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					5     Viruses and Other Acellular Infectious Agents

Viruses are small, acellular entities that usually possess only a single type of nucleic acid and must use the
metabolic machinery of a living host in order to reproduce. Viruses have been and continue to be of
tremendous importance because many human diseases have a viral etiology. The study of viruses has
contributed greatly to our knowledge of molecular biology, and the blossoming field of genetic engineering is
based on discoveries in the field of virology. This chapter focuses on the general properties of viruses, their
structure, reproduction, infectivity, and cultivation. The discussion concludes with the features of viroids,
virusoids, and prions.

After reading this chapter you should be able to:

•     define viruses and discuss the implications of the concepts embodied in the definition
•     discuss the composition and types of viral capsids
•     discuss the variety found in viral genomes
•     contrast virulent and temperate phage life cycles
•     discuss the various requirements for culturing viruses
•     discuss the nature of viroids, virusoids, and prions

I.    Viruses
      A. Viruses are acellular infectious agents that cannot reproduce outside of living cells; virology is the
           study of viruses
      B. Viruses can infect all types of cells but are specific for certain organisms; bacteriophages (phages)
           infect bacteria
II.   Structure of Viruses
      A. Virion size—ranges from 10 nm to 400 nm
      B. General structural properties
           1. Nucleocapsid—the nucleic acid plus the surrounding capsid (protein coat that surrounds the
                 genome); for some viruses this may be the whole virion; other viruses may possess additional
           2. Three types of capsid symmetry: icosahedral, helical, complex
           3. Viral capsids are constructed from many copies of one or a few types of proteins (protomers),
                 which are assembled together with the viral genome
           4. Enveloped viruses have an outer membranous layer (envelope) surrounding the nucleocapsid;
                 naked (nonenveloped) viruses lack an envelope
      C. Helical capsids—hollow tube with a protein wall shaped as a helix or spiral; may be either rigid or
      D. Icosahedral capsids—regular polyhedron with 20 equilateral triangular faces and 12 vertices;
           appears spherical; constructed of capsomers (ring or knob-shaped units), each usually made of five
           (pentamers or pentons) or six protomers (hexamers or hexons); viral capsids self-assemble
      E. Viruses with capsids of complex symmetry
           1. Poxviruses are large (200 to 400 nm) with an ovoid exterior shape
           2. Some bacteriophages have complex, elaborate shapes composed of heads (icosahedral
                 symmetry) coupled to tails (helical symmetry); the structure of the tail regions is particularly
                 variable; such viruses are said to have binal symmetry

     F.   Viral envelopes and enzymes
          1. Envelopes are membrane structures surrounding some (but not all) viruses
               a. Lipids and carbohydrates are usually derived from the host membranes
               b. Proteins are virus-specific
               c. Many have protruding glycoprotein spikes (peplomers) such as the enzymes
                     neuraminidase and hemagglutinin
          2. Although viruses lack true metabolism, they may carry one or more enzymes, many of which
               are involved in viral nucleic acid replication; in some cases the enzyme is capsid-associated,
               but in most cases the enzyme is located within the capsid
     G. Viral genomes
          1. Viral genome may be either RNA or DNA, single- or double-stranded
          2. DNA viruses
               a. Most use double-stranded DNA (dsDNA) as the genome; the DNA can be linear or
               b. Many have one or more unusual bases (e.g., hydroxymethylcytosine instead of cytosine)
          3. RNA viruses—most have single-stranded RNA (ssRNA) as their genome; many have
               segmented genomes (genomes consisting of more than one molecule); each being unique and
               frequently encoding a single protein
III. Virus Multiplication
     A. Common steps in viral life cycles
          1. Attachment (adsorption) to the host cell
          2. Entry of the nucelocapsid or viral genome into the host cell
          3. Expression of viral genes in host cell (synthesis stage); virus takes control of cell's machinery
               and produces viral proteins and genomes
          4. New virions self-assemble into mature virions
          5. Virions released by budding or cell lysis
     B. Attachment (adsorption)
          1. Virions attach to specific receptors, usually cell surface proteins or glycoproteins that are
               required by the cell for normal cell functioning
          2. receptor distribution often varies over the surface of the host cells and lipid rafts seem to be
               involved in both virion entry and assembly
     C. Entry into the host
          1. Shortly after adsorption, viruses penetrate and enter the host cell; virus uncoating (removal of
               the capsid and release of viral nucleic acid) occurs for some virions during or shortly after
          2. There appear to be three common modes of entry
               a. Fusion of the viral envelope with the host cytoplasmic membrane results in deposition of
                     the nucleocapsid core within the cell
               b. Endocytosis; lysosomal enzymes and low endosomal pH often trigger the uncoating
               c. Some nonenveloped viruses directly inject their genome into the cytoplasm
          3. Once in the cytoplasm the nucleic acid may function while still attached to capsid components
               or may only function after completion of uncoating
     D. Synthesis stage
          1. Viral life cycles are specific for the type of viral genome; dsDNA viruses follow the normal
               flow of genetic information; RNA viruses need to carry enzymes for genome replication not
               found in the host
          2. Expression of early viral genes is devoted to taking over the host cell; proteins synthesized late
               in the infection are usually involved in capsid synthesis and assembly
     E. Assembly
          1. Capsid proteins are synthesized by host cell ribosomes under the direction of viral late genes,
               often as several subassemblies
          2. Empty procapsids are produced and the nucleic acid is inserted within a "packasome" protein

