Exam 2 Viruses

A virus may interconvert among three different forms ___, ____, and _____

Virion, or virus particle, intracellular replication complex, and viral genome integrated within host DNA

Explain how oncogenes in viruses cause cancer

When oncogenic viruses infect a cell, instead of destroying it the virus may transform the cell using oncogenes that encode for an abnormal form of a host protein that controls cell proliferation.

How does the cell eventually lyse?

a "late gene" from the phage genome expresses an enzyme that lyses host cell wall, releasing the mature virions

What is a virome?

a community of viruses within a host ecosystem.

a viroid is

a nucleic acid genome, does not contain a capsid or anything else and is an infectious particle all by itself

endogenous virus

a permanently integrated provirus transmitted via the germ line

a prophage is.....

a virus that integrates its genome into the DNA of a bacterial genome

provirus

a virus that integrates its genome into the DNA of a human cell genome

Viruses are classified by the ICTV by several criteria which are

genome composition capsid symmetry envelope size of the virus particle host range

an empty capsid on a T4 bacteriophage is termed a ____

ghost (because of its appearance on an electron micrograph

the particular group of species that a virus can infect is called its ________

host range

the lytic replication cycle requires these steps ____ ____ ____ ____

host recognition and attachment genome entry assembly of phages exit and transmission

a symmetrical virus may have a capsid of one of two types

icosahedral or filamentous (helical)

how does a prion work?

it acts by binding to normally folded proteins of the same class and altering their conformation to that of a prion

What are some methods that viruses can potentially use to cause cancer?

oncogenes, genome integration cell cycle control

giant viruses may have evolved from ___ whereas small viruses are believed to have evolved from ___

parasitic cells / cell parts

viruses that do not immediately kill host are termed

persistent viruses (they remain in hosts) (endogenous)

When a cell is lysed, their appearance can be observed as

plaque

What are PFU's?

plaque forming units, once a host cell is lysed and the left plaque can be counted and used to calculate the concentration of phage particles

The HIV virus derives its envelope from the host ____ whereas the herpes virus derives its envelope from ______

plasma membrane, intracellular organelle membrane

what is the name of a protein that infects a host and propagates with no known genome?

prion

the two functions of the viral capsid

protects the viral genome from degradation, and enables it to be transmitted outside the host

Acute viruses_____________?

rapidly kill their host, also act as predators or parasites to limit the host population density

for an RNA virus such as poliovirus or hepatitis C virus, virions are assembled within "virus factories", virus induced cell compartments called a ______

replication complex

What is the viral shunt

returns some organic matter to microbial consumers in the upper region of the ocean

3 diseases believed to be caused by prions are

scrapie (sheep) kuru (cannibals) Creutzfield Jacobs Madcow

When dealing with viral integration there are two scenarios that can happen, what are they

some may integrate within a host chromosome and replicate as part of the host, alternatively the viral genome may lay dormant and be reactivated later to start assembling virions (Integration may or may not be permanant)

what does temperate phage mean?

such as phage lambda, a phage can infect and lyse cells like a virulent phage, but it also has an alternative pathway: to integrate its genome as a prophage.

what is tropism

the ability to infect a particular tissue type within a host.

How can you determine the lysate?

the burst size together with the cell density prior to lysis, determines the concentration of the resultant suspension of virus particles called a lysate

What is dysbiosis?

the deterioration to loss of health enhancing bacteria (largely due to

In research viruses provide both tools and model systems for our discovery of the fundamental principles of molecular biology, which include _____________, _______________, and_____________.

the first genes mapped the first regulatory switches defined, first genomes sequenced

A surprising source of giant viruses is____

the frozen polar environments of the arctic and antarctic regions

What does host DNA being transferred by virus particles mean in a bigger sense?

the genome can sometimes be incorporated into the infected host genome providing genes that express products useful to hosts.

how is prophage DNA replicated in lysogeny?

the integrated genome is replicated along with that of the host cell as the host reproduces

what is transduction?

the process of transferring host genes during the exit from lysogeny

How does a prohphage in a lysogenic state enter the lytic phase?

the prophage directs its own excision from the host genome by an intramolecular process of site specific recombination, as the phage DNA exits the host genome, it circularizes and initiates a lytic cycle, destroying the host cell and releasing phage particles

a core particle is

the protein capsid of an enveloped virus

Describe what is happening during the eclipse period of culturing a virus

the virions have attached to the host cells and are undetectable in the medium.

