14 Viruses (DIY)

• Reasons why all viruses rely on host cells for their reproduction


  1. Absence of translation machinery such as ribosomes and the building blocks amino acids, have to rely on host ribosomes and the building blocks amino acids for production of viral proteins

  2. Absence of transcription machinery such as RNA polymerase and free ribonucleotides, have to rely on host RNA polymerase and free ribonucleotides for formation of mRNA for the purpose of translation

  3. Absence of DNA replication machinery such as DNA polymerase and free deoxyribonucleotides, have to rely on host DNA polymerase and free deoxyribonucleotides to replicate genome
• Role of viral DNA in the infection process of the T4 bacteriophage

  1. Viral DNA codes for/is transcribed and translated to produce enzymes and structural components of phage which are important for infection of bacterial cell

  2. Enzymes hydrolyse the DNA of host cell to nucleotides which can be used by host DNA polymerase to replicate viral DNA

  3. Enzyme lysozyme which is released by phage to digest bacterial cell wall to trigger lysis of host cell for release of newly formed virions/to trigger injection of viral DNA into host cell

  4. Phage proteins which form tail fibres which can recognise and bind to receptors on surface of bacterial cell

  5. Phage proteins which form base plate which can change shape in response to molecules released from bacterial cell to cause contraction of contractile sheath for injection of viral DNA
• Suggest the advantages of the lysogenic pathway to the lambda phage virus

  • Via the lysogenic pathway, the lambda phage DNA is integrated into the bacterial DNA forming a prophage
  • Every time the bacterial chromosome is replicated, the prophage is also replicated along with it
  • This allows continuous replication of the lambda phage DNA/ prophage without killing the host bacteria
• How new strains of influenza virus may arise

  1. Antigenic drift

  2. Antigenic shift
• Antigenic drift


  New strains of viruses are formed as a result of accumulation of mutations of the genome leading to the changes in the ribonucleotide sequence
• Antigenic drift

  • Lack of proofreading ability of RNA-dependent RNA polymerase in influenza
  • Fast/high rate of replication of the virus
  • Changes in the conformation and charge of the glycoproteins
• Antigenic shift


  New viral strains are formed when 2 or more strains of influenza viruses infect a common/same host cell<|>Reassortment of the different RNA segments occur resulting in a new combination of RNA segments in a virion
• Antigenic shift


  • New combination of hemagglutinin and neuraminidase at the viral envelope
• Describe how HIV acquires the outer envelope

  • Viral glycoproteins (gp120 and gp41) are translated at rough endoplasmic reticulum from the mRNA of the provirus transcribed in the host
  • These glycoproteins are then transported and inserted into the host cell membrane via vesicles
  • The nucleocapsid will then be assembled near the cell surface, and it will bud off from  host cell membrane that is studded with viral glycoproteins to form a new virus
• Explain how the 2 reproductive cycles of bacteriophages – lytic and lysogenic cycle, differ in bacterial cells (Control of host cell's protein synthesising machinery)


  1. Lytic Cycle

  • Host cell DNA is degraded immediately upon virus entry allowing
  • Enzymes encoded by the virus take complete control of the bacterium’s macromolecular (DNA, RNA, protein) synthesis.

  2. Lysogenic Cycle

  • Host cell DNA is not degraded upon virus entry.
  • Phage partially control the bacterium’s macromolecular synthesis to synthesize repressor proteins.
• Explain how the 2 reproductive cycles of bacteriophages – lytic and lysogenic cycle, differ in bacterial cells (Integration into host cell genome)

  1. Lytic Cycle

  • Phage does not incorporate genome into host cell DNA

  2. Lysogenic Cycle

  • Phage incorporates its genome into the host cell DNA. Virus is now called a prophage
• Explain how the 2 reproductive cycles of bacteriophages – lytic and lysogenic cycle, differ in bacterial cells (Repressor protein)

  1. Lytic cycle

  • No repressor protein is encoded or synthesised

  2. Lysogenic cycle

  • Prophage gene expresses two repressor proteins which block expression of other phage genes involved in phage replication.
• Explain how the 2 reproductive cycles of bacteriophages – lytic and lysogenic cycle, differ in bacterial cells (Latent stage/ induction into lytic cycle)

  1. Lytic Cycle

  • Phage synthesizes enzymes and phage components immediately after infection. /There is no latent stage as the virus replicates once inside the host cell.

