chapter 13 viruses

explain the maturation step for enveloped and non-enveloped animal viruses

Involves bringing together newly formed viral nucleic acid with capsid proteins and packaging them to form the nucleocapsid. This process is a spontaneous self-assembly that occurs when an appropriate amount of viral nucleic acid and capsid proteins have accumulated in the host cell The site of assembly and maturation differs according to the virus: Non-enveloped viruses - mature fully in the host cell cytoplasm Non-enveloped viruses are released through ruptures in the cell membrane which kill the cell Enveloped viruses - some maturation steps occur as the virion leaves the host cell. Components of the envelope and spikes are incorporated into the membrane The virus deposits protein into the host cytoplasmic membrane The assembled nucleocapsid then binds to these regions of the membrane before exiting the host cell

what are late proteins? and what does the phage have to do with it?

Late proteins are structural proteins that make up the phage, specifically makes up the head and tail. toward the end of the infection cycle, the phage directs the bacterial cell to produce Late proteins.

name three viruses that have the helix structure and describe the structure

appear cylindrical, their capsomeres are arranged in a helix, similar to a spiral staircase. rabies influenza or ebola.

name three viruses that have a polyhedral (icosahedral) structure and describe the structure

appear spherical under and electron microscope but their surface is actually 20 flat triangles arranged like on a soccer ball. polio herpes or papilloma.

what is capsid, what is its function, and what role does it play for viruses?

capsid consists of nucleic acid surrounded by a protein coat, it protects the nucleic acid from enzymes and toxic chemicals in the environment. It also carries enzymes required by the virus for infection of a host cell

Define viroids

consists only of a small single-stranded RNA molecule that forms a closed ring Viroids only infect plants, where they causes serious diseases such as, potato spindle tube, and chrysanthemum tube Viroids enter plants through wound sites rather than binding to a receptor

what type and how are embryonated eggs used in terms of dealing with viruses

embryonated (fertilized) chicken eggs were used to grow viruses Part of the process for making most flu vaccines involves growing influenza viruses in embryonated chicken eggs Inoculate various membranes Observe pox, lesions, and death of an embryo

True or false - Mutations that either increase the expression of proto-oncogenes or decrease the expression of tumor suppressor genes are the least common cause of abnormal/uncontrolled growth

false

true or false - Lysogenized cells are not immune to reinfection by the same phage but not towards a different phage,

false

true or false - nearly all viruses are enveloped viruses

false

where does a virus obtain its envelope?

from the host cell

what is the difference between generalized transduction and specialized transduction?

generalized transduction is when bacteriophages can pick up any portion of the host's genome Results from a DNA packaging error Results from a lytic cycle specialized transduction is when Bacteriophages can only pick up specific portions of the Host's DNA Only bacterial genes adjacent to the integrated phage DNA can be transferred Results from a lysogenic cycle Results from an error in excision of a prophage

What are tumor suppressor genes?

genes that inhibit cell growth

What are proto-oncogenes?

genes that stimulate cell growth (controlled cell growth)

what are the key characteristics used in the current classification scheme for viruses

genome structures (strandedness), hosts they infect, viral shape, disease symptoms, nucleic acid compositions.

describe the complex symmetry and a virus that has this structure

has an icosahedral nucleocapsid; referred to as the head and has a long helical protein component, called the tail. (Bacteriophage). Pox.

what is and what does the synthesis of phage proteins and genomes (biosynthesis) entail?

host proteins synthesis is halted by viral degradation of host DNA Viral proteins interfere with transcription and repress translation of the host cell Phage uses the host's nucleotides and polymerase to synthesize its DNA Phage mRNA, enzymes and proteins are synthesized using the host's ribosomes, enzymes, and amino acids. An eclipse period lasts for several minutes until the complete phage can be found

what are capsomere subunits?

identical protein subunits that form the capsid.

what is the uncoating process that viruses have?

A process in all viruses, where the nucleic acid separates from its protein coat before the start of replication (separation occurs because of enzymes).

