Exam 2 - Mastering Microbiology - Chapter 5: Viruses Part II

How is penetration different in animal viruses as compared to bacterial viruses? Hint(s): Viral Penetration - During the life cycle of any virus, once the virus has attached to the surface of the target cell, penetration must occur. Part of the viral particle or the entire particle must enter the target cell in order for viral replication to occur. • The viral genome can penetrate an animal cell, while the entire viral particle penetrates a bacterial cell. • There is no difference; the entire viral particle penetrates both cell types. • The entire viral particle can penetrate an animal cell, while only the viral genome can penetrate a bacterial cell. • There is no difference; only the viral genome penetrates both cell types.

The entire viral particle can penetrate an animal cell, while only the viral genome can penetrate a bacterial cell.

How is the lytic cycle different from the lysogenic cycle with respect to the infected host cell? • The host cell dies during the lytic stage. • The viral DNA may integrate into the host genome during the lytic stage. • The host cell is allowed to live during the lytic stage. • The host cell can only divide during the lytic stage.

The host cell dies during the lytic stage.

What would be the fate of a lytic bacteriophage if the host cell died prior to the assembly stage? • The virus would not be able to infect new hosts. • The cell could still be revived by the virus. • The virus would infect new hosts.

The virus would not be able to infect new hosts.

Megaviruses and virophages share characteristics but differ in some important ways. Q2.B - What is a Virus? The introductory passage describes ways that virophages use megavirus-producing factories in Amoeba to reproduce because they are unable to do so independently. Compare characteristics of viruses and virophages by dragging the characteristics into the correct bin to indicate whether each is a characteristic of virophages only, viruses only, both, or neither. Hint(s): 1.) How do viruses differ from other microbes? Viruses are non-cellular infectious agents. Think about the parts of cells that differ from viruses, including their organelles, so that you can eliminate phrases that contain these components. 2.) How large are different types of microbes? The introductory passage discusses the relative sizes of cells, megaviruses, and virophages, mentioning that megaviruses are comparable in size to bacterial cells. How do virophages compare? Drag and drop the items into the appropriate bins. (match the bulleted items to the appropriate category) Category 1. Virophages only Category 2. Non-virophage viruses only Category 3. Both virophages and other viruses Category 4. Neither virophages nor other viruses • They are always smaller than Bacteria and Archaea. • They do not belong to any of the three domains (Bacteria, Archaea and Eukarya). • They generate energy through mitochondria. • They have a protein capsid surrounding their nucleic acid. • They use their own ribosomes to make proteins. • They cannot replicate on their own. • The genetic information of can be in the form of DNA or RNA. • They have a protein capsid surrounding their nucleic acid. • They lack the genes for proteins needed to replicate themselves.

*Category 1. Virophages only:* • They are always smaller than Bacteria and Archaea. • They lack the genes for proteins needed to replicate themselves. *Category 2. Non-virophage viruses only:* • The genetic information of can be in the form of DNA or RNA. *Category 3. Both virophages and other viruses:* • They cannot replicate on their own. • They do not belong to any of the three domains (Bacteria, Archaea and Eukarya). • They have a protein capsid surrounding their nucleic acid. *Category 4. Neither virophages nor other viruses:* • They generate energy through mitochondria. • They use their own ribosomes to make proteins. (note: While megaviruses are comparable in size to bacterial cells, the introductory passage explains that the tiny virophages are found around the structures that they use to replicate. Viruses are not classified within the domains Archaea, Bacteria, or Eukarya and do not have cellular structures such as ribosomes and mitochondria. However, megaviruses and virophages both have nucleic acids and protein capsids like all viruses. Viral nucleic acids can be DNA or RNA (sometimes with both at different parts of the life cycle).)

