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What is a bacteriophage?A virus that infects bacteria
What is a virus?Infectious nucleic acid surrounded by protein
Why is the virus considered ambiguous lifeform?&nbsp;Living - because it can proliferate within a cell<br>Non-living - Can't reproduce on its own; Just a bag of nucleic acid&nbsp;
What term does virus mean in latin?Poison
What makes the virus an obligate intracellular parasite?Genetic element cannot replicate independently of a living cell<br>&nbsp;(Can't replicate on its own)&nbsp;
What is a virus particle?Viron
What is a viron?Extracellular form of a virus
Are all viruses obligate intracelllular parasite?Yes
"When do we call a virus ""virion""?&nbsp;"When it is outside of the cell just floating around
Does the virion use ATP when outside the cell?No, the functions are automated&nbsp;
What are two types of nucleocapsid viruses?&nbsp;Naked<br>Enveloped&nbsp;
What is a naked virus?When nucleic acid is only surrounded by protein (Capsid)&nbsp;
What is an enveloped virus?A naked virus enveloped by an outer layer&nbsp;
What is the enveloped consisiting of? Where is it sourced from?&nbsp;A phospholipid bilayer<br>From host cell membrane
What is a survival mechanism that envelopes provide for viruses?&nbsp;Camoflage from immune system&nbsp;
What is a capsid?&nbsp;Protein shell that surrounds genome of a virus
What is a nucleocapsid?&nbsp;Nucleid acid + protein in enveloped viruses&nbsp;
What types of genomes do viruses have?&nbsp;Single or double stranded DNA or RNA
What is plus sense?The coding strand
What is minus sense strand?&nbsp;"The non-coding strand ""Complimentary strand""&nbsp;"
What shapes can the genome take?Linear<br>Circular&nbsp;
Why does the body automatically attack dsRNA?Because it is extremely rare and easily identifiable.&nbsp;
What unit is the viral genome typically?kbp&nbsp;<br>kilobasepairs&nbsp;
What are viruses classified on?The host they infect&nbsp;
What is the model system of viruses?Bacterial viruses (bacteriophages)
What is the range of size of viruses?&nbsp;20 - 300 nm
What is one of the largest viruses that is barely seen under a light microscope? What is size of it?Mimivirus&nbsp;<br>750 nm&nbsp;
What makes up a capsid?Capsomere&nbsp;
What is a capsomere?&nbsp;Individual protein molecules arranged in a precise and repetitive pattern around nucleic acid&nbsp;
What are two ways capsids put together?&nbsp;Self-assembly (spontaneous)&nbsp;<br>Host cell folding assistance&nbsp;
What is the symmetry of viruses? What are three types of folds?&nbsp;icosahedral<br>5-fold, 3-fold, 2-fold
What are types of enzymes inside virons?Lysozyme<br>Neuraminidases<br>Nucleic acid polymerases&nbsp;<br>- RNA replicases<br>- Reverse transcriptase
What do lysozyme allow virions to do?Make hole in cell wall to allow nucleic acid entry&nbsp;<br>Lyses bacterial cell to release new virions
NeuraminidasesDestroy glycoproteins and glycolipids&nbsp;<br>Allows liberation of viruses from cell&nbsp;
RNA replicases&nbsp;RNA dependent RNA polymerases&nbsp;
Reverse Transcriptase (which type of viruses uses it?)Retroviruses
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What is the major difference between prokaryotic and eukaryotic viruses&nbsp;Nucleic acid entry into the cell&nbsp;
What are the steps for viral replication in a permissive bacterial host?&nbsp;Attachment<br>Penetration<br>Synthesis<br>Assembly<br>Release
What is the curve that virus replication characterized by?One-step growth curve<br>Increase occurs when cell bursts
What is the latent period?Eclipse + maturation
What are phases of the one-step growth curve?&nbsp;Eclipse<br>Maturation<br>Release&nbsp;
What is eclipse?Genome replicated and proteins translated&nbsp;
what is maturation?Packaging of nucleic acids in capsids&nbsp;
What is release?Cell lysis<br>Budding<br>Excretion<br>
What is the burst size?&nbsp;Number of virions released&nbsp;
Which type of viruses is the easiest to grow?&nbsp;Bacterial viruses&nbsp;
Where can animal viruses (or plant viruses) be cultivated in?Tissue cultures (from animal organ in culture medium)&nbsp;
What is needed to detect and count viruses?Plaque assay
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Where is plating efficiency used?Used in quantitative virology&nbsp;
Will efficiency of infection usually be 100%?&nbsp;No, much less
Which number will always yield a lower count? Plaque-forming units or electron miscroscopy?Plaque-forming units will always be lower
Why is plaque always lower than electron microscope?Inactive virions or inappropriate conditions for infectivity<br>efficiency of infection less than 100%&nbsp;
What is the main bacteriophage we looked at in class?T4
What does attachment require?&nbsp;Complementary receptors on surface of susceptible host
