Genetics of Viruses and Bacteria

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Genetics of Viruses and Bacteria
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Viral structure

• Virus poison (Latin) infectious particles
  consisting of a nucleic acid in a protein coat
  (there are MANY, MANY types of viruses)
• Composition of virus
• Capsid protein shell that encloses the viral
  genome (the protein subunits are called
  capsomeres)
• DNA or RNA that is inserted into infected cells

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Examples of viruses
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Virus structure (cont.)

• Other accessories for viruses/virus types
• Membranous envelope that allows a virus to fool
  a cell membrane and allow the virus to enter the
  cell (viral envelope)
• Bacteriophage (phage) viruses that are able to
  infect bacteria

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General features of viral reproduction

• Viruses are intracellular parasites
• They need a host cell to reproduce
• They lack enzymes, ribosomes and all other
  machinery needed to make proteins
• Viruses can only infect a limited range of cells
  (host range)
• This is why diseases are usually species or
  tissue specific

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Lytic Cycle

• The lytic cycle is a viral reproductive strategy
  that results in the death of the host cell
• Attachment virus binds to a specific receptor
  site on the outer membrane
• Injection the viral DNA/RNA is inserted into
  the cell membrane
• Synthesis the viral DNA directs the production
  of viral proteins and the synthesis of viral
  nucleotides
• Assembly the synthesized viral material is
  assembled
• Release the viral particles are released from
  the organism, thereby destroying the host cell
• Virulent virus (phage reproduction only by the
  lytic cycle)

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Lytic cycle
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Lysogenic Cycle

• Genome replicated w/o destroying the host cell
• Very similar to the lytic cycle
• Key differences
• Genetic material of virus becomes incorporated
  into the host cell DNA by recombination (uses
  crossing-over)at a specific chromosomal loci
• The incorporated viral DNA is known as a prophage
• Once the prophage synthesizes its material, it
  circulates in the cell
• Temperate virus (phages capable of using the
  lytic and lysogenic cycles)
• May give rise to lytic cycle

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Lysogenic cycle
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Animal Viruses

• Viruses that infect animals are extremely varied
• They can be double stranded or single stranded
• They can be made of DNA or RNA
• They can have an outer membrane (viral envelope)
  or not
• PURPOSE The reason for the extreme variability
  in viral composition is to enter cells and
  utilize their reproductive machinery

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Retroviruses (class of RNA Viruses

• Retroviruses a class of RNA virus that can use
  an RNA template to transcribe its nucleotides
  into the DNA template
• Uses an enzyme called reverse transcriptase
• One deadly example of a retrovirus is HIV
• This is the virus that leads to the disease known
  as AIDS

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Retrovirus (HIV)
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HIV (cont.)

• Unlike a prophage in bacteria, the integrated
  viral DNA (provirus) is a permanent part of the
  cells genotype
• The cell will continue to synthesize the virus
  for the life of the cell

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How do we fight viruses?

• Viruses are extremely damaging
• They utilize our own cellular machinery to
  produce, infect and destroy our own cells
• With the creation of vaccines (harmless variants
  of pathogenic microbes), we can condition our
  body to destroy the infection before it can
  result in illness

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Why do we still have viruses?

• With the advent of vaccination, a lot of diseases
  have become extinct (polio or small pox)
• Yet, viruses have a high level of mutation
• They are constantly changing to fool your
  bodies immune system
• Even the influenza virus (flu) mutates every year
  so that you must get a new flu vaccine each
  season
• Also we do not understand enough about some
  viruses to create a vaccine

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Viroids and prions

• Viroids tiny, naked circular RNA that infect
  plants do not code for proteins, but use
  cellular enzymes to reproduce stunt plant growth
• Prions infectious proteins mad cow
  disease trigger chain reaction conversions a
  transmissible protein

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Bacterial genetics

• Nucleoid region in bacterium densely packed
  with DNA (no membrane)
• Plasmids small circles of DNA (separate from
  bacterial genome)
• Reproduction binary fission (asexual)

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Bacterial DNA-transfer processes

• Transformation genotype alteration by the
  uptake of naked, foreign DNA from the environment
  
• Transduction phages that carry bacterial genes
  from 1 host cell to another
• Generalized random transfer of host cell
  chromosome
• Specialized incorporation of prophage DNA
  into host chromosome
• Conjugation direct transfer of genetic
  material cytoplasmic bridges pili sexual

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Bacterial Plasmids

• Small, circular, self-replicating DNA separate
  from the bacterial chromosome
• F (fertility) Plasmid codes for the production
  of sex pili (F or F-)
• R (resistance) Plasmid codes for antibiotic drug
  resistance

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Transposable elements

• Transposable elements nucleotide sequences that
  can move from one site in a chromosome or plasmid
  to another site
• Insertion sequence (only in bacteria) can move
  one gene from one site to another
• Transposons transposable genetic element piece
  of DNA that can move from location to another in
  a cells genome (chromosome to plasmid, plasmid
  to plasmid, etc.) jumping genes
• This allows genetic information to be
  incorporated or passed on to other bacteria

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Incorporation of a plasmid
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Operons (the basic idea)

• For many proteins, there is a segment of DNA
  where all of the necessary genes are grouped
  together
• Therefore, you only need a single promoter site
  where RNA polymerase can begin to transcribe the
  DNA code
• Near the promoter site is a stretch of DNA that
  controls whether RNA polymerase can bind. This
  is called the operator
• The promoter site, the operator and the stretch
  of DNA that codes for the protein(s) is called
  the operon

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Operons (the trp operon)

• An example of an operon is the tryptophan (trp)
  operon in E. coli that produces the amino acid,
  trp
• The way it works
• Trp operon is usually on . . . RNA polymerase
  has access to the promoter
• To stop the production of trp, the operon has to
  be turned off
• A protein called the trp repressor binds to the
  operator and blocks the attachment of RNA
  polymerase
• This repressor protein is specific to the trp
  operator site and stops transcription
• The trp repressor is the product of another
  regulatory gene with its own operon
• When trp is absent, the repressor is inactive and
  the production of trp proceeds normally
• When trp is present in higher concentrations, it
  acts as a corepressor
• It binds with the repressor protein and
  activates it so that it can bind to the
  operator and turn off transcription

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Repressible operon

• The trp operon is called a repressible operon
• This means that the trp operon is usually in the
  on condition . . . it can transcribe the DNA
  normally
• Transcription can only be inhibited when trp
  binds with the repressor protein
• This allows the repressor protein to bind to the
  operator and prevent transcription

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Inducible operon

• In an inducible operon, the operon is usually
  off
• It is not possible to transcribe the DNA
• There must be some sort of signal (molecule) that
  can turn the operon on
• An example of an inducible operon is the lactose
  (lac) operon

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Operons (the lac operon)

• In E. coli, the enzyme beta-galactosidase is
  needed to break lactose into glucose and
  galactose
• Normally, E. coli does not have a large amount of
  this enzyme present
• The operon to create beta-galactosidase is
  normally in the off position
• A regulatory gene, lacI, creates a repressor
  protein that is normally bound to the operator of
  the lac operon
• When lactose is present, it will bind to the
  repressor protein and inactivate it
• Since this molecule is needed to start DNA
  transcription, it is called an inducer

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