The genetic information of viruses is highly variable. Beyond the differences in nucleic acid type, the strands can be plus-sense or minus-sense. Q2.C - Viral Replication and Synthesis The type of genetic material found in viruses, including virophages, affects the pathways for replication and synthesis of new viral genetic information. Match the viral genetic category to the correct description, using information from the introductory passage and from the chapter. While it is not mentioned elsewhere, note that known virophages have double-stranded genetic material. Hint(s): 1.) What do plus-sense and minus-sense mean? "Plus-sense" means the viral genome has the exact sequence of the viral mRNA, while "minus-sense" means that it has a complementary sequence. 2.)What does the prefix "retro" indicate? The prefix "retro" comes from the Latin word meaning "backwards." How can genetic information flow backwards? ______________ viruses have genome configurations that are either plus-sense or minus-sense. ______________ and ______________ viruses carry their own nucleic acid polymerases (called replicases) to replicate the viral genome with no DNA intermediate. ______________ viruses contain an RNA-dependent DNA polymerase called reverse transcriptase that is used generate a DNA intermediate. ______________ and ______________ viruses replicate using DNA polymerases, either their own or from those of the host. ______________ viruses have processes of replication, transcription, and translation that are the most similar to those used by cells. ______________ viruses have replication that involves first generating a complementary DNA strand. ______________ is the genetic material of virophages. word bank: • retro- • single-stranded RNA • double-stranded RNA • double-stranded DNA • single-stranded DNA

*Single-stranded RNA* viruses have genome configurations that are either plus-sense or minus-sense. *Single-stranded RNA* and *double-stranded RNA* viruses carry their own nucleic acid polymerases (called replicases) to replicate the viral genome with no DNA intermediate. *Retro-* viruses contain an RNA-dependent DNA polymerase called reverse transcriptase that is used generate a DNA intermediate. *Single-stranded DNA* and *double-stranded DNA* viruses replicate using DNA polymerases, either their own or from those of the host. *Double-stranded DNA* viruses have processes of replication, transcription, and translation that are the most similar to those used by cells. *Single-stranded DNA* viruses have replication that involves first generating a complementary DNA strand. *Double-stranded DNA* is the genetic material of virophages. (note: The variations in the genetic material in viruses makes studying viruses as a single group very challenging. This variability in genetic information, however, provides evidence for the evolution of viruses and their contribution to the evolution of cells.)

What is the benefit for a bacteriophage to be a temperate (or lysogenic) virus? Hint(s): Temperate Viruses - Bacterial viruses can be lytic or temperate (lysogenic). Lytic viruses infect a cell, replicate, assemble, and then lyse the cell to release new viral particles. Temperate viruses infect a cell and integrate into the genome of the host. Each time the cell replicates, the viral genome is replicated as well. • A single infection event can allow other host cells to be infected by the same virus. • A single infection event can allow the virus to live in the host cell indefinitely. • A single infection event can produce hundreds of new viral particles. • A single infection event can produce millions of new viral particles instead of hundreds of viral particles.

A single infection event can produce millions of new viral particles instead of hundreds of viral particles.

Viruses only contain genetic information, and they lack all of the enzymes necessary for replication. In order for viruses to replicate, divide, and reproduce, they must hijack the replication machinery and enzymes of cells. Viruses accomplish this task by infecting a cell. Q2.D - How Do Cells Evade Viral Infection? The introductory passage discusses the way that virophages interfere with the ability of megaviruses to reproduce and the possible selective benefits of this. However, there are many ways that cells attempt to survive attacks by viruses. According to the chapter, what is another way that cells have evolved to avoid viral infection? Hint(s): 1.) Stages of viral infection - In order to avoid viral infection, the host cell must adapt by making it impossible for the virus to carry out one or more of the steps leading to infection. Think about the steps required for a virus to infect a cell, and consider ways a host cell could prevent each from happening successfully. 2.) Advantageous mutations vs. disadvantageous mutations - A mutation in the host is advantageous if it prevents viral infection without compromising its own integrity and function. A mutation is disadvantageous to a host if the cell cannot survive because of it even if virus reproduction would be prevented. Select the best answer. • Cells undergo a phenomenon called circular permutation, in which the same set of genes is arranged differently in each individual. • The host develops enzymes that cleave the restriction endonucleases of the virus. • A mutation in the host blocks translation at the ribosome. • An attachment receptor on the host cell surface that is recognized by the virus is mutated.

An attachment receptor on the host cell surface that is recognized by the virus is mutated. (note: External components of the virion must interact with external components of its target cell, called receptors. If the specific receptor is absent or mutated, the virus cannot attach, and the host may become resistant to viral infection. The host range of a given virus depends on the presence of these specific recognizable receptors.)

