Taxonomy of viruses Flashcards
What does -viridae ending mean
When viruses are grouped into families
What does -virus ending mean
When viruses are given a genus name
What name is given in English to viruses
Species names
On what characteristics (5) classification is based
- Nature of the host (animal,plant, bacteria,etc.
- Type of disease caused (enteric, leukemia,pneumonia)
- Life cycle(pathways of nucleic acid replication and transcription)
- Type of nucleic acids and strandedness (+strand: same as mRNA)
- Naked or enveloped
The Baltimore classification scheme is based on ____. It is useful because ____
-Based on the type of genome. Useful becasue the kind of genome will dictate the replication mechanism
What is plus RNA configuration and minus RNA configuration
- Plus configuration: same strand that mRNA( can be translated directly)
- Minus configuration: complementary to mRNA ( needs to be transcribed into plus strand before transcribed)
6 stages of life cycle of viruses
- Absorption
- Penetration
- Uncoating
- Replication
- Maturation
- Release
Describe absorption as a stage in life cycle and how plant viruses get in
Attachment of the virus to specific receptors on the surface of the cell. Plant viruses are usually introduced into the host by insect vectors, or following mechanical damage
Describe penetration as a stage in life cycle and what happens with different viruses when diffusing
Virus genome enters the cell
- In enveloped and naked viruses, the complete virion may enter the cell.
- In enveloped viruses, the envelope may be left at the cell surface such that only the nucleocapsid enters the cell
- In naked viruses, the capsid may be left at the surface
Describe uncoating as a stage in life cycle
Removal of the envelope and/or the capsid by host enzymes, sometimes within lysosomes (in eukaryotes)
Most envelope viruses of eukarytes use ___ to get in. Such viruses are then delivered to ___ where
endocytoses or viropexis, where everything gets in
They are delivered to lysosomes which degrade the capsid and the nucleic acid is release into the cytoplasm
Describe replication as a stage in life cycle
Replication of nucleic acid, transcription and protein synthesize
Describe maturation as a stage in life cycle
Assembly of virus components, nucleic acid, nucleocapsid and accessory proteins to form new virons. Usually, the assembly is spontaneous (occurs by itself)
Describe release as a stage in life cycle
Mature virions exit the host cell by means of budding or by causeing lysis of the cell. Plant viruses exit and are transmitted by means of vectors
Two periods of virus replication
- Latent period
- Rise period
What is included in latent period and rise period
Latent period: eclipse and maturation
Rise period: release
Explain eclipse
Time necessary for the host cells to replicate the viral genome and synthesize the viral components
Explain maturation
Time needed for the different components to be assembled
Explain rise period
Virions are detected outside the cell
two things can happen why the virus are detected outside:
-Lysis: virus-encoded proteins damage the cytoplasmic membrane. In bacteria, a virus-encoded protein destroys the peptidoglycan layer.
-Budding (enveloped virus)
What is burst size
Number of virions released (varies according to the virus, host cell, etc.)
What is the usual time for virus replication cycle in bacterial and animal viruses
Bacterial: 20-60 min
Animal: 8-40 h
Best-studied bacteriphages infect ___
E.coli (gram-negative)
Most phages contain ___ genomes. Most are ___, nut some have ___
dsDNA genomes
Most are naked, but some have lipid envelopes
Two types of bacteriophages
- Virulent phages
- Temperate phages
Explain what is virulent phage and give examples
Infection of host cells always leads to replication resulting in host cell lysis (lytic pathway)
Example: T4
Explain what is temperate phage and give examples
Have two options:
1) lytic pathway
2)Lysogenic pathway- the genome becomes incorporated into the bacterial host genome.