Define the first catagory of animal virus infections.

Acute Infections - characterized by the sudden onset of symptoms of a relatively short duration Results in a burst of virions being released from infected host cells Example, Influenza, Mumps, Poliomyelitis

animal virus infections can be divided into 2 catagories, what are they?

Acute infection and Persistent Infection

what is the integration step in the lysogenic infection cycle?

Circular phage DNA recombines with the bacterial chromosome. This results in the prophage being integrated into the chromosome ( latent state) The integration process uses a phage encoded enzyme called an Integrase that inserts the phage DNA into the host cell chromosome at a specific site.

what is the cell division step in the lysogenic infection cycle?

Continued cell division makes many cells with the prophage Each time a host cell divides, the prophage is copied along with the host DNA, getting a free ride

what is a continuous cell line?

Continuous cell lines are immortalized cell lines with an infinite lifespan. These usually either come from tumor tissue or have been deliberately immortalized or transformed

what are the three different symmetry types

Cubic Symmetry Helical symmetry Complex

list the 3 general catagories of the replication strategies of viruses

DNA viruses, RNA Viruses, retroviruses

What are diploid cell lines?

Diploid cultures have a finite lifespan. They usually can undergo a maximum of 20-80 PDLs (Population Doubling Level) before they senesce.

what two distinct but interrelated events does the production of viral particles in an infected cell need and why?

Expression of viral genes to produce structural and catalytic proteins, such as capsid proteins and any enzymes required for replication Synthesis of multiple copies of the viral genome The viral proteins are sometimes synthesized as a polyprotein that is subsequently cleaved by viral proteases into individual proteins.

what is a virion?

Free viral particle, consisting of just nucleocapsid, or nucleocapsid plus envelope.

name three DNA viruses that cause cancer and what type of cancer they cause

HPV - cervical cancer Epstein-Barr virus - Burkitt's lymphoma Hepatitis B - liver cancer

name an RNA retrovirus that causes cancer and what type it is.

HTLV-1 - adult T-cell leukemia

name an RNA virus that causes cancer and what type of cancer it causes

Hepatitis C - hepatocellular carcinoma

what is the phage induction process?

If a lysogenic culture is treated with a DNA-damaging agent, the SOS repair system comes into play. This system activates a protease that destroys the repressor protein responsible for maintaining the integration of a prophage, as a consequence, the prophage is excised from the chromosome, allowing the phage to enter the lytic cycle.

describe the DNA virus replication strategy.

Most DNA viruses replicate in the nucleus of the host cell and uses the host cells components such as (ribosomes and enzymes) for DNA synthesis and gene expression. These viruses often encode their own DNA polymerase, which allows them to replicate even if the host cell is not actively duplicating its own chromosome. +-dsDNA - The genome of a Double-stranded DNA virus can be referred to as (+/-) to indicate that it has both (+) and (-) strands These (+) and (-) genomes can be transcribed to produce mRNA (+ssRNA) The mRNA is then translated to make viral proteins +ssDNA - similar to the replication of a +-dsDNA, except that a complement to the single stranded DNA molecule must be synthesised to generate a double stranded (+/-) DNA molecule. Once that has occurred, the genes can be expressed to produce the encoded proteins.

how are tissue cultures used to cultivate animal viruses? what problem does this approach have?

One way to obtain animal cells for culture is to remove tissue from an animal, and process it to get individual cells. These cells can then be grown in a flask with a liquid nutrient medium. Cells acquired in this way form primary cultures. ( a problem with this approach is that normal cells can divide only a limited number of times so new primary cultures must be regularly made)

Define the second catagory of animal virus infections

Persistent Infection - can continue with or without symptoms for years or even for the life span of the host cell. 2 general types of persistent infections : Chronic Infections and Latent Infections : Chronic Infections - characterized by the continuous low level production of viral particles In some cases, the infected cell lyses, but only a small proportion of cells is infected at any given time; which results as a low number of viral particles being continuously released In other cases, the infected cell survives and slowly releases viral particles Latent Infections - the viral genome remains silent within a host cell, yet can be reactivated to cause a productive infection After the initial infection, the virus is maintained in neurons in a non-infectious state. Later on, The virus reactivates again to produce disease symptoms

what is attachment (adsorption)?

