Chapter 18: Genetics of Bacteria and Viruses

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Chapter 18 Genetics of Bacteria and Viruses

• AP Biology Ms. Rader

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Viruses

• Viruses are obligate intracellular parasites
• They lack the necessary ribosomes or machinery to
  replicate themselves or have any metabolism
• The host range is the species that a virus can
  infect. Very often a virus is limited to one or
  just a couple of species that have suitable cells
  for the virus to infect.
• Viruses recognize host cells by binding to
  specific membrane receptors. These cells are
  usually tissue specific. For example, influenza
  virus infects the cells of the respiratory tract.
  

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Influenza
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Viral Structure

• Viruses are pieces of nucleic acids (either
  dsDNA, ssDNA, dsRNA or ssRNA) and a protein coat
  called a capsid.
• Some viruses have a membranous envelope, usually
  derived from the host cell membrane.

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Bacteriophages

• Viruses that attack bacteria are called
  bacteriophages or just phages.
• The most studied phages are those that infect the
  E. coli bacterium. The seven phages are named T2,
  T4, etc. They all have very similar structures
  that has become the stereotypical virus structure
  taught in biology.

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Viral Reproduction Lytic Cycle

• The virus infects the cell by attaching to
  receptors on the cells surface using its tail
  fibers.
• The tail sheath facilitates the injection of the
  virus DNA into the E. coli.

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Viral Reproduction Lytic Cycle

• The capsid remains on the outside of the
  bacterium and the DNA in the cell is hydrolyzed.
• The phage DNA takes over the cells proteins and
  enzymes to start replicating, transcribing, and
  translating the viral DNA.
• The phage parts start to assemble and then
  directs the production of lysozyme that ruptures
  the cell wall releasing the phages (100-200
  particles can be released from one bacterial cell)

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Lytic Cycle
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Viral Reproduction Lysogenic Cycle

• Some viruses replicate their genome and do not
  destroy the host cell.
• The l phage attaches to the host cell receptor
  and injects its DNA.
• Instead of hydrolyzing the host cell DNA the
  viral DNA is incorporated into the host genome.
  This is called a prophage and it is replicated
  each time the host cell replicates its genome.
• One of the prophage genes codes for a protein
  that inhibits the expression of the other viral
  genes. This gene is called the repressor protein.
  

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Viral Reproduction Lysogenic Cycle

• The virus remains quiet and its DNA is
  transferred to each subsequent daughter cell as
  the host cell replicates, more or less, normally.
• At certain times the virus can be activated and
  enter the lytic cycle. This is usually at times
  of stress, concurrent illness, or some other
  external factor that triggers the virus to enter
  this cycle.
• The viral genome leaves the bacterial chromosome
  and circularizes and starts to actively make
  viral components that assemble into virus
  particles. The virus then ruptures the cell and
  is released to infect other cells.

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Lysogenic cycle
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Viral Reproduction

• Viral Envelopes Viruses with membranous
  envelopes use them to enter and exit the cell.
• The membrane is typically a lipid bilayer with
  glycoprotein spikes protruding from the surface
• The glycoprotein spikes bind to receptors on the
  host cell membrane and then the viral membrane
  fuses with the host membrane, releasing the viral
  capsid into the host cell
• Enzymes in the host cells cytosol break the
  capsid apart, releasing the viral genome (DNA or
  RNA) into the cytosol.

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Viral Envelopes

• The viral genome is copied, transcribed, and
  translated. The viral genome codes for the
  glycoprotein spikes which are produced in the
  lumen of the endoplasmic reticulum.
• The glycoprotein spikes are transported to the
  host cells membrane and become a part of the
  exterior of the cell. This becomes the exit point
  for the new viral particles
• As the viral particles emerge from the host cell
  they become wrapped in the host cells membrane
  and covered in the glycoprotein spikes.