Tropism may depend on two things _____ and _____

the viruses ability to interact with the cytoplasm, the presence of an appropriate host cell receptor protein that can bind to the viral surface attachment protein

T2 and T4 phages are _______ whose ________ has a tail that inserts the viral ________ into the host cell

"tailed", capsid, genome

Group IV

(+) sense single stranded RNA

Group V

(-) sense single stranded RNA

smaller viral genomes typically are comprised of fewer than

10 genes

What percentage of human cancers are caused by oncogenic viruses?

20%

Roughly how many genes do giant viruses have?

200-2,000

how many jointed tail fibers (which are used for stabilization) does the T4 bacteriophage have?

6

Showed that DNA was the hereditary material that is passed on to the next generation

Alfred Hershey, Martha Chase

& groups used to classify viruses by genome is termed the _________, named after its founder, ______

Baltimore Classification, David Baltimore

TF? unlike an icosahedral capsid, which usually has a fixed size, a helical capsid can vary in length to accommodate different lengths of nucleic acid

True

What does CRISPR stand for?

Clustered Regularly Interspaced Short Palindromic Repeats

Awarded Nobel Prize for discovering how tumor viruses cause cancer

David Baltimore, Renato Dulbecco, Howard Temin

mimi virus was discovered by

Didier Raoult

Group I

Double Stranded DNA viruses

Group III

Double Stranded RNA

TF? The plaque count unfortunately does not represent the number of individual infective virions from the phage suspension that was spread on the plate.

False

TF? viruses are not major players in the cycling of atmospheric CO2

False

TF? Ebola is a virus that exhibits a narrow tropism

False, Ebola shows broad Tropism

A virus that "jumps" from an animal host is initially more chronic and has a lower mortality

False, a virus "jumping" across species is typically more acute and has a higher mortality

In the case of bacteriophages a lysate of phage particles can be extremely unstable , eukaryotic viruses however tend to be more stable and remain infective at room temperature for years

False, bacteriophage lysates are VERY stable and CAN remain infective at room temperature for years, while eukaryotic viruses tend to be LESS stable and need to be maintained in culture of deep freeze

TF? one disadvantage of geometrical symmetry is that it lacks a way to form a package out of repeating protein units generated by a small number of genes encoded by a short chromosomal sequence.

False, geometrical symmetry does allow for this advantage

TF? the virion may be only either symmetrical or asymmetrical

False, may be symmetrical, asymmetrical or combine aspects of both

TF? Plants and Animals essentially contract viruses in the same way

False, plant cells usually require MECHANICAL TRANSMISSION (nonspecific access through physical damage to tissues)

TF? some evidence supports that low level chronic viral infections might actually cause a weakened immune system leaving us more susceptible to further viral infection.

False, some evidence actually supports the idea that low level chronic viral infections may ENHANCE the function of our immune system

TF? envelopes on viruses can only be drawn from the plasma membrane of a host cell

False, the envelope can also be gained from exiting organelles within the host cell

TF? HERV's are reverse-transcribing RNA viruses whose DNA copies become temporarily fixed in our chromosomes.

False, they are permanently fixed

HERV stands for

Human endogenous retroviruses

How were integrated viral genomes discovered?

In the 1950s genetic analysis of bacteriophage lambda in E.Coli showed evidence of phage gene expression from within host genomes. ( Cancer Researcher Peyton Rous discovered that some avian viruses cause tumors, the tumor generation results from integration of a viral genome)

What does ICTV stand for

International Committee on Taxonomy of Viruses.

To observe one cycle of phage reproduction, phages are added to host cells at a

MOI multiplicity of infection (ratio of phage to cells) such that every host cell is infected

Group VII

Pararetroviruses (DNA reverse transcribing viruses)

Group VI

Retroviruses (RNA reverse transcriptase transcribing viruses)

Group II

Single stranded DNA viruses

What is an advantage of the icosahedral capsid?

