Viruses may be living organisms because:

a) they can 'reproduce' (replicate) in their intracellular state

Viruses are nonliving organisms because they:

a) lack cellular organelles though they have a protein capsid enclosing a nucleic acid core &
sometimes a viral envelope (Cell theory: all living organisms are composed of cells)

b) are unable to carry out metabolism, do not require nutrition and neither grow or excrete etc

Viruses are obligate parasites because:

a) requires host cell to complete its reproductive cycle

b) they lack cellular structures such as :

- enzymes for most metabolic processes
- protein synthesizing machinery ( ribosomes, RNA polymerases)
- energy in the form of ATP to drive replication, transcription, translation and cellular metabolism
- building blocks such as DNA/RNA and amino acids
and hence, have to hijack host cell metabolic machinery f or its replication, transcription and
translation.

Basic structure of a virus:

a) Viral genome- 1. contains either RNA o r DNA
2. can be circular or linear
3. can be double-stranded (ds) or single-stranded (ss)

b) Capsid- 1. a protein coat which encloses the viral genome

2. comprises capsomeres
3. various shapes (icosahedral, helical, spherical)

c) Envelope- 1) derived from the host CSM when the virus b uds off
2) contains viral glycoproteins which help the virus attach itself to the host cell
3) protects the viral genome from the effects of various genomes & chemicals

d) Other proteins such as reverse transcriptase (for animal viruses)

e) tail pins and tail fibres (for bacteriophages)

Comparing and contrasting between structures of bacteriophages and animal viruses:

1. Presence/absence of a viral envelope
2. presence/absence of glycoproteins
3. presence/absence of tail pins/tail fibres
4. ssRNA genome vs dsDNA genome
 Viral Infection:

Temperate phages: bacteriophages which are capable of a lysogenic life cycle

Lytic phages: bacteriophages which undergoes the lytic life cycle

Lytic- reproductive cycle that involves the l ysis of the host cell

Lysogenic- reproductive cycle that involves the i ntegration of the viral genome into the host
genome. The viral genome is replicated as host genome is replicated.

Comparison Lytic (T4) Lysogenic (Lambda)

Purpose ass reproduction of

For m For integration into host
viruses genome and to remain
dormant until appropriate
environmental stimulus
triggers mass reproduction

Gene Expression Genes coding for structural Genes coding for a

components such as capsid
and enzymes such as
lysozymes are synthesized for
the assembly of new viruses
repressor protein and an
integrase are expressed to
allow for the phage genome
to be integrated into host
genome.

Reproduction of virus Newly assembled phages No new viruses are formed.

formed are ready and will be Instead, viral DNA replicates
released from the host cell as part of the host genome.

Replication of viral genome Replication of phage DNA Viral DNA replicates as part
sing the host cell
occurs u of the host genome each
DNA polymerase. time the host cell divides.

Fate of host ies upon the

Host cell d Host cell survives and all the
release of new phages daughter cells will contain
the viral genome as part of
their genomes

Viral reproductive cycle consists of mainly: adsorption, penetration, replication, maturation

and release.
T4 reproductive cycle:
Adsorption: Tail fibres of T4 phage recognises and binds to specific receptor sites on the host
bacterium surface. The base plate comes into contact with the surface of the host bacterium
cell.
Penetration: The base plate and tail sheath then undergoes conformational change. The tail
sheath contracts to drive the tail tube through a hole in the bacterial cell wall (degraded by
lysozyme). The phage DNA is injected into the cytoplasm while the empty capsid is left outside
the cell.

Replication: The phage DNA directs the synthesis of phage proteins such as lysozymes, tail
and capsid proteins using the host cell RNA polymerases (for transcription) and ribosomes (for
translation). Lysozymes produced is used to degrade the host cell DNA and halt the host
macromolecular synthesis and replication processes. Viral DNA is replicated using the host cell
replication machinery such as nucleic acids.

Maturation: The capsid proteins spontaneously self-assemble around the phage DNA to form
new phages.

Release: The phage-encoded lysozyme is released in the host cell, causing osmotic lysis of the
host cell and the release of new phages.

Lambda reproductive cycle:

Adsorption: Tail fibres of T4 phage recognises and binds to specific receptor sites on the host
bacterium surface. The base plate comes into contact with the surface of the host bacterial cell.

Penetration: The base plate and tail sheath undergoes a conformational change. The phage
DNA is injected into the cytoplasm while the empty capsid is left outside the cell.

Integration: The phage DNA circularises and is integrated into a specific site of the bacterial
chromosome via integrase to become a non-infectious prophage.

Prophage replication: 1 prophage gene codes for repressor protein that prevents transcription
of most of the other prophage genes. Thus, the phage genome is mostly silent within the
bacterium. Each time the host cell divides, phage DNA replicates as part of the host bacterial
DNA, and every daughter bacterium now contains a prophage.

Activation: An environmental signal can trigger the destruction of repressor proteins. Repressor
proteins are no longer made and phage genome is excised from bacterial DNA in a few
bacteria.

Replication: Phage genes are activated. Phage components are made using the host
bacteriums machinery like DNA polymerase for replication of phage DNA, and RNA
polymerases and ribosomes for synthesis of new phage proteins.
Maturation: New phages are self-assembled spontaneously, with capsid proteins surrounding
phage genomes.

Release: A phage-encoded enzyme breaks down the bacterial cell wall, causing osmotic lysis
and release of intact lambda bacteriophages.