Ex.: Lambda
Lambda was discovered by
Ester Lederberg
T4 virus looks like
Usual complex virus, spider
How does T4 gets absorbed
T4 attaches to the core region of LPS by the tail fibers
What is the genome of T4
ds DNA, linear
What happens after T4 gets attached
The tail sheath contracts, forcing the central core through the outer membrane. Tail lysozymes digest the peptidoglycan layer, forming a small pore
What happens after the formation of the pore in peptidoglucan by T4
The phage DNA is then injected onto the cytoplasm of the host cell
Steps of T4 inside of bacteria
Nucelases, DNA polymerases, New sigma factors help in translation of phage DNA-> phage head proteins, tail, etc.-> mature phage particle-> T4 lysozyme prodiction->lysis
Explain lambda structure
Has no tail fibers
Has only one tail
Explain Lambda replication
As a temperate phage it can be integrated into the host genome and remain silent and under certain conditions it can exit the chromosome and continue the lytic pathway
The exit of the prophage from the choromosome is called
Excision
What is lysogeny
Latent sate of infection when phage is carried on the chromosome
What is prophage
Phage genome within the host cell chromosome
What is lysogen
Batcerum that contains a prophage
Phage Lambda’s genome is ___
Linear dsDNA with cohesive ends, a region of single stranded complimentary DNA
What is happening with cohesive ends
They join, forming a circular molecule of dsDNA
Explain how Lambda genome is incorporated into bacterial genome
It is incorporated into specific site: at attlamba site of bacterial chromosome. The at region in the phage genome is homologous to the attlambda site. The enzyme lambda intergrase(site-specific nucleases) catalyzes integration of the phage genome at this site. The lambda integrase is encoded on the phage genome
Phage фX174 is ___ genome
plus strand DNA (same strand as mRNA)
What Phage фX174 should do first
The minus strand must be synthesized first to produce a dsDNA genome, the replicative form
Step by step replicaton of ssDNA strand in Phage фX174
-Formation of negative DNA strand inside circle plus strand.
-Cutting of the plus strand is accomplished by the A
protein
-Continued rotation of the circle leads to the
synthesis of a linear fX174 genome(counterclock wise)
-When the growing viral strand reaches unit length , the A protein cleaves it and then ligates the two
ends of the newly synthesized single strand to give a singlestranded
DNA circle
The result of one replication cycle in fX174),
One relication form ( two circles)
One ssDNA positive form
What is MS2 (genome)
Plus strand RNA phage (same strand as mRNA). For replication minus strand should be synthesized
Explain how the replication of MS2 occurs
The genome first used as an mRNA and directs the synthesis of an RNA replicase (RNA-dependent RNA polymerase, this functin is not performed by th ehost) and other viral proteins.
Then the RNA replicase synthesizes a minus strand RNA that is used to produce additional mRNA and additional copies of the genome (plus strand) for the production of new virions
Where the replication of the viral genome will occur (animal viruses)
DNA viruses-> in the nucleus
RNA viruses->cytoplasm
Examples of animal viruses with DNA genome
Herpesvirus
Papovavirus (human papilomavirus)
How the penetration of Herpesvirus ,Papovavirus occurs
Fusion of the cell cytoplasmic membrane with the virus envelope. Nucleocapsid is transported to the nucleus where viral DNA is uncoated
How the transcription/ translation of Herpesvirus
Papovavirus genome occurs
- Immediate early proteins (transcription factors and, in some cases, virus specific RNA polymerase)
- Delayed early proteins (viral-specific DNA polymerase, and other viral proteins necessary for replication)
- Late proteins:nucleocapsid
How the replication of DNA virus occurs
Through rolling circle replication
How does assembly of DNA virus occurs
Assembly occurs in the nucleus, envelope is added via budding process through the inner membrane of the nucleus. The complete virions are then secreted out of the cell by the ER-Golgi pathway
If ssDNA genome comes into the cell , what happens first
It is converted to a dsDNA replicative form
Example of plus RNA genome viruses (animal)
Poliovirus
Hepatitis A
The genome of plus RNA viruses can be ___
Translated directly
In poliovirus, what happens to proteins
The plus-strand RNA serves as a template for synthesis of a large polyprotein that is cleaved into proteins
Poliomyelitis is transferred through
Faecal-oral route
explain polimyelitia as a disease and if it is treated
Little to no symptoms in 99% cases
Paralytic poli in 0.5-1% cases( usually in legs)
-Skeletal deformities post-paralytic polio
-No cure, but safe and effective vaccine
Example od minus strand RNA viruses
Measles, Rabies (rhabdovirus), Influenza (orthomyxovirus)
How the genome of minus strand RNA replicated
Cannot be translated directly. It is first transcribed into a plus-strand RNA by an RNA-dependent RNA polymerase carried inside the virions
Did we get rid of of measles
Yes
What are severe complications of measles
Pneumonia
Encephalitis(deafness, intellectual disability)
Death
What are long term complications of measles
-Subacute sclerosing panencephalitis(SSPE): progressive fatal neurodegenerative disease
What can be done to prevent measles
Safe and effective vaccine
The example of dsRNA virus
Rotavirus (reovirus)
How dsRNA replicates
The dsRNA can not be translated as it is. First, a plus strand RNA must be synthesized by a viral-encoded RNA dependent RNA polymerase using minus strand as a template.