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RNA virus Reproduction

• There are three types of single stranded RNA
  viruses.
• Some of these viruses use their RNA directly as
  mRNA. This viral genome can be directly
  transcribed into proteins.
• Others use their RNA as a template to make mRNA.
  These viruses use their own enzymes to synthesize
  RNA from RNA.
• The third type of ssRNA viruses are called
  retroviruses. The most infamous of the
  retroviruses is HIV (Human Immunodeficiency
  Virus) the causative agent of AIDS (Acquired
  Immunodeficiency Syndrome)

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Retrovirus Reproduction

• Retroviruses use their own enzyme called a
  reverse transcriptase to transcribe RNA into DNA.
  This DNA integrates into the host cell DNA.
• This incorporated DNA is called a provirus.
  Unlike the prophage we discussed earlier the
  provirus does not leave the host DNA.
• The host cells RNA polymerase transcribes the
  viral DNA into mRNA for protein synthesis and RNA
  for the genome of the new viral particles.

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Retrovirus Reproduction
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Recombination Genetics of Bacteria

• Bacterial genome is concentrated in one area of
  the bacteria in a region referred to as the
  nucleoid.
• Bacteria reproduce by binary fission and most
  offspring of a single bacterium are identical to
  the parent cell.
• Individual mutations occur rarely, but in a
  rapidly reproducing organism mutations can
  provide significant diversity in a population

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Transformation

• Transformation is the alteration of bacterial DNA
  by incorporation of a naked piece of foreign DNA
  from outside of the cell.
• Many species of bacteria have special proteins on
  the outside of their cell surface that facilitate
  the uptake of foreign DNA from the surrounding
  solution.
• Even bacteria that do not possess these proteins
  are able to take in foreign DNA. E. coli can be
  stimulated to take in the DNA by placing the
  bacterium in a culture containing a high
  concentration of Ca2 ions. This process is used
  to get the E. coli to take in genes for proteins.
  We use this technique to get the bacteria to make
  proteins and hormones in large quantities.
  Examples are insulin and growth hormone.

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Transduction

• In transduction, viruses carry bacterial genes
  from one host cell to another and insert those
  pieces of DNA into new host cells.
• There are two ways this can occur
• Generalized Transduction Where pieces of the
  lysed host cells DNA are packaged into the
  capsid of the viral particle instead of the viral
  genome. The virus is defective but it can still
  attach to a bacterial cell and inject this DNA.
• Specialized Transduction Where a host bacterial
  cell is infected by a temperate phage (one that
  enters the lysogenic cycle.) When the viral DNA
  comes out of the bacterial chromosome sometimes
  it takes some of the bacterial DNA with it. When
  the phage exits the cell it takes this new DNA
  with it and then infects the next host cell with
  the new bacterial DNA and its viral DNA.

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Conjugation in Bacteria

• Another way that bacterial cells can get
  recombinant DNA is through conjugation with
  another bacterial cell.
• Conjugation is direct transfer of genetic
  material from one bacteria to another while they
  are temporarily joined.
• This is a form of primitive sexual reproduction
  for bacteria. It allows for greater genetic
  diversity without relying the random occurrence
  of mutations.

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Conjugation

• The transfer occurs when the donor bacteria uses
  the male appendage, called sex pili, to attach
  to the recipient or female bacteria.
• The pili then pulls the recipient cell toward the
  donor cell and a temporary cytoplasmic bridge is
  formed between the two cells.
• The DNA transfer happens along this bridge.

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Plasmids

• The ability to form the sex pili in bacteria is
  determined by the presence of a set of genes on a
  piece of DNA called the F factor.
• The F factor can be either a part of the
  bacterial chromosome or on a separate piece of
  DNA called a plasmid.
• Plasmids are small, circular pieces of DNA that
  can replicate themselves. These pieces of DNA are
  separate from the bacterial chromosome. Plasmids
  are similar to temperate phages in that they can
  sometimes reversibly incorporate into the
  bacterial genome.
• The key differences between plasmids and
  temperate or lysogenic phages is that plasmids do
  not posses a protein coat and can not exist
  outside of the bacterial cell. Also, plasmids are
  generally beneficial to the cell, whereas phages
  are detrimental to the host cell.

