Genetics of Viruses

Question 1

(f) Discuss how viruses challenge the cell theory and concepts of what is considered living.

Answer 1

A virus is considered as a living organism as it is able to:

1. Reproduce: It takes over the genetic machinery of its host cells to replicate more viral particles.
2. Adaptable: Viruses have high mutation rates so as to have genetic variation and have a higher chance of survival in unfavourable environments.
3. Metabolism: Viruses direct its host cells to provide the energy needed to produce more viral particles.

It is considered non-living as:

1. Does not reproduce independently.
2. Unable to adapt independently.
3. Unable to metabolise on its own.
4. Does not grow or increase in size. It merely replicates to produce more viruses in terms of numbers.
5. Is not a cell or composed of cells, thus does not carry out metabolism on its own.
6. Does not have the ability to carry out homeostasis since it usually contains no more than a genome in a protein coat.
7. Does not seem to have the ability to respond to stimuli, since it does not move on its own.

Question 2

(e) Describe the structural components of viruses, including enveloped viruses and bacteriophages, and interpret drawings and photographs of them
(d) Describe the structure and organisation of viral genomes (including DNA/RNA, single-/double-stranded, number of nucleotides, packing of DNA, linearity/circularity and presence/absence of introns)

Answer 2

All viruses have a genome and capsid but can be categorized as enveloped or non-enveloped
a) Genome
The genome of a virus varies according to the type of virus:
- A virus is called a DNA virus or an RNA virus,
depending on whether the genome consists of DNA
or RNA respectively.
- For viruses with RNA genome,
–> they may possess either positive-sense RNA
(i.e. identical to viral mRNA and thus can be
immediately translated or)
–> negative-sense RNA (i.e. complementary to
viral mRNA and thus must be converted to
positive-sense RNA by RNA polymerase
before translation).
- The genome is usually organized as a linear or
circular molecule of nucleic acid, depending on the
type of virus.
- In some viruses, the nucleic acid is single-stranded,
whereas in others, it is double-stranded.
- Some kinds of viruses may have more than one copy of the genome.
- Viral genomes also vary considerably in size, ranging
from a few thousand to more than a hundred thousand nucleotides in length. Fewer genes have been related to a less complex viral structure

(b) Capsid
- The capsid is a protein coat enclosing the viral genome.
–> There is a variety of shapes, including helical and
polyhedral.
–> Capsids are built from a large number of protein
subunits called capsomeres.
- Some viruses carry a few viral enzyme molecules within their capsids.
- The most complex capsids are found among viruses that infect bacteria, called bacteriophages / phages.
–> The capsids of phages have elongated icosahedral
heads enclosing their genome.
–> Attached to the head is a tail sheath with fibres that
the phages use to attach to a bacterial cell wall. Generally, capsids serve to protect the viral genome.

(c) Envelope
- The viral envelope encloses the capsids of many viruses which infect animals.
–> These viral envelopes comprise of:
1. Host cell phospholipids from the cell surface membrane of the host cell
2. Embedded with virally encoded spike
glycoproteins
–> The viral envelope protects the virion from enzymes
and other chemicals, giving them an advantage over
capsid-only virions.
- Glycoproteins on viral envelopes help viruses enter host cells by recognizing and binding to receptor molecules on specific host cells.
- Each type of virus can infect only a limited host range.
This host specificity results from the evolution of
recognition systems by the virus, via a “lock-and-
key” fit between glycoproteins on the surface of the
virus and specific receptor molecules on the surface of
host cells.

Question 3

(e) Describe how the genomes of viruses are inherited through outlining the reproductive cycles of:
i. bacteriophages that reproduce via a lytic cycle, including T4 phage

Answer 3

Phage T4 / T4 phage is a virulent phage (i.e. a phage that reproduces only by lytic cycle)

The main steps of lytic cycle are as follows:

• Attachment / Adsorption:
  –> T4 phage uses its tail fibres bind to specific
  receptor sites on the outer surface of an
  Escherichia coli (host cell).
• Entry / Penetration:
  –> The sheath of the tail contracts, injecting the
  phage DNA into the cell and leaving the empty
  capsid outside.
• Synthesis of viral components:
  –> The phage DNA directs synthesis of phage
  proteins and replication of phage DNA by the host
  cell machinery.
  –> One of the first phage genes expressed codes for
  an enzyme that degrades the host cell’s DNA.
  The phage DNA is protected from degradation
  because it contains a modified form of cytosine
  that is not recognized by the enzyme.
• Viral assembly / Maturation:
  –> Phage components (head, tail and tail fibres) are
  assembled with the help of non-capsid proteins to
  form new phages.
  –> The phage DNA is packaged inside the capsid as
  the head is being formed.
• Release:
  –>The phage directs production of an enzyme
  called lysozyme that damages the bacterial cell
  wall, allowing fluid to enter.
  –> The host cell swells
  and lyses, releasing 100 to 200 new phages.

