Genetics of Virus Flashcards
Defn. Viruses
Viruses are obligate parasites as they can reproduce only within a host cell as they lack
organelles and metabolic enzymes necessary for protein synthesis and replication of the
viral genome.
What characteristics of life does the virus exhibit
- virus is a living organism because
- Reproduce within host cells: It takes over the genetic machinery of its host cells to
replicate more viral particles. - Adaptable: Viruses have high mutation rates so as to have genetic variation and have a higher chance of survival in unfavourable environments.
- Metabolism: Viruses direct its host cells to provide the energy needed to produce more viral
particles.
What characteristics of life does the virus not exhibit
- Virus is not a living organism because
- Does not reproduce independently.
- Unable to adapt independently.
- Unable to metabolise on its own.
- Does not grow or increase in size. It merely replicates to produce more viruses in terms of numbers.
- Is not a cell or composed of cells, thus does not carry out metabolism on its own.
- Does not have the ability to carry out homeostasis since it usually contains no more than a genome in a protein coat.
- Does not seem to have the ability to respond to stimuli, since it does not move on its
own.
- Therefore the answer as to whether viruses are living or non-living remains inconclusive.
Structure of virus
- 20-400nm in diameter
- genome
- capsid
- enveloped/ non-enveloped
Definition of life
The consensus is that life is a characteristic of organisms that exhibit all
or most of the following phenomena:
- Organisation – Being structurally composed of one or more cells which are the basic units
of life. - Metabolism – Consumption of energy by converting chemicals into cellular components
(anabolism) and decomposing organic matter (catabolism). Living things require energy to
produce phenomena associated with life. - Growth – A growing organism increases in size of all of its parts, rather than simply accumulating matter. The particular species begins to multiply and expand as the evolution
continues to flourish. - Homeostasis – The ability to regulate and maintain a constant internal environment.
- Adaptation – A population of living organisms has the ability to change over a period of time
in response to the environment, an ability that is fundamental to the process of evolution. - Response to stimuli – A response that can take on many forms from contraction of a
unicellular organism to external chemicals to complex reactions involving senses of higher
animals. A response is often expressed by motion for example the leaves of a plant turning
towards the sun, otherwise known as phototropism. - Reproduction – The ability to produce new organisms.
Structure of virus: genome
- DNA virus
- RNA virus
-> positive-sense RNA
-> negative-sense RNA - Linear vs Circular
- single-stranded vs double-stranded
- may have more than one copy of the genome
- viral genomes range from a few thousand to more than a hundred thousand nucleotides in length
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.
* 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
Envelope
The viral envelope encloses the capsids of many viruses which infect animals.
➢ These viral envelopes comprise of:
o host cell phospholipids from the cell surface membrane of the host cell
o 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.
Defn. lytic cycle (eg T4 phage)
A phage reproductive cycle that culminates the death of the host cell is known
as a lytic cycle. The bacterium lyses and releases the phages that were produced
within the cell.
* Phage T4 / T4 phage is a virulent phage (i.e. a phage that reproduces only by
lytic cycle) with about 300 genes which are transcribed and translated using the
host cell’s machinery.
Lytic cycle (eg T4 phage)
- 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 double-stranded
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.
o One of the first phage genes expressed codes for an enzyme that degrades
the host cell’s DNA. - Viral assembly/ maturation
o Phage components (head, tail and tail fibres) are assembled with the help
of non-capsid proteins to form new phages.
o The phage DNA is packaged inside the capsid as the head is being
formed. - Release
o The phage directs production of an enzyme called lysozyme that
damages the bacterial cell wall, allowing fluid to enter.
o The host cell swells and lyses, releasing 100 to 200 new phages.
Defn. Lysogenic cycle (eg. lambda phage)
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.
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:
o Lambda phage uses its tail fibres bind to specific receptor sites on the
outer surface of an Escherichia coli (host cell).
➢ Entry / Penetration:
o The lambda phage makes use of specific pores in the cell surface of E. coli
to inject its double-stranded DNA into the cell. Within the host cell, DNA
molecule circularizes.
➢ Integration:
o Lambda phage carries a gene that encodes an enzyme called integrase,
which is expressed soon after entry.
o 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.
o 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.
o 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.
enveloped viruses eg influenza
- infectious disease caused by RNA viruses
- Viral genome of type A virus comprise 8 negative-sense, single-stranded, RNA segments
- end of each RNA segment is attached to an RNA-dependent RNA polymerase. these viral RNA-dependent RNA polymerases uses the (-) strand RNA as a template to synthesise the complementary (+) strand RNA
- The influenza A virus sub-types are further classified and labeled according to an H number (for type of haemagglutinin) and an N number (for type of neuraminidase), each with different pathogenic profiles
influenza A virus sub-types glycoprotein
- Haemagglutinin (HA) glycoprotein
➢ For binding of viruses to sialic acid / neuraminic acid-containing receptor sites
on the surface membrane of epithelial cells of respiratory tract.
➢ Facilitates the fusion of the viral envelope and the endosomal membrane (i.e.
involved in viral entry).. - Neuraminidase (NA) glycoprotein
➢ An enzyme that 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 (i.e. involved in viral release).