Phage particles collide with with their host cells by chance, once contact is made, the phage attaches to a receptor on the host cell's surface or to an appendage such as a pilus. The receptor used by phages perform important functions for the cell, the phage merely exploit the molecules from the cells for themselves.

what are primary cell lines (primary culture)

Primary culture refers to the stage of the culture after the cells are isolated from the tissue and proliferated under the appropriate conditions until they occupy all of the available substrate (i.e., reach confluence). At this stage, the cells have to be subcultured (i.e., passaged) by transferring them to a new vessel with fresh growth medium to provide more room for continued growth.

what are the two different strategies for phage replication and what do they mean?

Productive Infection- new viral particles are produced Some types of viruses kill their host while others don't Latent State- the viral genome remains silent within the cell but is replicated along with the host cell's genome

describe the replication strategy of retroviruses

Retroviruses encode the enzyme called reverse transcriptase, an RNA-dependant DNA polymerase, which synthesizes DNA from an RNA template. Retroviruses such as HIV, have a (+) strand RNA genome, and carry reverse transcriptase within the virion After entering a host cell, the reverse transcriptase uses the RNA genome as a template to make 1 strand of DNA The complement to that DNA strand is then synthesized to make double-stranded DNA, which integrates into the host cell chromosome Once integrated, the viral DNA may remain in a latent state, or it may be transcribed into RNA that is translated to synthesize new viral proteins needed for production of new virions

t4 phage is a member of the __-_______ ________, a group including entero ___________ ____ and ____

T-even Phages, Bacteriophages T2 and T6

how many mechanisms does the penetration step use for animal viruses, and what are they and what do they depend on?

The mechanism an animal virus uses to enter its host cell depends on whether the virion is enveloped or non-enveloped. Enveloped viruses - enter the host cell by one of 2 mechanisms : Fusion with the host membrane or Endocytosis Membrane Fusion - the lipid envelope of the virion fuses with the cytoplasmic membrane of the host cell after the virion attaches to the host cell receptors. As a result of fusion, the nucleocapsid is released directly into the cell's cytoplasm Entry by Membrane Fusion : Attachment- spikes of the virion attach to specific host cell receptors Membrane Fusion - Enveloped of the virion fuses with the cytoplasmic membrane Nucleocapsid Released into the Cytoplasm - The viral envelope remains apart of the cytoplasmic membrane Uncoating - Nucleic acid separates from the capsid Endocytosis - viruses that enter by endocytosis take advantage of the receptor- mediated endocytosis, a normal mechanism by which cells bring certain extracellular material into the cell The viral particles bind to receptors that normally trigger and facilitate the process, causing the cell to take them up For example, the influenza viruses use their HA envelope glycoproteins to bind to host cell membrane, facilitating endocytosis and entry into that cell After a virion is taken into the cell, the viral envelope fuses with the membrane of the endosome, releasing the nucleocapsid from the cytoplasm. Entry by Endocytosis : Attachment - attachment to the receptors triggers endocytosis Endocytosis - The cytoplasmic membrane surrounds the virion, forming an endocytic vesicle Release from Vesicle- The envelope of the virion fuses with the endosomal membrane Uncoating - Nucleic acid separates from capsid Non-enveloped viruses - which have no lipid envelope, can't fuse to host membranes to enter cells Therefore, the virions only enter via endocytosis

what does it mean when a virus uses penetration (genome entry)?

The tail contracts so that phage particles appear to squat (sit) on the surface of the cell. (Contraction of tail sheath) a bacteriophage then injects its genome into the cell. T4 phage does this by degrading a small part of the bacterial cell wall, using an enzyme (T4 lysozyme) located in the tip of the tail. This action injects the phage DNA through the host cells wall and membrane, into the cell The capsid remains on the outside of the cell The separation of nucleic acid from its protein coat before replication is a feature of all viruses T4 lysozyme is functionally similar to lysozyme found in tears and eggs. Degrades peptidoglycan.

what is transduction?

