Virology Final Flashcards
Virion:
A complete virus particle outside of the host cell
What does a virion consist of? (3)
A nucleic acid genome
A protective protein coat (capsid)
Some contain a lipid envelope
Nucleic acid genome
Encodes for proteins that allow the virus to replicate in the host and transmit from one cell to another or one host to another.
Once inside of a host cell a virus will undergo uncoating of its _____ to release its genetic material inside the cell. This goes on to the hijacking of host machinery in order to synthesise viral ____ and ____. After the virus has replicated its genetic material (DNA or RNA), the viral structural proteins surround and ____ the newly made genome to protect it. Once the viral genome is encapsulated, the fully formed virus particles are considered “_____ viruses,” ready to infect other cells
capsid
mRNA
proteins
enclose
new progeny
Viral structural proteins ______ the newly replicated genome → new progeny virus particles
encapsidate
How does mutation connect with evolutionary lineage?
Use a constant mutation rate and cross reference it with the molecular clock
In DNA what are both the positive and negative strands responsible for?
“+” strand virus encodes for protein, the “-” strand encodes for the complementary strand
What are potential issues of having RNA genomes
- mRNA must be synthesised from a RNA template instead of DNA template
- RNA genome must be replicated
* This is problematic because the host cell doesn’t have the machinery to do that therefore most RNA viruses encode their own RNA-dependent RNA polymerases
_______ have RNA genome which gets converted to DNA by the host cell using ____ ____ (cDNA copy of RNA) encoded by viral genome e.g. HIV
Retroviruses
reverse transcriptase
Describe the hershey chase experiment
demonstrated that DNA is the carrier of genetic information. They used two scenarios: one with radioactively labeled DNA (using phosphorus-32) and another with labeled proteins (using sulfur-35). When bacteriophages infected cells, only the radioactive DNA entered the cells, while the labeled proteins remained outside. This indicated that DNA, not protein, carries genetic material, confirming its role in heredity.
Describe Tobacco Mosaic Virus
Tobacco Mosaic Virus (TMV) is the first identified plant virus, responsible for tobacco mosaic disease. Dimitri Ivanovski (1892) and Martinus Beijerinck (1898) discovered that the agent causing the disease could pass through fine filters that blocked bacteria, revealing the existence of infectious agents smaller than bacteria. TMV has a rod-shaped structure consisting of RNA surrounded by a protein coat and leads to mottled discoloration in infected plants. This research laid the foundation for virology and techniques like filter sterilization, which are still used in labs today. TMV’s discovery also influenced the identification of other viruses, such as those causing foot-and-mouth disease and yellow fever.
Describe plaque assays
- Measure concentration of bacteriophages by their ability to lyse bacteria.
- Bacterial growth is measured using a spectrophotometer; intact bacteria refract light, making cultures appear cloudy.
- Phages bind to bacterial cells, replicate, and release progeny, leading to cell lysis and loss of light diffraction (clearing).
- In solid cultures, phages infect surrounding cells, causing repeated lysis and forming clear areas (plaques) against uninfected cells.
- Plaques are counted as plaque-forming units (PFU), indicating the number of infectious virus particles in a suspension.
How are plaque assays done in eukaryotic cells
How are red blood cells commonly used to measure/detect viruses?
How do you interpret hemagglutination assays?
What is the implication of electron microscopy in viral analysis
Virus particles can be seen and counted by electron microscopy (cannot tell infectious vs not)
E.g. virus particles are mixed with an electron dense stain (e.g. phosphotungstate, uranyl acetate) → viruses do not take up the stain → observed as light image against a dark background (negative staining)
Describe negative staining
In negative staining, the stain does not bind to the virus itself. Instead, the negatively charged stain surrounds the virus particles, creating a dark background. The virus particles appear lighter in contrast, which makes them easier to visualise under an electron microscope. The stain does not bind to positively charged molecules on the virus surface.
How do plaque assays and electron microscopy relate to the ratio of infectious particles (if desired)
Describe the multiplicity of infection (MOI)
Multiplicity of infection (MOI) = Number of infectious virus particles per susceptible cell e.g MOI of 10-100 PFUs / cell is often used
Infect with excess virus to ensure that each cell receives at least one infectious particle.
Infects nearly all cells simultaneously, leaving few uninfected cells
Limitation: steps in replication cycle overlap → difficult to study
How do you calculate the percentage of the viral genome’s coding capacity used by the protein?
- Determine the nucleotide requirement for the protein:
* Each amino acid is encoded by 3 nucleotides (a codon).
* The protein is 100 amino acids long.
* So, the number of nucleotides required to encode the protein is: 100 amino acids×3=300 nucleotides - Convert the genome size to nucleotides:
* The genome size is given in kilobases (kb), which means 1 kb = 1000 nucleotides.
* The viral genome is 6.3 kb, so it contains: 6.3 kb×1000=6300 nucleotides - Calculate the percentage of the genome used by this protein:
* (300 nucleotides / 6300 nucleotides)×100=4.76%
Look at this
Analysis of viral macromolecules (proteins, mRNAs, genomes) can reveal the detailed
pathways of virus replication. Can be studied using assays involving what?
- Radiotracers (radioactive compounds incorporated into viral or cellular DNA, RNA,
proteins, lipids, carbohydrates) - Antibodies against specific proteins
- Molecular hybridization (labelled DNA or RNA probes)
- PCR
- Gel electrophoresis
- Microscopy
Describe the viral replication cycle
Describe the binding to cell receptor phase of the viral replication cycle