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GENETICS OF VIRUSES (STRUCTURE OF VIRUSES (STRUCTURE (genome (nucleic acid…

- - - - DNA virus or RNA virus depending on nucleic acid
    - - nucleic acid
        
        DNA or RNA (hence DNA virus/RNA virus)
        
        single or double stranded
        
        linear or circular
        
        single or multiple copies
      - 4 to 1000 genes (vs bacterial genome of 200-few thousand) --> much smaller and simpler in function
      - codes for viral proteins
        
        viral enzymes for replication
        
        form protein capsid coat
        
        glycoprotein inserted into lipid envelope
    - - forms enveloped viruses (otherwise naked viruses)
      - formed by budding out of host cells
        
        composed of phospholipids and glycoproteins (ie cell surface membrane of host cell)
        
        composed of it's own proteins incorporated into envelope --> glycoprotein spikes
        
        function: attach viruses to specific receptors on susceptible host cells
    - - composed of capsomeres protein subunit
        
        number of capsomeres is high but type of protein is low
      - encloses nucleic acid (ref. virus genome)
        
        forms nucleocapsid
      - functions
        
        protect nucleic acid from digestion by enzymes
        
        contain special sites (on surface) for attachment to host cell
        
        enable virus to penetrate cell membrane of host cell or inject viral nucleic acid into cytoplasm of host cell (basically ensures nucleic acid gets in)
  - - - reproduce within host cells
      - contain genes - have inheritance (heredity controlling growth and development)
      - undergo mutation - evolution is possible
    - - non-cellular
        
        lack organised structures (cytoplasm/organelles)
      - obligate intracellular parasites
        
        don't carry out metabolism
        
        don't generate usable chemical energy (- don't acquire, process and utilise energy unless it's in the cell)
      - can't synthesise own nucleic acids or viral proteins
  - - - all living things are composed of cells
      - cell is smallest and most basic unit of life
      - cells arise from pre-existing cells
    - - non-cellular (no cytoplasm)
      - smaller and more basic than cell, but exhibits some characteristics of life
      - don't undergo cell division
        
        ref. reproduction cycle of virus
- - - - 8 separate segments (identification)
      - single-stranded, negative sense RNA
      - codes for viral proteins
        
        Haemagglutinin (HA)
        
        glycoprotein on viral envelope
        
        facilitates attachment of virus to target cell (ATTACHMENT)
        
        Neuraminidase (NA)
        
        glycoprotein on viral envelope
        
        facilitates release of newly formed viruses from infected cells (EXIT)
        
        RNA-dependent RNA polymerase
        
        involved in replication (REPLICATION)
        
        lacks proof-reading mechanism
        
        high mutation rate in replication
        
        rapid viral evolution
        
        capsomere
        
        forms capsid coat
  - - - ENTRY
        
        REPLICATION
        
        ASSEMBLY AND MATURATION
        
        EXIT
        
        viruses obtain virus envelopes from host cell membrane
        
        bud at exit points (process)
        
        2 more items...
        
        HA and NA are transported (from GA - secretory vesicles) to the cell membrane
        
        inserted at exit point
        
        point where viral release occurs
        
        newly synthesised viral proteins (note: found inside capsid)(free ribosomes) transported back into nucleus
        
        assemble with viral RNA genome (negative sense) to form nucleocapsid
        
        nucleocapsid leaves nucleus and transported to cell membrane
        
        accessory proteins and viral RNA (genome) form a complex
        
        transported into nucleus
        
        RNA dependent RNA polymerase enters nucleus and catalyses synthesis of positive sense RNA from negative sense RNA genome (template)
        
        newly synthesised complementary positive sense RNA acts as a template to synthesise more copies of viral negative sense RNA
        
        1 more item...
        
        newly synthesised complementary positive sense RNA is a template for translation of viral proteins
        
        3 more items...
        
        enters by endocytosis (ref. transport across membrane)
        
        membrane invaginates (flask-like depression) and pinches off
        
        placing virus in an endosome (phagocytic vesicle)
        
        uncoating occurs: release of viral genome from rest of virus
        
        low pH of endosome causes conformation change in HA
        
        viral envelope and endosome membrane fuses
        
        1 more item...
        
        endosome containing entire virus is now inside cytoplasm
      - HA binds to sialic acid on specific receptors on host cells (epithelial cells of respiratory tract)
      - spread through aereolized viral particles
  - - - lack of proof-reading mechanism in replication
        
        RNA dependent RNA polymerase (also HIV reverse transcriptase)
        
        error prone replication enzymes
    - - antigenic drift
        
        results in slightly modified glycoprotein
        
        mechanism
        
        mutation to viral RNA coding for viral glycoproteins (HA,NA)
        
        changes in structural conformation of HA, NA
        
        over a long period of time (gradual)
        
        effect
        
        renders antibodies ineffective
        
        antibodies give people immunity to virus after they've recovered from it
        
        people are susceptible to infection again
        
        can be infected multiple times
      - antigenic shift
        
        results in novel combination of glycoprotein
        
        major change to virus structure to create new subtype of influenza virus
        
        mechanism
        
        formed in species that can be infected by different types of influenza virus
        
        eg: pigs - swine influenza, avian influenza, human influenza
        
        different types of influenza infect same cell
        
        newly synthesised viruses contain RNA segments from different virus types
        
        genetic reassortment
        
        effect
        
        new subtype of human influenza virus produced
        
        with surface glycoproteins from avian virus
        
        human immune system hasn't encountered surface proteins before
        
        surface proteins are needed to identify that they are viruses to be attacked by T cells - specific receptors
        
        can't combat viral infection effectively
        
        1 more item...
- - - - 2 identical strands
      - single stranded, positive sense RNA molecules
      - codes for viral proteins
        
        gp120, gp41
        
        glycoproteins on viral envelope
        
        recognition and binding of virus to target cell (ENTRY)
        