The plus-strand is then translated into proteins and is used as a template to synthesize a minus strand to yield ds RNA genomes
Example of retrovirus
HIV
Rous sarcoma virus(causing cancer)
Genome of retrovirus
The virons carries two identical copies of the genome( plus,strand ssRNA), reverse transcriptase , intergrase and proteases
Explain the replication of the genome in retro viruses
Th reverse transcriptase is an RNA-dependent DNA polymerase that reverse trasnscribes the RNA genome into DNA
The DNA genome travel to the nucleus and is integrated into the host DNA
What LTR and what is their function
Long terminal repeats.
Contain promoters for trasncription and participate in the integration process
What is provirus
ingrated viral DNA. Contrary to the lambda, the provirus cannot excise from the host genome
What are the consequnces of viral infection in animal cells
- Tumor cell-> tumor cell division
- Lysis( release of virus and death of cell)
- Persitent infection (slow release of virus without the death of the cell)
- Latent infection(virus present , but not replicating)
- Cell fusion
How does cell fusion happens with virus
Enveloped viruses that fuse with the host cell cytoplasmic membrane carries viral proteins that fuse biological membranes
cells fusion result in hybrid cells that have chromosomal aberrations, and are short lived
What is transformation
Conversion of a normal cell into a tumor, a cell has acquired immortality and unconrolled replication. Can be caused by a viral infection. The cell can be already predisposed to it and the virus just pushes
Both __ viruses are known to cause tumors in animals and in humans
DNA and RNA viruses
Four different mechanisms how viruses can make the cell oncogenic
- Transduction
- Insertion of a strong promoter
- Inactivation of a tumor suppresor gene
- Expression of a viral protein that induces transformation (DNA virus)
What viruses are associated with human cancer
-Epstein -Barr virus (DNA)
-Hepatitis C Virus (RNA)
-Human T-lymphotropic virus type 1 (retrovirus)
Hepatitis B virus (RNA)
Human papillomavirus (DNA)
How does transduction scenario occurs with cancer and by what type of viruses
By RNA viruses (Rous Sarcoma Virus)
The virus carries one or many oncogenes, called v-oncogenes (for virus-encoded oncogene). The v-oncogene was acquired from the host, This process is called transduction. Oncogenes are similar to normal genes found in eukaryotes, known as proto-oncogenes or c-oncogenes. High expression of the oncogene affects the regulation of replication and/or cell death and causes transformation
What is the purpose of proto-oncogene
The proto-oncogene is usually involved int he regulation of the cell cycle or in safety mechanisms that prevent transformation
What is src
an adaptor protein in viral genome that orchestartes signal transduction in animal cells. Expression of v-Src is locked in an “ON”mode. When expressed in a cell, v-Src activates numerous pathways that should not be active, resulting in transformation of the cell
Explain the mechanism of cancer development through promoter
The virus does not encode an oncogene.
insertion of a strong promoter of the provirus next to a proto-oncogene, he proto-oncogene is then expressed at high levels and results in misregulation of the pathway that prevents transformation. the site of integration of the provirus is very important and transformation will occur only if a proto-oncogene is affected
Who usually does cancer development through a promoter
Retrovirus
Who usually does cancer development through an inactivation of a tumor suppressor gene
retrovirus
how does cancer development through an inactivation of a tumor suppressor gene occur
The virus does not have an oncogene
Insertion of the provirus in a gene involved in the regulation of proto-oncogene expression. Insertion causes inactivation of the tumor suppressor gene and uncontrolled expression of the proto-oncogene, resulting in transformation
Who usually does cancer development through expression of a viral protein
DNA virus
How does cancer development through expression of a viral protein occur
The viral protein does not have a cell counterpart.
Integration of the viral genome into the host genome may occur (such as int he case of adenovirus,dsDNA) or the viral genome may persist in the cell as an extrachromosomal episome.
Some DNA viruses that cause tumor do so because they have infected a nonpermissive host, in which they cannot complete their infection cycle. The cell is infected and undergoes uncontrolled replication. Because the virus cannot complete its replication, the cells will never die
Example of viruses that make cancer through viral protein
Human papilloma virus(HPV)
Gene E6 and E7 induce transformation
How HPV work
Infects epidermal or mucosal epithelial cells that are still able to proliferate( basal layer cells)
Basal layer:viral gene expression is largely suppressed, but limited expression of specific “early” viral genes (E5,E6 and E7)->enhanced proliferation infected cells and their lateral expansion