In which stage does formation of mature viruses occur? • Penetration • Assembly • Biosynthesis • Attachment • Release

Assembly

The host DNA is usually degraded during which stage? • Penetration • Assembly • Attachment • Release • Biosynthesis

Biosynthesis

Some viruses, especially animal viruses, have an envelope surrounding their nucleocapsid. This envelope may have viral proteins embedded in it. Why are the viral proteins more readily recognized and targeted by the immune system than the envelope? Hint(s): [[Viral envelopes]] As enveloped viruses enter a cell, their envelope often fuses with the cell membrane. As they leave, they generally take cell membrane material with them, which becomes a major component of the envelope. To answer this question, consider how the immune system recognizes foreign versus self in order to respond to foreign material. • The envelope is not capable of stimulating an immune response because of its makeup. • Only proteins can stimulate the immune system, so the phospholipids and glycoproteins of the envelope are not immunogenic. • Enveloped viruses are often coated with animal cell membrane as they leave the cell. This membrane is a major component of the viral envelope. The viral proteins are more readily recognized by the immune system, as they are more distinct from the materials normally found in and on the cells. However, the envelope can contain several types of viral components as well. • Viral proteins are highly immunogenic in order to facilitate uptake by host cells, while the envelope is not important in uptake by host cells.

Enveloped viruses are often coated with animal cell membrane as they leave the cell. This membrane is a major component of the viral envelope. The viral proteins are more readily recognized by the immune system, as they are more distinct from the materials normally found in and on the cells. However, the envelope can contain several types of viral components as well.

Which of the following events might trigger induction of a temperate bacteriophage? • Normal cell division of an infected cell • Bacterial conjugation • Exposure to UV light • An infected cell entering the logarithmic phase of growth

Exposure to UV light

Differentiate between persistent and latent animal virus infections. Hint(s): [[animal virus infections]] Infection of an animal cell by a virus can lead to different results. Some viruses immediately replicate the virus and lead to viral release by cell destruction. Others keep the host cell alive for long periods of time while releasing new virus particles. • Persistent infections can cause transformation of the host cell, which can lead to the development of cancer. Latent infections do not cause transformation. • In a persistent infection, the host cell is continually releasing new viral particles slowly. In a latent infection, there are periods of time where the virus is not replicating and creating new viral particles. • Persistent infections always lead to cell lysis, while latent infections never lead to cell lysis. • In a latent infection, the host cell is continually releasing new viral particles slowly. In a persistent infection, there are periods of time where the virus is not replicating and creating new viral particles.

In a persistent infection, the host cell is continually releasing new viral particles slowly. In a latent infection, there are periods of time where the virus is not replicating and creating new viral particles.

What is the fate of the prophage during the lysogenic stage? • It is packaged into viral proteins and maintained until the host is exposed to an environmental stress. • It is copied every time the host DNA replicates. • It is released from the cell by lysing the cell. • It is degraded by the activity of host defense enzymes.

It is copied every time the host DNA replicates.

Q2.A - What Makes Something a Virus? Based on your understanding of the chapter material and the information in the passage, which of the following best defines something as a virus? Are virophages a type of virus or something different? Hint(s): 1.) A capsid is a protein coat made of capsomeres. 2.) What types of nucleic acid are found in viruses? Viral nucleic acids can be circular or linear and double-stranded or single-stranded. Select the best answer. • It must have a capsid and double-stranded or single-stranded DNA. Virophages are therefore a type of virus. • It must have a capsid and a linear nucleic acid that encodes replication enzymes. Virophages are therefore not a type of virus. • It must have an envelope, capsid, and nucleic acid, which can be double-stranded or single-stranded, and DNA or RNA. Virophages are therefore not a type of virus. • It must have a capsid and a nucleic acid, which can be double-stranded or single-stranded, circular or linear, and DNA or RNA. Virophages are therefore a type of virus. • It must have a capsid and single-stranded nucleic acid. Virophages are therefore not a type of virus. • It must have a capsid and linear nucleic acid. Virophages are therefore a type of virus.

It must have a capsid and a nucleic acid, which can be double-stranded or single-stranded, circular or linear, and DNA or RNA. Virophages are therefore a type of virus. (note: A virus must have a nucleic acid and a capsid, although the nucleic acids vary greatly and can be RNA or DNA, double-stranded or single-stranded, and circular or linear. Virophages have these components even though they lack genes for replication proteins, so they are technically viruses.)

