Chapter 19: Viruses
Overview: A Borrowed Life
 virus- infectious particle consisted of genes packaged in a protein coat
 In the 1800s, researchers thought viruses were the simplest living form because they’re
capable of causing a wide variety of diseases & can be spread between organisms
 Viruses aren’t living because they can’t reproduce or carry out metabolic activities outside a
host cell.
 Molecular biology was born in the lab of biologists studying viruses that infect bacteria.
 Viruses were valuable experimental systems. Experiments with viruses provided important
evidence that genes are made of nucleic acid, working out the molecular mechanisms of the
processes of DNA replication, transcription, & translation.
 The study of viruses has led to the development of techniques that allow scientists to
manipulate genes & transfer them from one organism to another, which are important in
applications.
19.1 A virus consists of a nucleic acid surrounded by a
protein coat
The discovery of viruses: Scientific Inquiry
 Tobacco mosaic disease stunts the growth of tobacco
plants & gives their leaves a mottled (mosaic)
coloration
 In 1883, Adolf Mayer discovered that he could
transmit the disease from plant to plant by rubbing
sap extracted from diseased leaves onto healthy
plants. He suggested that the disease was caused by
super small bacteria invisible under microscopic
view.
 Dimitri Ivanowsky tested the hypothesis by passing
sap from infected tobacco leaves through a filter that
removed bacteria. After filtration, the sap still
produced mosaic disease. But he still hypothesized
that bacteria caused the tobacco mosaic disease. He
thought the bacteria were small enough to pass
through the filter, or that it made a toxin that could
do so.
 Martinus Beijerinck carried out an experiment that
showed that the infectious agent in the filtered sap
could replicate. The pathogen replicated only within
the host it infected. It couldn’t replicate on its own, in test tubes.
 Wendell Stanley crystallized the infectious particle, tobacco mosaic virus (TMV).
Structure of Viruses
Viral Genomes
 Viruses’ genomes may consist of double-stranded DNA, single-stranded DNA, doublestranded RNA, or single-stranded RNA, depending on the type of virus
 The genome’s usually organized as a single linear or circular molecule of nuleic acid
 Viruses can contain 4 – 1000 genes
Capsids & Envelopes
 Capsid- protein shell enclosing the viral genome; shape (rod-shaped, polyhedral, more
complex) varies with type; built from large number of protein subunits called capsomeres, but
the number of different kinds of proteins in a capsid is small
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TMV has a rigid, rod-shaped capsid made from 1000(+) molecules of a single type of protein
arranged in a helix; a helical virus (rod-shaped)
Adenovirus- infect respiratory tracts of animals; have 252 identical protein molecules
arranged in a polyhedral capsid with 20 triangular facets (icosahedron); an icosahedral virus
Some viruses have accessory structures that help them infect their hosts
Viral envelope- membranous envelope that surrounds the capsids of viruses found in animals
(ex: influenza); derived from membranes of host cell, contain host cell phospholipids &
membrane proteins; contain proteins & glycoproteins (proteins with carbohydrates covalently
attached) of viral origin.
Bacteriophage (phage)- viruses that infect bacteria
The first phages studied included 7 that infected E. coli, named T1 – T7, in the order they
were found.
o The T-even phages (T2, T4, T6) were very similar in structure. Their capsids have
elongated icosahedral heads enclosing their DNA. Attached to the head is a protein
tail piece with fibers by which the phages attach to a bacterium.
19.2Viruses replicate only in host cells
 Viruses lack metabolic enzymes needed for making proteins
 They are obligate intracellular parasites – they can only replicate within a host cell
 Each particular virus has a host range- the limited number of cells of host species that a virus
can infect
 Viruses identify host cells by a lock & key fit between viral surface proteins & specific
receptor molecules on the outside of cells.
 Different viruses have different host ranges.
o West Nile & equine encephalitis viruses (distinctly different) have a broad range and
can infect mosquitoes, birds, horses, & humans
o Measles virus has a narrow range and can only affect humans.