        3. Some viruses assemble in the cytoplasm, while others assemble in the nucleus
     F. Virion release
        1. Nonenveloped viruses are often released when the host cell lyses
        2. Enveloped viruses are usually released by the following mechanism
              a. Virus-encoded proteins are incorporated into the host cell’s plasma membrane (some
                    viruses use the host’s nuclear membrane, endoplasmic reticulum, Golgi apparatus, or
                    other membranes)
              b. The nucleocapsid buds outward, forming the envelope during release; actin cytoskeleton
                    microfilaments can aid virion release
IV. Types of Viral Infections
    A. Infections of bacterial and archaeal cells: lysis and lysogeny
        1. Virulent phages are only capable of the lytic cycle, where multiplication begins once entering
              the host and continues until the host lyses
        2. Temperate phages are capable of lysogeny, a nonlytic relationship with their hosts (virulent
              phages lyse their hosts), in addition to the lytic cycle
              a. In lysogeny, the viral genome (called a prophage) remains in the host (usually integrated
                    into the host chromosome) but does not kill (lyse) the host cell; the cells are said to be
                    lysogenic (or are called lysogens)
              b. It may switch to the lytic cycle at some later time; this process is called induction
        3. Lysogenic conversion is a change that is induced in the host phenotype by the presence of a
              prophage, and that is not directly related to the completion of the viral life cycle; examples
              a. Modification of lipopolysaccharide structure in infected Salmonella
              b. Production of diphtheria toxin only by lysogenized strains of Corynebacterium
        4. Most bacteriophages are temperate; it is thought that being able to lysogenize bacteria is
              advantageous; supporting this is the observation that certain conditions favor the establishment
              of lysogeny
    B. Infection of eukaryotic cells
        1. Cytocidal infections lead to cell death; some viruses persist in the host for many years; in some
              cases degenerative changes occur in cells (cytopathic effects) without causing lysis
    C. Viruses and cancer
        1. Cancer is a disease where there is abnormal cell growth (neoplasia) and spread of the abnormal
              cells throughout the body (metastasis); tumors are growths or lumps of tissue that can be
              benign (nonspreading) or malignant (cancerous)
        2. Carcinogenesis is a group of complex, multistep processes that involve a triggering event and
              the activity of oncogenes; cells revert to less differentiated states (anaplasia)
        3. Viruses have been implicated in a number of human cancers including, Epstein-Barr virus
              (Burkitt's lymphoma), human herpesvirus 8 (Kaposi's sarcoma), Hepatitis B and C (liver
              cancer), human papillomavirus (cervical cancer), human T-cell lymphotropic virus I (T-cell
        4. Viruses may cause cancer by a variety of mechanisms
              a. Viruses may carry one or more cancer-causing genes (oncogenes)
              b. Viruses may produce a regulatory protein that activates cell division
              c. Viruses may insert a promoter or enhancer that causes abnormal expression of a cellular
                    proto-oncogene (a cellular gene that regulates cell growth and reproduction), and thereby
                    deregulating cell growth
              d. Viral proteins can inhibit the activity of tumor suppressor proteins (e.g., Rb and p53) that
                    regulate cell cycling and monitor or repair DNA damage
V. Cultivation and Enumeration of Viruses
    A. Cultivation requires a suitable host since viruses cannot reproduce outside of cells
    B. Bacterial and archaeal viruses are usually cultivated in broth or agar cultures of suitable host cells;
        broth cultures are usually clear, while areas of localized destruction (plaques) form in bacterial
        lawns on agar plates