Transduction is the transfer of genetic material from one organism to another by a phage

what is Transformed Cell Line?

Transformed cell lines usually have an increased growth rate and higher plating efficiency, are continuous, and require less serum in media, but they have undergone a permanent change in their phenotype through a genetic transformation.

what are the steps of a T4 Phage Infection?

Within minutes after the T4 DNA is injected into the host cell, some of the genomes on that viral genome are transcribed and translated by the infected cells The phage encoded proteins are made in a specific time sequence to control the cause of infection Early Proteins: early on, a phage directd the bacterial cell to synthesize proteins. They are needed to initiate phage replication. Biosynthesis of prerequisite proteins, required before replication can take place, such as replicase enzymes or enzymes that inhibit host-cell synthesis. For example, a nuclease degrades a host cell, DNA is made The phage genome is then synthesized

what is the western blot?

a common method to detect and analyze proteins. It is built on a technique that involves transferring, also known as blotting, proteins separated by electrophoresis from the gel to a membrane where they can be visualized specifically.

what is an envelope?

a lipid bilayer outside the capsid

what is a defective phage?

a phage that doesn't carry a complete set of phage genes.

what is peptidoglycan?

a substance forming the walls of many bacteria.

what are transferred tumor cells

an abnormal growth of tissue resulting from a malfunction in the normally highly regulated process of cell growth. Some tumors are are Benign - meaning that they don't spread or invade nearby normal tissue Other tumors are Cancerous or Malignant, meaning that they have the potential to metastasize (spread)

What is a T-antigen and what does it do?

an antigenic substance produced in tumor cells Triggers an immune response in the host Useful tumor marks in identifying tumor cells with certain diagnostic tests

What is an oncogene?

is a proto-oncogene that had been changed in such a way that it promotes uncontrolled growth. Numerous events, including spontaneous and induced mutations, can lead to the conversion of a host's normal proto-oncogene into an oncogene

what factors cause the excision(phage induction) of a

it can be caused by phage encoded enzymes and phage encoded regulatory proteins. also by upon detection of a damged cell host ( can happen from damage from uv light, chemicals or spontaneous event)

what is lysogenic infection?

it is when the phage DNA exists within the cell without causing damage. In this state, the integrated phage DNA, called the Prophage, is replicated along the host cell chromosome. When the cell divides, the prophage is passed on to the cell's progeny

describe the replication strategy of RNA viruses

most RNA viruses are single stranded and they replicate in the cytoplasm. RNA viruses require a virally encoded RNA polymerase (replicase) for replication The replicase is an RNA-dependant RNA polymerase, meaning that it uses an RNA template to synthesize a new strand of RNA RNA Polymerase involved in Transcription - this enzyme synthesizes a strand of RNA from a DNA template = is thus a DNA-dependant RNA polymerase. The replication strategy for RNA viruses depends on the type of viral genome Single stranded RNA viruses (+) - that have a (+) RNA strand genome, which also serves as mRNA The replication strategy is relatively simple because the genome functions as mRNA The viral RNA can immediately bind to host cell ribosomes and be translated to make proteins One of the proteins encoded is a viral replicase and once this is made, it can be used to synthesize more copies of the viral genome To do this, it first makes multiple complementary (-) RNA strands using the original (+) RNA strands as a template These (-) RNA strands then act as templates to produce more (+) RNA strands The newly synthesized (+) RNA strands can either be translated to make more viral proteins or be packaged as genomes into new virions being formed. Single stranded RNA viruses (-) - that have a (-) RNA strand genome, meaning that the genome is the complement to mRNA Replication of a single stranded (-) virus is more complicated because a (-) RNA strand cannot be translated directly. instead , it must first be copied into a (+) RNA strand. This is done by a replicase carried into the host cell by the virus Once the (+) RNA stand has been produced, it can be translated to make viral proteins and can be used as a template for forming new (-) RNA strands Double stranded RNA viruses- have a genome that consists of both a (+) strand and (-) strand. Double stranded RNA viruses, which are uncommon, must also carry their own replicase because the host cell machinery is unable to translate double-stranded RNA The replicase immediately uses the (-) RNA strand of the double-stranded RNA molecule as a template to make a (+) RNA strand. This molecule is then translated to make more replicase, and the infection cycle can continue.

