virology exam 1

what is a virus

a small obligate intracellular parasite

what is a virus composed of

genetic material (DNA or RNA) surrounded by a protein coat and/or membrane

what does a virus require in order to do its job

it requires the host cell to supply the complex machinery required for replication

why do we study viruses? (7)

• they’re everywhere

• they infect all living things

• “virosphere”

• they can be beneficial

• they can cause human disease

• they can cross species boundaries

• can be used as a tool to study biology

how are viruses everywhere

they are the most abundant entities in the biosphere and they outnumber cellular life by at least 10:1

how are viruses beneficial

• they regulate harmful gut bacteria populations

• drive evolutionary change

• collapse large blooms of phytoplankton (ocean viruses)

how are viruses used as a tool to study biology

• viruses based vectors used in gene therapy

• they are used in vaccine development

the vast majority of viruses infect us have little to no impact on our health, why? (3)

• most viruses pass through us

• we have an amazing immune system

• not all viruses cause disease

how do most viruses pass through us

• we ingest many non-animal viruses with foods

  • most RNA virus sequences in human feces are similar to plant viruses (PMMov)

what is meant by: not all viruses cause disease

anelloviruses are small circular, single-stranded DNA viruses that colonize over 90% of healthy humans

what are the 3 hypotheses for where viruses originated from

• escape

• reduction

• virus-first

what is the escape hypothesis

viruses may have originated from rogue genetic elements (plasmids or transposons) inside ancient cells that gained the ability to escape and move between other cells

what is the reduction hypothesis

they may be the remnants of once-living, complex cellular organisms that stripped down their genetic machinery over time to live as obligate parasites

what is the virus-first hypothesis

viruses may predate cellular life, originating from self-replicating RNA molecules in the ancient “pre-cellular” world

as early as 1728 what was the word virus used to describe

“virus” was used to describe an unknown agent that causes infectious diseases

in 1884, Charles Chamberland developed what

he developed a porcelain filter that could retain bacteria, the filters were initially used to provide bacteria-free water for the lab

what did pasteur find out about viruses using this filter

he found that the rabies agent passed through it, but thought it was a small bacterium

in 1892, Dmitri Ivanovski show about viruses with the filters

he showed that the agent of tobacco mosaic disease to be small enough to fit through filters and still cause disease

in 1898, Martinus Beijerinck repeated the finding of Ivanovski and what was his important insight from doing so

he found that the pathogen could only be propagated in plants, not in broth as was known for bacteria

what was the finding of Wendell Stanley in 1935

he was able to take the TMV liquid virus, isolate it, and then view via electron microscopy that the virus is actually particles

what is a complete virus particle called

a virion

what is the main function of the virion

the main function is to deliver its genome (DNA or RNA) into the host cell so that the genome can be expressed to replicate and make new virus

what is the range of size for a virus

20 to 400 nm in diameter

what is the nucleic acid genome covered in

it is covered by a protein coat; called a capsid

some animal viruses are further packaged into what

a lipid membrane or envelope that is derived from the host cell

what are the protein structures on the surface of virus particles called and what are they involved in

they are called spikes and they are involved in receptor binding on host cells

what is the function of the viral capsid

• protects the viral genome

• helps the virus attach to and enter the host cell

• helps the virus release its genome into the host cell

what are the 3 basic shapes of capsids

• helical

• icosahedral

• complex

what is the function of matrix proteins for the viral envelope

they serve as a bridge between the nucleocapsid and the inside of the viral membrane (envelope)

why is the envelope essential for the infectivity of the virus

because anything that destroys that envelope will eliminate the infection of said virus

what is a nucelocapsid

it is defined as the nucleic acid-protein assembly within the virus particle when the assembly is a discrete substructure in the particle

what is the replication steps for viruses (4)

• eclipse period

• latent period

• burst period

• plateau period

what happens during the eclipse period of viral replication

the viral nucleic acid is uncoated from its protective shell and no infectious virus can be detected inside cells

what happens during the latent period of viral replication

the time it takes to replicate and assemble new virus particles before lysis

what happens during the burst period of viral replication

corresponds to the coordinated lysis (bursting) of the host cell, releasing mature virions out into the environment

what happens during the plateau period of viral replication

this is the final stage of the viral replication cycle where the extracellular viral titer stops increasing and levels off

virologists divide the infectious cycle into steps to facilitate their study, what are those steps (5)

