Deck 11: Viral Molecular Biology

Question 1

The segmentation of the influenza genome is conducive to ________, which can be defined as the process by which two different viruses swap genome segments to form a new genome.

A) recombination
B) hybridization
C) ligation
D) reassortment
E) shuffling

Answer 1

D

Question 2

The HIV genome can be characterized by all of the following EXCEPT

A) 5'-"cap."
B) 3'-poly A-"tail."
C) a Lys-specific tRNA.
D) a DNA primer.
E) a coated nucleoprotein.

Answer 2

D

Question 3

Which of the following is FALSE regarding the establishment of lysogeny?

A) Lambda phage DNA integrates as a prophage in the host genome at the att site by site-specific recombination.
B) Rolling-circle replication generates multiple genomes in tandem, which are eventually cleaved by the enzyme terminase.
C) Production of the repressor CI by the integrated prophage prevents superinfection by other lambda phages.
D) A CI lambda repressor dimer binds to the major groove of a specific DNA sequence in the bacterial host, preventing the transcription of lytic promoters.
E) Once integrated in the host's DNA, gene expression from the prophage is limited to a few proteins, including the repressor C1.

Answer 3

B

Question 4

The director of a laboratory in charge of making the flu vaccine for the upcoming season is planning her production strategy. She must consider the phenomenon of reassortment, in which

A) two different viruses contribute genome segments to a reassorted genome that remains segmented.
B) two different viruses contribute genetic material to form a recombinant molecule.
C) genes within a genomic segment of a virus undergo a fast mutation rate in the presence of another virus.
D) there is antigenetic shift.
E) there is antigenetic drift.

Question 5

The figure below is a transmission electron microscopy image of an influenza A virion. Hemagglutinin (HA) is one of the spike proteins. Which is the other spike protein on the envelope of influenza A?

A) nucleocapsid protein
B) ion channel
C) matrix protein
D) nuclear export protein
E) neuraminidase

Question 6

RNA synthesis of influenza virus is primed by 7-methylguanine fragments of host mRNA, obtained by

A) telomerase activity.
B) the rolling-circle mechanism.
C) endocytosis.
D) exocytosis.
E) cap-snatching.

Question 7

The figure below shows a partial map (0 to about 22 kbp) of the lambda DNA genome. Which gene or gene set is mislabeled?

A) A-lysis/lysogeny switch
B) B-head
C) C-tail
D) D-tail tip
E) E-tail fibers

Question 8

What is the cause for cloudy centers appearing in lambda plaques on an Escherichia coli confluent plate?

A) A low multiplicity of infection prevents the appearance of large numbers of lysed cells.
B) Cell debris forms a physical barrier between uninfected cells and virions.
C) Compounds in agar or nutrient medium protect bacterial cells from infection.
D) A large number of infected cells become resistant to bacteriophage infection.
E) Some infected cells become lysogens and start growing up where the infection began.

Question 9

The lambda genome is replicated by a rolling circle mechanism. What is the end result after a round of replication?

A) a single-stranded DNA that is immediately packaged in the phage head
B) two molecules resulting from a step of circle-to-circle replication
C) several circular molecules inserted into each other; the circles are cleaved at the cos sites and eventually relegated
D) a concatemer (i.e., multiple genomes joined end to tail, which are cleaved at cos sites by a terminase), producing linear double-stranded DNA prior to packaging
E) several Okazaki fragments that are subsequently ligated

Question 10

Which host protein cleaves CI and triggers up to 100% lysis after lysogenic Escherichia coli cells are exposed to ultraviolet light?

A) primase
B) DNA polymerase III
C) RecA
D) terminase
E) Lon protease

Question 11

Influenza shows cyclic appearance of extremely virulent strains that may cause widespread infection with high mortality, such as that of 1918, which infected 20% of the world's population and killed more people than World War I. What is this type of infection called?

A) mutagenic
B) endemic
C) epidemic
D) pandemic
E) transgenic

Question 12

Proteolysis of the influenza ________ produces a fusion peptide, which initially binds to a ________ glycoprotein on the host's cell membrane that serves as a receptor.

