chapter 19: viruses

figure 19.5 the lytic cycle of phage T4, a virulent phage. what are the five steps of this lytic cycle?

1. attachment. 2. entry of phage DNA and degradation of host DNA. 3. synthesis of viral genomes and proteins. 4. assembly. 5. release.

figure 19.5 the lytic cycle of phage T4, a virulent phage. what is the first stage of this lytic cycle?

1. attachment. the T4 phage uses its tail fibres to bind to specific receptor sites on the outer surface of an E. coli cell.

figure 19.7 the replicative cycle of an enveloped RNA virus. what is the first step of this replicative cycle?

1. glycoproteins on the viral envelope bind to specific receptor molecules (not shown) on the host cell, promoting viral entry into the cell.

figure 19.7 the replicative cycle of an enveloped RNA virus. what are the eight steps of this replicative cycle?

1. glycoproteins on the viral envelope bind to specific receptor molecules (not shown) on the host cell, promoting viral entry into the cell. 2. the capsid and viral genome enter the cell. digestion of the capsid by cellular enzymes releases the viral genome. 3. the viral genome (red) functions as a template for synthesis of complementary RNA strands (pink) by a viral RNA polymerase. 4. new copies of viral genome RNA are made using complementary RNA strands as templates. 5. complementary RNA strands also function as mRNA, which is translated into both capsid proteins (in the cytosol) and glycoproteins for the viral envelope (in the ER and Golgi apparatus). 6. vesicles transport envelope glycoproteins to the plasma membrane. 7. a capsid assembles around each viral genome molecule. 8. each new virus buds from the cell, its envelope studded with viral glycoproteins embedded in membrane derived from the host cell.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the first step of this cycle?

1. the envelope glycoproteins enable the virus to bind to specific receptors on certain white blood cells.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what are the ten steps of this replicative cycle?

1. the envelope glycoproteins enable the virus to bind to specific receptors on certain white blood cells. 2. the virus fuses with the cell's plasma membrane. the capsid proteins are removed, releasing the viral proteins and RNA. 3. reverse transcriptase catalyses the synthesis of a DNA strand complementary to the viral RNA. 4. reverse transcriptase catalyses the synthesis of a second DNA strand complementary to the first. 5. the double-stranded DNA is incorporated as a provirus into the cell's DNA. 6. proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral protein. 7. the viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER). 8. vesicles transport the glycoproteins to the cell's plasma membrane. 9. capsids are assembled around viral genomes and reverse transcriptase molecules. 10. new viruses bud off from the host cell.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the tenth step of this cycle?

10. new viruses bud off from the host cell.

figure 19.5 the lytic cycle of phage T4, a virulent phage. what is the second stage of this lytic cycle?

2. entry of phage DNA and degradation of host DNA. the sheath of the tail contracts, injecting the phage DNA into the cell and leaving an empty capsid outside. the cell's DNA is hydrolysed.

figure 19.7 the replicative cycle of an enveloped RNA virus. what is the second step of this replicative cycle?

2. the capsid and viral genome enter the cell. digestion of the capsid by cellular enzymes releases the viral genome.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the second step of this cycle?

2. the virus fuses with the cell's plasma membrane. the capsid proteins are removed, releasing the viral proteins and RNA.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the third step of this cycle?

3. reverse transcriptase catalyses the synthesis of a DNA strand complementary to the viral RNA.

figure 19.5 the lytic cycle of phage T4, a virulent phage. what is the third stage of this lytic cycle?

3. synthesis of viral genomes and proteins. the phage DNA directs production of phage proteins and copies of the phage genome by host and viral enzymes, using components within the cell.

figure 19.7 the replicative cycle of an enveloped RNA virus. what is the third step of this replicative cycle?

3. the viral genome (red) functions as a template for synthesis of complementary RNA strands (pink) by a viral RNA polymerase.

figure 19.5 the lytic cycle of phage T4, a virulent phage. what is the fourth stage of this lytic cycle?

4. assembly. three separate sets of proteins self-assemble to form phage heads, tails, and tail fibres. the phage genome is packaged inside the capsid as the head forms.

figure 19.7 the replicative cycle of an enveloped RNA virus. what is the fourth step of this replicative cycle?

4. new copies of viral genome RNA are made using complementary RNA strands as templates.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the fourth step of this cycle?

4. reverse transcriptase catalyses the synthesis of a second DNA strand complementary to the first.

figure 19.7 the replicative cycle of an enveloped RNA virus. what is the fifth step of this replicative cycle?

