Old Exam 1 Questions Flashcards
What is meant by the term open reading frame
- a combination of nucleotide triplets that start with a start codon and stop with a stop codon
What is a cap structure?
- found on the 5’ end of the mature mRNA and helps prevent against degradation by exonuclease and helps the ribosome recognize the mRNA to begin. translation linked to 5’ of 7-methylGTP (Guanosine triphosphate)
On what kind of macromolecular would a cap structure be found?
- mature mRNA
Describe the process of ribosome scanning
1) 40s subunit binds to the cap with help from the translation initiator factor (adaptor)
2) Once bound ribosome scanning beings moving 5’-3’ one nucleotide at a time (towards start codon)
3) Once AUG is found in the A-site, tRNA then 60s subunit binds and we can begin translation
Two basic structural forms of viral nucleoprotein?
- rod-shaped
- spherical
Which of these two structural forms best describes picornavirus particles?
spherical
What are two different viral assembly mechanisms?
- nucleation
- shell stuffing
To what kinds of virus particles does each mechanism apply?
- nucleation is for all rods and most spheres
- shell stuffing is for some spheres
Picornaviridiae
family
Human rhinovirus A
Species
Human enterovirus C
Species
Why are biological properties of viruses, such as mode of transmission, not generally useful criteria for assigning them to specific families?
If they were used, there would be few, large families with viruses that are otherwise unrelated to each other. Many varying viruses have the same biological properties, so this is not an accurate measurement of their similarity.
Virion morphology classification
- shape and size of virions
- presence/absence of envelope (membrane)
Virion structural protein classification
molecular weight (size)/number of distinct proteins
Virion genome properties classification
- type of nucleic acid: DNA, RNA, ds, ss (+/-)
- size and number of nucleic acid molecules
- structure features:
- DNA(ds, ss), circular/linaer genome
- (+)- ssRNA, 5’-cap/VPg/poly(A) tail - nucleotide sequence
What are the humoral and cellular components of the innate and adaptive immune responses of mammalian hosts that are important for controlling virus infections?
Humoral
Innate: a/b-interferon
adaptive: antibody
Cellular Innate: Macrophages, Dendritic cells, NK cells Adaptive: CD8+s, CD4+s, TH1, TH2, CTLs
What fundamental process of the innate immune response underlies most kinds of immunopathology
inflammation
Give the names of the two types of hypersensitivity reaction
Type III and Type IV
Give the name of the adaptive immune system effector component on which each is dependent
Type III - antibody
Type IV - TH1 T cells
Which arm of the immune system is vaccination intended to stimulate
adaptive
What are the three basic types of antiviral vaccines?
- live attenuated
- inactivated
- subunit
Which of these vaccine types have been employed in immunization programs intended to prevent poliomyelitis
- live attenuated and inactivated
population
group of organism (individuals) under study
susceptibles
subset of population which is potentially infectable (naive host)
infections
individuals in which virus is reproducing
cases
individuals that show symptoms/clinical signs of disease
fatalities
(excess) deaths in the population
Explain the distinction between exposure and infection, as these terms are used in epidemiology
- exposure is coming into contact with a virus, but not necessarily becoming infected.
- to be infected you have to be exposed to a virus first
What is meant by the term case infection ratio?
fraction of infections that result in disease
Give an example of a disease with viral etiology in which the case infection ratio is (i) very high; (ii) very low
(i) smallpox
(ii) poliomyelitis
What are two routes of transmission by which viruses can enter human populations from extra human reservoirs?
- animal-to-human
- vector-to-human
For viruses that are maintained within a single host species, what are the three primary routes by which viruses are transmitted horizontally between individuals?
1) respiratory-aerosol
2) urogenital-sexual
3) fecal-oral
Which of these transmission routes is/are utilized by viruses classified in the genera (i) Hepatovirus, and (ii) Enterovirus?
Hepatovirus
- fecal oral
Enterovirus
- respiratory-aerosol - rhinovirus
- fecal oral - poliovirus
List, in the order in which they typically occur, the eight stages of the cellular viral infection cycle
- attachment
- penetration
- uncoating
- gene expression
- genome replication
- assembly
- release
- Maturation (may occur before, during, or after release)
What two types of protein are encoded by a viral genome?