A) hemagglutinin; syalic acid
B) neuraminidase; N-acetylglucosamine
C) matrix; fucose
D) nuclear-packaging protein; mannose
E) nucleocapsid protein; glucosamine

Question 13

The term "________" describes the mutation-caused emergence of multiple viral strains that present differing properties of replication, tissue tropism, and drug resistance within a single infected individual.

A) hybrid species
B) candidatus species
C) quasispecies
D) lethal species
E) type species

Question 14

What vertebrate groups harbor influenza viruses capable of mutating into strains infective to humans?

A) cattle and horses
B) swine and cattle
C) birds and swine
D) mice and rats
E) canines and felines

Question 15

The capsid of the bacteriophage lambda is composed of two types of protein subunits, namely, D and E, arranged in a(n)________ shape.

A) icosahedral
B) rhomboidal
C) pyramidal
D) triclinic
E) cubic

Question 16

The neuraminidase inhibitor ________ is currently used to treat influenza infections.

A) Pleconaril
B) Tamiflu
C) Zidovudine
D) Acyclovir
E) Vitravene

Question 17

The genome of the influenza virus is best described as

A) (-) strand segmented RNA.
B) (+) strand segmented RNA.
C) (-) strand single-piece RNA.
D) (+) strand single-piece RNA.
E) double-stranded RNA.

Question 18

The figure below shows a partial map of the lambda DNA genome (23-48 kb). The early left and right operons as well as the late operon are indicated. Which gene or gene set is mislabeled?

A) A-integration to host chromosome
B) B-lysis/lysogeny switch
C) C-DNA replication
D) D-lysis
E) E-terminase

Question 19

Control proteins Cro and CII lead to lysis or lysogeny, respectively. What environmental signal in the host contributes to regulate the amount of CII by influencing the activity of the protease HflB?

A) Mg2+ ion concentrations
B) temperature
C) water availability
D) nutrient concentrations
E) helper phages

Question 20

Which of the following statements is FALSE regarding phage lambda as a temperate phage?

A) The genome of phage lambda integrates into the genome of the host cell and becomes a prophage.
B) The phage DNA replicates as an integrated prophage but does not produce phage particles.
C) Lambda phage immediately kills its host after infection.
D) The presence of the lambda prophage confers resistant to new infections by lambda.
E) Incorporation of lambda phage DNA into the bacterial genome is called lysogeny.

Question 21

The reverse transcriptase complex is a crucial enzyme for retroviruses. Which catalytic activity does reverse transcriptase have?

A) RNA-dependent RNA synthesis
B) RNA degradation via RNase H
C) DNA-dependent DNA synthesis
D) RNA-dependent DNA synthesis
E) DNA-dependent RNA synthesis

Question 22

Which HIV protein is mismatched with its function?

A) nef-virion component
B) vpu-membrane protein
C) rev-reverse transcriptase
D) tat-transcription factor
E) env-envelope protein

Question 23

To decrease risks, viruses used for gene therapy are extensively engineered to incorporate safety features such as

A) the presence of virulence genes.
B) ensuring insertion in regions near oncogenes.
C) pseudotyping to alter tissue specificity.
D) alteration of the germ line.
E) ensuring deletions in regions near oncogenes.

Question 24

Antiviral agents have been synthesized against specific processes of HIV. Which of the following is a mismatched pair?

A) CCR5 blocking-maraviroc
B) integrase inhibition-raltegravir
C) reverse transcriptase inhibition-azidothymidine (AZT)
D) Gag-Pol cleavage-protease inhibitors
E) nef inhibition-oseltamivir

Question 25

Worldwide, HIV infects one in ________ adults.

A) 20
B) 50
C) 100
D) 500
E) 1,000

Question 26

Which are the main open reading frames (ORFs) present in all retroviruses, including HIV?

A) vif, vpi, vpu
B) env, pol, gag
C) tat, nef, rev
D) vif, pol, tat
E) tat, nef, vpu

Question 27

Which of the following viral groups has been successfully utilized as vector in gene therapy?