        HIV reverse transcriptase
        
        catalyses synthesis of viral double-stranded DNA from single stranded positive sense RNA template (REPLICATION)
        
        no proof-reading mechanism
        
        HIV integrase
        
        inserts viral DNA into host DNA, forming provirus (REPLICATION)
        
        HIV protease
        
        cleave synthesised viral polyproteins to form functional proteins
        
        capsomeres
        
        form capsid coat
  - - - ENTRY
        
        REPLICATION
        
        ASSEMBLY AND MATURATION
        
        EXIT
        
        viruses obtain viral envelopes from host cell
        
        by budding at exit points (process)
        
        1 more item...
        
        since viral envelopes (structure) is cell membrane + gp120, gp41
        
        gp120, gp41 transported (from GA - in golgi vesicles) to cell membrane
        
        inserted at exit point
        
        newly synthesised viral proteins assemble with viral RNA (in cytoplasm) to form nucleocapsid
        
        HIV reverse transcriptase transcribes single stranded RNA (template) into double stranded DNA
        
        Single stranded DNA synthesised using viral RNA as template
        
        RNA-DNA hybrid formed
        
        HIV reverse transcriptase removed RNA and uses single stranded DNA to synthesise complementary DNA strand
        
        viral DNA enters nucleus
        
        HIV integrase inserts viral DNA into host DNA
        
        integrated viral DNA forms provirus
        
        provirus is replicated with host DNA when host cell undergoes cell division (ref. lysogenic cycle)
        
        2 more items...
        
        viral envelope fuses with the cell surface membrane of the host T helper cell
        
        nucleocapsid released into cytoplasm
        
        uncoating occurs
        
        capsid is enzymatically removed, releasing viral RNA and enzymes into cytoplasm (HIV reverse transcriptase, HIV integrase, HIV protease)
      - GP120 binds to specific receptor CD4 on host T-helper cells
- - - - linear, double stranded DNA
        
        same as host bacterium genome
      - capsid coat composed of capsomeres
    - - hollow tube which viral DNA enters host cell through
      - contractile sheath surrounding tail that can contract
      - base plate at the end with tail fibres
        
        for attachment of phage to bacterial cell
  - - - results in death of host cell
        
        virulent phage
      - ATTACHMENT
        
        ENTRY
        
        REPLICATION
        
        ASSEMBLY AND MATURATION
        
        EXIT (RELEASE)
        
        phage coded lysosome breaks down bacterial peptidoglycan wall
        
        1 more item...
        
        happens very quickly
        
        T4 phage enzymes and structural components assemble around genome
        
        forming mature phage particles
        
        in the cell: viral particles detected --> end of eclipse period
        
        one of the first phage genes expressed (transcribed and translated) codes for a phage enzyme that degrades DNA of host cell
        
        so only phage genes is expressed
        
        shuts down bacterium protein, DNA, RNA synthesis
        
        phage replicates it's own genome using bacteria's protein synthesis machinery
        
        1 more item...
        
        penetration of bacterium cell wall (process)
        
        contractile sheath of tail contracts
        
        drives hollow tube into host bacterium
        
        entry of viral DNA through hollow tube
        
        1 more item...
        
        phage enzyme can drill a hole in bacterial wall (not for t4)
        
        inject DNA into host cell
        
        results in eclipse period
        
        amt of viruses detected goes to 0: viral DNA is in host cell so virus particles in host cell is 0
        
        between infection and appearance of mature virus
        
        tail fibres and base plate recognise and bind to specific receptors on cell surface of host cell
      - LIFE CYCLE
        
        eclipse period: just after entry to replication
        
        infectious phage can't be detected in host cell
        
        ends when intracellular infectious mature viruses occur (assembly occurs)
        
        latent period: from infection to release of mature viruses (until extracellular phage particles detected starts to rise)
        
        burst period is from lysis (release) until all phages are extracellular (per bacteria)
    - - replicates phage genome without destroying host bacterium
      - temperate phage: LAMBDA PHAGE
        
        combination of both lytic and lysogenic cycles
        
        structure
        
        one tail fibre only
        
        ATTACHMENT
        
        ENTRY
        
        REPLICATION (lysogenic cycle feature)
        
        ASSEMBLY AND MATURATION
        
        linear viral DNA molecule circularises (same as bacterial DNA)
        
        phage viral DNA integrates itself into specific site in bacterial chromosome
        
        forms prophage (integrated viral DNA ONLY - not bacteria DNA)
        
        1 more item...
        
        bacterial: lysogen