what outer covering, family, and representative disease does the double stranded DNA have?

non-enveloped, papillomaviridae, human papillomavirus.

what outer covering, family, and representative disease does the single stranded DNA have?

non-enveloped, parvoviridae, Human parvovirus B19 (5th disease).

what outer covering, family, and representative disease does the single stranded RNA have?

non-enveloped, picornaviridae, Polio viruses (poliomyelitis) Hepatitis A Virus (hepatitis A)

what outer covering, family, and representative disease does the double stranded RNA have?

non-enveloped, reoviridae, human rotaviruses. diahrheal

what is assembly (maturation)?

phage heads and tails are formed separately, the heads are filled with DNA and the tails are then attached. Once multiple copies of the phage genome and the structural components of the phage are made, they assemble to form new phage particles. Which is a complex multistep process: Once the phage phage head is formed, it is filled with DNA The tail is then attached followed by the addition of tail spikes Some of these components self assemble, meaning that the proteins join together spontaneously to form specific structures

how big are small and large viruses

small - 10 nm, big - 800 nm

what are spikes and what do they allow to happen?

spikes are protein structures that stick out from either the lipid bilayer of enveloped viruses or the capsid of non-enveloped viruses. Spikes allowing virions to attach to specific receptor sites on host cells

what is the cytopathic effect?

the effect a virus has on a given culture. many viruses can be detected by their effect on cells in a culture.

describe the release mechanism in enveloped and non-enveloped animal viruses

the release mechanism of a host cell depends on whether the virion is enveloped or non-enveloped. Enveloped viruses - are released by budding, a process whereby the virus acquires its envelope. Enveloped viruses are released through budding and usually do not kill the cell Before budding occurs, virtually encoded protein spikes insert into specific regions of the host cell's membrane Matrix protein then accumulates on the inside surface of those same regions Assembled nucleocapsids are then extruded from the cell protein and lipid envelope in the process Not all enveloped viruses have a cytoplasmic membrane derived envelopes. However, some obtain their envelope from the membrane of an organelle such as the Golgi Apparatus or the rough endoplasmic reticulum. They do this by budding into the organelle. From there, they are transported in vesicles to the outside of the cell. Budding may not destroy the cell because the membranes can be repaired after the viral particles exit Non-enveloped viruses - are released when the host cell dies. Released through ruptures in the cell membrane which kill the cell. (apoptosis) -programmed cell death, prior to the release of viral particles.

what is the role of the matrix protein? where can it be found?

the role of the matrix protein is for virus assembly forming links and bridges between the envelope and nucleocapsids. they can be found sandwiched between the nucleocapsids and the envelope of a cell.

define prions

they are composed only of protein and have no nucleic acid These agents have been linked to a number of slow, always fatal, human diseases: Creutzfeldt-jakob and Kuru Linked to animal diseases : scrapie, and mad cow disease Transmissible Spongiform Encephalopathies - sponge like appearance of the brain tissues, refers to all prion diseases

what temperate phages do?

they have the option of either directing a lytic infection (productive infection) or incorporating their DNA into the host cell genome, which is the latter situation called a Lysogenic infection (latent infection).

true or false - T4 is capable of undergoing only a lytic life cycle and not the lysogenic life cycle.

true

true or false - viruses that have the matrix protein are unique to enveloped viruses

true.

What is an oncogenic virus?

viruses that lead to cancer formation

what is an established cell line

when tumor cells are used in cell cultures. These cells multiply indefinitely in vitro.