The DNA is typically tightly coiled and pressurized within the capsid, the pressure of the spooled DNA can be as high as 50 atm.

Why do plant virions spread differently from that of which human viruses spread?

The cell wall prevents lytic burst or budding

TF? Bacteriophages have provided some of the most fundamental insights in molecular biology

True

TF? Humans harbor many obscure herpes and cold type viruses that stimulate normal development of the immune system.

True

TF? In animal viral infections such as herpes, an environmental stress triggers reactivation of a virus that was dormant within cells, (a latent infection)

True

TF? In one type of transduction, the entire phage genome is replaced by host DNA packaged in the phage capsid, resulting in a virus particle that transfers only host DNA

True

TF? In the oceans, viruses are the most numerous and genetically diverse forms of life.

True

TF? Increasing environmental change increases the number of emerging viral pathogens

True

TF? RNA interference is known to be widespread amongst all eukaryotes and archaea

True

TF? Some endogenous viral genomes express placental proteins that are essential for early development of human embryos

True

TF? Some human viruses appear in our bodies indefinitely causing either mild disease or none.

True

TF? The burst size of animal viruses is typically several orders of magnitude larger than that of phages

True

TF? The more complex structure of eukaryotic cells requires viral replication cycles that are more complex

True

TF? Viral gene transfer is a major source of cell genome evolution

True

TF? Viruses that have been long associated with a particular host, tend to have evolved a moderate disease state that provides ample opportunities for host transmission

True

TF? a virion can possess a genome of DNA or RNA

True

TF? acute viruses limit host population densities

True

TF? all cellular organisms are infected by viruses

True

TF? because two or more viruses can coinfect a cell and exchange components, the genomic content of a virus can be influenced by its host range.

True

TF? in a lytic cycle when a phage particle injects its genome into a cell, it immediately reproduces as many progeny phage particles as possible

True

TF? most animal viruses, unlike bacteriophages enter the host cell as virions

True

TF? prophages and endogenous viruses can function and benefit the host, often by increasing virulence

True

TF? prophages can express virulence factors that help defend the bacterium from the immune system.

True

TF? some phages digest the host DNA to increase the efficiency of phage production

True

TF? some viruses (such as the mimivirus) are so large that they can become infected by smaller viruses themselves

True

TF? some viruses can only infect a single species

True

TF? sometimes a transducing bacteriophage picks up a bit of host genome and transfers it to a new host cell

True

TF? spike proteins allow the virus to attach and infect the next host cell

True

TF? the number of viruses infecting bacteria and algae can reach 10^7 (10million) per milliliter

True

TF? the presence of a prophage prevents further infection (superinfection) by other virions of the same type.

True

TF? throughout the ocean viruses play a decisive role in controlling algal blooms

True

for a host cell that has been infected by a phage utilizing a slow release cycle, what effects does the phage have on the host

although the host cell will continue to reproduce, it will do so more slowly than uninfected cells do, because many of its resources are diverted to virus production

What is a Virion

an inert particle consisting of nucleic acid enclosed by a protein capsid. Some viruses package enzymes and posses a lipid envelope, A virion does not carry out any metabolism or energy conversion.

How does CRISPR work?

analogous to human immune system, if bacterium enzymes succeed in destroying phage, the may copy a tiny piece of phage DNA's CRISPR segment, now the adapted host cell "remembers" infection by the specific phage and prevents phage replication from that phage if it were to infect that cell again.

another focus assay used for quantifying viruses in animal tissue(that do not kill host) dealing with cancer is .....?

another type of focus assay can be used to isolate oncogenic viruses, which transform their host cells into cancer cells, the host cells lose contact inhibition and the grow up in a pile instead of remaining the normal monolayer, these piles of transformed cells or transformed foci can easily be visualized and counted, this procedure is known as the transformation focus assay

What are restriction endonucleases?

bacteria modify their DNA by adding methyl groups to bases within certain sequences the bacteria then can express restriction endonucleases (enzymes) that cleave DNA lacking the methylated pattern,-which includes potential virus DNA (HOWEVER phage genomes composed of RNA or of modified DNA escape cleavage by these enzymes.

a virus that infects a bacteria is called a _____

bacteriophage

What is a main complication of culturing viruses of multicellular animals?

because viruses show tropism for particular tissues or organs

Lysis is also referred to as a burst, and the number of virus particles released is called the___

burst size

How can a bacteria show genetic resistance to a phage?

by expressing a gene that encodes an altered host receptor protein, which fails to bind the viral coat protein. Alternatively a different cellular protein evolves to block phage binding to the receptor. An evolutionary arms race ensues, in which phages may evolve enzymes that cleave the host defense molecules.