       C. Embryonated eggs have long been used to culture animal viruses
       D. In tissue (cell) culture monolayers of animal cells host viruses, resulting in plaques and cytopathic
     E. Plant viruses can be cultivated in plant tissue cultures, cultures of separated plant cells, plant
          protoplast cultures, or whole plants; in whole plants they may cause localized necrotic lesions or
          generalized symptoms of infection
     F. Virus assays
          1. Particle counts
                a. Direct counts can be made with an electron or epifluorescence microscope
                b. Indirect counts can be made using methods such as hemagglutination (virus particles can
                       cause red blood cells to clump together or agglutinate)
          2. Measures of infectivity
                a. Plaque assays involve plating dilutions of virus particles on a lawn of host cells; clear
                       zones result from viral damage to the cells; results are expressed as plaque-forming units
                       (PFUs); similar measurements can be made by counting the number of pocks or necrotic
                b. Infectious dose assays are an end-point method for determining the smallest amount of
                       virus needed to cause a measurable effect, usually on 50% of the exposed target units;
                       results are expressed as infectious dose (ID50) or lethal dose (LD50)
VI. Viroids and Virusoids
     A. Viroids are circular ssRNA molecules that lack a capsid and cause a variety of plant diseases; the
          ssRNA molecules do not act as mRNAs (do not encode genes) and appear to be replicated by host
          RNA polymerases
     B. Pathogenicity of viroids may result from RNA silencing, where viroid RNA forms dsRNA by
          pairing with host mRNAs; these dsRNA are destroyed by host cell defenses and, hence, certain host
          genes are not translated, leading to disease
     C. Virusoids are circular ssRNA molecules (satellite RNAs) that encode proteins and need helper
          viruses for infectivity; the hepatitis D virusoid requires the help of the hepatitis B virus
VII. Prions
     A. Prions are proteinaceous infectious particles (PrP) that are not associated with a nucleic acid
     B. Genes that encode PrP have been identified in normal animal tissue
          1. It is hypothesized that abnormal PrP causes prion diseases by inducing a change from the
                normal conformation of the cellular PrP to the abnormal form
          2. This new abnormal PrP then causes other normal cellular PrP molecules to change to the
                abnormal form
     C. Prions cause progressive, degenerative central nervous system disorders, including scrapie (sheep
          and goats), bovine spongiform encephalopathy (mad cow disease), Kuru (related to New Guinea
          tribal ritual cannibalism), Creutzfeldt-Jakob disease (CJD), fatal familial insomnia and Gerstmann-
          Strassler-Scheinker syndrome


Place the letter of each term in the space next to the definition or description that best matches it.