Reproductive cycle of enveloped viruses (eg. influenza)
- Attachment/adsorption
o Haemagglutinin glycoproteins on viral envelope recognize and bind to
specific receptor molecules containing sialic acid on cell surface membrane
of epithelial cells of the respiratory tract, promoting viral entry into the cell. - Entry
o Virus enters the host cell via endocytosis, forming an endosome.
o Viral envelope fuses with endosome’s membrane, exposing the capsid to
digestion by cellular enzymes.
o This releases the viral RNA molecules, viral proteins and enzymes into the
cytoplasm.
o The viral RNA genome / RNA segments then migrate to the nucleus. - Synthesis of viral components
o 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:
▪ 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.
▪ templates for replication of new copies of viral RNA genome
(negative-sense RNA) within the nucleus. This process is also catalysed
by viral RNA-dependent RNA polymerase. - Viral assembly/mutation
o Capsid proteins enclose the viral genome and viral proteins.
o Capsid then assembles with viral glycoproteins during budding. - Release/budding
o Each new virus buds from the cell, surrounded by the host cell surface
membrane (consisting of the viral glycoproteins), which then forms the
viral envelope.
o Neuraminidase is then able to play the final role in virus budding – cleaving
the sialic acid residues from the host cell surface membrane receptors, thus
releasing the new viral particles from the infected host cells.
o Budding itself does not necessarily kill the host cells (as opposed to lysis
in the lytic cycle of phages), but eventually, the host cell will die due to
depletion of energy and resources.
o The enveloped viruses are now free to infect other epithelial cells.
Structure of HIV
The RNA animal viruses with the most complicated reproductive cycles are the
retroviruses. These viruses are equipped with reverse transcriptase, which serves to
form double-stranded viral DNA from (+) single-stranded RNA viral genome. It is able
to do so as the reverse transcriptase consists of the following activities:
i. forms single-stranded complementary DNA (cDNA) from a (+) single-stranded RNA
template.
ii. removes single-stranded RNA from the viral RNA-DNA hybrid.
iii. uses the single-stranded cDNA as template to form double-stranded viral DNA.
Reverse transcription is prone to errors and the enzyme reverse transcriptase does not
proofread. Hence errors and new mutations are introduced during this process. This is one
reason why HIV is difficult for the immune system to eliminate
(e.g. shape of viral surface proteins (e.g. gp120) is altered, so the antibodies that are made
against the earlier strains of HIV can no longer bind).
The Human Immunodeficiency Virus (HIV) is an example of a retrovirus. It causes
Acquired Immune Deficiency Syndrome (AIDS).
HIV is an enveloped virus that contains two identical molecules of single-stranded
RNA and important enzymes like reverse transcriptase, integrase and protease.
The envelope has embedded glycoproteins (spikes) - gp120 and gp41. Both are involved
in viral entry.
Target cells:
o CD4 T lymphocytes (i.e. white blood cells)
o Macrophages
Reproductive cycle of retroviruses (eg. HIV)
- Attachment / Adsorption:
o gp120 glycoproteins on viral envelope recognize and bind to specific
complementary receptor molecules (CD4) on cell surface membrane of
helper T-cell (a type of white blood cell), promoting viral entry into the cell. - Entry:
o 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:
o Reverse transcriptase catalyses the synthesis of a single DNA strand
complementary to the viral RNA.
o The viral RNA is degraded and reverse transcriptase catalyses the
synthesis of a second DNA strand complementary to the first.
o 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:
o With host cell activation, proviral genes are transcribed into RNA molecules
by the host’s RNA polymerase. These RNA molecules function as:
▪ Viral genomes for the next viral generation
▪ mRNAs, which is translated into both viral and capsid proteins (in the
cytosol) and viral glycoproteins (in the ER and modified in GA).
o Note: HIV mRNA is polycistronic (i.e. one mRNA → many proteins)
o The viral polyproteins are then cleaved by HIV protease to form functional
viral proteins.
o Vesicles embedded with viral glycoproteins (gp120 & gp41) migrate
towards and fuse with the cell surface membrane. As such, the viral
glycoproteins become embedded on the cell surface membrane. - Viral assembly / Maturation:
o Capsid proteins enclose the viral genome and viral proteins.
o Capsid then assembles with viral glycoproteins during budding. - Release / Budding:
o Each new virus buds from the cell, surrounded by the host cell surface
membrane studded with viral glycoproteins.
Antigenic Drift and Shift
- Antigens refer to a substance 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. 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. One or more amino acids are
changed, hence the shape of the glycoproteins (antigens) are slightly modified.
➢ Antigenic drift may result in a new strain of influenza and can cause epidemics. This
makes it different from previous strains, hence it is necessary to reformulate the flu
vaccine every year.
➢ 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 can only occur in viruses with segmented genomes, with genes found on
each distinct segment (e.g. influenza virus). - It is a sudden process.
- It involves a major change to the viral surface glycoproteins, caused by reassortment
of their segmented genome with that of another virus.
Viral Infections and Diseases
The link between a viral infection and the symptoms it produces is often obscure. The extent of
damage a virus causes depends partly on the ability of the infected tissue to regenerate by
cell division
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
- Inhibition of normal DNA, RNA or protein synthesis
- Viral genome may be expressed in the host to produce toxins that disrupts host organism’s homeostatic mechanisms.
- 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.