• recognition and attachment

• entry (penetration and uncoating)

• mRNA and protein synthesis

• genome replication

• virus assembly and release

how does recognition and attachment work in plant cells

• plant cells do not express classic surface receptors for viruses

• due to rigid cell wall, plant viruses do not use receptor-mediated entry

  • enter through mechanical wounds or via vectors like insects

how does recognition and attachment work in bacterial cells

• they express surface molecules that act as specific receptors for viruses

  • these receptors are normal structural components of the bacterial cell envelope that viruses exploit for attachment and entry

how does recognition and attachment work in animal cells

they express specific surface molecules that act as receptors for viruses

what is the process for the recognition and attachment step of the infectious cycle

• a host cell expresses a functional receptor on the cell surface that can be recognized by a virus

• a virus particle contains components (spikes) that allow it to recognize the host receptor and attach to the cell

what is the process for the penetration and uncoating step of the infectious cycle

• viruses must deliver their genome into the host cell to replicate

• viruses can penetrate the plasma membrane via direct fusion with the cell membrane or via endocytosis

• once inside the cell, the viral genome is released

what allows the viral genome to release

the drop in acidic pH

what are the 2 aspects of the macromolecule synthesis step of the infectious cycle

• mRNA synthesis

• protein synthesis

what are the aspects of mRNA synthesis within the macromolecule synthesis step of the infectious cycle

• early mRNA

• late mRNA

what happens during early mRNA

enzymes and proteins that function to take over cell processes

what happens during late mRNA

structural proteins take over

what occurs during protein synthesis during the infectious cycle

precursor polypeptides are cleaved by proteases and post-translationally modified

how is viral genome replication considered virus dependent

• most DNA viruses replicate in the nucleus

• most RNA viruses replicate in the cytoplasm

what occurs during the assembly and release step of the infectious cycle

individual virus components are then packaged and assembled into new viruses for subsequent release from the cell

how to enveloped viruses release from the cell

most viruses exit the cell via budding and release

how to non-enveloped viruses release from the cell

most viruses exit by lysing the cell to release its contents

what is tropism

the ability of viruses to infect different cell types and produce a successful infectious cycle

what is cellular tropism and 1 example

preference to infect specific cell types

• rabies virus exhibits neurotropism (infects neurons)

what is tissue tropism and 1 example

preference to infect specific tissues

• influenza A demonstrates tropism for the respiratory tract

what is host tropism and 1 example

preference to infect specific hosts

• HIV exhibits strict tropism for humans

what is a susceptible cell

a cell that has a functional receptor for a given virus to allow attachment and entry

what is a resistant cell

a cell that has no receptor to allow virus attachment and entry

what is a permissive cell

a cell that has the capacity to support virus replication

what does it mean for a cell to be susceptible and permissive

means that the cell can take up a virus particle and support its replication

what was the Hershey and chase breakthrough (1952)

used radioactive isotopes to label bacteriophages, proving that DNA is the genetic material that enters bacteria to direct viral replication

what was the Fraenkel-Conrat and Williams breakthrough (1955)

demonstrated that Tobacco Mosaic Virus could be separated into pure RNA and protein and then spontaneously self-assemble back into fully infectious viruses

how did Hershey-Chase prove that DNA is the genetic material

• they used radioactive isotopes to label the protein coats or DNA of bacteriophage viruses before allowing them to infect bacteria

• by spinning the samples in a blender and centrifuge, they discovered that only the radioactive viral DNA entered the bacteria to guide the production of new viruses

what is the Baltimore classification

a system that groups virus families into classes whose members have a common strategy for dealing with genome expression and replication

what are the 7 groups within the Baltimore classification system

1. dsDNA

2. ssDNA

3. dsRNA

4. ss(+)RNA

5. ss(-)RNA

6. ss(+)RNA with DNA intermediate

7. gapped dsDNA

mRNA (ribosome ready) is always what strand

positive

DNA of equivalent polarity is what strand

positive

RNA and DNA complements of (+) strands are what strands

negative

what information is encoded in a viral genome? (7)

1. replication of viral genome

2. efficient expression of the genome

3. Assembly and packaging of the genome

4. Regulation and timing of the replication cycle

5. Modulation of host defenses

6. Spread to other cells and hosts

7. some protein synthesis (mainly giant viruses)