(1.5) Viruses and Subviral Particles

1) T/F: All viruses contain envelopes 2) The envelope surrounds the _____________ and is composed of ____________ and ______________. 3) The envelope is very sensitive to ______________, ________________, and ____________. 4) T/F: Enveloped viruses are harder to kill than non-enveloped viruses.

1) False 2) Capsid, phospholipids, virus specific proteins 3) heat, detergents, desiccation. 4) False - Enveloped viruses are easier to kill because their envelopes are so sensitive. On the other hand, viruses that do not have an envelope are more resistant to sterilization and are likely to persist on surfaces for an extended period of time.

1) T/F: Once a bacteriophage goes through a lysogenic cycle and integrates into the bacterial host's genome, it stays in a lysogenic cycle forever. 2) Trapping of segments of the bacterial genome can occur when a provirus finally does decide to leave the genome, this allows for __________________ of genes from one bacterium to another.

1) False - Although the virus may remain integrated into the host genome indefinitely, some sort of stimulus, usually environmental factors (radiation, light, or chemicals), will cause the provirus to leave the genome and revert to a lytic cycle at some point. 2) Transduction

Briefly describe the pathway of retroviral nucleic acids from infection of a host cell to release of the viral progeny.

1) Proteins on the virus's surface bind cell surface receptors. 2) Virus fuses with cell and empties it's contents into the host cell's cytoplasm. 3) Reverse transcriptase copies the virus's RNA genome into double stranded DNA. 4) Integrase inserts the DNA into the host cell's genome 5) Cell machinery transcribes viral genes back into mRNA, and ribosomes produce the encoded proteins 6) Translated viral proteins (as well as non translated viral mRNA strands, which serve as the viral genome for new virions) travel to the membrane and gather into a budding virus particle, which is released and becomes an immature virion. 7) Viral proteases modify some viral protein chains which make the virion mature, and ready to infect a new cell.

1) Retroviruses carry an enzyme known as______________, which synthesizes DNA from single stranded RNA. 2) Provide an example of a commonly known retrovirus.

1) Reverse transcriptase 2) HIV

1) How is diversity generated amongst retroviral copies? 2) The enzyme ______________ is responsible for inserting the synthesized double stranded DNA (created by reverse transcriptase) into the host cells genome.

1) Reverse transcriptase often makes errors when synthesizing double stranded DNA from viral RNA. 2) integrase

Identify and explain the three processes through which viral progeny may be released from a host cell.

1. The viral invasion may initiate cell death, which results in the spilling of the progeny 2. The host cell may lyse s a result of being filled with extremely large numbers of virions 3. Extrusion - a process where the virus leaves the cell by fusing with its plasma membrane, keeping the host cell alive.

What is the difference between a positive sense single-stranded RNA virus and a negative sense single-stranded RNA virus?

A positive sense single stranded virus has a genome that can be directly translated to functional proteins by the ribosomes of the host cell, as if it were the cells own mRNA. A negative sense single stranded virus requires its "negative sense" RNA strand to be replicated into a complimentary template strand. This is what is translated into functional proteins.

Explain how there may be some benefit to a bacterium being integrated into a virus's lysogenic life cycle.

Although bacteriophages eventually kill the host bacterium, Infection with one strain of phage generally makes the bacterium less susceptible to simultaneous infection from other phages (i.e., superinfection) and because the provirus is relatively non-harmful, there may be some evolutionary advantage to this association.

_______________ are viruses that specifically target bacteria.

Bacteriophages

Why must viruses replicate and express genetic information inside a host cell?

Because they lack ribosomes to carry out protein synthesis.

A viruses protein coat is called a _______________

Capsid

Contrast the two main life cycles of bacteriophages.

Depending on growth conditions and the specific virus, bacteriophages may enter a lytic or lyogenic life cycle. During a lytic cycle, the bacteriophage makes maximal use of the cell's machinery with little regard for the survival of the host cell. The bacteriophage replicates inside the host cell in extremely high numbers until the host cell lyses and releases the virions allowing other bacteria can be infected. The other option is a lysogenic cycle, in which the virus does not create/release progeny, but instead enters the host genome and replicates with the bacterium as a provirus.

T/F: Viroids only infect plants.

F: Viroids are classically thought of as plant pathogens, but a few examples of human viroids do exist (e.g. hepatitis D)

Identify what structures bacteriophages have that allow them to inject their genetic material into a host bacterium, and explain the relative function of each.

In addition to a capsid, bacteriophages contain a tail sheath and tail fibers. The tail sheath can act like a syringe, injecting genetic material into a bacterium. The tail fibers help the bacteriophage to recognize and connect to the correct host cell. (pg. 29) They can also have enzymatic activity that allows for both the penetration of the cell wall and the formation of pores in the cell membrane.

Viruses are considered obligate intracellular parasites. What does this mean?

It means they cannot reproduce independently, so they must express and replicate genetic information within a host cell.

1) Which viral progeny release mechanism is actually a disadvantage for the virus and why?

Lysis. This is because after the cell lyses the virus can no longer use the cell to carry out its life cycle.

Viruses hijack a cell's transcription and translation machinery to make it's own proteins. What kinds of proteins are these?

Many of these proteins are structural capsid proteins and allow for the creation of new virions in the cytoplasm in the host cell.