____ 1.     The complete virus particle as it exists extracellularly
____ 2.     The localized areas of cellular destruction and lysis that appear as clear zones on confluent lawns of
            host cell growth
____   3.   Microscopic or macroscopic degenerative changes or abnormalities in infected host cells or tissues
____   4.   The clumping of red blood cells in the presence of a virus suspension
____   5.   The viral nucleic acid plus the surrounding protein coat
____   6.   The protein coat surrounding the viral nucleic acid
____   7.   Viral genetic material that is divided into separate parts, which may be packaged together or
            separately; all parts are needed to establish a productive infection
____ 8.    Glycoproteins on the envelope of a virus that project outward from the surface of the virion
____ 9.    A membranous structure that surrounds the nucleocapsid of some virions
____ 10.   The localized areas of destruction occurring on plants infected by a virus
____ 11.   The term that describes the time immediately after infection during which no infective virions are
____ 12.   The mRNA that is made before viral nucleic acid has been replicated
____ 13.   The mRNA that is made after viral nucleic acid has been replicated
____ 14.   Viruses that can only establish a lytic infection
____ 15.   An infection that kills the cell by causing it to burst open and release virus particles
____ 16.   Viruses that can either establish a lytic infection or lysogeny
____ 17.   An infection that does not kill the host and that maintains the viral genome in a dormant state; this
           dormant genome is replicated when the host genome is replicated
____ 18.   A change in the phenotype of a lysogenized cell that is not directly related to the completion of the
           virus life cycle
____ 19.   The switching of an infected bacterial lysogen to the active production of viral progeny
____ 20.   An infected bacterium carrying a dormant prophage in the lysogenic state
____ 21.   Abnormal cell growth and reproduction
____ 22.   Genes whose expression or abnormal expression leads to the development of cancer
____ 23    Causative agents of plant disease that consist of small, circular RNA molecules but lack protein
____ 24.   Causative agents of progressive degenerative diseases in humans and other animals that consist of
           small proteinaceous particles but apparently lack nucleic acid genomes
____ 25.   Genes expressed early in a viral infection; they are often involved in taking over host cell functions
____ 26.   Circular ssRNA molecules that code proteins but need helper viruses for infectivity

    a.     capsid
    b.     cytopathic effects
    c.     early genes
    d.     early mRNA
    e.     envelope
    f.     hemagglutination
    g.     induction
    h.     late mRNA
    i.     latent period
    j.     lysogen
    k.     lysogenic conversion
    l.     lysogeny
    m.     lytic infection
    n.     necrotic lesions
    o.     neoplasia
    p.     nucleocapsid
    q.     oncogenes
    r.     plaques
    s.     prions
    t.     segmented genome
    u.     spikes or peplomers
    v.     temperate phages
    w.     virion
    x.     viroids
    y.     virulent bacteriophages
    z.     virusoids