Question 4

(e) Describe how the genomes of viruses are inherited through outlining the reproductive cycles of:
ii. bacteriophages that reproduce via a lytic and lysogenic cycles, including lambda phage

Answer 4

Temperate phages are capable of using two modes of reproduction (both lytic and lysogenic) within a bacterium. Unlike the lytic cycle, the lysogenic cycle allows for replication of the phage genome without destroying the host. Lambda phage is an example of a temperate phage and it is also known as a non-contractile tailed phage.

The main steps of the lysogenic cycle are as follows:

• Attachment / Adsorption:
  –> Lambda phage uses its tail fibres bind to specific
  receptor sites on the outer surface of an
  Escherichia coli (host cell).
• Entry / Penetration:
  –> The lambda phage makes use of specific pores in
  the cell surface of E. coli to inject DNA into the
  cell. Within the host cell, Lambda DNA molecule
  circularizes.
• Integration:
  –> Lambda phage carries a gene that encodes an
  enzyme called integrase, which is expressed soon
  after entry.
  –> Integrase cuts the host’s chromosomal DNA
  and inserts the phage DNA into the host DNA.
  Once integrated, the phage DNA in a bacterium is
  called a prophage.
  –> A prophage gene could code for a protein that
  prevents transcription of most of the other
  prophage genes. Thus, the phage genome is
  remains dormant within the bacterium.
  –> Every time the E. coli cell prepares to divide, it
  replicates the phage DNA along with its own and
  passes the copies on to daughter cells. A single
  infected cell can quickly give rise to a large
  population of bacteria carrying the virus in
  prophage form. This mechanism enables the
  phage to propagate without killing the host cells on
  which they depend.
• Environmental signals, such as high-energy radiation and the presence of certain chemicals can induce the phage to transit from the lysogenic cycle to the lytic cycle.
• The prophage is excised and phage enters lytic cycle, via synthesis of viral components, assembly these viral components and subsequent release of new phages

Question 5

(e) Describe the structural components of enveloped viruses (Influenza)
(e) Describe how the genomes of viruses are inherited through outlining the reproductive cycles of:
iii. enveloped virus, including influenza

Answer 5

The viral genome of Type A viruse comprise 8 negative-sense, single-stranded, RNA segments.

Haemagglutinin glycoprotein:

• -> is responsible for determining strain infection i.e which species an influenza strain can infect and where in the respiratory tract an influenza strain will bind.
• -> Binds to specific receptor molecule (sialic acid) on glycoproteins / glycolipids on cell surface membrane of epithelial cells of respiratory tract.
• -> Facilitates the fusion of the viral envelope and the endosomal membrane.

Neuraminidase glycoprotein:

• -> catalyze the hydrolysis of terminal sialic acid residues from the newly formed viral glycoproteins and from the host-cell membrane glycoproteins.
• -> This facilitate the budding of the virus from the infected host cell and spread the infection to other cells

The main steps of the reproductive cycle of the influenza virus are as follows:

• Attachment / Adsorption:
  –> Haemagglutinin glycoproteins on viral envelope
  recognize and bind to specific receptor
  molecules (sialic acid) on cell surface
  membrane of epithelial cells of the respiratory
  tract, promoting viral entry into the cell.
• Entry:
  –> Virus enters the host cell via endocytosis, forming
  an endosome.
  –> Viral envelope fuses with endosome’s membrane,
  exposing the capsid to digestion by cellular
  enzymes.
  –> This releases the viral RNA molecules, viral
  proteins and enzymes into the cytoplasm.
• Synthesis of viral components:
  –> The viral genome (negative-sense RNA) functions
  as template for synthesis of complementary
  (positive- sense) RNA strands by viral RNA
  dependent RNA polymerase (i.e. a RNA
  polymerase that uses RNA as a template to
  synthesize new complementary RNA strands).
  The complementary RNA functions as:
  1. mRNA, which is translated into capsid proteins (in
  the cytosol) and viral glycoproteins (in the ER and
  modified in GA). Vesicles embedded with viral
  glycoproteins migrate towards and fuse with
  the cell surface membrane. As such, the viral
  glycoproteins become embedded on the cell
  surface membrane.
  2. templates for replication of new copies of viral
  RNA genome (negative-sense RNA).
• Viral assembly / Maturation:
  –> Capsid proteins enclose the viral genome and viral
  proteins.
  –> Capsid then assembles with viral glycoproteins
  during budding.
• Release / Budding:
  –> Each new virus buds from the cell, surrounded
  by the host cell surface membrane studded with
  viral glycoproteins.

Question 6

Describe the structural components of retroviruses (HIV)

(e) describe how the genomes of viruses are inherited through outlining the reproductive cycles of:
iv. Retroviruses, including HIV

Answer 6

HIV is an enveloped virus that contains two identical molecules of single-stranded RNA and important enzymes like reverse transcriptase, integrase and protease.