 Viral infection of multicellular eukaryotes is limited to particular tissues
o Human cold viruses infect only the cells lining the upper respiratory tract
o AIDS virus binds to receptors present only on certain types of white blood cells
General Features of Viral Replicative Cycles
 A viral infection beings when a virus binds to a
host cell & the viral genome makes its way inside
 The way a genome enters depends on the type of
virus & type of host cell
o T-even phages use their tail apparatus to
inject DNA into a bacterium
o Others are taken up by endocytosis
o Enveloped viruses are taken up by fusion
of the viral envelope with the plasma
membrane
 Once the viral genome’s inside, the proteins it
encodes can hijack the host, reprogramming the
cell to copy the viral nucleic acid & manufacture
viral proteins.
 The host provides the nucleotides for making viral
nucleic acids, enzymes, ribosomes, tRNAs, amino
acids, ATP.
 Many DNA viruses use the DNA polymerases of
their host cell to synthesize new genomes along the
templates provided by the viral DNA
 RNA viruses use virally encoded RNA
polymerases that can use RNA as a template to
replicate their genome
 After the viral nucleic acid molecules &
capsomeres are produced, they self-assemble into
new viruses.
 The simplest type of viral relicative cycle ends with the exit of hundreds of viruses from the
infected host cell, which damages or destroys the cell, which causes many symptoms of viral
infections. The viral progeny that exit a cell can infect additional cells
Replicative Cycles of phages
 Some double-stranded DNA viruses can replicate by 2 alternative mechanisms: the lytic cycle
& the lysogenic cycle
The Lytic Cycle
 Lytic cycle- ends in death of host cell; bacteria lyses (breaks open) & releases the phages that
were produced within the cell; each of the phages can then infect healthy cells
 Virulent phage- replicates only by a lytic cycle
 Successive lytic cycles can destroy an entire bacterial population in just a few hours, but
bacteria aren’t extinct because they have defense mechanisms.
1. Natural selection favors bacterial mutants with receptors that are no longer recognized
by a particular type of phage
 Natural selection also favors phage mutants that can bind to altered receptors
or are resistant to certain restriction enzymes
2. When phage DNA successfully enters a bacterium, the DNA often is identified as
foreign & cut up by cellular enzymes called restriction enzymes, which restricts the
ability of the phage to infect the bacterium
 Bacterial cell’s own DNA is methylated in a way that prevents attack by its
own restriction enzymes
3. Instead of lysing their host cells, many phages coexist with them in lysogeny
The lytic cycle of phage T4, a virulent phage
 T4’s genes are transcribed & translated using the host cell’s machinery. One of the 1st
translated genes after the viral DNA enters codes for an enzyme that degrades the host cell’s
DNA. The phage DNA’s protected from breakdown because it contains a modified form of
cytosine that’s not recognized by the enzyme.
1. Attachment: T4 phage uses its tail fibers to bind to specific receptor sites on the outer surface
of an E. coli cell
2. Entry of phage & degradation of host DNA: cover of tail bonds, injecting the phage DNA into
the cell & leaving an empty capsid outside. The cell’s DNA is hydrolyzed
3. Synthesis of viral genomes & proteins: The phage DNA directs production of phage proteins
& copies of the phage genome by host & viral enzymes, using components within the cell wall
4. Assembly: 3 separate sets of proteins self-assemble to form phage heads, tails, & tail fibers.
The phage genome is packaged inside the capsid as the head forms.
5. Release: the phage directs production of an enzyme that damages the bacterial cell wall,
allowing the fluid to enter. The cell swells & finally bursts, releasing 100s of phage particles.
The lysogenic cycle
 Lysogenic cycle- allows replication of the phage genome without destroying the host
 Temperate phages- phages capable of using both modes of replicating within a bacterium
 Phage  (lambda) is a temperate phage widely used in biological research that resembles T4,
but its tail has only one short tail fiber.