5. complementary RNA strands also function as mRNA, which is translated into both capsid proteins (in the cytosol) and glycoproteins for the viral envelope (in the ER and Golgi apparatus).

figure 19.5 the lytic cycle of phage T4, a virulent phage. what is the fifth stage of this lytic cycle?

5. release. the phage directs production of an enzyme that damages the bacterial cell wall, allowing fluid to enter. the cell swells and finally bursts, releasing 100 to 200 phage particles.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the fifth step of this cycle?

5. the double-stranded DNA is incorporated as a provirus into the cell's DNA.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the sixth step of this cycle?

6. proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral protein.

figure 19.7 the replicative cycle of an enveloped RNA virus. what is the sixth step of this replicative cycle?

6. vesicles transport envelope glycoproteins to the plasma membrane.

figure 19.7 the replicative cycle of an enveloped RNA virus. what is the seventh step of this replicative cycle?

7. a capsid assembles around each viral genome molecule.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the seventh step of this cycle?

7. the viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER).

figure 19.7 the replicative cycle of an enveloped RNA virus. what is the eighth step of this replicative cycle?

8. each new virus buds from the cell, its envelope studded with viral glycoproteins embedded in membrane derived from the host cell.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the eighth step of this cycle?

8. vesicles transport the glycoproteins to the cell's plasma membrane.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. what is the ninth step of this cycle?

9. capsids are assembled around viral genomes and reverse transcriptase molecules.

figure 19.2 what causes tobacco mosaic disease? experiment in the late 1800s, Martinus Beijerinck, of the Technical School in Delft, the Netherlands, investigated the properties of the agent that causes tobacco mosaic disease (then called spot disease). results when the filtered sap was rubbed on healthy plants, they became infected. their sap, when extracted and filtered, could then act as the source of infection for another group of plants. each successive group of plants developed the disease to the same extent as earlier groups. conclusion the infectious agent was apparently not a bacterium because it could pass through a bacterium-trapping filter. the pathogen must have been replicating in the plants because its ability to cause disease was undiluted after several transfers from plant to plant. source M. J. Beijerinck, Concerning a contagium vivum fluidum as cause of the spot disease of tobacco leaves, Verhandelingen der Koninkyke akademie Wettenschappen te Amsterdam 65:3-21 (1898). translation published in English as Phytopathological Classics Number 7 (1942), American Phytopathological Society Press, St. Paul, MN. what if? if Beijerinck had observed that the infection of each group was weaker than that of the previous group and that ultimately the sap could no longer cause disease, what might he have concluded?

Beijerinck might have concluded that the agent was a toxin produced by the plant that was able to pass through a filter but that became more and more dilute. in this case, he would have concluded that the infectious agent could not replicate.

table 19.1 classes of animal viruses. what are the six classes of animal viruses?

I. double-stranded DNA (dsDNA) II. single-stranded DNA (ssDNA) III. double-stranded RNA (dsRNA) IV. single-stranded RNA (ssRNA); serves as mRNA V. ssRNA; template for mRNA synthesis VI. ssRNA; template for DNA synthesis

concept check 19.1 compare the structures of tobacco mosaic virus (TMV) and influenza virus (see figure 19.3).

TMV consists of one molecule of RNA surrounded by a helical array of proteins. the influenza virus has eight molecules of RNA, each surrounded by a helical array of proteins, similar to the arrangement of the single RNA molecule in TMV. another difference between the viruses is that the influenza virus has an outer envelope and TMV does not.

epidemic

a general outbreak of a disease.

pandemic

a global epidemic.

vaccine

a harmless variant or derivative of a pathogen that stimulates a host's immune system to mount defences against the pathogen.

viral envelope

a membrane, derived from membranes of the host cell, that cloaks the capsid, which in turn encloses a viral genome.

figure 19.9 influenza in humans. what makes a pandemic different from an epidemic?

a pandemic is an epidemic on a global scale.

prophage (prō'-fāj)

a phage genome that has been inserted into a specific site on a bacterial chromosome.

temperate phage

a phage that is capable of replicating by either a lytic or lysogenic cycle.

virulent phage

a phage that replicates only by a lytic cycle.

viroid (vī'-royd)

a plant pathogen consisting of a molecule of naked, circular RNA a few hundred nucleotides long.

lysogenic cycle (lī'-sō-jen'-ik)

a type of phage replicative cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage, is replicated along with the chromosome, and does not kill the host.

lytic cycle (lit'-ik)

a type of phage replicative cycle resulting in the release of new phages by lysis (and death) of the host cell.

