.microbio E2: Viral Intrxn, Replication, Protein Expression, Viral Pathogenesis

Front 1

Differentiate the bacterial growth curve and the viral growth curve.

Back 1

Bacterial growth curve has four phases (lag phase, log phase, stationary phase, death phase). Viral growth curve only has one growth phase and two decline phases since it uses the host cell's machinery. The first decrease is due to viral entry into cells, the second decrease is due to host cell destruction. Without a host, a virus cannot replicate.

Front 2

The general pattern of viral multiplication includes six steps. Name em.

Back 2

1. Attachment
2. Entry
3. Uncoating
4. Replication
5. Assembly / Maturation
6. Release

Front 3

Attachment, the FIRST step of the multiplication stages, is NOT dependent on which of the following things?
A. pH
B. temperature
C. physiological state of the cell
D. availability of receptors on the cell
E. virus-specific neutralizing antibodies' presence
I. ionic-strength

Back 3

B. temperature

Attachment is temperature INDEPENDENT. (Though the next step, entry, is temperature dependent.)

Front 4

Viruses have viral attachment proteins on their surfaces that are similar to receptor ligands. For naked viruses, ________________ attach to the host cell receptor. For enveloped viruses, __________ attach to host cell receptors.

Back 4

For naked viruses, capsomere proteins found in the capsid attach to the host cell receptor.

For enveloped viruses, spikes are used.

Front 5

At what stage/point of the viral multiplication process do vaccines work?

Back 5

ATTACHMENT. (First step!) ! If you have a high enough antibody titer that is type specific for that virus, the antibody will coat the virus and obscure the attachment sites of the virus and the virus cannot attach to the host cell it would have infected. We have 14 vaccines for viruses. Most research is thus focused on this.

Front 6

True or False:
There are structural similarities between viral attachment proteins (epitopes on the virus) and receptor ligands. Thus, any and every receptor can act as a virus ligand.

Back 6

True.

SO HOW DO YOU DEAL WITH AN ANTIBODY THAT WILL MASK THE SITE BUT ALSO CROSS REACT WITH YOUR BODY?
That’s the problem.

Thru moleculary mimickry , every virus has the ability to imitate things in your body – chemokine, cytokine, or anything like that.

Reciprocally, every receptor in your body can recognize viruses that look similar to things they would naturally bind.

Front 7

State where the cell attachment site is for the following select viruses:
A. HIV
B. Polioviruses
C. Orthomyxoviruses
D. Paramyxoviruses
E. Rabies viruses
F. EB virus

Back 7

A. HIV: CD4 receptors on T cells, macrophage subsets, and microglial cells in the brain.
B. poliovirus receptor similar to tissue specific inter-cellular adhesion molecules (ICAMs) in the gut.
C.& D. mucoprotein receptors in respiratory tract
E. nicotinic ACh receptors on neurons
F. C3d receptor on B lymphocytes

Front 8

Match where the cell attachment site is for the following select viruses: EB virus, HIV, Orthomyxoviruses, Paramyxoviruses, Polioviruses, Rabies virus.

1. mucoprotein receptors in respiratory tract
2. CD4 receptors on T cells, macrophage subsets, and microglial cells in the brain.
3. nicotinic ACh receptors on neurons
4. C3d receptor on B lymphocytes
5. poliovirus receptor similar to tissue specific inter-cellular adhesion molecules (ICAMs) in the gut.

Back 8

1. mucoprotein receptors in respiratory tract = Orthomyxoviruses, Paramyxoviruses
2. CD4 receptors on T cells, macrophage subsets, and microglial cells in the brain = HIV
3. nicotinic ACh receptors on neurons = Rabies virus.
4. C3d receptor on B lymphocytes = EB virus
5. receptor similar to tissue specific inter-cellular adhesion molecules (ICAMs) in the gut = polio virus

Front 9

Entry, the second step of the multiplication stages, is NOT dependent on which of the following things?
A. pH
B. temperature
C. physiological state of the cell
D. availability of receptors on the cell
E. virus-specific neutralizing antibodies' presence
I. ionic-strength

Back 9

Not dependent on everything listed EXCEPT temperature, for which is IS dependent upon.

Viropexis (microphagocytosis) following attachment.

