Introduction, Section 6.1, Section 6.2 (except Viroids and Prions), Section 6.

3 (only Baltimore Virus Classification), Section 6.4 (except Gut

Bacteriophage Community), Section 6.5 (except Plant Virus Replication Cycles)
Read: Introduction, Section 11.2
Study tip: Describe where in the environment would you find viruses: everywhere, carried by molecules such as water
6.1 Explain the difference between a bacteriophage and virus that infects human cells; a prophage, a provirus and an
endogenous virus: prophage is the genetic material of a phage. Endogenous viruses are native genetic material that can be linked to
retroviruses.
6.3 Contrast the differences between the forms of a virus: virion, intracellular replication complex, viral genome integrated in
host DNA: virioids have no capsid, just RNA molecules. They may have catalytic ribozymes. Prions are just messed up proteins which
multiply and aggregate leading to cell death. Viria are capsids with a nucleic acid genome outside of the host cell.
6.4 Define the term "host range" and answer Thought Question 6.2: host range can refer to diverse infectable hosts by similar
viruses.
6.5 Draw and label the parts of symmetrical or tailed virus and an asymmetrical virus by including the following features as
warranted by the structure: genome, capsid, envelope, spike proteins, tegument proteins, tail-baseplate-tail fibers, accessory proteins

6.6 Categorize each group of viruses: +RNA viruses, -RNA viruses and double stranded DNA viruses according to method of
genome replication as shown with the Baltimore classification in Figure 6.19 and Table 6.1

6.7 Using four or less sentences for each step, summarize the steps of bacteriophage lytic replication and a separate step for
lysogenic infection (use Fig. 6.23 for additional help and lambda phage information from Ch. 11)

6.8 Describe the ways a bacterial cell can defend itself against bacteriophage infection
Endonuclease, CRISPR, mutation
6.9 In animal virus infection, detail the role of host receptors that correspond to host range: To commence an infectious life
cycle, bacteriophages need to
contact and attach to the surface of an appropriate host cell.
Contact and attachment is mediated by cell surface recep-
tors, proteins on the host cell surface that are specifi c to the
host species and that bind to a specifi c viral component.
Receptor proteins. The cell surface receptor for a virus
is actually a protein with an important function for the
host cell, but the virus has evolved to take advantage of its
existence. An extensively studied model system of virus-
receptor binding is that of bacteriophage lambda (see
Table 6.1, top row). The phage lambda virion attaches
specifi cally to the maltose porin in the outer membrane
of Escherichia coli (Fig. 6.17). Although the protein is often
called “lambda receptor protein,” it actually evolved in
the host as a way to acquire the sugar maltose to metabo-
lize. Thus, natural selection maintains the maltose porin
in E. coli despite the danger of phage infection.
The precise domain of the maltose porin that binds
to phage lambda was defi ned experimentally by muta-
tions in E. coli that cause amino acid substitution in the
protein. Some of the mutant E. coli strains were resis-
tant to phage lambda infection. The mutations that con-
ferred host resistance mapped to the domain of maltose
porin that binds the phage capsid. / The host receptors play a key role in determining the
host range, the group of host species permitting growth.
Within a host, receptor molecules can also determine the
tropism, or tendency to infect a particular tissue type.

6.10 Contrast the genome entry and uncoating of a non-enveloped virus vs. an enveloped virus. (use Fig. 6.27)
Some animal viruses, such as
poliovirus, attach to the host cell surface and insert
their genome into the host cell, as do bacteriophages.
In animal virology, this process is called “extracellular
uncoating” of the genome. Most animal viruses, how-
ever, enter the host cell as intact virions, then undergo
intracellular uncoating, a process of virion disassem-
bly in which the genome is released for replication and
gene expression

6.11 Contrast the replication of a DNA virus to that of an RNA virus

Animal DNA viruses either
inject their genome or enter the
host cell by endocytosis. The
viral genome requires uncoating for gene expression.
■ RNA viruses use an RNA-dependent RNA poly-
merase to transcribe their messenger RNA.
■ Retroviruses use a reverse transcriptase to copy
their genomic sequence into the chromosome of a
host cell.

