Virology Flashcards
What is the difference/similarity between a bacteriophage and a virus?
-Virus is the general class of organism.
-Phage is a subclass of virus that infects bacteria
How big is a typical bacteriophage or virus?
-MUCH smaller than cell it infects.
-Most are 30 to 300 nm (bacteria average 1000 nm in diameter)
What is the basic structure of a bacteriophage or virus?
-Nucleic acid surrounded by protein capsid
What types of nucleic acids are present in their genomes?
-All varieties, ssDNA, dsDNA, ssRNA, and dsRNA
What steps are involved in the reproductive cycle of a T4 lytic phage?
Eary-Takeover of host cell machinery
Middle-Replication of phage genome
Late-Capsomer production, Capsid assembly, Genome packaging, Host cell lysis
What is happening during the latent period of a phage lytic infection?
-No increase in the number of plaque-forming units=early and middle function
-PFU only increase during packaging
What is involved in the reproduction cycle of a lambda lysogenic phage?
-Most phage go into lytic cycle
-some go into lysogenic cycle where phage gene expression is silenced and the phage DNA is inserted into the host chromosome
-the phage DNA is replicated along with the host DNA during all “LYSOGEN” cell growth and division
-eventually the “PROPHAGE” can be induced, it exits the host chromosome and starts a new lytic cycle.
How can you measure the abundance of bacteriohages?
-Plaque assay
-Spread phage sample on plate along with host cells
-incubate to get bacterial lawn
-count the number of clear spots where cells were lysed=plaques
-each plaque derived from one phage particle
What is involved in the reproductive cycle of a retrovirus?
-ssRNA is used as template to produce dsDNA by REVERSE TRANSCRIPTION
-DNA inserts into host cell chromosome by INTEGRASE
-HIV genes are expressed from that PROVIRUS to produce mRNA, which is also the + strand RNA assembled into viral particles
-Translation produces polyprotein, which is cleaved into individual viral protein components by HIV protease
What is an enveloped virus and what types of molecules make up the envelope?
-A virus that has a membrane surrounding the nucleocapsid
-generally these infect animal cells
-the envelope contains lipids from the host cell cytoplasmic membrane plus viral “spike” protein that were inserted into the membrane during viral growth.
What is the difference between “RNA replicase” and “Reverse transcriptase”?
-RNA-direct RNA synthesis versus RNA-directed DNA synthesis
How do influenza viruses undergo antigenic shift?
-They acquire a significantly different gene encoding one of the two major antigens (H or N) when a single cell is infected by two different influenza virus strains
-this can happen only because the influenza genome is made up of 8 separate RNA molecules, each encoding a different protein
What is a viroid?
-is an infectious RNA molecule
-infects plants
-does not encode any protein
What is a prion?
-is an infectious protein molecule that is not produced from any infectious nucleic acid
-the gene is in the host chromosome
-protein is only infectious when it is improperly folded and able to catalyze the further misfolding of host-produce proteins
What are plus and minus strand RNA?
-(+) strand is mRNA
-(-) strand id the complement of mRNA which can be used as a template by RNA replicase to produce + strand RNA
Bacteriophages
-infect bacteria
Viruses
-NOT FREE LIVING
-obligate intracellular parasites
-not cellular
-infect eukaryotes or archaea
-need a host and their machines to make copies/reproduce
-no metabolism
Are viruses smaller or bigger than living cells? and do they have small or big genomes?
-smaller in size than living cells
-Small genomes
Baltimore Classification Scheme
-based on the nucleic acid metabolism of the virus
-7 classes
-Baltimore got a noble prize
Viral Class
-DNA viruses
-RNA viruses
-RNA - DNA viruses
Viral Genome
-DNA viruses = ssDNA and ds DNA
-RNA viruses = ssRNA and ds DNA
-RNA-DNA viruses = ssRNA (retroviruses) and dsDAN (hepadnarviruses)
Virus Structure
-Nucleocapsid
-Sometimes covered by an envelope (membrane)
-Sometimes carries specialized enzymes
-genome protected by protein coat
-Helical vs Icosahedron shapes
Nucleocapsid
-nucleic acid plus capsid
-composed of proteins
-naked virus
Enveloped viruses
-form of nucleocapsid
-composed of lipids, and brown balls - are proteins that code the outside and allow the virus to enter the host cell
What are the types of protein coats that protect genome?