The main steps of the reproductive cycle of the HIV are as follows:

• Attachment / Adsorption:
  –> gp120 glycoproteins on viral envelope
  recognize and bind to specific receptor
  molecules (CD4) on cell surface membrane of
  helper T-cell (a type of white blood cell), promoting
  viral entry into the cell.
• Entry:
  –> The virus envelope fuses with the cell surface
  membrane. The capsid proteins are degraded by
  host cell’s enzymes, releasing the viral RNA and
  reverse transcriptase into the cytoplasm.
• Integration:
  –> Reverse transcriptase catalyses the synthesis of
  a single DNA strand complementary to the viral
  RNA.
  –> The viral RNA is degraded and reverse
  transcriptase catalyses the synthesis of a second
  DNA strand complementary to the first.
  –> The newly synthesized double-stranded viral DNA
  then enters the cell’s nucleus and integrates, as a
  provirus, into the host cell DNA via the action of
  integrase. The provirus never leaves the host’s
  genome, remaining permanently in the host cell.
• Synthesis of viral components:
  –> With host cell activation, proviral genes are
  transcribed into RNA molecules by the host’s RNA
  polymerase. These RNA molecules function as:
  1. Viral genomes for the next viral generation
  2. mRNAs, which is translated into both viral and
  capsid proteins (in the cytosol) and viral
  glycoproteins (in the ER and modified in GA).
  –> Vesicles embedded with viral glycoproteins migrate
  towards and fuse with the cell surface membrane.
  As such, the viral glycoproteins become
  embedded on the cell surface membrane.
• Viral assembly / Maturation:
  –> Capsid proteins enclose the viral genome and viral
  proteins.
  –> Capsid then assembles with viral glycoproteins
  during budding.
• Release / Budding:
  • -> Each new virus buds from the cell, surrounded by the host cell surface membrane studded with viral glycoproteins.

Question 7

(f) describe how variation in viral genomes arises, including antigenic shift and antigenic drift

Answer 7

Antigenic Drift & Shift

• Antigens refer to the molecules on the surface of viruses that are recognised by the immune system and are capable of triggering an immune response (such as antibody production).
• Antigenic drift refers to the process by which virus
  varies genetically in minor ways from year to year.
  Spontaneous point mutations in viral genes cause
  small differences in the structure of the viral surface
  antigens (viral glycoproteins).
  –> RNA viruses must replicate their genomes
  using viral RNA-dependent RNA polymerases,
  which lack the proofreading ability of DNA
  polymerase. A consequence of this is that RNA
  viruses have a greater rate of mutation than DNA
  viruses. Thus, small point mutations will occur.
  –> For influenza virus, point mutations in the genes
  encoding the two major viral surface glycoproteins,
  hemagglutinin and neuraminidase, happen
  continually over time as the virus replicates.
  –> Antigenic drift may result in a new strain of
  influenza and can cause epidemics.
  –> For HIV, antigenic drift occurs due to error-prone
  reverse transcriptase that produces mutations in
  the genes encoding the two major viral surface
  glycoproteins, gp120 and gp41, as the virus
  replicates.
• Antigenic shift refers to a major change in the
  surface antigens of virus, caused by reassortment
  of their segmented genome with that of another virus.
  –> When more than one strain of influenza virus
  coinfect a single cell in a single host, genetic
  reassortment / recombination occurs whereby
  there is random assembly of different RNA
  segments from different strains, producing a virus
  with novel combinations of RNA segments.
  –> For influenza, both pigs and birds can harbour
  human influenza A viruses, as well as their own
  and maybe those of other species, making them
  perfect conduits for in vivo genetic reassortment
  between human influenza A viruses
  –> Antigenic shift will result in a new subtype of
  influenza and cause global pandemics.

Question 8

Describe how Viral infections can cause Diseases.

Answer 8

There are several mechanisms through which viral infections can cause diseases in animals:

• Change in antigenic surface of host cell surface membrane, resulting in it being recognized as foreign and destroyed by the host’s immune system.
• Inhibition of expression of host cell’s genes
  –> Adenovirus interferes with the transport of mRNAs
  from nucleus to cytoplasm.
  –> Influenza virus cleaves the capped ends from
  cellular mRNA’s causing them to be degraded by
  exonucleases.
  –> Herpes virus also degrades host cell’s mRNA’s.
• Inhibition of normal DNA, RNA or protein synthesis –
  –> Poxvirus codes for a protein that degrades single-
  stranded DNA, disrupting host cell DNA synthesis
  by destroying DNA used as template at replication
  forks.
  –> Herpes virus displaces host chromatin from its
  normal association with nuclear matrix proteins,
  inhibiting replication and transcription.
• Viral genome may be expressed in the host to produce toxins that disrupts host organism’s homeostatic mechanisms.
  –> Rotavirus produces toxins that cause severe
  diarrhoea in the host organism.
• Some viruses are oncogenic, causing normal cells to become malignant, resulting in cancers, e.g. Human papillomavirus and polyomavirus.
• Trigger release of hydrolytic enzymes from host cell’s lysosomes leading to lysis of infected host cells
• Depletion of host cell’s cellular materials e.g. amino acids, nucleotides, that are essential for normal functioning