A) rhabdoviruses
B) parvoviruses
C) lentiviruses
D) orthomyxoviruses
E) bacteriophages

Question 28

How many genomes does an HIV particle have and what is their biochemical nature?

A) two RNA molecules
B) eight RNA molecules
C) a DNA/RNA hybrid
D) a single RNA molecule
E) a DNA molecule and a noncomplementary RNA molecule

Question 29

Retroelements are remains of retroviral genomes in various states of decay. Which of the following are NOT retroelements?

A) Alu sequences
B) HERVs
C) LINE
D) Gene transfer vectors
E) SINE

Question 30

The pol open reading frame of HIV encodes

A) reverse transcriptase.
B) integrase.
C) protease.
D) gyrase.
E) ligase.

Question 31

The lymphocyte protein chemokine receptor 5 (CCR5) is involved in HIV. Functionally, CCR5 is a(n)

A) antagonist.
B) coreceptor.
C) cofactor.
D) inhibitor.
E) regulator.

Question 32

Cyclophilin A is a host protein that

A) acts as a coreceptor for HIV.
B) facilitates HIV entry into the nucleus.
C) is incorporated in the HIV envelope.
D) inhibits HIV replication.
E) cuts the polyprotein into subunits.

Question 33

Glycosylation and packaging of the HIV env proteins occur in the

A) endoplasmic reticulum.
B) nucleus.
C) membrane.
D) Golgi.
E) cytoplasm.

Question 34

Integrated retroviral genomes that have accumulated mutations and can no longer generate virions are known as ________ retroviruses.

A) lysogenic
B) temperate
C) virulent
D) exogenous
E) endogenous

Question 35

Which of the following primers for nucleic acid replication is linked to the appropriate virus?

A) M2 and poliovirus
B) host caps and poliovirus
C) VPg and influenza virus
D) virus tRNA and herpes virus
E) host tRNA and HIV

Question 36

Retroelements and transposons compose about what percentage of the sequence of the human genome.

A) 8
B) 25
C) 33
D) 50
E) 90

Question 37

The figure below shows the structures involved in attachment of HIV to a host cell. The protein gp120 is represented by the number ________; CCR5 is indicated by ________ and CD4 by ________.

A) 1; 2; 3
B) 2; 3; 4
C) 3; 1; 2
D) 4; 1; 2
E) 5; 3; 4

Question 38

The figure below shows the process attachment of HIV to a host cell. Which step is blocked by the antiviral agent maraviroc?

A) 1, CD4 binding
B) 1, CCR5 binding
C) 2, formation of the fusion peptide
D) 3, release of gp120
E) 4, reverse transcriptase activity

Question 39

The lack of ________ in some people makes them resistant to HIV infection.

A) CD4 receptors on the macrophages
B) CCR5 receptors on the macrophages
C) T4 lymphocytes
D) B-cell receptors
E) nuclear factor kappa beta in the B cells

Question 40

HIV-infected cells can fuse with neighboring cells, subsequently forming a giant multinucleate cell known as a

A) transgene.
B) syncytium.
C) hypha.
D) tumor.
E) coenocyte.

Question 41

Herpes simplex virus latent infections are seen more frequently in nerve cells, such as

A) the trigeminal ganglion.
B) the glia.
C) multipolar neurons.
D) the basal nuclei.
E) astrocytes.

Question 42

The lysis/lysogeny switch has been used in synthetic biology applications that take advantage of the properties of the interaction between Cro and CI. Give two examples of such an application.

Question 43

Approximately 60%-80% of Americans acquire herpes simplex, usually HSV-1, in epithelial lesions commonly known as

A) chancres.
B) pox.
C) cold sores.
D) shingles.
E) hives.

Question 44

What is the Escherichia coli protein used by bacteriophage lambda as a receptor? Why has this protein not been lost in the process of evolution?

Question 45

Why do highly virulent strains of the influenza virus appear periodically? Give one example.

Question 46

Replication of herpes viruses requires all of the following elements EXCEPT

A) primase.
B) helicase.
C) single-strand DNA binding proteins.
D) ligase.
E) viral DNA polymerase.

Question 47

What regulatory elements of herpes genes do NOT resemble those of eukaryotic genes?