In which stage is the viral DNA introduced into the cell? • Penetration • Biosynthesis • Assembly • Attachment • Release

Penetration

Which of the following examples is an example of lysogenic conversion? Hint(s): [[Lysogenic conversion]] When a bacteriophage integrates its genetic material into a bacterial chromosome (a prophage) during the lysogenic life cycle, it may sometimes cause lysogenic conversion. • An RNA virus infects a cell and causes the production of new viruses. • A lambda phage infects E. coli and enters the lytic cycle. • Vibrio cholerae bacteria produce cholera toxin when infected with a phage. • T4 phages infect E. coli bacteria and are resistant to destruction by restriction enzymes.

Vibrio cholerae bacteria produce cholera toxin when infected with a phage.

Which of the following is true about viral infection? Hint(s): Viral Infection - In order to infect cells, viruses have to attach to the cell. They do this by finding appropriate receptors. Receptors differ in different species and even in different cells within a single organism. That is why some viruses can cause infection only with particular types of exposure (e.g., HIV cannot cause infection through a handshake) and may infect only particular tissues (e.g., viral upper respiratory infections are located in the tissues of the upper respiratory tract). • Viruses can infect any cell in a particular species; it does not matter which tissue they infect as long as the species (or group of similar species) is correct. • Viruses have what is needed to infect a host cell; they do not need anything specific from the host cell in order to cause infection and therefore can infect a wide range of cells. • Viruses can infect any cells within a large group, but they are not more specific than that. For example, there are plant viruses that can affect many types of plants, bacteriophages that affect many types of bacteria, and animal viruses that affect a range of viruses. • Viruses are very specific in which cells they infect. For a virus to be taken up by a cell, it must find a cell with appropriate receptors on the surface; it cannot be taken up by cells without the appropriate receptors.

Viruses are very specific in which cells they infect. For a virus to be taken up by a cell, it must find a cell with appropriate receptors on the surface; it cannot be taken up by cells without the appropriate receptors.

Lysogenic viral DNA integrating into the host genome is referred to as ___________. • lytic. • a prophage. • lysogeny. • induction.

a prophage.

Which of the following are viable methods of release of newly assembled viral particles? Hint(s): Viral Life Cycle-Release - Once a virus has infected a cell and replicated its genome, the next steps are to assemble new viral particles and then release them. If a virus is unable to release the new viral particles, the lifecycle is interrupted and there will be no further infections. • budding • lysis of host cell • budding or lysis of host cell • lysogeny

budding or lysis of host cell

Considering T4 bacteriophage infection of a bacterial cell, which would be an example of the earliest phage proteins transcribed and translated? Hint(s): In the lytic cycle, a bacteriophage infects a bacterium and immediately begins the process of forcing the host cell to make new viruses. The bacteriophage rapidly bursts and releases the new viruses. • portal proteins • enzymes for the synthesis and glucosylation of the unusual T4 base 5-hydroxymethylcytosine • T4 lysozyme • capsid proteins

enzymes for the synthesis and glucosylation of the unusual T4 base 5-hydroxymethylcytosine

In general, whether viruses are infecting bacterial cell or animal cells, they follow the same general steps of infection. In doing this, viruses will damage, distort the function, and cause the death of the host cell. Q2.E - Viral Life Cycles Virophages interfere with the life cycle of megaviruses by competing with them for replication enzymes, causing defective megaviruses to be produced. When the life cycle occurs correctly, what are the steps? Hint(s): 1.) What is lysis? "Lysis" means that the cell bursts. When would this occur in the viral life cycle? 2.)Unsuccessful viral infection - If an infected cell lyses immediately after the nucleic acid enters, the virion is no longer an infectious entity because the genome is no longer enclosed. List the items into the correct order of start to finish, from left to right • Host cell enzymes and replication machinery are used to synthesize new viral genetic and capsid material. • The host cell lyses, releasing the newly assembled virus particles. • The virus attaches to the host cell, which can be mediated by cell surface receptors. • Penetration of nucleic acids into the host cell and the capsid is discarded. • Newly synthesized viral genomes and capsids are assembled into complete viral particles.

from start to finish: (far left) 1. The virus attaches to the host cell, which can be mediated by cell surface receptors. 2. Penetration of nucleic acids into the host cell and the capsid is discarded. 3. Host cell enzymes and replication machinery are used to synthesize new viral genetic and capsid material. 4. Newly synthesized viral genomes and capsids are assembled into complete viral particles. 5. The host cell lyses, releasing the newly assembled virus particles. (far right) (note: Viruses attach to the host cell, and then nucleic acids penetrate the cell. Host cell enzymes and replication machinery are used to make new viral components, during which time virophages may interfere with the process. New viral particles are assembled, and then the cell lyses to release them.)