Front 10

There are three modes of entry into a host cell for the second stage of viral multiplication. Name em.

Back 10

direct penetration- naked viruses inject their DNA through this method, pinocytosis, membrane fusion - enveloped viruses do this such that the envelope fuses with the host cell membrane and results in the entry of the capsid and enclosed nucleic acid.

Front 11

True or False:
Uncoating, the third step in viral replication, occurs in a multistep fashion in the cytoplasm of the cell and involves host cell enzymes only.

Back 11

FALSE. This is a partial truth! Take out the last word "only" and add virus-specific enzymes too.

Front 12

Following uncoating, the virus nucleic acid is transported to either the _______ or _______ in the cytoplasm of the host cell.

Back 12

nucleus or ER

Front 13

Replication stage in viral multiplication is broken down into "early" transcription and translation, genome replication, and "late" transcription and translation. What occurs in each?

Back 13

"Early" transcription and translation occurs before genome replication. Gives rise to virus enzymes and regulatory proteins required for replication of the virus genome. Genome replication occurs. Then "late" transcription and translation occurs after viral genome replication and yield structural virus proteins which make up the capsid and the envelope proteins.

Front 14

Some early transcription is carried out by host-cell enzymes and some by virion enzymes. Which four use a CELLULAR DNA-dependent RNA polymerase like RNA polymerase II?

Back 14

all Adenoviridae, all Papovaviridae, some Parvoviridae, all Herpetoviridae

Front 15

Some early transcription is carried out by host-cell enzymes and some by virion enzymes. Which utilize virion enzymes, specifically:
A. Which one uses viral DNA-dependent RNA polymerase?
B. Which six use virion associated RNA-dependent RNA polymerase?
C. Which one uses virion associated RNA-dependent DNA polymerase?

Back 15

A. Which one uses viral DNA-dependent RNA polymerase? POXVIRIDIAE
B. Which six use virion associated RNA-dependent RNA polymerase? Bunyaviridae, Arenaviridae, Orthomyxoviridae, Paramyxoviridae, Rheoviridae, Rhabdoviridae.
C. Which one uses virion associated RNA-dependent DNA polymerase? RETROVIRIDAE

Front 16

The genomes of which three serve as their own mRNA and are not transcribed into early mRNA?

A. Bunyaviridae
B. Picornaviridae
C. Togaviridae
D. Rheoviridae
E. Coronaviridae

Back 16

B. Picornaviridae
C. Togaviridae
E. Coronaviridae

Front 17

Assembly of virus subunits occur in many different places. Which assemble:
A. in the nucleus? (3)
B. in cytoplasmic "cell factories"? (2)
C. at the nuclear membrane (1)
D. at the cell surface membrane (3)

Back 17

A. in the nucleus? (3: Adenoviridae, Papoviridae, Parvoviridae)
B. in cytoplasmic "cell factories"? (2: Picornaviridae, Poxviridae)
C. at the nuclear membrane (1: Herpetoviridae)
D. at the cell surface membrane (3: Orthomyxoviridae, Paramyxoviridae, Rhabdoviridae)

Front 18

Release of progeny virus particles can occur in many ways. Which occurs by:
A. cell lysis? (2)
B. budding from cytoplasmic membrane? (5)
C. through ER and Golgi apparatus (1)

Back 18

A. cell lysis? (2:Picornaviridae and Rheoviridae )
B. budding from cytoplasmic membrane? (5: Orthomyxo, Paramyxo, Rhabdo, Retro, Toga)
C. through ER and Golgi apparatus (1: Herpetoviridae)

Front 19

All animal DNA viruses replicate in the nucleus of the infected cell with the exception of ________ which replicates in the cytoplasm.

Back 19

Poxviridae

Front 20

All animal DNA viruses utilize DNA-dependent RNA polymerases for early transcription except for ______ and some _______.

Back 20

Poxviridae (has a virus-associated DNA-dependent RNA polymerase) and some Parvoviridae

Front 21

Most RNA viruses replicate in the ____________.

Back 21

cytoplasm. Orthomyxoviridae and retroviridae are exceptions in that they have both cytoplasmic and nuclear phases of replication.