-capsid
-capsomere (individual subunits that make up capsid)
Helical
-ex. Tobacco
-long and hollow
-capsids are in a spiral shape around the RNA
Icosahedron
-20 sides
-12 vertices
-sides are triangular shape
-2, 3, and 5 fold symmetry
What type of microscope are you able to viral structures under?
-Electron microscope
Parts of a bacteriophage T4 structure
-head (nuclide capsule)
-collar
-tail
-tail pins
-base plate
-tail fibers
What does bacteriophage T4 infect and what does it look like?
-E. coli
-moon lander
Steps of viral repliaction
-Attachment
-Penetration (punch it way through)
-Synthesis (make nucleic acid and viral proteins)
-Assembly and packaging
-Release (Outside!)
Can a virus infect if it doesn’t attach?
-No
Detail steps viral replication
-attachment (absorption of phage virion)
-Penetration of viral nucleic acid, viral DNA enters, and protein coat remains outside
-Synthesis of viral nucleic acid and proteins using cellular machinery and subunits
-Assembly and packaging of new viruses (make head like structure)
-cell lysis and release of new virions
Parts of a one-step growth curve for virus replication
-virus added -> latent period -> increase slope
-eclipse and maturation
-look at slides
Parts of the eclipse section on the graph
-early enzymes
-nucleic acid
-proteins coats
Parts of the maturation section on the graph
-assembly and release
Blast Size
-number of virions released from an infected host cell during the lytic cycle of viral replication
Quantification of Viruses: bacterial cells
-based on destruction of bacterial cells
-plaque assay for bacteriophage
-isolation of pure virus strain in a plaque
-confluent
Quantification of Viruses: eukaryotic cells
-based on the destruction of eukaryotic cells
-plaque assay for animal viruses uses tissue culture cells
-confluent monolayer of tissue cells
-stain dyes all red
Attachment and Penetration by Bacteriophage
- Tail compress to eject T4 to the peptidoglycan layer
Does a hole punched through the peptidoglycan layer kill the cell?
-No, the hole has to go through the cytoplasmic membrane to kill the cell
Synthesis of viral nucleic acids: DNA
-Class I
-Class II
-Class VII
Class I
-dsDNA (+) virus
-classical semiconservative
-transcription of minus strand
-no rRNA
Class II
-ssDNA (+) virus
-classical semiconservative
-discard (-) strand
-synthesis of other strand, ds DNA intermediate, transcription of minus strand
Class VII
-dsDNA (+) virus
-transcription followed by reverse transcription
-transcription of minus strand
-has rRNA
what does (+) mean?
-mRNA coding
Synthesis of viral nucleic acids: RNA Viruses
-Class III
-Class IV
-Class V
-Class VI
Class III
-dsRNA virus
-transcription of minus strand
-makes ssRNA (+) and transcribe from this to give ssRNA (-) genome
Class IV
-ssRNA virus (+)
-used directly as mRNA
-makes ssRNA (-) and transcribe from this to give ssRNA (+) genome
Class V
-ssRNA (-) virus
-transcription of minus strand
-make ssRNA (+) and transcribe from this to give ssRNA (-) genome
Class VI
-ssRNA (+) retrovirus
-reverse transcription
-dsDNA intermediate
-transcription of minus strand
-integrate into chromosome
-make ssRNA (+) genome by transcription off of (-) strand of dsDNA
Types of bacteriophage that infect bacterial cells
-RNA= ss MS2 and ds O6
-ssDNA = Ox174 and fd, M13
-dsDNA = T3, T7 (T odd) and Mu and Lambda and T2, T4 (T even)
Lytic/Virulent phage: T4 phage
-early gene expression
-middle gene expression
-late gene expression
Early gene expression
-takeover of cellular machinery
-T4 nucleases
-DNA polymerase
-new sigma factors
Late gene expression
-phage head proteins
-tail, collar, base plate and tail fibers
What happens in the lysis stage in T4?
-mature T4 virion
-T4 lysozyme production
How long does Lytic phage take to mature?
-25 minutes
What type of phage is Lambda phage?
-Lysogenic/temperate phage
-prophage when inserted into genome
Lysogenic Pathway
-Attachment of the virus to the host cell
-injection of viral DNA
-Viral DNA is integrated into host DNA
-Viral DNA is replicated with host DNA at cell division
Lytic Pathway
-Attachment of the virus to the host cell
-injection of viral DNA
-Lytic events are initiated
-Induction
-Phage components are synthesized and virions are assemble
-Lysis of the host cell and release of new phage virions
Are lysogenized cells immune to reinfection from same phage?