Note: Glycoproteins are translated in RER while capsid proteins and other viral enzymes (HIV
protease) are translated by free ribosomes.
Influenza reproductive cycle:
Adsorption: Haemagglutinin (HA) on viral envelope binds to sialic acid receptors on the host
cell membrane.
Penetration: After binding, host cell surface membrane invaginates and places the virus in an
endosome. The lowered pH in the endosome triggers a conformational change of the HA,
causing fusion of endosomal membrane and viral envelope, releasing the nucleocapsid into the
cytoplasm. The cellular enzymes remove the capsid, virus then dispatches its genetic material
and internal proteins into nucleus.

Replication: Viral genome acts as a template for synthesizing complementary RNA strands via
RNA-dependent RNA polymerases. Complementary RNA strands then served as templates for
making new RNA genome OR mRNA for producing viral proteins such as capsid proteins and
glycoproteins using host cells ribosomes.

Maturation: Glycoprotein HA and enzyme NA transported via vesicles to host cell surface
membrane. Capsid proteins transported back into the nucleus for self-assembly with viral
genome. Mature viruses then transported to the host cell surface membrane where HA and NA
had been incorporated into.

Release: Mature viruses bud off from the host cell covered with an envelope derived from the
host cell surface membrane which has viral HA and NA inserted. Sialic acid receptors are
cleaved off the surface of the new viral particles through viral NA, and this facilitates the release
of viral particles from the host cell.

HIV reproductive cycle:

Adsorption: GP120 on the viral envelope binds to CD4 receptors and co-receptors CCR5 on
the host cell membrane.

Penetration: Binding of GP120 to the host receptors triggers conformational change in GP41,
causing viral envelope to fuse with host cell surface membrane, and the virus releases its
nucleocapsid into the cytosol. The capsid is degraded, releasing enzymes such as integrase
and reverse transcriptase as well as RNA into cytoplasm.

Reverse Transcription: Reverse transcription of RNA genome into a single-stranded DNA via
Reverse transcriptase. A second complementary DNA is then synthesized by Reverse
transcriptase to form a linear double-stranded DNA copy of the original genome.

Integration: Viral DNA is integrated into the host DNA through reactions catalysed by integrase,
forming provirus (remains latent for years and undergoes retroviral replication)

Provirus activation: due to extracellular stimuli, theres an activation of provirus which forces
the cell to produce more virions.

Replication: Proviral genes (DNA) is transcribed to produce copies of RNA. Transcribed RNA
serves as new viral genomes OR mRNA to be translated into viral proteins and enzymes by
host ribosomes. gag mRNA and pol mRNA are translated into polyproteins that are then
cleaved by HIV protease to form capsid proteins and enzymes such as Reverse Transcriptase,
Integrase and HIV Protease, respectively. env mRNA is translated into GP160 which is then
cleaved into gp120 and gp41 by protease.

Maturation: gp120 and gp41 is then transported by golgi vesicles to be incorporated into the
host cell surface membrane. Capsid proteins formed around viral RNA and enzymes for
self-assembly. Nucleocapsid then transported to sites at the host cell surface membrane where
gp120 and gp41 have been incorporated into.

Release: Mature viruses bud off covered with an envelope derived from the host cell surface
membrane incorporated with glycoproteins.

Question: Explain the new combination of RNA segments in H7N9.

Antigenic shift occurs when 2 or more influenza strains infect the same intermediate host cell
simultaneously.
The cell replicates the viral genome of the 2 strains at the same time, random assembly of RNA
segments from the 3 different influenza viruses- reassortment of NA and HA genes occur
leading to new combination of RNA segments in influenza virus when it exits by budding.

Question: the need for frequent new flu vaccines.

Influenza viruses undergo antigenic drift frequently due to the high mutation rate during its
genome replication.
Lack of proofreading activity of RNA-dependent RNA polymerase as well as its fast replication
involving 2 rounds of complementary RNA strands formed accounts for its high mutation rate.
This leads to change in conformation of HA and NA on its viral envelope. Antibodies induced by
earlier strains of influenza viruses can no longer bind to the HA since HA is no longer
complementary in shape to the antibodies.
Hence, new vaccines must be developed frequently.

The viral RNA contains PB2, PB1 and PA which codes for viral RNA polymerase. Explain
why such RNA segments are needed by the virus.
Viral RNA polymerases required by the viruses would not be present in the host cell.
Viral RNA polymerases are able to recognise viral RNA and synthesize complementary RNA
strands which serve as template for replication of new viral RNA as well as mRNA for making
viral proteins.

Explain why HIV protease inhibitors work in treating HIV infection.

HIV proteases cleave HIV polyprotein into several functional proteins such as Reverse
Transcriptase, HIV protease and Integrase, required for the formation of mature HIV virions.
HIV protease inhibitor is a competitive inhibitor which is complementary to and binds to the
active site of the HIV protease, preventing HIV protease from functioning properly so that there
is no maturation of HIV virions.
This prevents other cells from being infected with HIV and the spread of HIV among human
cells.

Researchers have recently discovered that the entry of MERS-CoV into its host cells is
similar to how Human Immunodeficiency Virus (HIV) enters its host cells.
Suggest how MERS-CoV genome enters its host cell.
Spike proteins on viral envelope binds to specific receptors on host cell surface membrane.
Upon binding, conformational changes occur to the spike proteins that promotes the fusion of
the viral envelope and the host cell surface membrane, resulting in the release of MERS-CoV
genome into the cytoplasm of the host cell.

Researchers predict that MERS-CoV is infectious because as it mutates, it is able to bind

to different host cell proteins, leading to viral entry.
Suggest why coronaviruses mutate faster than DNA viruses.
RNA viruses have higher rates of mutation because the RNA-dependent RNA polymerase/
Reverse transcriptase that synthesizes the RNA genome lacks the proof-reading activity that of
DNA polymerases synthesizing DNA viruses genomes.