What receptor does sars-covi-2 attach to?ACE 2
What do receptors include?Proteins<br>Carbohydrate<br>Glycoproteins<br>Lipids<br>Lipoproteins
What is a determinant that host will be susceptible to virus?The attachment
What are the receptors on host cell?Normal functional proteins&nbsp;
What does T4 bind to on bacteria?&nbsp;LPS&nbsp;<br>lipopolysaccharide&nbsp;
What does T4 release to make a small pore in peptidoglycan layer?&nbsp;Lysozyme
Does the capsid of T4 become part of the membrane?&nbsp;No, capsid stays outside
What does T4 proteins do the host RNA polymerases?&nbsp;Modify them to recognize only phage promoters and transcribe viral RNA&nbsp;
Is the host DNA and metabolic functions still operation when the virus takes over?&nbsp;No, host systems and trancription shuts down&nbsp;
What proteins does T4 modify?&nbsp;RNA polymersases&nbsp;
How long does T4 virion synthesis take inside the bacterial cell?about 30 minutes
How many parts is T4 genome translated in?&nbsp;3&nbsp;<br>Early, Middle, Late proteins
What are early proteins?Needed for DNA rep, transcription, and breakdown of bacterial cell chromosome.&nbsp;
What are middle and late proteins?Head n Tail proteins and enzymes required to liberate mature phage particles.&nbsp;
If you have a small genome, how many proteins do you code for?&nbsp;Smaller amount of proteins
Circular permutationSame genes get arranged in different orders
What is terminally redundant?DNA sequences duplicated on both ends&nbsp;
What do small DNA viruses use for genome replication?Host DNA polymerase
What does virus use to protect itself against bacteria?Methylate cytosine<br>Hydroxylmethylcytosine
What is packaging?T4 genome and virion assembly&nbsp;
How is genome pumped into head?Use ATP<br>Proheads and motor to form capsid&nbsp;
What do bacteria do to stop the spreading of the virus?"Create toxin-antitoxin molecules&nbsp;<br>Antiviral <span style=""color: rgb(255, 170, 0);"">CRISPR</span><br>Restriction endonucleases<br>"
What do toxin-antitoxin molecules cause to bacteria?The cell undergoes apoptosis (cell suicide) to prevent the spread of virus&nbsp;
What are a large majority of DNA in viruses?&nbsp;dsDNA&nbsp;
How does CRISPR work? What protein it use?&nbsp;Keeps RNA copy of viral RNA/DNA<br>&nbsp;if virus attacks again, they attack viral DNA if it matches.&nbsp;<br>Cas9 Protein&nbsp;
What does restriction endonucleases specifically for?dsDNA<br>Cleave at specific sites
Phases of lytic cycleAttachment<br>Penetration<br>Biosynthesis<br>Assembly<br>Release&nbsp;
VirulentViruses always lyse and kill host after infection&nbsp;<br>Causes host lysis&nbsp;<br>Don't give a fuck about host&nbsp;
TemperateViruses replicate their genome in tandem with host genome and without killing host.&nbsp;<br>Establish long-term, stable relationship
can a temperate virus be lytic/virulent?&nbsp;Yes&nbsp;
What is lysogeny?Viral genes is replicated into host chromosome and passed to daughter cells&nbsp;
What is a lysogen?Cell that harbors temperate virus
What is lysogenic conversion?Cells&nbsp;
What are examples we covered in class of temperate phages?&nbsp;Lambda&nbsp;<br>P1
What form is the DNA of P1 viruses?Exists as a plasmid&nbsp;
What does the lambda DNA do? (Think about what type of cycle it uses)&nbsp;Integrated into bacterial chromosome
What is a prophage?Integrated viral DNA into host DNA&nbsp;
What it is and how is lysogeny maintained?Phage-encoded repressor protein<br>Means virus is dormant until inactivation of repressor (cell stress)&nbsp;
What induces the change from lysogenic to lytic?Cell stress
What is an intergrase?Protein used to excise and integrate viral DNA&nbsp;
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"
What are two repressor proteins?cl protein<br>cro repressor
"
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"
What is cl protein?Causes repression of lambda lytic events
What is a cro repressor?Controls activation of lytic events&nbsp;
What controls infection outcome?First repressor that accumulates&nbsp;
What are retroviruses?Genome is +ssRNA, but converts RNA to DNA and enters chromosome
How can viruses enter animal cells?Envelope fuses with cell membrane<br>Endocytosis
Do animal viruses need specific receptors?Yes, still needed&nbsp;
What is latent infection?Viral DNA exists in host genome but no virions produced<br>Host cell is unharmed unless virulence is triggered&nbsp;<br>Similar to lysogenic&nbsp;
Persistent infectionsRelease of virions from host cell by budding does not result in cell lysis<br>Infected cell used to produced virus<br>Hep B and C&nbsp;
TransformationCan cause normal cell to turn into tumor cell
Are animal cells able to replicate RNA?No they aren't capable of it.&nbsp;
How do retroviruses get around replicating DNA from RNA?&nbsp;Use reverse transcriptase&nbsp;
What is a reverse transcriptase?Convert RNA to DNA&nbsp;
