Chapter 2 Flashcards
Domain includes?
archaea
bacteria
eukarya
what does kingdoms include?
monera protists fungi plantae animalia
what was added in 2012 for the 5 domain system?
prionobiota (accelular without nucleic acid) and virusobiota (accellular with nucleic acid)
order is derived from ______ -_________
common ancestor
what are the 4 orders that infect humans?
- mononegavirales
- nidovirales
- herpesvirales
- picornavirales
what is the ICTV cirteria for classification?
- Morphology of virions
- Physical properties of virions
- Properties of the genome
- Properties of proteins
- Lipids
- carbohydrates
- genome organization and replication
- antigenic properties (epitopes)
- biological properties
what is metagenomic?
analyzing genomic sequences in environmental samples, able to obtain sequences from non cultural organisms
what is the baltimore system?
morphological based classification system that places viruses into one of seven groups depending on a combination of their genome (RNA or DNA), strandedness (single-stranded or double-stranded), sense of genome (positive or negative) and method of replication
does the baltimore system handle complex viruses?
no
viruses may have _______ or ________ stranded ____ or _____
single, double, dna , rna
(+) sense genome are?
viral RNA is identical to viral mRNA and can be immediately translated into protein by the host cell machinery
(-) sense genomes are?
viral RNA is completely to mRNA and must be converted to (+) sense RNa by an RNA polymerase before translation
what are the 7 types of genomes?
- dsDNA genomes
- ssDNA genomes
- dsRNA genomes
- ssRNA genomes (+)
- ssRNA genomes (-)
- RNA genome that used reverse transcriptase to make DNA intermediate that is used to make the RNA genome
- DNA genomes with an RNA intermediate stage used to produce a DNA genomes
classifications categories for viruses that infect humans
- no enveloped (with helical capsid, with icosohedral capsid)
- enveloped (with helical capsid, with icosohedral capsid)
- complex (everything else)
Class 5 ssRNA has been subdivided into ______ and _________
segmented and non segmented
what are quasispecies?
within an infected individual there are a large number of variants with different genomic sequences
strains means?
variations within a subtype, share similar physiological effects
what are variants?
variations within a strain (differs between infected individuals)
*In viral taxonomy a virus family ends in…
Viridae
*You can classify viruses based on their?
all of the above
structure, genome type, genome sequence
*The definition for species is the same for animals and viruses. (T F)
F
*The definition for species is the same for animals and viruses. (T F)
F
the smallest bacterial genome was around _________bp
490885
__________ large DNA viruses thought to be the largest viruses
Nucleocytoplasmic (NCLDVs)
New organism within an aquatic amoeba, first identified as a gram-positive bacteria due to size, could be what?
mimivirus
what is the single species of mimivirus?
Acanthamoeba polyphaga mimivirus (APMV)
describe mimi virus
dsDNA virus
90% coding capacity
10%junk dna
1.2 million base pairs
satelite virus resepmbles a replicative capable virus but needs a _____ virus co infecting the ______ cell to complete its replication cycle
helper, same
what is the only known satelite virus of humans?
Parvoviridae AAV
satellite viruses often have a _____ impact on the helper virus
negative, parasitic relationship
how do satellite viruses work in absence of helper?
AAV integrates into the host genome and goes latent
what are virusoids?
- associate with plant viruses
- no human examples
- circular ssRNA
- need helper to make structural proteins
- formerly called satelite RNAs
what are viroids?
- Produce a range of diseases in plants
- Circular RNA molecules (220-375 bp)
- Smallest self-replicating infectious agents
- Similar to virusoids, but can replicate without a helper virus
- Belong to 2 families
(Avsunvirodidae and Pospiviroidae)
what is this describing:
Single stranded, but strands pair with other regions to form a tightly coiled structure
Protects the naked nucleic acids from nuclease degradation
viroids
describe viroid replication
DNA-dependent RNA polymerase makes multiple copies of the viroid sequence in a row
what is a concatamer?
moves around the circular sequence
viroid RNA itself functions as a ______ to cut the nucleic acid
ribozyme
describe the hepatitis delta virus
- Circular, ssRNA genome
- 1680 bp
- Codes for two proteins
- Needs helper virus, hepatitis B virus, to make structural proteins to form HDV particle
replication defective viruses do not contain a complete ________-
genome
replication defective viruses cannot replicate unless what?
there is a co-infection with a virus that can provide the functions missing from the defective virus
RNA genome viruses replicate very quickly, and many produce ______ _________ ________during high multiplicities of infection (MOI) (ratio of virus titre to host cell)
defective interfering (DI) particles
DI particles compete with the_______ -_____ for enzymes in the host cell
‘helper virus’
what are two examples of mobile genetic elements?
- Bacterial plasmids
( Code for transfer-associated structures on the cell surface) - Transposons (jumping genes)
(Eukaryotic equivalent of plasmids)
what are retrotransposons?
- Homology to retrovirus genes
- DNA in host genome that has an RNA stage during replication
- DNA –> RNA (many copies) –>DNA via reverse transcriptase then inserted into genome
- Some code for proteins
(Some can assemble into virus-like particles)
___% of human genome is retrotransposons
42
what is an endogenous virus?
- A DNA sequence derived from a virus and is present in the genome of a non-viral organism
- Requires the virus sequence to be integrated into the genome
- Can be a genetic fragment or entire viral genome (provirus)
- Most common EVs are derived from retroviruses, which integrate into the nuclear genome of the host cell as part of their replication cycle
- Account for ~8% of human genome
most endogenous viruses infect _______ cells but can occasionally infect germline cells
somatic
what are prions?
- Actually an infectious protein
- No nucleic acid present
- (mutated protein PrPsc) structure change causes the formation of fibrils in the brain
_____ now accepted as human form of BSE transmitted to humans from the consumption of contaminated tissue
vCJD
*What is a satellite virus?
A virus that can’t replicate without a helper virus
*What about hepatitis delta virus makes it like a viroid?
RNA genome with complex secondary structure
*What is a concatamer?
A circular genome copied many times
*Despite its size relative to other viruses, Mimivirus is still smaller than the smallest bacteria. ( T F)
F
- Creutsfeldt-Jacob disease can be inherited (familial) or contracted from consumption of contaminated tissue. What zoonotic disease was initially considered the source of BSE?
scrapie