provirus

a viral genome that is permanently inserted into a host genome.

bacteriophage (bak-tēr'-ē-ō-fāj) phage

a virus that infects bacteria.

phage (fāj) bacteriophage

a virus that infects bacteria.

figure 19.3 viral structure. what are the four most common viral structures?

a) helical viruses. b) icosahedral viruses. c) viruses with membranous envelope. d) bacteriophage capsids.

figure 19.3 viral structure. describe the structure of tobacco mosaic virus.

a) tobacco mosaic virus has a helical capsid with the overall shape of a rigid rod.

figure 19.6 the lytic and lysogenic cycles of phage λ, a temperate phage. what are the two different ways in which this lytic cycle can proceed after the λ DNA enters the bacterial cell?

after entering the bacterial cell and circularising, the λ DNA can immediately initiate the production of a large number of progeny phages (lytic cycle) or integrate into the bacterial chromosome (lysogenic cycle).

retrovirus (re'-trō-vī'-rus)

an RNA virus that replicates by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.

restriction enzyme

an endonuclease (type of enzyme) that recognises and cuts DNA molecules foreign to a bacterium (such as phage genomes). the enzyme cuts at specific nucleotide sequences (restriction sites).

reverse transcriptase (tran-skrip'-tās)

an enzyme encoded by certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.

prion

an infectious agent that is a misfolded version of a normal cellular protein. they appear to increase in number by converting correctly folded versions of the protein to more of these agents.

virus

an infectious particle incapable of replicating outside of a cell, consisting of an RNA or DNA genome surrounded by a protein coat (capsid) and, for some viruses, a membranous envelope.

figure 19.7 the replicative cycle of an enveloped RNA virus. name a virus that has infected you and has a replicative cycle matching this one. see table 19.1

any class V virus, including the viruses that cause influenza (flu), measles, and mumps.

test your understanding level 1: knowledge/comprehension draw it redraw figure 19.7 to show the replicative cycle of a virus with a single-stranded genome that can function as mRNA (a class IV virus).

as shown here, the viral genome would be translated into capsid proteins and envelope glycoproteins directly, rather than after a complementary RNA copy was made. a complementary RNA strand would still be made, however, that could be used as a template for many new copies of the viral genome.

figure 19.3 viral structure. describe the structure of adenoviruses.

b) adenoviruses have an icosahedral capsid with a glycoprotein spike at each vertex.

test your understanding level 2: application/analysis RNA viruses require their own supply of certain enzymes because a. host cells rapidly destroy the viruses. b. host cells lack enzymes that can replicate the viral genome. c. these enzymes translate viral mRNA into proteins. d. these enzymes penetrate host cell membranes. e. these enzymes cannot be made in host cells.

b. host cells lack enzymes that can replicate the viral genome. explanation RNA viruses require their own supply of enzymes that can replicate the viral genome as it consists of RNA. the cells of hosts of viruses have the machinery to replicate only DNA, and not RNA. in order to be replicated, viral genes lead to synthesis of proteins necessary for its replication. retroviruses, that have RNA as their genetic material, use reverse transcriptase to transcribe their RNA to DNA in order to integrate it into the host genome. if viruses were unable to replicate their RNA, they would not be able to increase in copy number and thus they could not produce a stable infection.

concept check 19.2 why is HIV called a retrovirus?

because it synthesises DNA from its RNA genome. this is the reverse ("retro") of the usual DNA → RNA information flow.

figure 19.1 are the tiny viruses infecting this E. coli cell alive?

because viruses are capable of causing a wide variety of diseases and can be spread between organisms, researchers in the late 1800s saw a parallel with bacteria and proposed that viruses were the simplest of living forms. however, viruses cannot reproduce or carry out metabolic activities outside of a host cell. most biologists studying viruses today would probably agree that they are not alive but exist in a shady area between life-forms and chemicals. the simple phrase used recently by two researchers describes them aptly enough: viruses lead "a kind of borrowed life."

concept check 19.2 make connections the RNA virus in figure 19.7 has a viral RNA polymerase that functions in step 3 of the virus's replicative cycle. compare this RNA polymerase to the one in figure 17.9 (p. 333) in terms of template and overall function.

both the viral RNA polymerase and the RNA polymerase in figure 17.9 synthesize an RNA molecule complementary to a template strand. however, the RNA polymerase in figure 17.9 uses one of the strands of the DNA double helix as a template, whereas the viral RNA polymerase uses the RNA of the viral genome as a template.