With regard to how protein translation is carried out, single stranded RNA viruses may be _____________ or _______________.

Positive sense or negative sense

What is a prion? Explain how they cause disease.

Prions are infectious proteins. They cause disease by triggering misfolding of other proteins, usually involving the conversion of a protein from an alpha helical structure to a beta pleated sheet. This drastically reduces the solubility of the protein, as well as the ability of the cell to degrade the misfolded protein. Eventually, protein aggregates form, and the function of the cell is reduced.

When a virus is releasing it's progeny via extrusion, thus continuously using the host cell, it is said to be in a ______________ cycle.

Productive

When a bacteriophage is going through a lysogenic cycle, it integrates into the host genome as a ______________ (or ________________).

Provirus (or Prophage)

A negative sense single-stranded RNA virus carries the enzyme ________________, which synthesizes an RNA compliment from it's negative sense strand before translation.

RNA Replicase

What is a retrovirus? What makes them unique with regard to how they infect a cell? How is this advantageous?

Retroviruses are enveloped, single stranded RNA viruses in the family retroviridae which contain two identical RNA molecules. These viruses carry an enzyme known as reverse transcriptase, which synthesizes DNA from single stranded RNA. The DNA then integrates into the host cell genome, where it is replicated and transcribed as if it were the host cell's own DNA. What makes this advantageous to the virus is that integrating their genetic material into the hosts genome allows the virus to infect the cell indefinitely, and the only way to cure the infection is to kill the infected cell itself.

A ______________ occurs when a bacterium is infected simultaneously by more than one bacteriophage.

Superinfection

Coronavirus, which causes the common cold, is described as an enveloped, single stranded positive sense RNA virus. What does this description indicate about structure/function of the virus?

The description indicates that the virus contains a outer layer of phospholipids with an inner capsid. Within the capsid, there is a single stranded RNA that can be immediately translated to protein by the ribosomes.

How do retroviruses show potential as therapeutics?

Theoretically, both retroviruses and transduction could be useful as methods of gene therapy. This is because both are capable of delivering functional versions of missing or altered genes so that the correct proteins can be synthesized and certain disease states can be alleviated.

T/F: The viral genome must be returned to it's original form before packaging

True - for example, retroviruses must transcribe new copies of their single stranded RNA from the DNA that entered the host genome.

T/F: Viruses do not actually enter cells in the process of transferring their genetic material.

True and False - it depends which type of virus you're taking about. This is true for bacteriophages, they simply "inject" it, while leaving the remains structures outside the cell. However, with other viruses, different portions of the virion will be inserted into host cells depending on the virus. Enveloped viruses (e.g. HIV) fuse with the membrane and enter the cell intact. Additionally, sometimes a host cell may misinterpret the binding of a virus to the membrane as nutrients or other useful molecules and will actually bring the virus into the cytoplasm via endocytosis.

T/F: Viruses can only infect a specific set of cells.

True: In order to infect a cell, the virus has to bind to specific receptors on the host cell. Without the proper receptors, the cell is essentially invisible to the virus.

What kind of variation do you see in viruses regarding the structure and organization of their genetic material?

Viral genetic information may be circular or linear, single or double stranded, and composed of either DNA RNA.

How many genes to viruses typically carry in their genome?

Viral genomes come in a variety of shapes and sizes. Some are made of only a few genes, while others have several hundred.

After hijacking a cell's machinery, a virus will replicate and produce viral progeny, called ______________.

Virions

_______________ and ______________ are very small (subviral) particles that can cause disease under certain circumstances.

Viroids and Prions

What is a Viroid?

Viroids are small pathogens consisting of a very short circular single stranded RNA that infect plants. Viroids can bind to a large number of RNA sequences and will silence genes in the plant genome. This prevents synthesis of necessary proteins and can subsequently cause metabolic and structural derangement in the plant cell.

A host bacterium that is infected by a bacteriophage which is going through a lytic cycle is said to be ________________

Virulent

After infection, translation of viral genetic material must occur in order for the virus to reproduce. This requires translocation o the genetic material to the correct location in the cell. For each of the following, explain where the genetic material must travel to be translated: a) DNA viruses b) Positive Sense Single Stranded RNA viruses c) Negative Sense Single Stranded RNA viruses d) Retroviruses

a) Most DNA viruses must go to the nucleus in order to be transcribed to mRNA, which then goes to the cytoplasm where it is translated into proteins. b) Genetic material for positive sense RNA viruses stays in the cytoplasm, where it is directly translated to protein by host cell ribosomes. c) Negative sense RNA viruses require synthesis of a complementary RNA strand via RNA replicase, which can then be translated to form proteins in the cytoplasm by host cell ribosomes d) DNA formed through reverse transcription in retroviruses must travel to the nucleus to be integrated into the host genome. From there, it is transcribed (in the nucleus) to mRNA which travels out to the cytoplasm to be translated by host cell ribosomes.

How many new virions does the typical virus create inside a host cell?

anywhere from hundreds to many thousands

After binding receptors on the cell surface, ________________ viruses are able to fuse with the plasma membrane of a cell, allowing entry of the virion into the host cell.

enveloped

What general structures make up a virus?

genetic material, a protein coat, and sometimes an envelope containing lipids.