oxidize methane back into CO2
- anaerobic methane-oxidizing archaeon (anme)
- regions of seafloor where methane seeps into surrounding cold water
what are halophiles?
- haloarchea
- are extreme halophiles, aerobic chromo heterotrophs
- grow optimal near 3 to 4M NaCl
- cell wall disintegrates if NaCl <1.5
- salt in approach - antiporters/symporters to concentrate ions
what are the two groups of eukaryotes?
protists and fungi
What are two organelles in protists?
- plasmalemma - identical to the cell membrane of multicellular organisms
- vacuoles - contractile, secretory, phagocytic
how can protists create energy?
- mitochondria in aerobic chemoorganotrophs
- chloroplasts in photosynthetic protest
- hydrogenosomes in aerobic chemoorganotrophs
what helps protists move?
- cilia and flagella may help motility and generate water currents for feeding and respiration
Trophozoites? what are the two pathways it can go through depending on environmental conditions?
- actively growing and replicating protists
1. Encystement
2. Excystement
what is encystment?
- formation of dormant cysts
- protect against environmental changes
- in parasitic species, they are infectious stages between hosts
- examples: oxygen depletion, crowding, stravation
What is excystment?
Escape from cyst when returning to favorable conditions
How do protist reproduce?
- most have both asexual (in stable environment, quicker, decrease in diversity) and sexual (more diversity, responds to change)
- multiple fissions and budding
What environments do protists inhabit?
Most are free living and inhabit freshwater environments
- in decaying organic matter and soil, chemoorganotrophic forms can be found - role in nutrient cycling
What are the three classes of protists?
- Plant-like (photosynthetic)
- fungi-like (slime molds)
- animal-like (protozoan)
Three types of plant-like protists and characteristics?
- features - has chlorophyll, performs photosynthesis, and contributes to carbon fixation in marine ecosystem
1. chloroplastida
2. diatoms
3. euglena
What are the two groups of slime molds?
- myxobacteria - acellular slime mold
- dictyostelia - cellular mold
- features: decomposes organic material, reproduces with spore formation and from multicellular structures under certain conditions
Three groups of animal-like protists? Defined by?
- differs in motility
1. pseudopods
2. cilia
3. flagellum
what is an important feature of animals like a protest?
- amoebozoa: important in terms of ecological relationships
= free-living, endosymbiotic, commensal and parasitic forms
= mosi environment
three categories of fungal groups?
- zoosporic fungi (animal-like pathogen)
- zygomycetous fungi
- dikarya
What are the two subgroups of zoosporic? features of zoosporic?
- endospores parasite with motile spores
- reduces genome size so that it can infect the host cell to complete life cycle
- polar tube for host invasion after germination
- Chytridiomycota
- microsporidia
What are the two subcategories of zygomycetous? Features of zygomycetous?
- spores dispersal by wind or animals, sexually reproduce when environment is not favorable, parasitic
- Mucoromycota - used for food production
- Glomeromycota: mycorrhizal associations
Functions of dikarya? 2 subgroups
- cells with two haploid cells and are always without flagella
1. ascomycete (sac fungi)
2. Basidomycota
What is ascomycete (sac fungi)? disease?
- spores created with sacs called asci
- food spoilage
- white noise syndrome - erodes tissue
two types of ascomycete?
- nidulans - eukaryotic model organism
- oryzae - fermentation of sake miso and soy sauce
Basidomycota
- club-shaped fruiting bodies that are hanging called basidia
- saprophytes - decay plant matter (cellulose and lignin)