figure 19.3 viral structure. describe the structure of influenza viruses.

c) influenza viruses have an outer envelope studded with glycoprotein spikes. the genome consists of eight different RNA molecules, each wrapped in a helical capsid.

test your understanding level 1: knowledge/comprehension to cause a human pandemic, the H5N1 avian flu virus would have to a. spread to primates such as chimpanzees. b. develop into a virus with a different host range. c. become capable of human-to-human transmission. d. arise independently in chickens in North and South America. e. become much more pathogenic.

c. become capable of human-to-human transmission. explanation H5N1 is a subtype of influenza A virus which causes infection in birds. the infection is highly contagious and it affects the respiratory system of the infected birds. however, there are some reported cases that H5N1 infection was found in humans and majority of these cases were linked in the direct or close contact of the individuals with sick or dead infected poultry. the term pandemic is defined as an epidemic that is occurring globally, crossing international boundaries and usually affecting great number of people. for H5N1 to cause human pandemic, it must first surpass the host-barrier (birds-human) in which transmission will be possible from human to human. hence, the answer is c.

test your understanding level 1: knowledge/comprehension which of the following characteristics, structures, or processes is common to both bacteria and viruses? a. metabolism b. ribosomes c. genetic material composed of nucleic acid d. cell division e. independent existence

c. genetic material composed of nucleic acid explanation bacteria are small unicellular organisms that can be found almost everywhere in the environment. they perform different metabolic processes and functions to maintain their homeostasis. they also have DNA which serves as their genetic material. viruses are microscopic infectious agents that live and reproduce inside of a living host. they infect all types of life forms including humans, animals and plants. they have no ribosomes and other metabolic processes since they are considered acellular. the genetic material of a virus can be either RNA or DNA. in addition, the arrangement of nucleic acid may also be single or double-stranded. hence, the correct answer is C. both bacteria and virus genetic material is composed of nucleic acids.

figure 19.3 viral structure. describe the structure of bacteriophage T4.

d) bacteriophage T4, like other "T-even" phages, has a complex capsid consisting of an icosahedral head and a tail apparatus.

test your understanding level 2: application/analysis a bacterium is infected with an experimentally constructed bacteriophage composed of the T2 phage protein coat and T4 phage DNA. the new phages produced would have a. T2 protein and T4 DNA. b. T2 protein and T2 DNA. c. a mixture of the DNA and proteins of both phages. d. T4 protein and T4 DNA. e. T4 protein and T2 DNA.

d. T4 protein and T4 DNA. explanation tf T2 phage protein coat and T4 phage DNA were introduced to a bacterium, after infection it would produce phages with T4 protein and T4 DNA. the reason for this is the fact that only DNA is the carrier of genetic material and it contains the information necessary for making an entire new phage including its DNA and protein component. T2 protein that was transferred did nothing in terms of contributing to production of new phages as it does not contain coding information.

test your understanding level 1: knowledge/comprehension emerging viruses arise by a. mutation of existing viruses. b. the spread of existing viruses to new host species. c. the spread of existing viruses more widely within their host species. d. all of the above. e. none of the above.

d. all of the above explanation viruses are microscopic infectious agents that live and reproduce inside of a living host. they infect all types of life forms including humans, animals, and plants. the genetic material of a virus can be either RNA or DNA. in addition, the arrangement of nucleic acid may also be single or double-stranded. emerging virus is the term to describe the newly discovered viral agent. this virus can be a result of various factors such as increased exposure of virus in the host which can lead to mutation, increase contact with the different hosts, and expansion of population overtime in which it can spread and maintain itself in a population. hence, the correct answer is D.

concept check 19.3 what if? TMV has been isolated from virtually all commercial tobacco products. why, then, is TMV infection not an additional hazard for smokers?

humans are not within the host range of TMV, so they can't be infected by the virus.

concept check 19.3 contrast horizontal and vertical transmission of viruses in plants.

in horizontal transmission, a plant is infected from an external source of virus, which could enter through a break in the plant's epidermis due to damage by herbivores. in vertical transmission, a plant inherits viruses from its parent either via infected seeds (sexual reproduction) or via an infected cutting (asexual reproduction).

figure 19.10 viral infection in plants. how does the presence of certain viruses in some plants manifest visually?

infection with particular viruses causes irregular brown patches on tomatoes (left), black blotching on squash (centre), and streaking in tulips due to redistribution of pigment granules (right).

concept check 19.2 compare the effect on the host cell of a lytic (virulent) phage and a lysogenic (temperate) phage.

