Viruses

Question 1

Virus Characteristics

Answer 1

• Obligate parasite, cannot replicate outside cellular host
• Acellular and lack cellular organelles
• Do not carry out metabolism/respiration/growth independently BUT can direct enzymes to carry out metabolism once inside cell
• Reproduce by copying viral genome inside cell using host cell machinery
• Do not respond to stimuli outside cell but can respond inside cell
• Viruses only evolve by natural selection within host

Question 2

Virus Structure

Answer 2

1. Genome (generally few genes)
   - Either DNA or RNA, often single stranded, either single or segmented, either circular or linear
   - Genome codes for synthesis of viral components and viral enzymes
2. Capsid
   - Protein coat that protects, attaches and introduces genome into host cells
3. Envelope
   - Phospholipid bilayer with glycoprotein spikes used for recognition and attachment of virus to specific receptors on host cell membrane

When comparing viruses, compare above 3 structures (type of genome, presence of envelope, mode of replication)

Question 3

Bacteriophage Structure

Answer 3

T4 (lytic)
- DNA genome
- Icosahedral capsid head
- Contractile tail sheath
- Base plate and tail fibre ending in tail pins

Lambda (temperate)
- Same except no base plate and small tail fibre

Question 4

Lytic Cycle

Answer 4

1. Attachment
   - Attachment sites on tail fibres recognise and attach to complementary receptor sites on bacteria by forming weak H bonds
   - Viral specificity: specific strains of phases only adsorb to specific bacteria strains
2. Penetration
   - Bacteriophage tail releases phage lysozyme to digest peptidoglycan cell wall, triggering a conformation change of base plate to initiate tail sheath contraction
   - This causes viral DNA to be injected into host cell
3. Replication
   - Early Replication (all genome): DNA immediately transcribed into mRNA using host RNA polymerase
   - Phage enzymes coded by genome takes over bacteria’s synthesising machinery, using host cell nucleotides, DNA polymerase and own enzymes to synthesise many copies of phage DNA via replication
   - Host Cell DNA is degraded by enzymes translated from viral DNA
   - Late Replication: mRNA used as a template to translate phage enzymes + capsid proteins
   - Eclipse period occurs when separate components are present but no complete infective virions present yet
4. Maturation
   - Bacteriophage DNA and capsid assembled into DNA-filled head
   - Parts assemble at plasma membrane in this order: tail fibres, base plate proteins, head
5. Release
   - Release of virions involving lysis of plasma membrane

Question 5

Lysogenic Cycle

Answer 5

1. Attachment and Penetration same
2. Replication
   - Originally linear phage DNA circularises and integrates into bacterial chromosome via integrase, viral DNA known as prophage
   - Entering lysogenic cycle allows prophage to replicate along w bacterial DNA, remaining latent in bacterial daughter cells
   - This occurs because most prophage genes are repressed by repressors, blocking transcription
3. Spontaneous Induction
   - Occurs spontaneously but frequently enhanced by irradiation w UV light or exposure to DNA damaging agents
   - This activates cellular proteases to destroy repressors proteins, allowing prophage to be excised from host genome and enter lytic cycle
   - Lytic cycle same: DNA transcribed to mRNA, translated to synthesise phage enzymes and capsid proteins
4. Maturation and Release same

Question 6

Influenza

Answer 6

1. Attachment
   - Haemagglutinin binds to sialic acid receptors on host cell membrane in epithelial cells of respiratory tract
2. Penetration and Uncoating
   - Virus enters by clathrin-mediated endocytosis, where host plasma membrane invaginates, placing virus in an endocytic vesicle.
   - Vesicle fuses with acidic lysosome, causing pH to drop and stimulating viral envelope to fuse w endocytic vesicle to release nucleocapsid into cytoplasm
   - 8 negative sense ssRNA segments enter nucleus through nuclear pore
3. Replication and Maturation
   - Negative sense RNA strand used as template to synthesise complementary positive sense mRNA strand catalysed by RNA-dependent RNA polymerase, using host cell ribonucleotides
   - + sense RNA acts as template for synthesis of new viral RNA
   - + sense RNA acts as mRNA that moves into cytosol to translate into viral structural protein
   - Glycoproteins to be embedded in plasma membrane synthesised at RER
   - Capsid proteins synthesised in cytosol by free ribosomes
   - Assembly of virion occurs when viral genome associates w proteins to form ribonucleoprotein and interact w capsid proteins to start budding process
4. Release via budding
   - Each new virus buds off from cell when host cell membrane evaginates, acquiring host membrane envelope w glycoproteins embedded
   - Neuraminidase cleaves sialic acid from cell surface membrane and progeny virgins, facilitating virus release

Question 7

HIV

Answer 7

1. Attachment
   - Viral glycoprotein gp120 binds to CD4 receptor on membrane of helper T cells/macrophages w help of co-receptor
2. Penetration and Uncoating
   - With the help of gp41, the viral envelope fuses w host plasma membrane (not endocytosis)
   - Capsid degraded to release viral enzymes and RNA into cytoplasm
3. Replication
   - Viral reverse transcriptase catalyses synthesis of DNA strand complementary to positive sense viral RNA, forming a RNA-DNA hybrid
   - RNA strand degraded and complementary DNA strand synthesised via CBP to form a double stranded viral DNA molecule
   - Viral dsDNA integrated into host genome catalysed by viral integrase, now known as a provirus that can persist in latent state for many years
4. Activation
   - Upon activation, provirus transcribed into viral RNA using host cell RNA polymerase
   - This serves as both mRNA for translation into viral polypeptides and as new viral RNA genomes
   - Glycoproteins gp120 and gp41 made in RER while viral polyproteins made in cytoplasm
5. Assembly and Release
   - Polyproteins and genomic RNA assemble at plasma membrane
   - Virus buds off from cell, with viral envelope acquired from host cell membrane containing gp41 and gp120
   -Polyproteins cleaved by HIV protease to form structural capsid proteins and 3 critical enzymes: integrase, reverse transcriptase and protease

Question 8

Antigenic Drift

Answer 8

• Occurs in accumulation of mutations in genes encoding surface glycoproteins, causing change in ribonucleotide sequence
• Resulting viruses have surface antigens w different conformation and new viruses can’t be recognised by antibodies
• Constant selection pressure from antibodies leads to rapid selection for new mutation by evading pre-existing host immunity

Small antigenic drift possible due to
1. Lack of proofreading ability of RNA-dependent RNA polymerase or reverse transcriptase for HIV
2. Fast rate of replication
3. Viral RNA is single stranded and does not have backup copy to carry out repair
4. RNA genome more reactive

Question 9

Antigenic Shift

Answer 9

• Sudden and major change in virus surface antigens
• Caused by 2 different influenza strains infecting common host cell, allowing RNA segments from different strains to be packaged into same virion
• This gives rise to random reassignment and new combination of RNA segments. These form a new subtype w new combinations of glycoproteins —> possible bcos RNA genome is segmented
• Often jumps across species barrier, especially with pigs as mixing vessels susceptible to both avian and mammalian influenza