Legarde, Manuel III Castones

Virology
Study questions for lecture 3 – Genomes and genetics

1. Describe two experimental approaches proving that viral DNA or RNA is the
genetic material.

The first experiment was the Hershey's experiment. It was known as the
Kitchen Blender Experiment. They used radioactive precursors on either DNA or
protein in Bacteriophages. The viral DNA is labeled with phosphorus, and the
radioactive DNA is in the progeny phase. Proving that DNA is one of the genetic
material of a virus.

The second experiment was the Fraenkel-Conrat Experiment. They

conducted using the Tobacco Mosaic Virus with its RNA wrapped in protein. By
adding the protein to the RNA, it reassembles and infects the leaves. They
concluded that it does not maintain the color/type of the coat because it is encoded
in the RNA.

2. How many genome types are known? Name all of them, including a
representative virus, and trace the pathway of each to mRNA.

There are seven (7) known types of genome found in viruses. It is classified
under seven (7) classes; Class 1, Class 2, Class 3, Class 4, Class 5, Class 6, and
Class 7. Underclass 1, has a genome consisting of double-stranded DNA. The
dsDNA will be directly used to transcribe by RNA polymerase to produce
+ssmRNA. Class 2 consists of Positive Single-Stranded DNA. It will build its DNA
complementary strand (Negative Single-Stranded DNA) to produce dsDNA and
transcribe by RNA polymerase to produce +ssmRNA. Class 3 is categorized as
double-stranded RNA and needs RNA-dependent RNA Polymerase (RdRp) to
make +ssRNA. The single-stranded positive RNA with single-stranded negative
RNA dependent, Class 4, also needed RdRp to make +ssRNA. Class 5, Single-
stranded Positive RNA, can be used directly to make proteins by the host's cells
ribosomes. Class 6 reverse transcribes the single-stranded positive RNA to make
the single-stranded negative DNA. That will be converted into dsDNA and will be
transcribed by RNA polymerase to produce +mRNA. Class 7 is the gapped DNA
which makes the host's cells ribosome think that the DNA is its owner to repair its
strand. After completion of sdDNA, RNA will be transcribed to produce +mRNA.

3. The genome inside a virus particle is always a nucleic acid. If you could get only
the genome into a cell, would it start the replication cycle? Consider this question
for each of the seven known viral genome types.

It is highly possible as long as it can produce +mRNA. The dsDNA is the

easiest genome to replicate as it only needs the host's machinery to reproduce.
+ssRNA can be directly made into proteins by the host ribosomes. The gapped
dsDNA will be repaired by the host and will later on transcribed by RNA
polymerase. RNA (single-stranded negative and double-stranded) is converted

Study questions 4310 2020 Lecture 3

into mRNA by a viral RNA-dependent RNA polymerase. Lastly, as long as the
host's machinery can reverse transcribe the Class 6, it can be replicated.

4. What is the source of the enzyme that copies the genome of DNA viruses? Why
are there different sources?

Class 1, dsDNA, only needed RNA Polymerase to produce +mRNA. Class

2 (single-stranded positive DNA) needs DNA polymerase to make its
complementary strand, and then it can produce +mRNA with the help of RNA
Polymerase. Class 6 needs the reverse transcriptase to convert the +ssRNA with
-ssDNA intermediate to dsDNA, which then produces +mRNA with the help of RNA
Polymerase. Class 7 (gapped double-stranded DNA) needs the help of DNA
polymerase to repair its DNA, and then it can produce +mRNA with the help of
RNA Polymerase. The reason there are different sources of the enzyme that
copies the genome of DNA viruses is that different viruses have different
evolutionary histories, especially DNA viruses can have implications for the
development of antiviral drugs.

5. What is the source of the enzyme that copies the genome of RNA viruses?
Explain why this always the source.

The source of an enzyme that copies the genome of RNA viruses is RNA-
dependent RNA Polymerase. RNA viruses don't have their DNA polymerase and
rely on a virally encoded RdRp to replicate their genomes. Also, RdRp is the cause
of mutation of RNA viruses because it lacks proofreading ability (only DNA
polymerase has).

6. What can viruses with segmented genomes do that other viruses with
unimolecular genomes cannot? Why is this process of evolutionary significance?

Segmented genome has the advantage of reassortment. The reassortment

of genomes from both parental genomes can mix to form new virus strains with
different combinations of genes. The process of evolutionary significance can help
the virus adapt to its host. This is why segmented genomes can be a problem and
lead to the emergence of pandemic situations.

7. There is an infectious DNA clone for at least one member of nearly every virus
family. How would these be used to produce a mutant virus? Why is this process
so important to the field of virology? Why is it a source of concern to some?

Through the process of transfection, it can introduce the infectious DNA

clone into a cell using a vector. Using the DNA copy of the reverse transcribed
RNA, we can manipulate and modify the virus. You cannot manipulate RNA, but
you can manipulate its DNA. The DNA will be replicated and expressed once it is
inside the cell. The importance of this function is to understand how the virus
behaves, observe its specific mutations, and control its spread. However, there are
numerous ethical concerns when it comes to transfection. If it falls into the wrong
hands, it can be used as a bioweapon of mass destruction.

Study questions 4310 2020 Lecture 3

Reference:

Flint, S. J., Racaniello, V. R., Rall, G. F., Skalka, A. M., & Enquist, L. W. (2015).
Principles of Virology (4th ed., Vol. 2nd). ASM Press.

MicrobeTV. (2023). Virology Lectures 2023 #3: Genomes and Genetics. YouTube.
Retrieved September 14, 2023, from
https://www.youtube.com/watch?v=YMQZOkm1CP4&t=1467s.

Study questions 4310 2020 Lecture 3