What proteins do retroviruses contain?Reverse transcriptase, integrase, protease&nbsp;
Are retroviruses enveloped?Yes&nbsp;
what&nbsp; disease is an example of a retrovirus?HIV&nbsp;
What are the specific genes of retroviruses?gag<br>pol<br>env&nbsp;
What cells does HIV affect?&nbsp;Leukocytes (WBC)&nbsp;
Why does HIV target leukocytes?&nbsp;Because it contains the specific receptors for leukocytes&nbsp;
"
<div id=""io-header"">steps of retrovirus infection </div>
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""
<div id=""io-header"">steps of retrovirus infection </div>
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"
<div id=""io-header"">steps of retrovirus infection </div>
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""
<div id=""io-header"">steps of retrovirus infection </div>
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"
<div id=""io-header"">steps of retrovirus infection </div>
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<div id=""io-header"">steps of retrovirus infection </div>
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<div id=""io-header"">steps of retrovirus infection </div>
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<div id=""io-header"">steps of retrovirus infection </div>
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<div id=""io-header"">steps of retrovirus infection </div>
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"
What is the genome of SARS-CoV-2Postitive sense single-stranded RNA virus
What are similar viruses to SARS-CoV-2?Rhinoviruses<br>HCV<br>West Nile<br>Dengue
What is the receptor used by COVID?Angiotensin-converting enzyme 2 (ACE2)&nbsp;
What is the evelope membrane composed of in enveloped viruses?&nbsp;Phospholipid bilayer
Does the entire eveloped virion enter the cell, or only the viral DNA?The entire virion
What is titer?&nbsp;Number of infectious units per volume of fluid
What is the plaque assay?Clear zones that develop where successful viral infection occurs.&nbsp;
What does the T1 virus attach to?&nbsp;Iron transport protein
What does the Chi virus attach to?Flagellum
What is glucosylation?The addition of a glucose molecule
Where is the glucose molecule added on the T4 base during glucosylationAdded to the T4 base hydroxymethylcytosine
What are two methods viral DNA is resistant to endonucleases?Hydroxymethyl cytosine<br>Glucosylation of the cytosine&nbsp;
What is the name of the site that make linear DNA into a circle?cos site
What is another form of DNA replication used by plasmids in the lytic cycle?Rolling circle replication&nbsp;
What proteins are used for the rolling circle replication?RepA<br>Host DNA poly (DNA poly III)<br>Helicase<br>Single-strand binding protein<br>DNA ligase<br>RNA polymerase
What end does RepA attach to to allow for DNA poly to bind?5'&nbsp;
What is the function of single strand binding proteins?&nbsp;To stabilize the replicated strand.&nbsp;
How does lambda synthesize long, linear concatemers of DNA when it enters the lytic pathway?Rolling circle replication
Where are the genome-sized lengths cut?At cos sites
If lambda is lysogenic, where does it integrate into E.coli chromosome?Lambda attachment site&nbsp;
What does lambda use to integrate into the chromosome?Lambda integrase
What occurs when tails are added to lambda phage head?Lysis
What is the cro repressor?Controls activation of lytic events
How are animal viruses classified?By genome
Virulent infectionLysis of host cell&nbsp;
Latent infectionViral DNA exists in host genome and virions not produced<br>Harmless until triggered
"
<div id=""io-header"">Identify the type of infection based on cause</div>
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""
<div id=""io-header"">Identify the type of infection based on cause</div>
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<div id=""io-header"">Identify the type of infection based on cause</div>
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<div id=""io-header"">Identify the type of infection based on cause</div>
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"
<div id=""io-header"">Identify the type of infection based on cause</div>
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<div id=""io-header"">Identify the type of infection based on cause</div>
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"
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<div id=""io-header"">Identify the type of infection based on cause</div>
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"
what is the <i>gag</i> gene?&nbsp;Encode structural proteins
What is the pol gene?Encode reverse transcriptase and integrase
what is the env gene?Encodes envelope proteins
What is TMPRSS2?Activates the viral spike glycoproteins<br>Facilitate virus-cell membrane attachment&nbsp;