Intro to virology

Question 1

What is a virus?

Answer 1

Nucleic acid(s) surrounded by a coat of protein

Cannot reproduce or carry out metabolic activities outside of a host cell. (This is why they are not considered living, because they cannot survive out of a host on their own.)

Question 2

The process of getting a soluble structure out of solution and getting a precipitate for analysis

Answer 2

Crystallization

Question 3

Protein coat surrounding nucleic acid

Answer 3

Capsid

Question 4

Protein subunit of the capsid

Answer 4

Capsomere

Question 5

Viral nucleic acid surrounded by it’s capsid

Answer 5

Nucleocapsid

Question 6

Membrane surrounding nucleocapsid

Answer 6

Viral envelope

Question 7

What are the steps of the infectious cycle/viral replication?

Answer 7

1) Attachment
2) Entry
3) Translation of viral mRNA & viral genome replication
4) Assembly
5) Release

Question 8

Lysis of the host cell and release of new viral progenies:

Answer 8

Lytic cycle of phage T4
“Virulent phage”

Question 9

Study and understand the lambda phage:

Answer 9

Excision of DNA from chromosomes

Triggered by UV light, carcinogens, X-rays

Question 10

Describe Baijernick’s experiment to explain the nature of the tobacco virus:

Answer 10

Transferred the the filtered sap from infected tobacco leaves to healthy ones. He found that the infectious agent was capable of multiplying and spreading, and did not behave like any other organism.

Question 11

What is x-ray crystallography? Why is this relevant?

Answer 11

Determines three dimensional structures.
This method uses a crystalline sample & analyzing the resulting diffraction pattern to reconstruct the molecular structure.

Relevance:
-Structural insight
-Vaccine development
-Drug design
-Mechanisms of Infection
-Mutations & Variants

Question 12

Describe in detail, the life cycle of the lytic phage T4:

Answer 12

1) Attachment & absorption: phage posses tail fibers with specific binding sites that recognize & attach to receptors on the bacterial cell wall.

2) Injection of genetic Material: consists of double stranded DNA The tail punctures the bacterial cell wall and allows the entrance of the viral DNA.

3) Expression of early genes: Once inside, the T4 DNA takes over the bacterial transcription & translation machinery. “early genes” code for DNA polymerase, nucleases, & other proteins that are necessary for the viral life cycle.

4) DNA replication: viral DNA forms a chain of connected DNA molecules

5) Expression of middle genes: Code for structural proteins required for the assembly of new phage particles. (capsid proteins and tail components)

6) Head assembly: Capsid proteins assemble into empty capsid shells, DNA packs into these shells.

7) Expression of late genes: encode for lysis proteins-holins(make holes in the inner membrane) & endolysins (degrade the peptidoglycan cell wall)

8) Lysis and release: accumulation of lysis proteins. The cell bursts releasing numerous phage particles that can infect new bacteria.

9) Propagation: The released phage T4 particles can then go on to infect other bacteria and repeat the process.

Question 13

Describe in detail the life cycle of the temperate phage lambda:

Answer 13

Lysogenic phase:
1) Attachment and integration: Lambda initially attaches to the E.coli cell using its tail fibers and injects its double stranded DNA into the host. (integrates into the hosts chromosomes)

2) Prophage formation: integrated lambda DNA; becomes part of the host and replicates with it (coexists w/ host)

3) Repression: Lambda prophage generally represses the transcription of most of it’s genes, preventing the synthesis of new phage particles. (lambda repressive protein)

4) Lysogeny: host bacterium w/ integrated lambda prophage is called “lysogen.” Lysogen continues to divide and replicate normally, and the prophage is passed on to daughter cells during cell division.

Lytic phase:
1) Induction: Under certain conditions, such as exposure to DNA-damaging agents (ex. UV radiation), the lambda prophage can be induced to switch into the lytic cycle. Leads to production of new phage particles.

2) Cleavage of cl repressor: Repressor protein cl, which maintained the prophages repressed state, gets cleaved and transcription is no longer repressed.

3) Expression of lytic genes: After cl cleavage expression of lytic genes is expressed including those involved in DNA replication, capsid, and tail assembly, and lysis of the host cell.

4) Replication & assembly: Lew lambda phage DNA is synthesised, and structural proteins are produced.

5) Lysis & release: Once the cells are ready the host cell undergoes lysis, releasing the newly formed lambda phage particles. Triggered by holins & endolysins.

6) Infection of new host: Released lambda phages infect the new host bacterial cells.