lytic phages can only carry out lysis of the host cell, whereas lysogenic phages may either lyse the host cell or integrate into the host chromosome. in the latter case, the viral DNA (prophage) is simply replicated along with the host chromosome. under certain conditions, a prophage may exit the host chromosome and initiate a lytic cycle.

concept check 19.3 describe two ways a pre-existing virus can become an emerging virus.

mutations can lead to a new strain of a virus that can no longer be effectively fought by the immune system, even if an animal had been exposed to the original strain; a virus can jump from one species to a new host; and a rare virus can spread if a host population becomes less isolated.

figure 19.11 model for how prions propagate. how do prions spread?

prions are misfolded versions of normal brain proteins. when a prion contacts a normally folded version of the same protein, it may induce the normal protein to assume the abnormal shape. the resulting chain reaction may continue until high levels of prion aggregation cause cellular malfunction and eventual degeneration of the brain.

chapter review: concept 19.2 describe enzymes that are not found in most cells but are necessary for the replication of viruses of certain types.

single-stranded RNA viruses require an RNA polymerase that can make RNA using an RNA template. cellular RNA polymerases make RNA using a DNA template. retroviruses require reverse transcriptases to make DNA using an RNA template. once the first DNA strand has been made, the same enzyme can promote synthesis of the second DNA strand.

concept check 19.1 make connections in figure 16.4 (p. 307), you learned how bacteriophages were used to provide evidence that DNA carries genetic information. briefly describe the experiment carried out by Hershey and Chase, including in your description why the researchers chose to use phages.

the T2 phages were an excellent choice for use in the Hershey-Chase experiment because they consist of only DNA surrounded by a protein coat, and DNA and protein were the two candidates for macromolecules that carried genetic information. Hershey and Chase were able to radioactively label each type of molecule alone and follow it during separate infections of E. coli cells with T2. only the DNA entered the bacterial cell during infection, and only labeled DNA showed up in some of the progeny phage. Hershey and Chase concluded that the DNA must carry the genetic information necessary for the phage to reprogram the cell and produce progeny phages.

human immunodeficiency virus HIV

the infectious agent that causes AIDS. it is a retrovirus.

host range

the limited number of species whose cells can be infected by a particular virus.

figure 19.8 the replicative cycle of HIV, the retrovirus that causes AIDS. make connections in figure 7.11 (p. 130), you learned how HIV binds to cells. describe what is known about this binding and how it was discovered.

the main protein on the cell surface that HIV binds to is called CD4. however, HIV also requires a "co-receptor," which in many cases is a protein called CCR5. HIV binds to both of these proteins together and then is taken into the cell. researchers discovered this requirement by studying individuals who seemed to be resistant to HIV infection, despite multiple exposures. these individuals turned out to have mutations in the gene that encodes CCR5 such that the protein apparently cannot act as a co-receptor, and so HIV can't enter and infect cells.

chapter review: concept 19.3 what aspect of an RNA virus makes it more likely than a DNA virus to become an emerging virus?

the mutation rate of RNA viruses is higher than that of DNA viruses because RNA polymerase has no proofreading function, so errors in replication are not corrected. their higher mutation rate means that RNA viruses change faster than DNA viruses, leading to their being able to have an altered host range and to evade immune defences in possible hosts.

capsid

the protein shell that encloses a viral genome. it may be rod-shaped, polyhedral, or more complex in shape.

acquired immunodeficiency syndrome AIDS

the symptoms and signs present during the late stages of HIV infection, defined by a specified reduction in the number of T cells and the appearance of characteristic secondary infections.

concept check 19.2 what if? if you were a researcher trying to combat HIV infection, what molecular processes could you attempt to block? see figure 19.8

there are many steps that could be interfered with: -binding of the virus to the cell -reverse transcriptase function -integration into the host cell chromosome -genome synthesis (in this case, transcription of RNA from the integrated provirus) -assembly of the virus inside the cell -budding of the virus many of these, if not all, are targets of actual medical strategies to block progress of the infection in HIV-infected people.

figure 19.4 a simplified viral replicative cycle. make connections label each of the straight black arrows with one word representing the name of the process that is occurring. review figure 17.26 (p. 348)

top vertical arrow: infection. left upper arrow: replication. right upper arrow: transcription. right middle arrow: translation. lower left and right arrows: self-assembly. bottom middle arrow: exit.

chapter review: concept 19.1 are viruses generally considered living or non-living? explain.

viruses are generally considered non-living, because they are not capable of replicating outside of a host cell. to replicate, they depend completely on host enzymes and resources.