Virology Chapter Review Questions

Chapter Questions 

Chapter 1

1. What is a virion? What is the difference between a virus and a virion? 

A virion is an infectious virus particle. The difference between a virus and a virion is that a virion is an external form of a virus. It consists of a genome that is either DNA or RNA. It also has a capsid and may or may not have an envelope. The term virus is referring to the entity as whole, meaning it includes the viral cycle and characteristic differences. 

2. Describe three reasons why it is important to study viruses. 

The first and most important reason to study viruses is because they can cause diseases with some being fatal if not treated promptly. Viruses can cause epidemics or pandemics. Studying viruses has helped in understanding how systems worked in living organisms. This was exemplified by the Hershey-Chase experiment that revealed how DNA is a hereditary matter. Lastly, the studying of viruses revealed that they could be used for treatment of bacterial infections. 

3. How was it determined that DNA, and not protein, encodes genetic information? 

The Hershey-Chase experiment helped determine that DNA encodes genetic information. They used radioactive ³²P  and ³⁵S. Phosphorus is found in DNA and Sulfur is found in proteins. They observed that the P DNA went into the cell and that ³²P was passed down into a new set of bacteriophages. The same observation was not found in the ³⁵S. 

4. How are viruses used therapeutically? 

Viruses were used for phage therapy, which used viruses for the treatment of bacterial infections when antibiotics did not exist yet. Viruses were also used for gene therapy, which was replacing defective genes to treat disease. 

5. List the characteristics of living things. Describe why viruses do or do not satisfy each criterion. 

For an organism to be considered alive, it must be able to meet certain criteria. The first being that there must be some type of genomic material. Viruses do meet this criteria because depending on the virus it has either DNA or RNA genomic material. The next criteria needed is the organism must be able to take part in metabolic reactions. Viruses do not meet this requirement because they can’t independently engage in metabolic reactions, they must use the host cell’s mechanisms. An organism must be able to independently reproduce and grow. While a virus can technically reproduce and grow, it cannot do so independent of a host cell. An organism also needs to be able to quickly adjust to changes in the environment to maintain homeostasis. A virus is not able to maintain a level of homeostasis because they lack the mechanisms that living organisms have. Finally, for a living organism to be able to adapt to its environment, it must be able to evolve. Viruses do meet this criteria because they can evolve to adapt to different environments for survival. 

6. How is virus replication different from cell division? 

In cell division, they are able to reproduce independently. Cells replicate its DNA, grow and divide both the cell and DNA in two. Viruses can not reproduce independently, it must enter a cell for it to reproduce. Unlike in cell division, a virus will disassemble once it enters and will make new virions from scratch. 

7. What hypotheses exist for the origin of viruses? Which do you think is most likely, and why? 

There are three hypotheses that exist for the origin of viruses. The first is the Pre-Cellular hypothesis, which states that viruses were present before or alongside early cells. This hypothesis believes that RNA was the first genetic material to exist on Earth. The second hypothesis is called the Escape hypothesis. This hypothesis stated that viruses are pieces of cells that escaped and were able to travel from cell to cell. This hypothesis believes that cells came before viruses unlike in the Pre-cellular hypothesis. The last one is called the Regressive hypothesis. This hypothesis states that viruses were at one point independent and regressed back to a state where they can’t replicate independently. 

The one that is most likely is the Regressive hypothesis. This hypothesis explains that viruses, particularly large, evolved which means that viruses have cellular ancestors. Also, the pre-cellular and escape hypotheses are essentially the opposites of each other. Both contradict one another that either RNA is the starting genetic material or it’s not.  

8. What characteristics of viruses made it difficult for scientists to discover them? 

Koch’s Postulates were created as a way of making it easier to distinguish and identify viruses. In actuality, his Postulates made it quite difficult. Not every virus was able to match these characteristics and thus making it hard to discover them. 