 Infection of E. coli cell by phage 
1. Phage binds to surface of cell & injects its linear DNA genome
2. Within the host, the  DNA molecule forms a circle.
3. This step depends on the replicative mode: lytic cycle or lysogenic cycle
 Lytic cycle- viral genes immediately turn the host cell into a -producing
factory & cell soon lyses & releases viral products
 Lysogenic-  DNA molecule is incorporated into a specific site on the E. coli
chromosome by viral proteins that break the circular DNA molecules & join
them to each other. When integrated into the bacterial chromosome in this
way, the viral DNA’s a prophage. 1 prophage gene codes for a protein that
prevents transcription of most of the other prophage genes. The phage
genome is mostly silent within the bacterium.
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Every time the E. coli cell prepares to divide, it replicates the phage DNA
along with its own & passes the copies on to daughter cells. A single infected
cell can give rise to a large population of bacteria carrying the virus in
prophage form, which enables viruses to propagate without killing the host
cells on which they depend
Lysogenic implies that prophages are capable of generating active phages that lyse their cells.
This occurs when the  genome is induced to exit the bacterial chromosome & initiate a lytic
cycle.
An environmental signal (ex: certain chemical or high-energy radiation) triggers the
switchover from lysogenic to lytic
Some prophage genes may be expressed during lysogeny. Expression of these genes may alter
the host’s phenotype, which has important medical significance
o 3 sepcies of bacteria that cause diphtheria, botulism, & scarlet fever wouldn’t be so
harmful to humans without certain prophage genes that cause the host bacteria to
make toxins
Replicative Cycles of Animal Viruses
 The nature of the genome (number of strands, type of nucleic acid) is the basis for the
classification of viruses.
 Single-stranded RNA viruses are classified into 3 classes (IV – VI) according to how the RNA
genome functions in a host cell
 Many animal viruses have both an envelope and RNA genome. Nearly all animal viruses with
RNA genomes have an envelope.
Viral Envelopes
 An animal virus with an envelope (outer membrane) uses it to enter the host cell. Protruding
from the outer surface of the envelope are viral glycoproteins that bind to specific receptor
molecules on the surface of the host cell.
 Ribosomes bound to the ER of the host cell make the protein parts of the envelope
glycoproteins; cellular enzymes in the ER & Golgi apparatus then add the sugars. The
resulting viral glycoproteins, embedded in the host cell membrane, are transported to the cell
surface.
 Like exocytosis, new viral capsids are wrapped in a membrane as they bud from the cell.
 The viral envelope is derived from the host cell’s plasma membrane. The enveloped viruses
are now free to infect other cells. This replicative cycle doesn’t necessarily kill the host cell.
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Some viruses have envelopes that aren’t derived from plasma membrane
1. Herpeviruses are temporarily cloaked in membrane derived from the nuclear envelope
of the host. They then shed this membrane in the cytoplasm & acquire a new envelope
made from the membrane of the Golgi apparatus. They have a double-stranded DNA
genome & replicate within the host cell nucleus, using a combo of viral & cellular
enzymes to replicate & transcribe their DNA. Copies of the viral DNA can remain
behind as mini-chromosomes in the nuclei of certain nerve cells, where they remain
latent until some physical or emotional stress triggers a new round of active virus
production.
The replicative cycle of an enveloped RNA virus
 A virus with asingle-stranded RNA genome functions as a template for synthesis of mRNA.
The formation of new envelopes for progeny viruses occurs like this:
1. Glycoproteins on the viral envelope bind to specific receptor molecules on the host
cell, promoting viral entry into the cell
2. The capsid & viral genome enter the cell. Digestion of the capsid by cellular enzymes
releases the viral genome
3. The viral genome functions as a template for synthesis of complementary RNA
strands 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 protein (in the cytosol) & glycoproteins for the viral envelope (in ER & Golgi
apparatus)
6. Vesicles transport envelope to plasma membrane
7. 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 host cell
New virus
RNA as viral genetic material
 Genome of class IV single-stranded RNA genomes in animal viruses can directly serve as
mRNA & can be translated into viral protein immediately after infection
 Class V- RNA genome serves as a template for RNA synthesis. RNA genome’s transcribed
into complementary RNA strands, which function both as mRNA & as templates for the
synthesis of additional copies of genomic RNA. All viruses that require RNA  RNA
synthesis to make mRNA use a viral enzyme capable of carrying out this process. The viral
enzyme’s packaged with the genome inside the viral capsid.