1.    A complete virus particle, or ____________, consists of one or more molecules of ____________ or
      ____________ enclosed in a coat of ____________.
2.    Viruses can be cultured by inoculating a layer of cells and then covering the cells with a thin layer of
      agar to limit their spread, so that only adjacent cells are infected by newly produced virions. As a
      result, localized areas of cellular destruction and lysis called __________ are formed. This
      phenomenon is the basis of a method for enumerating viruses called a              __          . In this
      procedure, each                     is assumed to have arisen from the reproduction of one virion.
      Therefore, the number of                  counted at a given dilution can be used to calculate the number of
      infectious virions, or                         .
3.    Virions range in size from about 10 nm to 300–400 nm. The smallest viruses are a little larger than
      ____________, while the largest viruses are about the same size as small ____________ and can be seen
      in the light microscope.
4.    Viruses that are regular polyhedrons with 20 faces are said to have ____________ symmetry, while those
      shaped like hollow cylinders have ____________ symmetry. Some                            viruses exhibit the
      former type of symmetry in the head region and the latter type in the tail. These viruses are said to have
      ____________ symmetry.
5.    Many viruses have an outer membrane layer called an ____________ surrounding the nucleocapsid.
      These viruses often have glycoprotein spikes or ____________ protruding from their outer surface,
      which may be involved in virus attachment to host cells.
6.    Viral capsids are constructed from many copies of one or a few types of protein subunits called
7.    Icosahedral viruses are constructed from ring- or knob-shaped units called ____________ that can either
      be ____________, which are located at the vertices, or ____________, which are located at the edges or
      the triangular faces.
8.    When biological effects are not readily quantified, an end-point dilution is often useful. The normal end
      point used is the dose necessary to affect 50% of the cultures. If the end point measured is host damage,
      that dilution is called the ____________ ____________; if the end point is the death of the culture or
      organism, it is called the ____________ ____________.
9.    Virus-specific mRNA that is synthesized before viral nucleic acid is replicated is called ____________
      mRNA, while that produced after viral replication is called ____________ mRNA.
10.   Phages that are capable only of the lytic infectious cycle are called ____________ phages, while those
      that are capable of both lytic infection and lysogeny, a dormant state, are called ____________ phages.
      The bacteria carrying these dormant phages are called ____________.
11.   A temperate phage may cause a change in the phenotype of the host that is not directly related to the
      completion of its life cycle. This process is called                                   .
12.   The numerous diseases collectively referred to as                      are characterized by abnormal cell
      growth called                 , which results in the formation of a lump of tissue called a               .
      Cells in malignant                  are able to spread throughout the body by a process known as                 .
13.   Some infections have a rapid onset and last for a relatively short time; they are called ____________
      infections. Others are long-lasting infections called                  infections. There are several types of
      these infections. In                virus infections, the virus is detectable and clinical symptoms are mild
      or absent for long periods (e.g., hepatitis B and HIV infections). In                    virus infections, the
      virus stops reproducing and remains dormant before becoming active again (e.g., herpes simplex virus
      infections). A small group of viruses cause extremely slow-developing infections. These infections are
      called             virus diseases (e.g., subacute sclerosing panencephalitis).
14.   Small ssRNA molecules that have no capsid and cause disease in plants are called ____________, while
      small proteinaceous particles that have no apparent nucleic acid and cause progressive degenerative
      diseases in humans and other animals are called ____________.
15.   Most               virions are released upon host cell lysis. In contrast, during                    virus
      reproduction, release and envelope formation occur simultaneously, without lysing the host cell.


For each of the questions below select the one best answer.

1.  Which of the following is NOT true about the word virus?
    a. It is of Latin origin and means poison.
    b. It is currently used to describe small, acellular entities that cause disease.
    c. It was used to describe disease-causing agents long before those agents were characterized.
    d. All of the above are true about the word virus.
 2. In which of the following ways do viruses differ from living microbial cells?
    a. Viruses are acellular.
    b. Viruses have RNA or DNA, but usually not both within the same virion.
    c. Viruses are obligate intracellular parasites that cannot reproduce independently of host cells.
    d. All of the above are ways in which viruses differ from living microbial cells.
 3. What viruses have a single-stranded RNA genome with the same base sequence as the viral mRNA?
    a. plus-strand RNA viruses
    b. minus-strand RNA viruses
    c. complementary-strand RNA viruses
    d. None of the above is correct.
 4. Which of the following is a viral genome that exists as several separate, nonidentical molecules packaged
    together or separately?
    a. diploid genome
    b. segmented genome
    c. polyploid genome
    d. fractionated genome
 5. What is the function of virus-specific enzymes produced before viral nucleic acid replication?
    a. degradation of host DNA
    b. modification of host RNA polymerase to recognize viral promoters
    c. production of any unusual bases required by the virus for DNA replication
    d. All of the above are functions performed by virus-specific enzymes.
 6. Which of the following is NOT a translation product of late mRNA?
    a. phage structural proteins
    b. phage assembly proteins that are not incorporated in the capsid
    c. phage proteins needed to replicate the phage nucleic acid
    d. phage release proteins
 7. Which of the following is NOT commonly used by animal viruses to enter host cells?
    a. capsid remains outside the cell, as the nucleic acid is injected through the plasma membrane
    b. fusion of envelope with plasma membrane
    c. endocytosis
    d. All of the above are ways that animal viruses enter host cells.
 8. Enveloped viruses, except poxviruses, acquire their envelopes in which of the following ways?
    a. during assembly but before release
    b. during release
    c. after release
    d. during penetration
 9. Which of the following diseases is/are thought to be produced by prions rather than viruses?
    a. kuru
    b. scrapie
    c. Creutzfeldt-Jakob disease
    d. All of the above are thought to be produced by prions.
10. Some cancer cells revert to a more primitive or less differentiated state. What is this called?
    a. anaplasia
    b. neoplasia
    c. metastasis
    d. carcinogenesis
11. Epstein-Barr virus (EBV) is one of the best-studied human cancer viruses. What does it cause?
    a. Burkitt’s lymphoma
    b. nasopharyngeal carcinoma
    c. infectious mononucleosis
    d. All of the above are caused by EBV.
12. Which of the following is NOT a way in which viruses cause cancer?
    a. introduction of an oncogene carried by the virus
    b. introduction of a viral promoter or enhancer next to a previously unexpressed gene that controls cell
    c. production of a regulatory protein that activates cellular genes controlling cell division
    d. All of the above are ways in which viruses cause cancer.
13. How do enveloped viruses acquire their envelopes?
    a. by budding through the plasma membrane
    b. by budding through internal cellular membranes
    c. For some viruses (a) is correct; for others viruses (b) is correct.
    d. Neither (a) nor (b) is correct.