9. How were Chamberland filters useful in the discovery of viruses? 

The Chamberland filters were useful because it helped identify if the infectious agent was bacterial or not. The Tobacco mosaic virus was much smaller than bacteria and was still infectious when passed through the filter. This discovery was useful because it provided a distinction between bacteria and viruses.  

10. How do light and electron microscopes work? What are the advantages and disadvantages of each?

Light microscopes work by having a light source shine through a specimen and lenses that focus the specimen to make it appear larger. Electron microscopes use electron beams that illuminate a specimen. The advantages of light microscopes is that they are less expensive, don’t need training, and can observe color. However, light microscopes have good resolution but it is not better than an electron microscope. The advantages of electron microscopes is that they have greater magnification and resolution. Electron microscopes allow for great visualization of the surface of a virus. The disadvantage is that electron microscopes are expensive and require training. They also don’t show color and specimens must be dead to be seen. 

Chapter 2

1. Why are viruses considered obligate intracellular pathogens? 

They are considered obligate intracellular pathogens because they depend on the cell’s internal environment to be able to create new virions. 

2. How does viral replication differ from cell reproduction? 

Viruses use the cell's mechanisms to replicate and create new virions from scratch, while cells will divide into two. 

3. What is the function of the capsid? Why must viruses repeat the same capsid protein subunits repeatedly, rather than having hundreds of different capsid proteins? 

The capsid is a protective shell that surrounds the nucleic acid of a virus. By repeating the same capsid protein, the capsid is stronger and flexible compared to having a bunch of different capsids. 

4. Explain what 2–3–5 symmetry is, pertaining to an icosahedron. 

2-3-5 symmetry refers to the ways that an icosahedron is able to rotate on its axis. 2-fold is when the axis is through the center of an edge. 3-fold is when the axis is through a face center. 5-fold is when the axis is through a vertex of an icosahedron. 

5. What is a structural unit? In a T = 3 virus that has three subunits per structural unit, how many total subunits form the capsid? 

A structural unit is a set of repeated viral proteins or a single viral protein that form the face of an icosahedron.  In a T = 3 virus, the total subunits that form the capsid is 3. 

6. List the seven groups of the Baltimore classification system.

Class 1: dsDNA

Class 2: ssDNA

Class 3: dsRNA

Class 4: +ssRNA

Class 5: -ssRNA 

Class 6: RNA viruses that can reverse transcribe

Class 7: DNA viruses that can reverse transcribe 

7. What taxa are used to classify viruses? How does this differ from the classification of a living organism? 

Viruses use: realm, kingdom, phylum, class, order, family, genus, and species. The realm in viruses is called the domain in living organisms. 

8. What viral properties are used to classify viruses?

There are several properties used to classify viruses. A virus's nucleic acid type and protein purpose is taken into account. The sequence of nucleic acid is also considered. The physical properties of viruses are also considered such as virion size, the capsid shape, whether it has an envelope or not. 

Chapter 3 

1. Describe the general process of expressing a gene (located in a chromosome) into a protein. Where does each step take place within the cell? 

The first step in expressing a gene into a protein is that the DNA needs to be replicated to be ready for transcription. Next, is the creation of a mRNA copy from a portion of the DNA. This is called transcription, which occurs in the nucleus with the DNA. The final step is translation which occurs in the cytoplasm. A ribosome will begin translating at the start codon and continue until it reaches a stop codon. 

2. A secreted protein has been synthesized by a ribosome. Describe the pathway it will take to leave the cell and what happens at each step. 

The secreted protein can either be free flowing in the cytosol or attached to the rough endoplasmic reticulum. Either way the protein is then folded into glycoproteins and transported via vesicles into the Golgi complex. From there, they can be shipped to other cellular parts or to outside the cell. 

3. What molecules do you know of that are hydrophobic or hydrophilic? 

Fatty acids are hydrophobic and phosphate groups are hydrophilic. 

4. Explain the fluid mosaic model of plasma membrane assembly. 

The fluid mosaic model says that the fluid nature of the model is because proteins and other phospholipids are not connected molecularly and can move around freely. 