- capsid protein for genome protection
- nucleic acid polymerase or modifier subunit for genome replication
Identify a stage of the cellular infection cycle at which each is required? (capsid protein, nucleic acid polymerase/modifer subunit)
- capsid protein - assembly
- nucleic acid polymerase or modifier subunit - genome replication
What stage of the cellular viral infection cycle would you expect to be blocked by
(i) virus-specific immunoglobulin
(ii) a/B interferons
(iii) chemical cross linking of proteins in virus particles
i. attachment - by sticking on the virus particle by blocking access to the canyon.
ii. gene expression - translation block
iii. uncoating (disassembly) - it won’t come to pieces because it is too stable.
What are three mechanisms by which viruses or viral genomes, may enter host cells?
- endocytosis
- direct fusion
- direct injection
Which of these mechanisms apply to viruses in the family Picornaviridae (for penetration)
direct injection
What occurs during leaky scanning
-The 40s subunit moves along one base at a time past the start codon BEFORE initiator tRNA can get to the binding site
What is a segmented viral genome?
- multiple nucleic acid molecules that collectively make up the genome
What are three processes by which genetic variability may be generated during the propagation of a virus with a segmented genome?
- mutation
- recombination
- pseudorecombination ( not for a nonsegmented genome)
Picornavirales
Order
Hepatovirus
Genus
What two mechanisms for penetration of a host cell are most commonly employed by enveloped viruses?
- direct fusion
- endocytosis
Define the term maturation as it applies in the context of a cellular viral infection cycle?
the changes in the virion required to make it infectious
What stage of the cellular viral infection cycle is blocked in cells that are responding to a/b-interferon?
gene expression
What is the route of entry into the host for a virus that is transmitted in the vector-human pattern?
- arthropod bite
What is the general name given to viruses that have this transmission pattern?
- arbovirus (arthropod borne viruses)
What are the three primary routes by which viruses are transmitted horizontally between individuals in a population?
- respiratory-aerosol
- urogenital-sexual
- fecal-oral
In the family Picornaviridae, which of these routes are utilized by members of the genus Enterovirus?
- fecal oral
- respiratory-aerosol
Among people who are infected with poliovirus, very few will develop the clinical signs of flaccid paralysis. Does this mean that the case:infection ratio is high, or low?
low; few cases come from infections
For wild, neurovirulent strains of poliovirus, a case–fatality rate of about 0.05 is observed. What does this mean?
what fraction of the population that is showing signs/symptoms will die
What are two routes by which poliovirus can spread systemically through a human host?
- nerves
- blood
What does the term ‘tissue tropism’ mean in relation to virus infection of a multicellular organism?
- specific tissue type infected by the virus
What are two factors that affect the tissue tropism observed for any given virus?
- presence of appropriate receptors for virus on host cells found in specific organ or tissues
- if the virus can gain access to the specific tissue
What is the name given to the tissue tropism that is characteristic of
(i) hepatitis A virus
(ii) poliovirus?
- hepatotropism
- neurotropism
Non-segmented (+)ssRNA genomes, such as that of SFV, can acquire genetic variability through RNA recombination. What is the name given to this mechanism?
-Copy Choice
Describe Copy Choice
1) RNA polymerase binds to the 3’ end
2) starts copying template
3) RNA polymerase detaches from template still holding stand
4) attaches to new or old template
5) net output depends if it binds back to the same analogous region (binds back to the same region then it is homologous or if it binds back to a different region its non-homologous which can result in duplication or deletion of a sequence)
To what taxonomic entity (i.e. order, family, subfamily, genus, or species) does each of the following belong?
(i) Enterovirus (ii) Picornaviridae
(iii) Human rhinovirus A
i) genus
ii) family
iii) species
What two mechanisms for penetration of a host cell are most commonly employed by non-enveloped viruses?
- direct injection
- endocytosis
What are three host and/or viral factors that can contribute to the occurrence of an epidemic?
- availability of susceptible host
- opportunity for hosts to be exposed to the virus
- transmission efficiency of virus
What is the mathematical relationship between the rate of asymptomatic carriage and the case:infection ratio for a virus in a given population?