A) Each gene has a promoter with control sequences such as a TATA box.
B) Genes are transcribed individually.
C) Different gene classes have their own specific regulatory elements.
D) tegument
E) Genes are translated individually.

Question 48

The causative agent of chickenpox is

A) herpes simplex virus 1.
B) herpes simplex virus 2.
C) varicella-zoster virus.
D) Epstein-Barr virus.
E) HIV.

Question 49

Which of the following is a mismatched pair?

A) herpes simplex virus 2-genital lesions
B) varicella-zoster virus-chickenpox, shingles
C) papillomavirus-genital warts
D) variola major virus-smallpox
E) None of the examples are mismatched.

Question 50

Pigs function as "mixing bowls" for avian, human, and swine influenza strains. What is the biochemical mechanism for this phenomenon?

Question 51

How does the herpes simplex virus genome reach the interior of an infected cell?

A) The core particle partly uncoats after entering the cytoplasm.
B) The intact viral capsid travels down a scaffold of microtubules to a nuclear pore.
C) The viral particle enters the cell by endocytosis and releases virion contents into the cytoplasm.
D) The capsid remains outside the cell; the nucleic acid is threaded through a receptor in the membrane.
E) DNA is forced into the capsid.

Question 52

Herpes simplex virus 1 capsids receive a primary envelope from ________, whereas secondary enveloping uses ________.

A) Golgi; the plasma membrane
B) the outer nuclear membrane; endoplasmic reticulum
C) vacuoles; lysosomes
D) lysosomes; the plasma membrane
E) endoplasmic reticulum; Golgi

Question 53

After Dr. Esther Lederberg crossed a standard stock of Escherichia coli K-12 with UV-mutagenized cells of the same strain, she observed the formation of plaques, but only among the mutagenized colonies. What was the explanation for this phenomenon?

Question 54

Viruses that specifically infect and lyse tumor cells are called

A) transfer vectors.
B) temperate.
C) lytic.
D) lysogenic.
E) oncolytic.

Question 55

Describe how priming for mRNA synthesis or template synthesis for viral progeny of influenza A virus differs from typical mRNA synthesis mechanisms.

Question 56

Use the figure below to describe the events leading to the fusion between influenza virus A and host membranes. What structures are indicated by the numbers?

Question 57

The segmented genome of influenza virus makes virus assembly problematic. Is there evidence that the assembly mechanism packages the eight unique segments correctly?

Question 58

Describe the replication process of the human immunodeficiency virus (HIV).

Question 59

How is lambda phage being used to fight the problem of antibiotic resistance in bacteria?

Question 60

Which type of virus has been successfully used in the treatment of diseases such as B-cell leukemia and adrenoleukodystrophy?

A) lentivirus
B) adenovirus
C) poliovirus
D) influenza virus
E) T4

Question 61

Endogenous retroviruses (ERVs) express viral components, including reverse transcriptase, as part of the host cell normal functions. What role do ERVs play in mouse B-cell immune response to carbohydrate antigens?

Question 62

What types of infections are caused by herpes viruses? Describe the two possible types of replication processes that occur with the herpes viruses.

Question 63

What is an oncolytic virus? Give an example.

Question 64

Describe the several features of lentivectors. What are their molecular sources?

Question 65

Explain what happens in individuals infected with HIV who are homozygous for functional CCR5, heterozygous for a CCR5 deletion, or homozygous for a CCR5 deletion.

Question 66

What are retroelements and why do they exist within the human genome?

Question 67

Sequences of endogenous retroviruses (HERVs) are remnants of retroviral infections. HERVs have accumulated over millions of years and comprise about 8% of the human genome. Briefly describe the evidence for the expression of HERV-K proteins and virus-like particles in the human embryo. What are the implications of HERV-K products interacting with embryonic factors?

Question 68

Why is it advantageous to use lentivectors to treat diseases that affect nondividing cells?

Question 69

Compare and contrast the advantages and disadvantages of lentiviral vectors with respect to adenoviral vectors.

Question 70

What is the mechanism by which the viriotherapeutic agent T-VEC specifically kills hard-to-treat tumors?