5. Which cellular organelles or processes are utilized by viruses? 

A virus utilizes many organelles such as the rER and the golgi complex. Viruses also use endocytosis (bulk and receptor-mediated) to enter the cell. 

6. Describe what happens during each of the four stages of the cell cycle. 

During the first phase (G1), the cells will grow. In the S phase, the cell will replicate and duplicate the chromosomes. The cell will prepare for either mitosis or meiosis in the G2 phase. Lastly the cell will divide into two through mitosis or meiosis. 

7. What is the central dogma of molecular biology? 

DNA is replicated in the nucleus and is then transcribed into mRNA. The mRNA is translated into proteins by ribosomes. 

8. Draw a double-stranded piece of DNA. Make sure to label the 5′ and 3′ ends. Now draw out the process of DNA replication, paying attention to the 5′ and 3′ ends and the direction that DNA polymerase synthesizes the new strand.

DRAW

9. Describe the three steps involved in RNA processing. 

The first step involved is the addition of a 5’ cap to the end of the transcript. The next is the addition of the poly A tail at the 3’ end of transcript. Finally, the introns are removed from the transcript. 

10. Use the genetic code in Fig. 3.19 to translate the following piece of mRNA: 

5′-GCCGCCAUGGCCA UAGCCGAUUGACCCGGA-3′ 

3’ -CGGCGGTACCGGT ATCGGCTAACTGGGCCT -5’

11. Determine the 5′ UTR and 3′ UTR in the sequence above. 

5’ UTR is highlighted yellow 

3’ UTR is highlighted green 

12. Describe what happens during the three stages of translation. 

The first stage of translation is the initiation. The ribosomes will assemble at the start codon of mRNA and a tRNA will transfer the RNA. In the next step, elongation, the protein is synthesized from amino acids. The last step, termination, is where the ribosome will arrive at a stop codon and the protein is released. 

13. Explain at least three translational processes involving the ribosome that occur with viral translation but do not normally occur with cellular translation of a protein. 

Ribosomal frameshifting occurs in viral translation but not cellular. This is when a ribosome changes the reading frame of mRNA and skip nucleotides. Viruses also have IRES that allows ribosomes to still bind to mRNA without the 5’ cap. Viruses can also engage in ribosomal skipping, which is when a ribosome continues translating. 

14. How do viruses ensure the preferential translation of their gene products over cellular gene products?

Some viruses are able to prevent enzyme activation and its breakdown. They can also degrade the host mRNA and interfere with the exportation of mRNA transcripts. 

Chapter 4

1. List what takes place at each of the seven steps of viral replication. 

• Attachment: A virus will attach to the cell via virus attachment proteins to attach to the host cell 

• Penetration: The virus enters through the host cell's plasma membrane through endocytosis or fusion 

• Uncoating: The virus’ capsid will dissolve and the genome of the virus will be released into the cell. 

• Replication: The virus' genome will replicate to form new virions but the type of genome replicated depends on the nucleic acid type. 

• Assembly: The newly created virions assemble their nucleocapsids for maturation

• Maturation: Any final changes or adjustments are made before release 

• Release: The viruses are released either through budding off or lysis of the cell. 

2. Considering that each virus must bind to a specific cell surface receptor for attachment, explain how you would create a drug that prevents viral attachment. 

I would first determine what the corresponding ligand of the virus and receptor of the host are. Then I create a drug that would prevent the binding of the receptor and the ligand. By preventing the binding of the receptor and the ligand, the virus would not be able to attach to the host.  

3. Focusing on the nucleic acids and enzymes involved, draw out the replication strategies of the seven classes of viruses. 

4. Regardless of the type of nucleic acid, what are the general requirements for a virus to create functional nascent virions? 

The virus must be able to replicate its genome regardless of the type of DNA or RNA it is. It also must be able to complete the other virus cycle steps such as; mutatration, assembly, and release. 