  2. Lysogenic Cycle

  • Phage synthesizes enzymes and phage components after the induction event in which prophage is excised from host genome and phage genes are activated /Phage undergoes a latent stage where it does not undergo replication
• Explain how the 2 reproductive cycles of bacteriophages – lytic and lysogenic cycle, differ in bacterial cells (Propagation of virus)

  1. Lytic Cycle

  • The viruses are released by lysing the host cell and infect new bacteria cell

  2. Lysgenic cycle

  • Virus replicate as the host cell genome is replicated and will be found in the bacteria progenies during latent stage
• Lamba phage replication process (1. Attachment)

  • Tail fiber adsorb to complementary receptor site on host bacterial surface (same as T4 phages)
• Lamba phage replication process (2. Entry - penetration)

  • Unlike T4 phage, lambda phage has a non-contractile tail without a contractile sheath
  • Phage genome enters the bacterium via hollow tube through the bacterial cell wall
• Lamba phage replication process


  1. Penetration into bacteria cell

  2. Linear phage DNA forms a circle

  3. Circular DNA can be replicated and transcribed leading to production of new phage and cell lysis (lytic cycle)

  4. Circular DNA can integrate into and become part of circular bacterial DNA (lysogenic cycle)
• Prophage

  Inserted phage DNA
• Prophage genes

  • Most are repressed by repressor proteins that are the products of phage genes
  • Repressors stop transcription of all the other phage genes, turning off genes that would otherwise direct synthesis and release of new virions
• Replication of prophage

  1. Each time the host cell's machinery replicates the bacterial chromosome, it also replicates the prophage DNA

  2. Prophage will be found in all progeny cells where it remains latent
• Lambda phage replication process: (4. spontaneous induction)

  • Occurs in one of every million to every billion bacteria containing a prophage
  • Induction occurs spontaneously but its frequency is enhanced by irradiation with ultraviolet light or exposure to agents that damage DNA
  • Activates the cellular proteases (cleave repressor proteins)
  • Under these conditions, repressor protein is degraded by increased protein activity
  • Prophage is no longer repressed but is instead excised and enters the lytic cycle
• Lambda phage replication process (5. Assembly)

  • Since phage genome is no longer repressed, phage components are produced using the host bacterium’s metabolic machinery
  • More copies of viral genome are produced by DNA replication using host cell machinery
  • Bacteriophage components then assemble into complete virions (same as T4 phages)
• Lambda phage replication process (6. release)


  The complete virions are then released from the host cell in the same manner as the lytic cycle (same as T4 phages)
• Retrovirus- HIV structure

  • 2 copies of positive-sense single-stranded RNA
  • RNA tightly bound to nucleocapsid proteins
  • contains 3 major genes, 5’ gag-pol-env 3’ which encode major structural proteins and enzymes (Gag: structural proteins, Pol: viral enzymes, Env: glycoproteins)
  • concial-shaped capsid containing 2 molecules of enzyme reverse transcriptase + integrase and protease
  • envelope surrounds the capsid, which contains gp120 and gp41 with specific conformation that allows the virus to bind to certain receptors on T-helper cells
• HIV replication process (1. Attachment)

  • Process begins when a viral particles comes into contact with a cell that carries on its surface a special protein called CD4
  • gp120 interacts with the receptor on the target cell (usually T-lymphocytes) with the help of a co-receptor
  • a conformational change in shape is triggered which involves a receptor
• HIV replication process (2. Entry - penetration and uncoating)

  • With the help of gp41, the viral envelope will fuse with the host cell membrane and the capsid is then released into the cell, leaving the envelope behind (alternatively can also enter via endocytosis)
  • Capsid and nucleocapsid protein are then degraded, releasing viral enzymes and the RNA into the cytoplasm
• HIV replication process