Describe what is happening during the rise period of culturing a virus `

cells begin to lyse and liberate progeny viruses and are thus then detectable in the medium

explain how cancer can be caused using cell cycle control

certain oncogenic proteins expressed by the virus can interact with the cell cycle and stimulate uncontrolled growth

Explain how genome integration can lead to cancer

certain viruses when integrated into the genome of a host chromosome express proteins that stimulate host cell division and may ultimately lead to the growth of tumors

What is a concern from the revival of ancient viruses?

concern is that as the tundra melts during inevitable climate change, the melting permafrost will release human pathogens from long dead hosts, such as buried victims of smallpox.

Most plant viruses gain entry to cells by one of three routes

contact with damaged tissues, transmission by an animal vector, transmission through seed

What is a batch culture?

culture in an enclosed vessel of liquid medium, enables growth of a large population of viruses for study

What is the slow release cycle?

differs from lysis and lysogeny in that phage particles reproduce without destroying the host cell.

tegument proteins are

enzymes that interfere with the host cell to depress its defense responses, they are expressed during infection of a host cell and then get packaged into the virion.

TF? bacteriophages typically attach via cell surface receptors, but only to certain proteins on the host cell surface that do not serve a critical function

false, bacteriophages typically attach to proteins that are most important to the cell,

What does the lytic cycle do?

generates a large number of progeny phages and then lyses the defunct cell

What are orthologs?

genes of common ancestry in two genomes that share the same function.

What are the three main forms of animal and plant host defenses?

genetic resistance immune system (interferons, RNAi (interference) (mechanism by which mRNA molecules expressed by a viral genome are recognized by a host protein RNA complex that shuts down further expression.

What are the three main bacterial defenses against phages?

genetic resistance restriction endonuclease CRISPR (bacterial immune system)

Why is the influenza virus capable of rapid evolution of new strains?

they are capable of packaging several genome segments into separate helical packages of different sizes contained together within a membrane envelope. Separate chromosome packaging enables influenza virus to pack different numbers of RNA segments into different virions, such virions are thus defective, but the process enables rapid evolution of new strains

What relevance does proteomics play in the world of viruses?

they are useful in sequencing information without requiring gene products common to all species, they study the proteome, proteins are identified through biochemical analysis of virus particles and through bioinformatic assays of protein sequences encoded in the genomes. (THIS IS MOST USEFUL BECAUSE PROTEIN SEQUENCES OFTEN SHOW RELATEDNESS THAT IS OBSCURED IN THE NUCLEIC ACID SEQUENCE BY SILENT MUTATIONS)

What makes viral genomes structurally more diverse than those of cells?

they can be either DNA RNA, single or double stranded, linear or circular and whole or segmented (that is, divided into separate "chromosomes")

How can animal viruses that do not kill their host cell be identified?

they can be identified using a fluorescent antibody called a fluorescent focus assay,

Why does a lysogen "decide" to reactivate and begin a lytic cycle?

they can occur at random , or can be triggered by stress on the host cell, indications that a host cell may not survive will trigger a lytic burst, whereas a healthy host cell will most likely keep the lysogen inactive.

How do plant virions spread?

through the plasmodesmata

TF? filamentous viruses show helical symmetry

true

TF? filamentous viruses have been used for production of material used in electronic devices?

true filamentous phages have been used in nanotechnology to nucleate the growth of crystalline nanowires for electronic devices

The burst size is

virus concentration at the end divided by the original concentration of inoculated phage

lysogeny is__

when a virus integrates its genome into that of a host cell (is then called a prophage)

Explain an intracellular replication complex

within a host cell, the viral gene products direct the cells enzymes to assemble progeny virions at "virus factories" called replication complexes. Assembly requires host ribosomes as well as intricate collaboration between host and viral proteins.