5. Make a chart that lists the location of transcription for each of the seven classes of viruses. 

6. Explain why +ssRNA viruses do not have to carry their own RdRp within their virions. 

+ssRNA do not have to carry their own RdRp because it is already ensconced into the genome. It has already been produced when its genome has entered the cell. 

7. What is the difference between recombination and reassortment? 

The major difference between recombination and reassortment is that recombination happens with two different strains but it is the same virus. The virus will exchange some of its genetic material with a different strain of the same virus. This creates a type of hybrid virus that is different from either parent strain. Reassortment is when two strains with segmented genomes are replicated but the segments from one virus will mix with the segments from the other. This creates a virus that is new in the sense it hasn't been seen before. 

8. List the steps involved in the reverse transcription and integration of a retrovirus genome. 

Reverse Transcription:

• The start of reverse transcription begins with a tRNA host that partially unwinds and binds to the PBS (primer-binding site). 

• The negative-strand strong-stop DNA is formed when the RT binds and adds DNA nucleotides to the sequence. 

• Next, the RT RNase H activity degrades the RNA from the RNA:DNA hybrid.  

• After it is degraded, the RT begins reverse transcribing the positive strand after binding the PPT primer. This forms the positive-strand strong-stop DNA

• The tRNA is then digested by the RT RNase H and RT will complete the replication of both strands. Thus creating lTRs on both ends of the double stranded cDNA. 

Integration: 

• Integrase will remove the two base pairs from both ends of proviral DNA

• It will create a nick in the chromatin of the host and join the proviral DNA to the host DNA. 

• The cellular DNA repairs the enzymes and seals the nick. 

9. Describe the steps involved in replicating the genome of HBV. 

The rcDNA is repaired into cccDNA and the cellular RNA polymerase II transcribes an RNA pregenome. RNA polymerase II transcribes the entirety of the negative-strand and continues on to DR1 after passing DR2. The repeat section folds into an epsilon shape and the pgRNA and P protein are formed into capsids. The P protein binds to the epsilon which reverse transcribes DNA base pairs. The entire negative strand is also reverse transcribed by the P protein and the RNase H degrades the RNA from the RNA:DNA hybrid.  The rest of the RNA segment is transferred to the opposite end of the negative strand and is binded to the DR2 sequence. The P protein continues to synthesize in the 5’ to 3’ direction. 

10. Both HIV and HBV use reverse transcription. Explain how reverse transcription is used differently in the replication of these two viruses. 

HIV uses reverse transcription the same way a typical retrovirus would. It transcribes RNA genomes into cDNA. HBV uses reverse transcription to create DNA that is partially single- and double-stranded. 

11. What generally determines whether or not a virus needs to gain entry into the nucleus to replicate? 

The type of genome that the virus has determines whether or not it needs to be in the nucleus. DNA viruses are typically in the nucleus when replicating and RNA viruses are in the cytoplasm. RNA viruses have RNA genomes which do not have a DNA intermediate. 

12. Make a table of the seven classes of viruses and list what the first event is that occurs after the virus enters the cell. Transcription? Reverse transcription? Translation? 

13. Which of the cellular processes described in this chapter are limited only to enveloped viruses compared to nonenveloped viruses? 

Only enveloped viruses use fusion to enter the cell because the envelope fuses with the plasma membrane of the target cell. Enveloped viruses are most commonly released from the cell via budding off. Nonenveloped viruses use endocytosis, either caveolin-mediated or clathrin-mediated to penetrate the cell. 

14. Which classes of viruses are more prone to introducing mutations during genome replication? Why? 

RNA viruses are prone to mutations because unlike DNA, RNA viruses don't have a proofreading ability that checks for incorrect sequences. 

15. What would be the result of interfering with the maturation of virions? 

The virions would not be able to infect new cells. 

16. Looking at the one-step growth curve (Fig. 4.19), extracellular virus disappears because the virus enters the cell. Why does the virus initially disappear from the intracellular samples, too?

The intracellular samples disappear because the assembly of the virions hadn't begun yet. 