-Yes
RNA phage: MS2
-genome encodes only 4 proteins
-Overlapping genes
-“+” RNA in virion serves as mRNA template for - RNA
-“-“ RNA is replication intermediate and template for + RNA
What are the 4 proteins that MS2 genome encode?
-Maturation protein (1 copy in viral particle)
-Coat protein (capsomere)
-Lysis protein
-RNA replicase
How can genes overlap?
-they are set in different frame
-look at notes for viral multiplication
Nonenveloped DNA viruses that infect Eukaryotic Host
-Parvovirus (ssDNA)
-Papovavirus (dsDNA)
-Adenovirus (dsDNA) = causes colds
-Iridovirus (dsDNA)
Viruses that Infect Eukaryotic Host
-Infect plants and animals
Enveloped DNA viruses that infect Eukaryotic Host
-Hepadnarvirus (partially dsDNA)
-Poxvirus (dsDNA)
-Herpesvirus (dsDNA) = causes cold sores and integrate into chromosome
Nonenveloped RNA viruses that infect Eukaryotic Host
-Picronavirus (ssRNA) = small
-Reovirus (dsDNA)
Enveloped RNA viruses that infect Eukaryotic Host
-all ssRNA
-Rhabdovirus
-Togavirus
-Orthomyxovirus
-Bunyavirus
-Coronavirus
-Arenavirus
-Retrovirus
-Paramyxovirus
Eukaryotic viruses
-possible outcome of infection
-most viruses are lytic
-very few cause cancer
What is the anti-cancer cell?
-P53
What can come from a eukaryotic virus cell?
-transformation into a tumor/cancer cell
-lysis of infected cell and release of virus
-Persistent infection
-Latent infection
-cell fusion (2 nuclei)
Persistent infection
-virus gets outside cell
-slow release of virus without cell death
Latent infections
-Virus present but not replicating
-Eukaryotic Viruses: Influenza
-RNA virus
-Genome is in eight segments of RNA
-Immunity is via antibodies against surface proteins
-various strains infect humans, pigs, birds and other animals
What surface proteins are against influenza immunity?
-Neuraminidase
-Hemagglutinin
How are new strains of influenza produced?
-Co-infection of one animal/cell by two strains of influenza can allow mixing of the segmented genome (Antigenic shift)
-this produces a new strand that human haven’t seen previously and no immunity against it
Steps of Eukaryotic Viruses: Retroviruses
-Retrovirus virion containing two copies of ssRNA
1. Entrance
2. Uncoating
3. Reverse Transcription
4. Travel to nucleus and integration into host DNA
5. Transcription - viral mRNA and genomic RNA
6. Encapsidation - nucleocapsid
7. Binding - host cytoplasmic membrane
8. Release - progeny retrovirus virions
Corona Viruses - COVID 19
-Spike protein binds to a receptor on the surface of susceptible cells
-receptor for COVID is the ACE-2 protein
What is ACE-2 and where is it found?
-angiotensin converting enzyme 2
-is found on the surface of many types of cells, including respiratory and intestinal epithelia (diarrhea)
Steps of corona virus
- Infection, ssRNA genome release
- Translation of replicase gene
- Synthesis of minus strand
- Synthesis of monocistronic mRNA and synthesis of genome copies
- Translation of yield viral proteins
- viral assembly
Stages of HIV and AIDS
-eukaryotic retrovirus
-symptom free
-swollen lymph glands
-Subclinical immune dysfunction
-opportunistic infection
-systemic immune dysfunction
Levels of T cells
-normal range
-significantly depressed
-severe T cell depletion
Viroid
-infectious RNA molecules
-small circular ssRNA molecules that cause plant diseases
-no protein coat
use plant machinery to replicate
-replication of virion in plants causes disruption of normal function
Prions
-Infectious proteins
-Normal protein is a normal component of nerve cells
-infectious form is improperly folded and catalyzes improper folding of native protein
-look at slides
Prion virus in animals
-Scrapie = sheep
-Chronic wasting disease (deer)
-Mad cow disease = humans
-Creutzfeldt - Jakob disease
-Kuru = caused by cannibals
Definition of Prions
-composed of proteins
-cause degenerative and fatal neurological disease
-protein misfolding
What is the difference between “RNA replicase” and “Reverse transcriptase”?
-RNA-direct RNA synthesis versus RNA-directed DNA synthesis
