Virus/Phage Flashcards
Why are viruses considered unicellular?
Psych. They are considered acellular
For which process will a virus require their host cells machinery?
replication, energy, metabolic intermediates, genome replication, protein synthesis?
All of those processes require the hosts machinery
By which method would a virus that normall injects itself into E.coli infect Shigella?
Viruses show high levels of specificity. If it normally infects E.coli it wont infect Shigella
What are the 2 classifications of virus? How do they differ?
- Baltimore Classification
- Based on Genome and mRNA production methods
- 7 classes
- ICTV Classification
- Based on phenotypes
- morphology
- nucleic acids
- mode of replication
- host organisms
- diseases
- Still 3,000 known viruses unclassified
- Based on phenotypes
What makes it hard to “classify” all the different viruses?
- Viruses do not all share 1 common trait -
- like the 16s rRNA in bacteria…or the sexual reproduction in Eukaryotes
What is the term used to describe the virus outside of a cell, or in the external environment?
Virion
What are the 2 primary forms the nucleocapsid of the virus will take?
What is the 3rd “form”
- Helical (rod)
- Spherical
- Icosahedral
- Complex
- Helical portion + Icosahedral portion
Define:
Capsid
Capsomere
Nucleocapsid
- Capsid - protein structure encasing the RNA/DNA of virus
- Capsomere - indivudual proteins making up the capsid
- Nucleocapsid - The Capsid and DNA/RNA all in one unit!
Can the Nucleocapsid contain other proteins besides capsomeres?
yes
How are nucleocapsids usually packaged? (2 types)
- Naked
- Enveloped (partial to Eukaryotes)
Why do enveloped virus “generally” not infect plants or bacteria?
- Plants and bacteria have cell walls.
- the enveloped virus are better at getting through the plasma membrane of animals.
Does and enveloped virus kill its host?
- It doesnt have to.
- The virus basically ‘blebs” out covering itself in the membrane of the host.
What determines the shape of enveloped proteins?
Capsomeres
Bacteriophage normally have what type of structure…?
What is a widely studied bacteriophage?
Complex
The T4 that attacks E.coli
What are 4 examples of, common, protiens found within a virus?
- Adhesion proteins
- ALL viruses need these to help find/target specific host cells
- Lysozyme
- breaks down NAG-NAM in peptidoglycan
- Punctures cell walls
- Polymerases
- Needs to replicate nucleic acids once inside a cell
- Reverse Transcriptase - turns RNA into DNA
- Neuraminidases
- Break glycoproteins and glycolipids in cell walls to free virions?
What is the term for the amount of “offpspring” from a virus?
Birth size
What are the 5 steps in Virus Replications?
- Attachment
- Penetration
- Synthesis
- Assembly
- Release
Viral Attachment:
- Mediated by:
- Each Virion will recognize a specific [] and maybe even a []
- VAPs can []. with their host and even evolve to [] in a certain population
- Viral Attachment Protein
- receptor….co-receptor
- Evolve/change….host jump?
What are the way a virus will penetrate the host cell?
- Injection
- this is used for hosts wil cell cells
- Complex virus (like T4) use this
- Fusion
- Used mainly by enveloped virus
- Also can be endocytosed
- Requires uncoating of nucleocapsid
What are 2 options for an RNA virus to replicate in the host cell?
Why are these necessary?
- Convert their RNA genome to dsDNA
- Reverse transciptase, Retroviruses
- Bring their own RNA-dependent RNA polymerase (RdRp)
- recognized RNA templates, makes copies of RNA
- this is Necessary because host cells do not have machinery to use RNA as a template. Needs to be converted to DNA first.
How does a Class II (+ ssDNA) virus replicate its genome?
How does a Class III (+/- dsRNA) virus replicate its genome
How does a Class IV (+ ssRNA) replicate its genome?
- Class II- makes a 2nd copy of its ssDNA and then uses host machinery
- Class III (+/- dsRNA)- Uses RdRp to transcribe - side into a + mRNA
- Class IV (+ ssRNA) - Can be used as mRNA
How does a Class V (- ssRNA) virus replicate its genome?
How does a Class VI (+ ssRNA) virus replicate its genome?
How does a Class VII (+/- dsDNA) virus replicate its genome?
- Class V (- ssRNA)- uses RdRp to make a dsRNA and then replicate genome
- Class VI (ssRNA +) - Retroviruses
- Uses reverse transcriptase to make RNA–> DNA
- Then makes ssDNA into dsDNA and then can use host machinery
- Class VII (dsDNA +) - hepatic viruses
- Starts with dsDNA –> RNA –> ssDNA –> dsDNA
- Uses host polymerase to make RNA –>then uses viral polymerase with reverse tranciprtase and DdDp to make dsDNA.