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F Plasmid

• In bacterial conjugation the sex genes the F
  factor can be conveyed to the bacteria in a
  plasmid.
• The F plasmid has about 25 genes
• A cell that has the F plasmid is referred to as
  F (positive for the F factor or male
  bacteria.) F- cells do not possess the F factor
  in either form and are considered female cells
  and are DNA recipients in conjugation.
• The F factor plasmid is heritable and F cells
  give rise to other F cells
• During conjugation a F cell mates with a F- cell
  only the F factor plasmid is transferred through
  the conjugation tube

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Integrated F factor genes

• Cells with the F factor integrated into the
  bacterial chromosome is called a Hfr cell because
  it has a high frequency of recombination.
• When these cells go through conjugation they act
  as the male cell, but they are able to transfer
  bacterial DNA from the Hfr cell to the recipient
  cell.
• The Hfr cell initiates conjugation and DNA
  replication starts at the point of the F factor
  genes.
• The leading end of the F factor genes are now
  dragging copied bacterial DNA behind it.
  Conjugation is almost always interrupted before
  the entire Hfr chromosome is replicated and the
  DNA fragment is left in the recipient cell.

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R plasmids

• The genes that carry resistance to antibiotics
  are carried on plasmids called R plasmids.
• The indiscriminate use of antibiotics can lead to
  resistance and the propagation of bacteria that
  carry R plasmids to particular antibiotics.
• Some R plasmids carry resistance to up to ten
  different antibiotics.

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Transposon

• Transposable genetic element
• Transposons are genes that can move from one
  position to another on the bacterial chromosome,
  from plasmid to bacterial chromosome, or from
  plasmid to plasmid.
• Transposons can be moved by cut and paste,
  where the set of genes are cut from one place and
  then sliced into another location.
• They can also be moved by replicative
  transposition. This is where the transposon
  replicates at its original site and the copy is
  transposed into the new site.

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Insertion Sequences

• Simplest form of a transposon is an insertion
  sequence. Contains only the genes for the
  transposase and inverted repeats on either side
  of the genes for the transposase enzyme. The
  enzyme cuts the DNA and facilitates the moving of
  the transposon.
• These transposons do not cause much change in
  the genome unless they land in the coding region
  of another gene.

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Composite Transposons

• Composite transposons are longer and more
  complicated transposons. They carry the
  transposase genes and some extra genes.
• Composite transposons are typically beneficial to
  the bacterium. Antibiotic resistance to multiple
  types of antibiotics is achieved by composite
  transposons.

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Operons

• Some genes are linked by their promoter region.
  This means that one promoter signals the
  transcription of more that more gene.
• The benefit of such a system is twofold first
  the genes and subsequent proteins can be made as
  a group when needed, second a on and off switch
  can be used to regulate the transcription of a
  group of related genes.
• The on and off switch is called an operon.
• The operon is located in the promoter region of
  the related genes or between the promoter and the
  coding region of the DNA.
• The operon controls access of the DNA to the RNA
  polymerase.

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Operons and Repressors

• By itself, the operon switch is in the on
  position, and transcription will take place.
• The off position of the operon is controlled by
  the presence or absence of repressors.
• Repressors are proteins that bind to the operon
  and inhibit transcription.

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Repressors

• Repressors are proteins that are product of
  regulatory genes. The genes code for the
  production of the repressor protein.
• For example, in the gene that codes for the
  enzymes responsible for the production of
  tryptophan, trp genes has the regulatory gene
  trpR.
• Feedback inhibition is the mechanism that
  controls whether the repressor actively represses
  the expression of the trp genes.
• Tryptophan is then a corepressor in this pathway
  as it activates the repressor protein.

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