Chapter 5

1. Make a table listing each portal of entry. What defenses does the host have at each location, and how are viruses able to successfully bypass them? 

2. Norwalk virus causes significant morbidity in developed nations, despite the fact that these countries have clean water supplies. How do you think the virus is transmitted, and why is it so successful?

The Norwalk virus is typically transmitted via the fecal-oral route. Individuals that eat contaminated food or touch contaminated surfaces can be infected. It is successful because it can spread through direct contact. 

3. Describe the architecture of the skin and how viruses gain access to each layer and the subcutaneous tissue. 

The skin has two layers of tissue: the epidermis, which is the outermost layer, and the subcutaneous layer, which is the underlying layer. The epidermis has five strata with the top strata not able to support virus replication. Viruses gain to the epidermis through small cuts or abrasions that allow it to go deeper into the skin. The subcutaneous layer is accessed through animal bites, needle punctures.  

4. How are vertical and horizontal transmission of viruses different from each other? 

Vertical transmission is when the virus spreads from parent to offspring or one generation to the next. The virus will cause long-term infection to the offspring. Horizontal transmission is when the virus spreads through direct contact from host to host. These viruses rely on a high infection rate to sustain the virus population. 

5. Which viruses are capable of initiating transplacental or intrapartum infections?

HIV and Herpes simplex virus  

6. How do localized infections become systemic infections? 

Localized infections become systemic infections by either neurotropic spread or hematogenous spread. 

7. Describe how different factors could affect the stability of virions within the environment. 

The type of nucleic acid the virion has could affect the stability. Also, the virion's sensitivity to pH changes and the presence/absence of an envelope. The temperature, pH, and humidity can also play a role in the stability of virions within the environment. 

8. Draw out the stages of infection after a person is infected with a virus. 

First is the incubation period, which is the time that the virus infects the host and symptoms begin to appear. The prodromal period is when the virus begins to quickly replicate and symptoms are generic. Next, the illness period is where the symptoms start to become more specific and the virus is multiplying at high levels. The immune system is activated at this stage as well. The convalescent period is the last stage in which the host begins to feel better and symptoms subside.  

9. Your friend walks into class, still sniffling occasionally from a respiratory viral illness. She reassures you that she’s “not infectious anymore.” You have your concerns. Why? 

She can still be infectious because she is still in the period of communicability. Even though the symptoms have subsided, the range of communicability can be before or after symptoms have subsided. 

10. How can persistent infections arise? 

They arise because the immune system cannot clear the virus completely. 

11. Describe the difference between endemic and epidemic. 

An endemic is the usual numbers of a disease that is present in a population. An epidemic is the unexpected number of cases for a disease in a population. 

12. Make a list of the three major aspects of the epidemiologic triad model and what factors could affect each aspect in promoting infection. 

• Host 

  • Age and gender of individual

  • Immune status 

  • Malnourished 

• Agent 

  • The stability of the environment 

  • Susceptibility to antiviral drugs 

  • Transmission of the pathogen

• Environment

  • Has proper sanitation 

  • Health services are available 

  • Climate 

  • Presence of vectors 

13. Create a list of control measures that could interfere with each variable in the chain of infection.

• Prevent the virus from leaving the infected individual 

• Isolate individuals that have been infected 

• Prevent direct contact with infected individuals by implementing hand washing and sterilization measures

• Wear ppe 

14. Consider the SARS-CoV-2 pandemic. Identify specific control measures that were used to interrupt the chain of infection. 

• Isolation of infected individuals (quarantine) 

• Handwashing 

• PPE (masks) 

• Cleaning and sanitization measures 

15. Design a case–control study that attempts to determine the precise food product that was the cause of a viral gastrointestinal illness.

By looking at the past events, the precise food product that caused a viral gastrointestinal illness will be determined. Determine if all the case patients had eaten the same precise food product. Then create a control group with a different food product and compare the infection rate. From there, determine what missed procedure caused the contamination of that food product.