Do viruses carry ribosomes?
No
What is the difference between positive RNA and negative strand RNA?
- Positive = sense
- its the coding strand, has RBS and AUG codon
- Must be positive to be recognized by ribosome
- Negative = antisense
- template strand; reverse complement of coding strand
Is there a “timing” for gene expression during viral synthesis/replication?
- Yes
- you’ll see early genes encode enzymes and regulatory protiens need to start viral replication
- RTs, transcription factors for late genes, RdRp
- You see late genes encod for structural proteins
- capsid
- VAP
- tail proteins, envelope proteins
What are the 2 “lifestyles” for a virus?
- Lytic
- Rapid progression through viral synthesis phase
- No viral DNA incorporation into host genome
- Lysogenic
- Incorporates viral DNA into host DNA (but not expressed)
- Virus lays dormant until conditions are right
- “Activation” (stimulus) will swith it to Lytic cycle
How does the virus assemble all of the proteins into its virion form?
- Self-assembly of all proteins into virion form inside the cytoplasm of host cell.
What are 2 methods of release for a virus?
- Budding
- induved extrusion carrying host membranes with it
- Lysis
- late viral genes encode protesin that break down membranes/wall and allow release
What are methods Eukaryotes use to halt viral synthesis?
- RNA interference-recognizes viral DNA and leads to degredation
- Innate and adaptive memory of previous pathogens and antibody production
What are ways that bacteria fight off viral infection?
- CRISPR - memory based short DNA fragments interference
- Restriction endonucleases - recognizes and clips DNA at certain sequences (palindromic sequences and methylated sequences)
Bacteriophage Facts
- Genome type?
- Enveloped?
- Physical Type?
- Life Style?
- Types?
- dsDNA
- naked
- Complex (head and tail)
- Lytic and lysogenic lifestyle
- Virulent Phage and Temperate Phage
Virulent Phages
- kill host []
- Best example []
- Encodes some of its own []
- T4 DNA contains 5 [] instead of cytosine = resistant to [] [] by hosts
- Express their own []
- rapidly
- T4 - infects E.coli
- tRNA
- hydroxymethylcytosine, restriction modification
- Endonuclease (chops up host DNA for use by virus)
Temperate Phage
- Capable of [] via lysogeny
- Exists as a [] in the genome
- Can be [] to become lytic
- Most well studied example - [] ?
- non-killing
- prophage
- induced
- bacteriophage lambda
Phage Lambda
- Uses [] sites to cyclize
- Inserts itself into host genome at [] sites (possesed by both virus and hose
- Can be [] or []
- Why does Phage Lambda want to cyclize?
- cos
- att
- lytic or lysogenic
- Linear DNA will be killed in E.coli
What are some of the possible outcomes of viral infections in Eukaryotes?
- Transformation - normal cell to tumor cell and so on
-
Lysis - death of cell and release of virus
- Influenze, Rhinovirus
-
Persistant Infection - slow release of virus without cell death
- Rubella, Adenovirus
-
Latent Infection - viruse present but not replicating..until necessary or stimulated…could revert to lytic
- Herpes, HIV
-
Cell Fusion
- 2 cells become one and now the body cant locate the virus becomes it moves back and forth between the fused cells
What is a defective virus?
- It is a virus that has lost the ability to do 1 of the 5 steps in teh viral process
- Requires a helper virus
What is a viroid?
- infectious RNA, LACKS CAPSID
- Found only in plants
- 246 to 339 nt long
What is a Prion?
- Infectious proteins that cuase aggregation or misfolding of host proteins
What makes a normal protein a “prion”?
- If the protein is misfolded, it can become infectious
- Once misfolded - it can induce other near proteins to misfold leading toinsoluble protein aggregates
- PrP^sc = infectious
- PrP^C = normal protiein
2 examples of examining viruses in vitro?
- Plaque Formation - hole in the lawn of host in a agar tray = a plaque
- Plaque Assay - infect layer of host cells with serial dilution froma virus stock
- stain host cells and observe number of plaque and multiply by dilution factor.
- in units of PFU/mL
What is the “Regressive/Reduction Hypothesis?”
Viruses are remnants of cellular organisms that lost their features.
How could retrotransposons be tied to viral evolution?
- mobile genetic elements may have evolved to travel between cells therby becoming infectious entities
Do viruses possess any hallmark genes?
- Yes
- There are many genes shared by different viruses.
