Viruses

• Why viruses are living organisms:

  • possess genetic material, can propagate genetic info
  • when inside host cell, can use host cell enzymes to carry out metabolic processes
  • undergo mutation and reassortment of genetic material
  • able to respond to stimuli when inside host cell
  • can evolve to adapt to new environment
• why viruses considered non-living:

  • lack cellular organelles
  • do not carry out metabolism, lack ability to reproduce independently
  • do not grow and undergo developmental changes
  • do not respond to stimuli outside host cell
  • can only evolve within host cell
• bacteriophages: viruses that only infect bacteria
• T4 bacteriophage

  
• main steps of viral replication:

  1. virus invades host cell via specific receptors/glycoproteins
  2. genetic material injected/whole virus enters
  3. virus uses host cell machinery to synthesise own nucleic acid
  4. virus uses host cell rna polymerase to transcribe own genes and ribosome for mRNA to form viral components
  5. components assemble, exit cell via budding, exocytosis or lysis of cell
• T4 bacteriophage attachment:

  • attachment sites on tail fibres recognise and attach to complementary receptor sites on bacteria surface
• T4 bacteriophage entry:

  • phage lysozyme hydrolyses bacterial cell wall, releases molecules that trigger change in shape of base plate -> tail sheath contracts, hollow core tube thrust through bacterial cell wall and cell membrane
  • viral genome (DNA) injected Into cell
• T4 bacteriophage replication:

  • phage DNA immediately transcribed using host RNA polymerase
  • enzymes coded by phage genome takes over bacterium‘s macromolecular synthesising machinery
  • use host cell nucleotides to synthesise copies of phage DNA
  • bacterium metabolic machinery used to synthesise phage enzymes and phage structural components
• T4 bacteriophage assembly:

  • bacteriophage dna and capsid assemble
  • head, tail, tail fibres assembled independently
• T4 bacteriophage release:

  • lysozyme hydrolyses bacterial cell wall
  • newly produced bacteriophages released, infect other susceptible cells
• lambda bacteriophage:

  
• Lambda bacteriophage attachment:

  • tail fiber (one only) adsorbs to complementary receptor site on host bacterial surface
• Lambda bacteriophage entry:

  • phage genome enters via hollow tube through bacterial cell wall and cell surface membrane
• lambda bacteriophage replication (lytic):

  • linear phage dna forms a circle
  • circular dna replicated and transcribed (using host cell machinery), new phages formed and cell lysis occurs
• lambda bacteriophage replication (lysogenic):

  • circular dna integrated into bacterial dna (Now called prophage), action by enzyme integrase
  • Prophage genes repressed by repressor proteins (products of phage genes), no release of virions
  • when bacterial chromosome replicated, prophage will be replicated along with it, remains latent
• Lambda bacteriophage spontaneous induction:

  • irradiation with uv light or agents that damage DNA, activates cellular proteases to degrade repressor proteins, allowing for lytic cycle to take place
• lambda bacteriophage assembly:

  • phage components produced using host bacterium’s metabolic machinery
  • assemble components
• Lambda bacteriophage release:

  • lysozyme hydrolyses bacterial cell wall, release of complete virions via cell lysis
• classification of viruses:

  • shape: helical/icosahedral/complex
  • type and structure of genome
  • presence/absence of envelope
  • mode of replication
• Structure of influenza virus:

  • enveloped virus, capsid lines inner side of envelope
• genome of influenza virus:

  • 8 segments of single-stranded RNA (-ve strand, complementary to mRNA)
  • 3 rna segments code for 3 different rna dependent rna polymerases
  • 5 rna segments code for viral proteins
• influenza attachment:

  • haemagglutinin on virus envelope binds to sialic acid receptor on host cell surface membrane
• influenza entry:

  • virus enters cell by endocytosis, where host cell surface membrane invaginates, pinches off and places virus in an endocytic vesicle
  • low pH in vesicle stimulates fusion of viral envelope with vesicle membrane, releasing nucleocapsid into cytoplasm
  • capsid degraded by cellular enzymes, leaving behind helical nucleoprotein that enters nucleus
• • Capsid and genome = nucleocapsid
  • many capsomeres form capsid
  • viral genome can associate with nucleoproteins found inside capsid
• influenza replication:

  • viral rna used as template for synthesis of viral mRNA, catalysed by RNA dependent RNA polymerase
  • mRNA produced will act as template to synthesise new viral rna genome
  • mRNA strands exit nucleus into cytosol to be translated into viral structural proteins at RER
• influenza maturation and assembly:

  • viral glycoproteins translated by vesicles form ER and incorporated into host cell surface membrane
  • capsid proteins associate with glycoprotins at host csm
  • viral genome associates with proteins to form helical nucleoproteins, interact with capsid proteins, initiates budding process
• influenza release:

  • host csm evaginates and pinches off, forms viral envelope with viral glycoproteins haemagglutinin and neuraminidase embedded
  • neuraminidase cleaves sialic acid from cell surface and progeny virions facilitating virus release (so that virions don’t bind tgt)
  • each new virus buds off from cell
• genome of HIV: 2 copies of single stranded RNA (positive strand) tightly bound to nucleocapsid protein

  • 3 major genes

  1. Gag: codes for structural proteins like capsid
  2. Pol: codes for viral enzymes
  3. Env: codes for glycoproteins gp 120, gp 41
• HIV capsid:

  • conical shaped
  • contains 2 molecules of reverse transcriptase
• HIV attachment:

  • gp 120 interacts with CD4 receptor on target cell (eg T lymphocytes like T helper cells) with help of co-receptor
• HIV entry:

  • gp 41 helps viral envelope fuse with cell surface membrane, capsid released into the cell
  • capsid and nucleocapsid protein degraded, viral enzymes and rna into cytoplasm
• HIV replication:

  1. reverse transcriptase catalyses synthesis of DNA strand complementary to viral RNA strand -> RNA-DNA hybrid
  2. RNA strand degraded, DNA strand complementary to the 1st is synthesised to form double-stranded DNA molecule
  3. viral DNA enters nucleus, integrated into host chromosome (catalysed by integrase), now is provirus (can persist in latent stage for years)
• HIV activation after replication:

  • transcription of viral DNA into RNA that serves as mRNA
  • mRNA exits nucleus, will be translated into viral polyproteins
  • gp 120 and gp 41 made in RER
  • Env polyprotein cleaved by host cell protease in RER
  • viral RNA becomes viral genome for next generation of viruses
• HIV assembly:

  • polyproteins and viral genome assemble at inner surface of host cell surface membrane
  • vesicles containing gp 41 and gp 120 embedded in vesicle membrane transported to csm
• HIV release:

  • host cell surface membrane evaginates and pinches off, forms viral envelope with gp 120 and gp 41 embedded
  • Gag and Pol polyproteins cleaved into functional proteins by HIV protease
• Antigens: specific molecular structures that antibodies and receptors in our immune systems recognise
• Antigenic drift:

  • accumulation of mutations in genes encoding surface glycoproteins of virus
  • will result in surface antigens/glycoproteins to have different conformation and charge to the previous strain
  • common in influenza virus due to lack of proofreading ability of RNA-dependent RNA polymerase and fast/high rate of replication of virus -> introduces mutations
• antigenic shift:

  • sudden and major changes in surface antigens/glycoproteins
  • occurs when 2 or more strains of virus infect the same host
  • reassortment of different RNA segments result in new combinations of RNA segments in a virion
  • new combinations of glycoproteins at viral envelope
• PA, PB1, PB2 in influenza will form a complex of RNA dependent RNA polymerase