Front 22

RNA viruses can be classified into four groups based on different pathways used to synthesize mRNA. List em.

Back 22

Front 23

Which viral RNA mRNAs are polycistronic and which are monocistronic? ( ssRNA+ , ssRNA - , dsRNA+ , dsRNA- )

Back 23

Poly: ssRNA+
Mono: ssRNA -, dsRNA+/-

Front 24

Members of the retrovirus family carry a special viral enzyme called reverse transcriptase. What does it do?

Back 24

Reverse transcriptase copies viral RNA into double stranded DNA which can then be incorporated into the host cell chromosome, It is then replicated when the host replicates.

Front 25

Transport of mRNAs from the nucleus to the cytoplasm is a highly regulated process. What usually needs to happen before export from nucleus can occur?

Back 25

splicing of transcripts.

Influenza's unspliced transcripts are not understood well.

Front 26

What is the importance of constitutive transport elements for RNA genomes?

Back 26

RNA genomes of simple retroviruses caontain constitutive transport elements, or cis elements, that render the unspliced RNA efficiently transported to the cytoplasm by host machinery.

Front 27

What mRNA transport does this detail? Explain it.

Back 27

HIV has a specific transport mech. When HIV reactivates from latent state, no Rev is present. Unspliced transcripts remain in the nucleus until spliced. As both Rev anad Tat are translated from spliced transcripts, Rev and Tat proteins are made. Tat increases trnascription making more Rev and Tat. Rev proteins transport out the mRNAs- spliced or not (most not). This impairs futher translation of Tat and Rev while providing ample unspliced RNAs that serve both as mRNAs for translation of the structural Ga proteins and as viral genomes for packaging.

Front 28

With regards to mRNA transport from the nucleus for HIV, what do Rev and Tat do?

Back 28

Rev and Tat proteins are made. Tat serves to increase transcription from the proviral LTR promoter, making more Rev and more Tat. Rev protein levels reach a point where most of the mRNAs are transported out of the nucleus by Rev before they can be spliced. This impairs further translation of Tat and Rev while providing ample unspliced RNAs that serve both as mRNAs for translation of the structural Gag proteins and as viral genomes for packaging.

Front 29

How does translation normally proceed in uninfected cells?

Back 29

1. mRNAs have 5' end caps, a 40S ribosomal cap binding complex binds the cap
2. This complex scans down the mRNA (5' to 3') until it encounters an AUG. The 60S subunit joins the complex and translation begins at this AUG and continues until a stop codon is encountered and the ribosome comes off the RNA.

Thus, under normal circumstances, mRNAs that are not capped are not translated and only the first open reading frame in mRNA is translated thus one mRNA = one protein.

Front 30

Viruses have mechanisms to manipulate the process to translate uncapped mRNAs or to express multiple proteins from one mRNA. What describes: one large polyprotein is expressed from a single open reading frame and this cleaved into several smaller peptides by one or more viral-encoded proteases.

A. Polyproteins
B. Leaky scanning
C. Reinitiation
D. Frame shifting
E. Suppression
F. Internal Ribosome Entry

Back 30

A. Polyproteins

Front 31

Viruses have mechanisms to manipulate the process to translate uncapped mRNAs or to express multiple proteins from one mRNA. What describes: Most AUGs can serve as start codons but their "context" (nature of nearby nucleotides) strongly influences whether the AUG is strong or weak. Sometimes viruses take advantage of this and express multiple proteins from one mRNA.
A. Polyproteins
B. Leaky scanning
C. Reinitiation
D. Frame shifting
E. Suppression
F. Internal ribosome entry

Back 31

B. Leaky scanning

ex. Sendai virus

Front 32

Viruses have mechanisms to manipulate the process to translate uncapped mRNAs or to express multiple proteins from one mRNA. What describes: Normally ribosomes fall off when an mRNA encounters a stop codon. With some viral mRNAs, the ribosome stops translation but fails to fall off. Instead i starts at a nearby AUG and translates a downstream open reading frame to make another protein.
A. Polyproteins
B. Leaky scanning
C. Reinitiation
D. Frame shifting
E. Suppression
F. Internal ribosome entry

