Viruses

Question 1

What is the difference between viruses and virions?

Answer 1

Virus - genetic elements with an obligate intracellular replication.

Virion - extracellular form which includes the nucleus acid and normally a protein coat and possibly outer envelope; genome can be DNA, RNA, double stranded, single stranded, linear or circular.

obligate intracellular replication - can only reproduce inside the cells of another organism (the host)

Question 2

What are the basic structures of viruses?

Answer 2

capsid, nucleocapsid, symmetry (either helical; tobacco mosaic virus or icosahedral; human papilloma virus)

Question 3

How does a virus differ from a plasmid?

Answer 3

Virus = genetic element, can be DNA or RNA and have an extracellular form.

Plasmid= doesn’t have an extracellular form, form is just DNA.

Both have genetic elements and can self-replicate.

Question 4

How does a virion differ from a cell?

Answer 4

Virions are essentially packages of genetic material (DNA or RNA) encased in a protein shell, while cells possess a nucleus, organelles, and a cytoplasm.

Question 5

What is a bacteriophage?

Answer 5

viruses that infect and replicate only in bacterial cells

Question 6

What is the role and makeup of capsids?

Answer 6

• protein coat that surrounds the nucleic acid
• subunits of capsid are capsomers
• capsomers self assemble to create capsid structure

Question 7

What is the role and makeup of envelopes?

Answer 7

• membranes are derived from host plasma membrane
• more common in animal viruses
• membrane proteins are normally encoded on the viral genome

Question 8

What are complex virus features?

Answer 8

• many phage of E. coli have been identified as complex
• additional elements: head, tail, tail pin, endplate, collar, tail fibers (ex: bacteriophage T4)
• complexity requires larger genome to encode extra proteins
• problem - more genetic to store within capsid

makes it pretty mobile

Question 9

What are the two enzymes discussed in class that may be packaged into virion structures?

Answer 9

Some viruses need enzymes to successfully infest their host; need to be attached to host for enzymatic activity to occur.
* lysozyme - used to allow for entry of viral genome
* polymerase - some viruses have genes that require viral polymerase for replication
* host-lytic enzymes - may be required for liberation of virions from the host cell

Question 10

What are viral plaques?

Answer 10

a zone that develops on a host cell area (ex: agar plate); where the bacteria not growing; analogous to bacterial colonies

Question 11

How are viral plaques used to quantify infectivity? What is PFUs?

Answer 11

• bacteriophage grow as plaques on petri plates or liquid culture
• determine plate efficiency by counting number of plaque forming units (PFUs)
• determines how infectious a virus is in a given situation

Question 12

What is plating efficiency?

Answer 12

refers to the fact that normally only a small portion of the virions result in plaques

Question 13

Why is it helpful to use cell culture for viral research?

Answer 13

provide a controlled environment for studying viral replication, interaction with host cells, and the development of new diagnostic and therapeutic tools. They facilitate the isolation, identification, and propagation of viruses, enabling scientists to study their lifecycle, pathogenesis, and host range.

Question 14

What are the steps for the quantification of viruses?

Answer 14

1. pour mixture (molten top agar, bacterial cells, diluted phage suspension) onto agar plate
2. creating sandwich of top agar and nutrient agar
3. incubate
4. lawn of host cells, phage plaques

small portion of virions result in plaques

Question 15

How is lytic viral replication different from bacterial batch culture growth?

Answer 15

Lytic viral replication involves a quick hijacking of the host cell, rapid viral replication, and cell lysis, resulting in a one-step growth curve. Bacterial batch culture, on the other hand, follows a typical growth curve with distinct lag, log, stationary, and death phases, where the bacteria multiply independently.

Question 16

What are the steps of a virus infection?

Answer 16

1. attachment to host cell - mediated by receptors on the host cell surface
2. penetration (injection) - use of strategies for viral entry into host cell; some only injection of nucleic acid is needed while others require packaged enzymes (retrovirus)
3. synthesis of nucleic acid and protein
4. synthesis of nucleic acid and protein
5. assembly and packaging
6. release (lysis)

Question 17

How does this penetration differ from that of many animal viruses?

Answer 17

While bacteriophages typically inject their DNA directly into the host cell, animal viruses generally enter the host cell entirely, often via endocytosis or membrane fusion.

Question 18

What does the term eclipse refer to?

Answer 18

the period after viral attachment and penetration but before the first appearance of infectious virions (new viral particles) outside the host cell. During this period, the virus is replicating and assembling its components inside the host cell, but no free virions are detectable.

Question 19

What events occur during the latent period of viral replication?

Answer 19

the virus exists in a dormant state within the host cell, meaning that viral replication is not active but the viral genome is retained.
* early enzymes, nucleic acid, protein coats produced; virus added

Question 20

What is the difference between a naked virus, enveloped virus, and complex virus?