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Retroviruses (class VI)- RNA animal viruses with the most complicated replicative cycles;
equipped with reverse transcriptase (transcribes RNA template into DNA, providing RNA
 DNA info flow)
o HIV (human immunodeficiency virus) causes AIDS (acquired immunodeficiency
syndrome)
 They’re enveloped viruses that contain 2 identical molecules of single-stranded RNA & 2
molecules of reverse transcriptase
 After HIV enters a host cell, its reverse transcriptase molecules are released into the
cytoplasm, where they catalyze synthesis of viral DNA.
 The newly made viral DNA then enters the cell’s nucleus & integrates into the DNA of a
chromosome
 Provirus, integrated viral DNA, never leaves the host’s genome, remaining a permanent
resident of the cell
 The host’s RNA polymerase transcribes the proviral DNA into RNA molecules, which can
function both as mRNA for the synthesis of viral proteins & as genomes for the new viruses
that’ll be assembled & released from the cell
The replicative cycle of HIV
1. The envelope of glycoproteins enable the virus to bind to specific receptors on certain WBCs
2. The virus fuses with the cell’s plasma membrane. The capsid proteins are removed, releasing
viral proteins & RNA
3. Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral
RNA
4. Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the 1st
5. The double-stranded DNA’s 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
generations & as mRNAs for translation into viral protein
7. The viral proteins include capsid proteins & reverse transcriptase (made in cytosol) &
envelope glycoproteins (made in ER)
8. Vesicles transport the glycoproteins to the cell’s plasma membrane
9. Capsids are assembled around viral genomes & reverse transcriptase molecules
10. New viruses bud off from the host cell
Evolution of viruses
 Viruses aren’t descendents of precellular forms of life, rather they’ve evolved after the first
cells appeared
 Most favored hypothesis of virus origin: viruses originated from naked bits of cellular nucleic
acids that moved from one cell to another via injured cell surfaces.
 The evolution of genes coding for capsid proteins have facilitated the infection of
uninjured cells.
 Candidates from the original sources of viral genomes (all are mobile genetic elements)
1. Plasmids- small, circular DNA molecules found in bacterial & unicellular eukaryotes
called yeasts. They exist apart from the cell’s genome, can replicate independently of
the genome, & are occasionally transferred between cells
2. Transposons- DNA segments that can move from one location to another within a
cells genome
 Viral genome can have more in common with the genome of its host than with the genomes of
viruses that infect other hosts.
 Some viral genes are identical to the hosts’
 Genetic sequences of some viruses are similar to seemingly distinct viruses. This
genetic similarity reflects the persistence of groups of viral genes that were favored by
natural selection during the early evolution of viruses & the eukaryotic cells that
served as their hosts.
 Debate about origin has been revived by reports of mimivirus, the largest virus discovered.
Virus most likely evolved before the first cells & then developed an exploitative relationship
with them.
 It is a double-stranded DNA virus with an icosahedral capsid 400 nm in diameter. Some of its
genes code for proteins involved in translation, DNA repair, protein folding, & polysaccharide
synthesis.
Virus Diseases in Animals
 Viruses may damage or kill cells by causing the different release of hydrolytic enzymes from
lysosomes
 Some viruses cause infected cells to produce toxins & lead to disease symptoms
 Some have molecular components that are toxic
 The degree of damage partly relies on the ability of the infected tissue to regenerate by cell
division.
o People recover from cols because the epithelium of the respiratory
 Many of the temporary symptoms associated with viral infections (ex: fever, aches) result
from the body’s efforts at defending itself against infection.