Back 32

C. Reinitiation

ex. influenza

Front 33

Viruses have mechanisms to manipulate the process to translate uncapped mRNAs or to express multiple proteins from one mRNA. What describes: Only in some retroviruses (ex. HIV). Gag and Pol are encoded by different overlapping open reading frames. Most of the time translation stops at the Gag stop codon, making only Gag protein but sometimes the ribosomes shifts into a different reading frame just before the Gag stop and continues to produce Pol.
A. Polyproteins
B. Leaky scanning
C. Reinitiation
D. Frame shifting
E. Suppression
F. Internal ribosome entry

Back 33

D. Frame shifting

ex. some retroviruses, like HIV

Front 34

Viruses have mechanisms to manipulate the process to translate uncapped mRNAs or to express multiple proteins from one mRNA. What describes: Only in some retroviruses (ex. HIV). Gag and Pol are encoded by different overlapping open reading frames. Most of the time translation stops at the Gag stop codon, making only Gag protein but sometimes the ribosome misreads the Gag stop codon and places an amino acid there instead so translation continues to produce Pol.
A. Polyproteins
B. Leaky scanning
C. Reinitiation
D. Frame shifting
E. Suppression
F. Internal ribosome entry

Back 34

E. Suppression

ex. some retroviruses, like HIV

Front 35

Viruses have mechanisms to manipulate the process to translate uncapped mRNAs or to express multiple proteins from one mRNA. What describes: Poliovirus mRNAs have no 5' cap. They do have a special RNA sequences called an IRES which the 40S ribosomal subunit binds to then scans down the RNA to the first AUG where it is joined by the 60S subunit to initiate translation.
A. Polyproteins
B. Leaky scanning
C. Reinitiation
D. Frame shifting
E. Suppression
F. Internal Ribosome Entry

Back 35

F. Internal Ribosome Entry

ex. Poliovirus

Front 36

Proteins are synthesized in the cytoplasm and assembly of viral particles in the nucleus requires them to localize to the nucleus. This occurs by normal cellular processes so those proteins usually have ___________ or partially assembled subunits "piggyback" onto ones that do.

Back 36

Nuclear localization signal (NLS).

This "piggyback" mech ensures that only components that are properly folded are imported into the nucleus, as well as ensuring the proper stoichiometries within the nucleus.

Front 37

Many viral envelope glycoproteins are expressed as single polypeptides that are proteolytically cleaved into two subunits that often remain associated in the viral envelope, sometimes by disulfide bonds. These proteolytic cleavages are usually carried out by [ host / viral ] proteases in the trans-Golgi.

Back 37

host proteases

Front 38

What are scaffolding proteins useful for?

Back 38

Scaffold proteins have to do with capsid assembly. The icosohedral capsids of adnovirus and herpesviruses require scaffold proteins to organize the assembling structures into completed capsids that contain scaffold proteins but no nucleic acid. Concomitant with DNA packaging, the scaffold is removed from the capsid.

Front 39

Describe the genome packaging process for herpesviruses.

Back 39

DNA docks with a procapsid. Then DNA is translocated into the capsid by an enzyme complex called "terminase". As the DNA goes in, the scaffold proteins come out. When a full genome length has entered, terminase recognizes specific DNA sequences that signal the end of the genome and cleave the DNA at precisely the correct nucleotide. This releases a full genome within the capsid.

Front 40

_________ reside outside the capsid but inside the envelope. These have functional activities that can take effect immediately upon entry of the viral particle such as phosphatases, kinases, ribonucleases, and transcriptional activator activities.

Back 40

Matrix / tegument proteins

Front 41

For herpesviruses, DNA containing capsids are believed to traverse the nuclear envelope by an envelopment/ deenvelopment process, then acquire their final envelope by budding into ___________ which then fuse with _________.

Back 41

budding into Golgi vesicles which then fuse with the cell membrane. Some tegument proteins appear to be acquired in the nucleus whereas others are acquired in the cytoplasm.

Front 42

For poxviruses, envelopment involves _________ producing many membrane layers. Most viral particles remain intracellular and are released by cell lysis; however, some particles are released by fusion with the cell membrane.

Back 42

wrapping of Golgi vesicles around virion core particles, producing many membrane layers

Front 43

True or False:
Proteolytic processing occurs in retroviruses.