11.1 Illustrate the structure and genome of influenza virus

The infl uenza virion, unlike that of polio, has no geo-
metrical capsid (Fig. 11.20A). Its RNA chromosome
segments are loosely contained by a shell of matrix pro-
teins (M1). Matrix proteins enclose the core or capsid,
supplementing its connection to the membrane envelope
(Fig. 11.21A). The envelope derives from the phospho-
lipid membrane of the host cell, which incorporates viral
proteins such as hemagglutinin (HA) and neuraminidase
(NA). These viral envelope proteins peg the membrane
to the enclosed capsid, maintaining its structure. Thus,
mutations in the gene encoding neuraminidase pro-
duce aberrant virions with highly irregular shapes (Fig.
11.20B).

11.2 Discuss why influenza must carry its own RNA polymerase into its host cell
. Genome of infl uenza
A includes eight RNA segments, each
encoding one protein. Each (–) strand
segment must be transcribed to a (+)
strand mRNA with a host-derived 5′
cap and viral RNA polymerase, and
3′ poly-A tail. Two of the segments (7
and 8) undergo additional processing
to express two additional proteins (M2
and NS2). The matrix shell contains the eight RNA segments,
which are noncoding (–) strands (Fig. 11.21B). The
RNA segments are coated with nucleocapsid proteins
(NP). The term “nucleocapsid” refers generally to pro-
teins coating a viral genome and packaged within or
as part of the viral capsid. Each NP-coated RNA seg-
ment also possesses a bound RNA-dependent RNA
polymerase complex

11.3 Outline how a segmented genome gives rise to reassortment and highly virulent strains of influenza: Highly virulent
strains of infl uenza usually result
from reassortment between distantly related strains. The
reassortment process is enhanced by a particular fea-
ture of their molecular biology, namely, the segmented
genome. A segmented genome of a virus consists of
multiple separate nucleic acids, like the multiple chromo-
somes of a eukaryotic cell. The infl uenza genome consists
of eight separate linear (–) strands of RNA, which can
combine from different strains to generate a novel hybrid
strain.
11.4 Compare replication of a +RNA genome to a –RNA genome in a virus
The prepackaged
RNA-dependent RNA polymerase uses each (–) strand
RNA segment to synthesize mRNA (Fig. 11.25, step 4).
The mRNA synthesis is primed by a 5-methylguanine-
“capped” RNA fragment (labeled C). The infl uenza poly-
merase had obtained the cap fragments from the previous
host by cleaving them from host nuclear pre-mRNA,
a process quaintly known as “cap snatching.” The (+)
strand mRNA molecules return to the cytoplasm (step
5) for translation to all types of viral proteins. Segments
encoding envelope proteins attach to the ER for ultimate
transport to the host cell membrane (step 6). The nucleo-
capsid RNA- packaging protein (NP), as well as newly
synthesized RNA- dependent RNA polymerase compo-
nents, subsequently return to the nucleus (step 7). Other
genome-packaging proteins (M1 and N2) also return to
the nucleus.
Synthesis of (+) strand and (–) strand genomic RNA.
Back in the nucleus, the original (–) strand RNA seg-
ments now serve as templates for RNA synthesis primed
not by cap snatching, but instead by one of the subunits
of nucleocapsid protein NP (step 8). The NP-primed (+)
strand RNA then becomes coated with the newly made
NP subunits imported from the cytoplasm. The NP-
coated (+) strand serves as template to synthesize (–)
strand RNA (step 9), which also becomes coated with NP
(step 10).
The NP-coated (–) RNA associates with a newly
made polymerase for a future cycle of viral replication.
The RNA is then complexed with matrix protein (M1)
and nuclear packaging protein (N2), proteins that were
imported from the cytoplasm earlier. At last, the fully
packaged (–) RNA segments exit the nucleus to the cyto-
plasm (step 11), where they approach the cell membrane
for packaging into progeny virions (step 12).