The result of viral infection on the host cell depends on the life cycle that a particular virus follows. Q2.F - Viral Life Cycles Megaviruses have a particular life cycle in which new viral particles are produced, and then the host cell lyses, although virophages can compete with them for replication enzymes. Viruses have many types of life cycles and can go through phases during which they are actively replicating and destructive to the host cell or dormant within the host cell. These life cycles differ in different types of viruses, so the cycle of megaviruses differs from those of bacteria and animals. During which part of the bacteriophage life cycle will the viral genome be replicated in synchrony with the host cell? Hint(s): 1.) How are life cycle options for bacteriophages and animal viruses different? There are two life cycles of bacteriophages, the lytic and lysogenic cycles. There are at least four possibilities for animal viruses, including virulent infection, latent infection, persistent infection, and transformation. 2.) What is transformation? Transformation by viruses refers to the ability of an animal virus to convert a normal cell into a tumor cell or to genetic recombination that results from a cell picking up genetic material from extracellular sources. Select the one best possible answer for the question. • latent infection • lytic • persistent infection • transformation • lysogenic

lysogenic (note: Some bacteriophages are only capable of a lytic life cycle, in which they rapidly kill their host, but others (temperate bacteriophages) are also capable of a lysogenic cycle. Animal viruses have a range of life cycles. These include virulent, latent, and persistent infections. In some cases, animal viruses can transform cells so that they become cancerous.)

Viral structural proteins and proteins involved in the release of new viral particles that are synthesized after genomic replication begins would be considered __________. Hint(s): Viral proteins - Once penetration occurs, the virus takes over the host cell and its metabolism. Very quickly, transcription and translation of viral genes occurs using the host cell enzymes. • middle proteins • early proteins • late proteins • middle and late proteins

middle and late proteins

Question 2. Q2.A - Q2.F The simplest definition of a virus is an infectious nucleic acid surrounded by protein. Viruses are also typically much smaller than bacteria. However, giant viruses comparable to some bacterial cells have been discovered. These "megaviruses" can actually be seen under the light microscope, as their diameters reach up to 0.75 μmμm, and because of their size, they clearly distort the line between a cell and a virus. Megaviruses infect protozoa such as Amoeba in diverse aquatic environments. Virologists have made several exciting discoveries about megaviruses other than their size. For example, for megavirus replication, infected amoeba cells form cytoplasmic "factories" dedicated to virus production, and these factories can be as large as the cell's nucleus. A particularly remarkable discovery was the detection of tiny virus-like particles surrounding intracellular megaviruses. These structures contain DNA surrounded by capsid proteins, and so by definition, they should be viruses. However, the DNA in these particles does not encode proteins required for their replication. With this in mind, how do these virus-like particles reproduce? Although they cannot replicate in amoeba cells by themselves, these tiny structures hijack the host's megavirus-producing factories for their own benefit. This leads to competition for virus-replicating enzymes and the ultimate formation of defective megaviruses, which are unable to infect new host cells. Because of this parasitic activity toward megaviruses, these pesky little structures are called virophages in analogy to the term bacteriophage, which describes viruses that infect Bacteria. The transmission electron micrograph here shows active cell infection by Samba megaviruses isolated from a river in the Amazon, along with their associated virophages (arrow). The dark mass in the bottom right is a viral factory (VF), and the inset illustrates the formation of a defective Samba virus that is unable to infect new amoeba cells. While it is unclear what role(s) virophages play in the biology of the amoeba cell, it is clear that the very existence of the virophage depends on its ability to parasitize the megavirus. Hence, the ability to inactivate megavirus replication and protect host cells from death may well be the selective force that maintains the virophage in this cozy arrangement of three different microbes. *image* Source: Campos, R.K., et al. 2014. Samba virus: A novel mimivirus from a giant rain forest, the Brazilian Amazon. Virol. J. 11: 95.

read for Q2.A - Q2.F

A retrovirus has a genome that consists of __________. Hint(s): [[Retroviruses]] Retroviruses contain an enzyme called reverse transcriptase to aid in the replication of the viral genome. They were the first viruses shown to be able to cause cancer and they are the causative agent of Acquired Immunodeficiency Disease (AIDS). • dsDNA • ssDNA • ssRNA • dsRNA

ssRNA