Question 14

Cell Culture:

Primary:
3 pros & cons

Answer 14

process of isolating and growing cells directly from living healthy tissues. (animal or human source)

Pros:
1) Close to in vivo conditions
2) Relevance to disease research
3) Heterogeneity & complexity

Cons:
1) Limited lifespan
2) Variability
3) Ethical & technical challenges

Question 15

Cell Culture:

Continuous:
3 pros & cons

Answer 15

Cells are maintained in an ongoing, uninterrupted state of growth & division.

Pros:
1) Unlimited replicative potential
2) Standardization
3) Ease of handling

Cons:
1) Altered phenotype
2) Loss of specialized functions
3) Cross-contamination & misidentification

Question 16

Cell Culture:

Suspension:
3 pros & cons

Answer 16

Cultivation of cells in a liquid medium, remain suspended in this liquid medium.

Pros:
1) High cell density
2) Scalability
3) Continuous agitation

Cons:
1) Shear stress
2) Limited attachment-dependent studies
3) Hydrodynamic stress

Question 17

Cytopathic effect:

Answer 17

structural and functional changes that occur in host cells as a result of a viral infection.

Question 18

Plaque assay:

Answer 18

used for quantifying the concentration of viral particles in a sample and determining the infectivity or titer of a virus.

1) Cell culture
2) Viral infection
3) Incubation
4) Plaque formation
5) Staining
6) Plaque counting

valuable for various purposes including determining the concentration of a virus sample, assessing the effect of antiviral agents, and characterizing the virulence and behavior of different viral strains.

Question 19

Describe the classical system for viral taxonomy:

Answer 19

Baltimore classification: classified into 7 distinct groups depending on the type of genetic material in the virus, and their mode of replication.

1) nature of the nucleic acid
2) Symmetry of the protein shell (capsid)
3) Presence or absence of a lipid membrane (envelope)
4) Dimensions of the virion and the capsid

Question 20

What are the 3 viral shapes?

Answer 20

Helical: long, cylindrical shape, with a central core of genetic material that is surrounded by a helical protein.

Icosahedral: Roughly spherical shape with 20 equilateral triangular faces. Constructed from repeating protein subunits, forming a geometrically regular structure.

Complex: Have more intricate and irregular shapes that result from their unique structural features.

Question 21

Define & describe the principle of host range:

Answer 21

Primarily determined by the interactions between viral surface proteins and host cell surface receptors.

Factors influencing host range:
1) Viral attachment proteins
2) Cell entry mechanisms
3) Host cell environment
4) Immune responses

Host range examples:
1) Species-specific host range
2) Tissue-specific host range
3) Broad host range

Question 22

Viral attachment:
Direct penetration=>

Answer 22

Typically occurs with non-envoloped viruses or naked viruses. Can be more efficient and rapid.

1) attachment to host cell: attachment proteins or capsid proteins (highly specific)

2) Receptor binding: typically proteins or carbohydrates.

3) Direct penetration:
a) Inject genetic material
b) pore formation
c) Membrane disruption
d) Initiation of replication

Question 23

Viral attachment:
Membrane fusion=>

Answer 23

Enveloped viruses posses an outer lipid membrane derived from a host cell, and use this to interact with host cell.

1) attachment to host cell

2) Receptor binding

3) Membrane fusion
a) Attachment
b) Conformational changes
c) membrane fusion
d) release of viral contents

4) Initiation of replication

Allows the virus to bypass endocytosis and directly infect the host.

Question 24

Viral attachment:
Endocytosis=>

Answer 24

Process involves the uptake of the entire cirus particle into the host cell through vesicle formation.

1) Attachment of host cell
2) Receptor binding
3) Internalization via endocytosis
4) Maturation of endosome
5) Release of viral contents
6) Initiation of replication

Question 25

Describe in detail, the Baltimore scheme:

Answer 25

1) Double stranded DNA (dsDNA) viruses: double-stranded genome. replicate by using their DNA as a template.

2) Single-stranded DNA (ssDNA) viruses: single-stranded genome. Replicate using their single strand, and turning it into double strand.

3) Double- stranded RNA (dsRNA) viruses: double stranded RNA genomes. Replicate using RNA-dependent RNA polymerase.

4) Positive sense single-stranded RNA [(+)ssRNA] viruses: Viruses with genomes of (+) ssRNA can be directly translated into proteins by the host.

5)Negative sense single stranded RNA [(-)ssRNA] viruses: Viruses with the genomes of (-)ssRNA require synthesis of complimentary (+)ssRNA strand before translation.