Back 43

True.

For example, in HIV, the final morphological change of the viral particle from spherical to somewhat conical results from autoproteolytic cleavage of the Gag polyprotein.

Front 44

Blood is the major transmission route for which of the following?
A. Cytomegalovirus
B. Enteroviruses
C. Hepatitis A
D. Hepatitis B
E. Hemorrhagic fever virus
F. Mumps

Back 44

D. Hepatitis B
E. Hemorrhagic fever virus

Front 45

Urine is the major transmission route for which of the following?
A. Cytomegalovirus
B. Hepatitis A
C. Hepatitis B
D. Hemorrhagic fever virus
E. Mumps
F. Rodent hantaviruses

Back 45

A. Cytomegalovirus
F. Rodent hantaviruses

Front 46

Semen is the major transmission route for which of the following?
A. Cytomegalovirus
B. Hepatitis A
C. Hepatitis B
D. Herpesviruses
E. Human simplex viruses
F. Varicella zoster virus

Back 46

C. Hepatitis B
D. Herpesviruses

Front 47

Breast milk s the major transmission route for which of the following?
A. Cytomegalovirus
B. Hepatitis A
C. Hepatitis B
D. Herpesviruses
E. Human simplex viruses
F. Mumps

Back 47

A. Cytomegalovirus
F. Mumps

Front 48

Skin lesions are the major transmission route for which of the following?
A. Cytomegalovirus
B. Ebola
C. Hepatitis B
D.Human simplex viruses
E. Mumps
F. Pox
G. Varicella zoster virus

Back 48

B. Ebola
D.Human simplex viruses
F. Pox
G. Varicella zoster virus

Front 49

Differentiate between virulence and pathogenicity.

Back 49

Virulence is defined as the capacity to cause disease in a host and is often used in a quantitative sense (highly-, moderately-, mildly-, avirulent). Pathogenicity is similar but usually used in an all or none context (pathogenic or apathogenic).

Front 50

List four general classes of viral genes involved in pathogenesis. (Viral genetics of virulence.)

Back 50

1. Genes that are needed for replication in certain cell types (HSV-1 and ICP34.5)
2. Genes involved in immune evasion
3. Genes involved in dissemination ( a single amino acid change in HSV-1's surface glycoprotein D blocks the ability of the virus to spread to the CNS via neuronal route)
4. Genes that produce toxic products (Rotavirus' NSP4 protein acts as a viral enterotoxin and causes diarrhea.)

Front 51

True or False:
Most causes of damage when it comes to viral infections are due the host's immune-mediated response.

Back 51

TRUE

Front 52

The paralytic effects of polio infection are due to [ host- / virus - ] induced lysis of neurons in the CNS.

Back 52

virus-induced (this is an exception to the general statement that most viral damage is done by host immune response)

Front 53

Lymphocytic choriomeningitis virus (LCMV) replicates in cells of the pituitary gland and thus viral infection results in a two-fold reduction in GH production, not because of damage to the cells, but because ....

Back 53

a protein encoded by the virus inhibits transcription from the GH promoter.

Front 54

The classic "flu-like" (fever, fatigue, sleepiness) symptoms of many acute viral infections are due largely to....

Back 54

CNS and systemic effects of circulating inflammatory cytokines (IL-1, IL-6, TNF-alpha and beta)

Front 55

The predominant form of antibody-mediated pathogenesis involves....

Back 55

deposition of antigen-antibody complexes in blood vessels, kidney and brain. Deposition results in constriction and blockage, leading to vasculitis, nephritis, and dementia.

Front 56

True or False:
In dengue hemorrhagic fever, preexisting antibodies to a different serotype (from a previous infection) actually facilitate viral infection of monocytes because the antibodies coat the viral particles and monocytes endocytose them. The infected monocytes produce large amounts of pro-inflammatory cytokines, which initiate a cytokine self-stimulating loop that culminates in severe leakage of blood vessels and hemorrhagic fever.

Back 56

TRUE

Front 57

In which virus/condition does preexisting antibodies to a different serotype (from a previous infection) actually facilitate viral infection of monocytes because the antibodies coat the viral particles and monocytes endocytose them. The infected monocytes produce large amounts of pro-inflammatory cytokines, which initiate a cytokine self-stimulating loop that culminates in severe leakage of blood vessels and hemorrhagic fever.

