Bacterial Viruses Flashcards
What is a virus?
Obligate intracellular parasite that can only multiply inside a host cell and must rely on it for energy, metabolic intermediates and protein synthesis.
What is the virion? What are its parts?
extracellular form of viruses that protect the viral genome when the virus is outside the host cell.
What is a capsid?
protein shell of a virion composed of a individual capsomere proteins that are often arranged in a precise and highly repetitive pattern around the nucleic acid
What is nucelocapsid?
Inner structure of ONLY nucleic acid and capsid protein. May be naked (no further layers) or enveloped in layers of phospholipids and glycoprotein to protect the genome and aid in attaching to host cell.
What are the two types of symmetry of a virion?
Rod shaped viruses: helical symmetry (e.g. human papillomavirus virion)
Spherical shaped viruses: icosahedral symmetry (ebola)
What is the difference in the way a virus enters a eukaryotic and prokaryotic cell?
Eukaryote: entire virion is taken up by the cell
prokaryote: only nucleic acid is taken up by the cell
Why do virus infections upset host bacteria’s regulatory systems?
there is a marked overproduction of viral nucleic acid and protein to make new virions
What are the two groups of proteins synthesized after infection?
early proteins: nucleic acid polymerases and other enzymes used to shut down host cell transcription and translation
late proteins: structural components of the virion and other components needed for assembly
what is burst size?
Average number of virions released from a host cell when it lyses.
What is the range in virus sizes?
viral genomes range almost a thousand fold from smallest to largest, and are grouped by genome structure
What is the baltimore classification of viral genomes?
7 class system (3 DNA, 4 RNA) of viral genome classification developed by virologist David Baltimore based on the relationship of viral genome to its mRNA.
What is the difference between plus and minus RNA and DNA strands?
(-) RNA: negative sense-RNA complementary to positive sense RNA. Cannot be directly translated into protein.
(+) RNA: positive sense-RNA. Can be directly translated into protein.
(-) DNA: strand is complementary to the (+) mRNA and serves as the template during transcription
(+) DNA: strand with the same sequence as the (+) mRNA (with T instead of U)
What is baltimore Class I form of genome, mRNA production, and replication?
Genome: dsDNA
mRNA Production: Host RNA polymerase transcribes viral DNA into mRNA.
Replication: Uses host or viral DNA polymerase.
What is baltimore Class VII form of genome, mRNA production, and replication?
Genome: dsDNA, but replicates via an RNA intermediate.
mRNA Production:
Host RNA polymerase transcribes viral dsDNA into mRNA. Reverse transcriptase converts mRNA back into DNA for new virions for infection.
Replication: Uses reverse transcriptase to return to DNA form.
What is baltimore Class II form of genome, mRNA production, and replication?
Genome: ssDNA
mRNA Production: by itself creates mRNA(-) so it is converted into dsDNA intermediate replicative form by host DNA polymerase, then transcribed into mRNA (+)
Replication: Uses host DNA polymerase on replicative dsDNA.
What is baltimore Class III form of genome, mRNA production, and replication?
Genome: dsRNA
mRNA Production:
Viral RNA-dependent RNA polymerase (replicase) transcribes the (-) strand of the two strands into mRNA(+).
Replication: Uses RNA replicase to copy RNA.
What is baltimore Class IV form of genome, mRNA production, and replication?
Genome: (+) ssRNA (acts as mRNA directly).
mRNA Production:
No transcription needed—ribosomes translate it immediately.
Replication: Uses RNA replicase to make a (-) RNA template, then more (+) RNA copies.
What is baltimore Class V form of genome, mRNA production, and replication?
Genome: (-) ssRNA (complementary to mRNA).
mRNA Production:
RNA replicase transcribes (-) RNA into (+) mRNA before translation.
Replication: Uses RNA Replicase to copy RNA.
What is baltimore Class VI form of genome, mRNA production, and replication?
Genome: (+) ssRNA but not used directly as mRNA.
mRNA Production:
Reverse transcriptase converts RNA to dsDNA. Host RNA polymerase transcribes viral DNA into mRNA.
Replication: Uses reverse transcriptase to turn to dsDNA and integrates into host genome.
What are bacteriophages?
Bacterial viruses intensively studied a model systems for the molecular biology and genetics of virus replication.
What is phage ɸX174? How does it work?
Parvovirus; Icosahedral Baltimore class II ssDNA (+) bacteriophage that binds specifically to the Lipopolysaccharides of E. coli and converted into double stranded replicative form by host enzymes.
What is the condition of overlapping genes?
When a phage genome has insufficient DNA to encode all viral specific proteins, parts of the genome are transcribed in more than one reading frame with different promoters.
How does phage ɸX174 undergo rolling circle replication?
- E. coli host’s primosome and DNA pol III synthesizes the (-) complementary strand to the (+)ssDNA, converting the genome into its double stranded replicative form.
- Viral A protein acts as endonuclease and “nicks” at the origin of replication in (+) strand of circular dsDNA, letting 3’ end act as a primer for rolling circle replication.
- (+) strand synthesis is initiated as dNTP’s are added to 3’ end using exposed (-) strand as template as 5’ peels away.
- Rotation of circle results in linear copy of (+) strand
- Viral A protein cuts out old (+) ssDNA and ligates ends of newly synthesized (+) ssDNA to make circular (+) genome.
- (+/-) dsDNA replicative form is ready for another round of replication, and there is an accumulation of (+) strand ssDNA genome copies to be packaged into capsid by single stranded DNA binding proteins.
How does E. coli host enzymes convert phage ɸX174 genome into the replicative form?
Secondary structure ssDNA folding allow recruiting primosome (helicase and primase) to lay down a primer.
What is a plaque?
a visible clearing or zone of bacterial lysis (cell death) on a bacterial lawn (a dense growth of bacteria) caused by the infection and replication of bacteriophages (viruses that infect bacteria)
What are the steps in a plaque assay?
- Mixture of top agar, bacterial cells and diluted phage suspension is poured onto a solidified nutrient agar plate
- Micture is left to solidify
- Incubation allows for lawn of bacterial growth and phage replication, creating plaques
What is Phage M13?
Filamentous ssDNA(+) virus with helical symmetry attaching to the pilus of its host cell. It replicates similarly to that of ɸX174 phage, but is released from host cell without cell undergoing lysis.
What are the stages in the Phage M13 life cycle?
- phage attaches to pilus of recipient cell allowing ssDNA(+) entry into the cell
- Host enzymes convert (+)ssDNA into double stranded replicative form to create the complementary (-)ssDNA for (+)mRNA transcription.
- Rolling replication occurs, creating new (+)ssDNA and peeling off the old (+)ssDNA. pV starts accumulating.
- Once enough pV proteins are present, they bind to displaced (+)ssDNA strands as they peel off, preventing it from being used as a template for (-) strand synthesis and marking it for phage assembly.
- pV coated (+)ssDNA is delivered to the phage assembly site at inner membrane in periplasm.
- pVIII replaces pV and coats the ssDNA forming the long filamentous structure
- pIII and pVI dock onto the assembling phage at the inner membrane.
- PIII releases particle from inner membrane and slides it out of outer membrane secretin protein (pIV) and out of the cell without killing the host.
What is steady state infection?
Also known as chronic infection: when a pathogen persists in the host cell for a significant period, continuously replicating and releasing progeny, without causing immediate death of the infected cells