(1-(C/I))
Generation time
average time between infection and transmission to new host (directly related to virus shedding)
Incubation Period
time from infection to onset of clinical signs/symptoms (overt disease)
Which transmission route is utilized by Hep. A virus?
fecal-oral
Which transmission route is utilized by Human Rhinovirus B?
Respiratory-aerosol (droplet)
Which transmission route is utilized by varicella zoster virus?
respiratory-aerosol (airborne)
Which transmission route is utilized by human papilloma virus?
urogenital-sexual
Which transmission route is utilized by herpes simplex virus?
Urogenital-sexual (horizontal) maternal parturition (vertical)
Which transmission route is utilized by rotavirus?
fecal-oral
Which transmission route is utilized by rubella virus?
vertical- placental fetal
**also can be horizontal which would be respiratory aerosol
Which transmission route is utilized by human immunodeficiency virus?
maternal-neonatal (vertical)
To what taxonomic entity (i.e. order, family, subfamily, genus, or species) does each of the following belong?
(i) Hepatovirus
(ii) Human enterovirus C
(iii) Picornaviridae
i) genus
ii) species
iii) family
name the stages of the cellular infection cycle that
must occur before translation of the viral genome can begin.
attachment
penetration
uncoating
What is the most important function of the cap structure during mRNA translation?
Where the 40s subunit binds to, so it can begin translation
What determines the likelihood that leaky scanning will occur?
the likelihood of leaky scanning occurring depends on a good kozak consensus sequence (if you have a good kozak sequence then leaky scanning will not occur), because it favors translation. Therefore it allows the 40s subunit to pause allowing the initiator tRNA to get there and bind resulting in translation.
You have a virus that infect only humans and they cannot be grown in continuous cell lines in culture. What type of vaccine could be developed for this virus, and what would be the key steps in its production?
-Subunit vaccine
Take a purified viral protein and use recombinant DNA technology to produce the vaccine
You have a virus that infects humans and several kinds of non-human animals. It can also be grown in cell culture, although strict safety precautions are required to protect workers from the virus. What type of vaccine(s) might be developed for this virus? Which vaccine would be most feasible based on safety considerations?
- live attenuated, inactivated, subunit would all work
- subunit, because it is the safest for the workers to use although it doesn’t give the best immune response compared to inactivated.
The host immune response significantly affects the interaction between a virus and a multicellular host organism. Describe three ways in which the immune system may affect the outcome of an infection
1) resolve the infection- through the humoral and cellular effectors, the immune system kills off all pathogens.
2) Immunopathology- the immune system ramps up and causes inflammation, cytokine effects can also cause non-specific flu like symptoms
3) Stop the spread (contain) of the infection-Humoral and cellular effectors can stop pathogen from spreading while the infection is occurring. Allowing the infection to stay localized/or with less pathogen load
If something is endotheliotropic what does that mean and what can happen?
- it means that the virus will infect the lining of the blood vessels
- this will lead to hemorrhaging.
5’ and cap located on
the left
3’ and poly A tail located on
the right
The ORF likely to encode RdRp
on the left because you genome replication comes first in the infection cycle so RNA polymerase needed
The ORF likely to encode capsid protein
in the middle or on the right depending on what is asked because assembly comes later in the infection cycle.
Ebola virus particles consist of an elongated, flexible nucleocapsid surrounded by a tightly-fitting envelope. Given this information, Ebola virus potentially could penetrate cells by one of two possible mechanisms. What are they?
- direct fusion
- endocytosis
For which of these mechanisms is/are penetration and uncoating combined?
- direct fusion
- direct injection
The Ebola virus genome consist of (-)-sense SSRNA. After the nucleocapsid has penetrated to the cytoplasm of a newly infected cell, what steps of viral gene expression would be required for the synthesis of new Ebola virus proteins?
- you would first have to make a +-sense ssRNA then you can translate the +-sense strand
Which of these steps requires the action of a virus-encoded protein, and what is the virus encoded protein?
- the first step would require the action of a virus-encoded protein
- that virus encoded protein is RNA polymerase
Newly synthesized Ebola virus nucleocapsids acquire an envelop as they leave the cell. What is the name given to this stage of the infection cycle?
- release
And what is the name for the mechanism of envelopment
budding
What are three factors that determine the efficiency of virus transmission?
- availability of susceptible hosts
- extent and duration of shedding
- infective dose of virus