Back 57

Dengue hemorrhagic fever (Dengue virus)

Front 58

What are the general 6 stages of the typical viral life cycle in vivo?

Back 58

1) Entry
2) Replication at primary (usually entry) sites of infection
3) Dissemination
4) Replication at secondary sites of infection
5) Secondary dissemination to tertiary sites also possible
6) Shedding

Front 59

Define dissemination and describe hematogenous and neuronal dissemination.

Back 59

To cause significant disease, viruses usually have to disseminate within the host - have to spread beyond the initial entry site and primary site of infection. Hematogenous dissemination is when the virus is disseminated throughout the body via circulatory system- either freely as virions (Hep B, polio) or by infected circulating blood cells. Neuronal dissemination is via neurotropic viruses, or viruses that have the ability to infect and replicated in neurons. Neuronal dissemination is spread throughout body via neurons (polio, rabies, HSV, varicella zoster).

Front 60

Define viremia.

Back 60

Cell-associated OR free infectious virus in the blood is called viremia.
The first wave that results in disseminaiton is primary viremia.

Front 61

True or False:
Many viruses use leukocytes as vehicles of dissemination.

Back 61

True

Front 62

The ability of a given virus to infect and replicate in a particular cell type is termed __________ and is often a major determinant of how the virus disseminates and in which secondary sites it replicates.

Back 62

Tropism

Usually the presence of cell surface receptors that can be used by the virus to gain entry defines the tropism. (ex. HIV and CD4+ receptors) But events after attachment and entry can also define tropism. (ex. JC virus replicates only in oligodendrocytes b/c viral enhancer is strictly dependent on transcription factors unique to oligodendrocytes.) Even extracellular factors can define tropisms. (Influenza's HA glycoprotein and Clara proteases.)

Front 63

The ability of a given virus to infect and replicate in a particular cell type is termed tropism. There are three determinants of tissue/cell tropism: presence of cell surface receptors that can be used by the virus to gain entry, events after attachment and entry , extracellular factors. Give an example of each.

Back 63

*presence of cell surface receptors that can be used by the virus to gain entry: HIV and CD4+ receptor. *events after attachment and entry: JC virus can only replicate in oligodendrocytes b/c dependent on transcription factors unique to oligos
* extracellular factors: Influenza surface HA glycoprotein must be proteolytically cleaved by Clara proteases before it can be infectious.

Front 64

The final stage of the viral life-cycle is to leave the host by a route that is likely to result in transmission to a new host. This may occur from ______________.

A. the primary site of infection
B. the secondary site of infection
C. the tertiary site of infection
D. any or all sites of infection

Back 64

D. any or all sites of infection

Front 65

Which mode of transmission and virus is MISMATCHED?
A. Hepatitis A = feces
B. Hepatitis B = blood, semen
C. Cytomegalovirus = breast milk, urine
D. HSV = skin lesions, genital lesions
E. Mumps = skin lesions

Back 65

E. Mumps = skin lesions

Mumps is spread by breast milk.

Front 66

What is the major transmission route for enteroviruses?

A. Respiratory secretions
B. Feces
C. Blood
D. Urine
E. Semen
F. Skin lesions

Back 66

B. Feces

Front 67

What is the major transmission route for Hepatitis A?

A. Respiratory secretions
B. Feces
C. Blood
D. Urine
E. Semen
F. Skin lesions

Back 67

B. Feces

Front 68

What is the major transmission route for Hepatitis B?

A. Respiratory secretions
B. Feces
C. Blood
D. Urine
E. Semen
F. Skin lesions

Back 68

C. Blood

Front 69

What is the major transmission route for Hemorrhagic fever viruses?

A. Respiratory secretions
B. Feces
C. Blood
D. Urine
E. Semen
F. Skin lesions

Back 69

C. Blood

Front 70

Feces is the major transmission route for which of the following?
A. Cytomegalovirus
B. Enteroviruses
C. Hepatitis A
D. Hepatitis B
E. Poliovirus
F. Mumps

Back 70

B. Enteroviruses
C. Hepatitis A
E. Poliovirus