Answer 20

naked - have nucleic acid + capsid (composed of capsomers)
enveloped - nucleocapsid + envelope

Question 21

How does a restriction system protect bacteria from phage infection?

Answer 21

• bacterial way of preventing viral infections inhibiting foreign DNA in the cell; host cell will methylate own DNA so it does not get cut
• restriction enzymes that will cut DNA that is not methylated
• ex: endonucleases

Question 22

What is bacteriophage T4?

Answer 22

• example of virus that has gotten around endonucleases because substituted cytosine is glucosylated

Question 23

How does bacteriophage T4 replicate?

Answer 23

DNA replication results in circular permutation of the packaged genomes.
* replicated genomes are joined to form a large concatemer.
* concatemer is cleaved into headfuls of DNA resulting in repeated terminal sequences.

• early genes are transcribed directly by host RNA pol-theta70.
• phage anti-sigma shuts down early mRNA synthesis.
• middle genes are transcribed by host RNA pol that has been modified to recognize phage middle promoters by phage early proteins.
• late genes are transcribed by RNA pol associated with a phage encoded sigma subunit.
• phage-encoded nucleases degrade host DNA –> lyse open the cell.

concatemer - a long DNA molecule formed by linking multiple copies of the same DNA sequence together end-to-end.

Question 24

What are the seven classes of viruses in the Baltimore Classification system?

Answer 24

most viruses are using the minus transcribe into mRNA (+).
Class I, VII - double stranded DNA (+) virus, transcription of minus strand.
Class II - single stranded DNA (+) virus, synthesis of other strand –> ds DNA intermediate –> transcription of minus strand.
Class III - double stranded RNA (+) virus, transcription of minus strand.
Class IV - single stranded RNA (+) virus, used directly as mRNA.
Class V - single stranded RNA (-) virus, transcription of minus strand.
Class VI - single stranded RNA (+) retrovirus, use reverse transcriptase –> ds DNA intermediate –> transcription of minus strand.

Question 25

Compare and contrast the infection cycles of the lytic bacteriophage T4 with that of the temperate bacteriophage lambda.

Answer 25

lytic - virus enters host cell and replicates and lyses host and finds other hosts to infect; occurs when Cro is the dominant regulatory molecule. lysogenic - integrates its genome into the host, integrates into host DNA without detection, replicating with the bacterium, eventually will trigger host to undergo lytic cycle; cl protein causes repression of lambda lytic events. - T4 does not do rolling circles --> overlaps. - headful mechanism - T4. - rolling circle; cut one genome at a time. ## Footnote temperate - has two alternate life cycles rather than one.

Question 26

How does Phage Lambda regulate between lytic and lysogenic cycle?

Answer 26

Agents that cause DNA damage induce lambda to excise from the chromosome and enter the lytic cycle from the lysogenic cycle. * The cI protein (the lambda repressor) causes repression of lambda lytic events; the Cro protein controls activation of lytic events. * RecA protease destroys the cI Lambda repressor resulting in Cro activation and entry into the lytic cycle.

Question 27

What are animal viruses?

Answer 27

* many are enveloped * include all known modes of viral genome replication * some can cause cancer * not all infections of animal host cells result in cell lysis or death: latent or persistent infections are common.

Question 28

What are the five potential consequences of virus infections in animals?

Answer 28

* transformation * lysis/death * persistent infection * latent infection - no virion produced during latent stage, recurring infection, won't replicate in healthy state.

Question 29

What are the viruses and diseases associated with the Influenza virus? What are their defining features?

Answer 29

* segmented RNA virus * undergo frequent mutagenesis * **antigenic shift:** rearrangement of genome segments to produce different viruses * **antigenic drift:** minor antigenic changes due to genetic mutations * both of these make it necessary to get a new flu shot every year. ## Footnote shift and drift are ways it can mutate.

Question 30

What are the viruses and diseases associated with retroviruses? What are their defining features?

Answer 30

It will go from RNA genome --> DNA --> transcribing back to RNA. - gag codes for structural proteins. - pol encodes reverse transcriptase. - env codes for envelope protein. - R is a terminal repeat region.

Question 31

What are the viruses and diseases associated with poxvirus? What are their defining features?

Answer 31

ds DNA

Question 32

What is the difference between prions and viroids?

Answer 32

Viroids - small circular ssRNA particles that infect plants, naked nucleic acid, no protein encoding regions. Prions - just proteins that cause neurological disease, misfolded; host contains normal info through a mechanism --> misfolding proteins --> more misfolded proteins produced through gene expression or directly misfolding them --> build up --> damage. ex: Creutzfeldt-Jakob disease and Kuru. ## Footnote PrPSc is a misfolded protein that affects more misfolding and accumulates aggregates.

Question 33

What is a famous prion disease found in cattle that may manifest in humans?

Answer 33

Bovine spongiform encephalopathies aka mad cow disease; vCJD in humans.