11.5 Describe the process of attachment and entry by influenza

Attachment and Entry to the Host Cell
An infl uenza virion attaches to a cell when its hemagglu-
tinin envelope protein binds to a host cell receptor pro-
tein that contains polysaccharide terminating with sialic
acid. The precise structure of the host receptor binding
the hemagglutinin may determine whether a strain such
as avian infl uenza H5N1 will spread directly between
humans. For example, the sialic acid connection in the
receptor polysaccharide can involve different OH groups
of the sugar galactose: a linkage to the OH-3 (α2,3) or to
the OH-6 (α2,6) (Fig. 11.23). The infl uenza strain H5N1
recognizes mainly the α2,3-linked protein, found in birds.
In humans, the upper respiratory tract contains mainly
α2,6-linked receptors; α2,3-linked receptors are found
only deeper within the lungs. Thus, avian infl uenza strain
H5N1 is rarely transmitted between humans. However,
more rapid transmission could arise from a mutation in
the avian hemagglutinin that binds the receptor, leading
to an infl uenza pandemic.
The hemagglutinin complex consists of a trimer of
subunits, each of which has an N-terminal fusion pep-
tide. A fusion peptide is a portion of an envelope pro-
tein that changes conformation so as to facilitate envelope
fusion with the host cell membrane.
Before membrane contact, the fusion peptides are
buried within the core of the hemagglutinin (HA) trimer
(Fig. 11.24 ). The HA C-terminal domains each bind a
sialic acid receptor in the host membrane. When the virion
is taken up by endocytosis, the endocytic vesicle fuses
with a lysosome and its interior acidifi es. The lowered pH
induces a conformational change shifting the C-terminal
ends back and the N-terminal fusion peptides outward to
face the vesicle membrane. The peptides extend into the
membrane, where they mediate fusion between viral and
host membranes. The fusion process expels the contents
of the virion into the host cytoplasm, where the RNA seg-
ments become uncoated. Unlike poliovirus, which injects
only its chromosome with an attached peptide, infl uenza
virus releases several enzymes and structural proteins
along with its genetic material.

11.6 Outline the replication of influenza virus (review from Fig. 11.18)
Replicative Cycle of Infl uenza A
The replication of infl uenza virus is more complex than
that of poliovirus because the viral components travel
in and out of the nucleus. In addition, envelope proteins
require transport through the ER and Golgi to the cell
membrane (Fig. 11.25 ). By contrast, for poliovirus no
envelope is assembled.

Infl uenza virus causes periodic pandemics of respi-

ratory disease. New virulent strains arise through
recombination of human and avian strains.
■ The infl uenza virus consists of segmented (–)
strand RNA. Each segment is packaged with nucleo-
capsid proteins. Segments from different strains
recombine through coinfection.
■ Capsid and matrix proteins enclose the RNA seg-
ments of the infl uenza virus. The matrix is enclosed
by an envelope containing spike proteins.
■ Spike proteins mediate virion attachment. The
spike proteins include a fusion peptide that under-
goes conformational change to cause fusion between
viral envelope and host cell membrane. For infl uenza,
the virion is internalized by endocytosis.
■ Lysosome fusion with endosomes triggers viral
envelope fusion with the endosome membrane. The
viral genome and proteins are then released into
the cytoplasm. Viral (–) strand RNA segments are
uncoated and enter the nucleus.
■ Infl uenza mRNA synthesis is primed by capped
RNA fragments, cleaved from host mRNA. The viral
mRNAs return to the cytoplasm for translation.
■ Genomic RNA synthesis is primed by the nucleo-
capsid protein (NP). First, (+) strand RNA is syn-
thesized as a template for (–) RNA strands, which are
then packaged in newly made nucleocapsid protein
and exported to the cytoplasm.
■ Envelope proteins of infl uenza virus are synthesized
at the ER for transport to the cell membrane.
■ Infl uenza viral assembly occurs at the cell mem-
brane, where capsid, matrix, and (–) strand RNA
components are packaged into envelope.