  1. Reverse transcriptase catalyses conversion of viral RNA into DNA

  2. Reverse transcriptase catalyses synthesis of DNA strand complementary to viral RNA, forming RNA-DNA hybrid

  3. RNA strand is degraded and second DNA strand complementary to first is synthesised to form double-stranded DNA molecule

  4. Viral DNA enters host cell nucleus and is integrated into host genetic material

  5. Enzyme integrase catalyses integration process

  6. Integrated viral DNA may persist in latent state for years

  7. Activation of host cell results in transcription of viral DNA into viral RNA which serves as mRNA

  8. mRNA exits nucleus into cytoplasm where it is translated into viral polyproteins

  9. Envelope glycoproteins gp120 and gp41 are made in ER and transported to cell membrane

  10. Env polyprotein is cleaved by host cell protease in ER

  11. Viral RNA forms genetic material for next generation of viruses
• Provirus


  Viral DNA integrated into host genetic material
• Reverse transcriptase is a viral enzyme
• HIV replication process (4. Assembly)

  • Polyproteins and viral genome assemble at the inner surface of the host cell surface membrane
• HIV replication process (5. Release)

  • After assembly at the host cell surface membrane, the virus buds off from the cell
  • Host cell surface membrane evaginates and pinches off, forming the viral envelope with viral glycoproteins (gp120 & gp41) embedded
  • Polyproteins will be cleaved into the functional proteins by HIV protease
  • The functional proteins include structural proteins (matrix, capsid, nucleocapsid proteins) and viral enzymes (reverse transcriptase, integrase, HIV protease)
  • The virion is now considered mature and ready to infect another cell
• Envelope viruses - influenza structure

  • spherical/ ovoid in shape
  • organised into 8 segments of single-stranded negative sense RNA strands
  • RNA is packaged with protein into a helical nucleoprotein form, with 8 RNA molecules
  • 3 polymerases form an enzyme complex, RNA-dependent RNA polymerase/ RNA replicate which functions in both replication and transcription of the viral genome
  • other 5 RNA segments code for other viral proteins such as glycoprotein (haemagglutinin) and enzymes (neuraminidase)and non-structural proteins
  • derived lipid bilayer from cell surface membrane
• Influenza replication process (1. attachment)

  • Protruding glycoproteins bind to specific receptor molecules on surface of host cell
  • In humans, haemagglutinin on the influenza virus binds to sialic acid receptor on the host cell surface membrane
• Influenza replication process (2. Penetration and unloading — entry)

  • The virus usually enters by endocytosis
  • Host cell surface membrane invaginates and pinches off, placing the virus in an endocytic vesicle/ endosome
  • Within the vesicle, the low pH environment will stimulate the viral envelope to fuse with lipid bilayer of the vesicle membrane and nucleocapsid is released into the cytoplasm
  • The capsid is degraded by cellular enzymes, leaving behind the helical nucleoprotein
  • The helical nucleoprotein then enters the nucleus of the cell
• Influenza replication process (3. Replication)

  • The viral genome is used as a template to synthesise the viral mRNA/ (+) strand RNA catalysed by the viral RNA-dependent RNA polymerase
  • mRNA produced in turn acts as a template for the synthesis of new viral RNA genome
  • mRNA strand then exit the nucleus to the cytosol and RER where they are translated into viral structural components, such as the glycoproteins to be incorporated into the viral envelope (at the ER) and capsid proteins (in the cytosol)
• Influenza replication process (4. Maturation - assembly)

  • Viral glycoproteins are transported by the vesicles from the ER
  • Incorporated into the host cell surface membrane
  • Capsid proteins then associate with these glycoproteins at the host cell surface membrane
  • Viral genome associates with proteins to form the helical nucleoprotein which then interacts with the capsid proteins at the host cell surface membrane
  • Interaction of the capsid with the nucleoprotein will initiate the budding process
• Influenza replication process (5. Release by budding)

  • Each new virus buds off from the cell
  • Host cell surface membrane evaginates and pinches off, forming the viral envelope with viral glycoproteins (haemagglutinin & neuraminidase) embedded
  • With enveloped viruses, host cells may or may not be lysed
  • The release is facilitated by neuraminidase
  • Neuraminidase cleaves sialic acid from cell surface and progeny virions, facilitating virus release from infected cells