____ 1.  In the extracellular phase, viruses possess few if any enzymes, and cannot reproduce independently
         of living cells.
____ 2. Like bacteria and eukaryotic microorganisms, viruses can be cultured on artificial media.
____ 3. Bacteriophages (phages) are viruses that have the typical prokaryotic appearance of bacteria.
____ 4. In viruses with helical symmetry, the nucleic acid is wound in a spiral and lies in the hollow interior
         formed by the protein subunits.
____ 5. All capsids with helical symmetry tend to be rigid.
____ 6. In viral envelopes, the lipids usually come from the host cell, while the proteins are coded for by
         viral genes.
____ 7. For some viruses with segmented RNA genomes, the segments may be packaged into separate
         virion structures.
____ 8. Viruses can be counted directly with a transmission electron microscope.
____ 9. Most DNA viruses have single-stranded DNA as their genome, and most RNA viruses have double-
         stranded RNA as their genome.
____ 10. The single-stranded genome of RNA phages serves both as a template for its own replication and as
____ 11. Prion-mediated pathogenesis may involve conformational change in the prion protein (PrP) to an
         abnormal form.

1.   Viruses are thought by some scientists to be among the most primitive of living organisms. Others
     suggest that they are not living organisms. Take a stand on this debate and defend your position. What
     would be the most likely arguments from those taking the opposing viewpoint? How would you counter
     their arguments?

2.    Consider the sequence shown below. It represents a segment of the mRNA produced by a virus. Suppose
      the virus was a double-stranded DNA virus; what would the corresponding genomic sequence be?
      Suppose the virus was a plus-strand RNA virus; what would the corresponding genomic sequence be?
      Finally, suppose the virus was a negative-strand RNA virus; what would the corresponding genomic
      sequence be?


Terms and Definitions

1. w, 2. r, 3. b, 4. f, 5. p, 6. a, 7. t, 8. u, 9. e, 10. g, 11. i, 12. d, 13. h, 14. y, 15. m, 16. v, 17. l, 18. k,   19. g,
20. j, 21. o, 22. q, 23. x, 24. s, 25. c, 26. z

Fill in the Blank

1. virion; DNA; RNA; protein 2. plaques; plaque assay; plaque; plaques; plaque-forming units (PFUs)
3. ribosomes; bacteria 4. icosahedral; helical; complex; binal 5. envelope; peplomers 6. protomers
7. capsomers; pentamers; hexamers 8. infectious dose (ID50); lethal dose (LD50) 9. early; late 10. virulent;
temperate; lysogens 11. lysogenic conversion 12. cancer; neoplasia; tumor; tumors; metastasis 13. acute;
persistent; chronic; latent; slow 14. viroids; prions 15. naked; enveloped

Multiple Choice

1. d, 2. d, 3. a, 4. b, 5. d, 6. c, 7. a, 8. b, 9. d, 10. a, 11. d, 12. d, 13. c


1. T, 2. F, 3. F, 4. T, 5. F, 6. T, 7. T, 8. T, 9. F, 10. T, 11. T