Tortora ch. 8

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Tortora ch. 8

• Microbial Genetics

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Ever feel like this?
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Terms to define

• Genetics-science of heredity
• Genome-genetic information in the cell
• Chromosomes-structures in the genome that contain
  DNA and genes
• Genes-segments of DNA that code for different
  things
• Genetic code-rules that determine how a
  nucleotide sequence is converted into protein

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Genotype and Phenotype

• Genotype-genetic makeup
• Phenotype-expressed properties of the genetic
  make up (the adjective)
• The genotype is the collection of genes
• The phenotype is the collection of proteins

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DNA and chromosomes

• Bacteria have a single loop shaped chromosome
  that is usually attached to the plasma membrane
• DNA is E. coli has 4.6 million base pairs and is
  1 mm long (1000 times longer than the whole
  cell!)
• DNA is twisted and takes up only 10 of cell
  volume
• See figure 8.2 for flow of genetic information

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DNA components

• Double helix
• Sugar phosphate backbone (sides of a ladder)
• Sugar is Deoxyribose
• Nucleotide bases include adenine, guanine,
  cytosine, and thymine (steps of the ladder)
• Watson and Crick

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DNA replication

• 1 parent divides into 2 daughter cells
• Requirements are complimentary base pairs, gyrase
  (relax supercoil), helicase (unwinds DNA), DNA
  polymerase (glues new nucleotides in place)
• Replication occurs at the replication fork
• Remember complementary base pairs are adenine
  (A)/thymine (T) and cytosine (C)/guanine (G)

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Replication

• Semi-conservative replication
• new DNA always has one conserved strand and one
  new strand
• DNA polymerase adds new nucleotides ONLY to 3
  end
• 3 end has a hydroxyl on it
• 5 end has phosphate on it.
• See figure 8.4
• http//www.mcb.harvard.edu/Losick/images/TromboneF
  INALd.swf

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Steps and oddities

• DNA unwinds
• Replication fork forms at origin of replication
• Leading strand is synthesized continuously at DNA
  polymerase moves toward replication fork in 5 ?
  3 direction
• Lagging strand-RNA primer begins synthesis then
  DNA polymerase adds nucleotides to 3 end of RNA
• DNA polymerase digests away the RNA as it makes a
  small piece of DNA (Okazaki fragments combined by
  DNA ligase)

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Links and games

• http//www.pbs.org/wgbh/aso/tryit/dna/
• Play with this link to make your own protein and
  match complementary base pairs.
• Play this game to create a protein
  http//library.thinkquest.org/20465/g_DNATranscrip
  tion.html
• http//highered.mcgraw-hill.com/sites/0072437316/s
  tudent_view0/chapter14/animations.html movie of
  DNA replication

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RNA and Protein synthesis

• RNA is a single strand copied from the DNA
  template
• Use the sense strand (the other side is called
  the anti-sense strand)
• RNA has ribose sugar, not deoxyribose
• RNA has 4 nucleotide bases, but thymine is
  MISSING! Replaced with uracil.

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Transcription

• Synthesis of a strand of RNA from DNA
• It is transcribed or copied
• 3 kinds of RNA are made using this process
• mRNA is messenger RNA (codon)
• tRNA is transfer RNA (anticodon)
• rRNA is ribosomal RNA (forms part of the ribosome)

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Requirements

• Complementary base pairs are A/U and C/G
• Requires RNA polymerase
• Begins at the promoter on DNA and proceeds in the
  5 ? 3 direction
• Polymerase assembles the nucleotides into a chain
• Continues until terminator is reached
• Polymerase and the new chain are released from DNA

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Translation

• mRNA contains the genetic code for making
  specific proteins (call it a recipe if you wish)
• This must be translated into english and that
  is the job of the tRNA
• The special language of RNA is based on groups of
  3 nucleotides called a triplet
• The tRNA has a triplet that will have a
  complementary triplet on the mRNA.
• The trick is to match them up!

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Miscellaneous information on Translation

• There are 64 possible codon combinations and 20
  amino acids. See figure 8.8 for the genetic code
  
• 61 codons are sense codons and 3 are non-sense
  codons that dont code for anything.
• These 3 are called stop codons (UAA, UAG, and
  UGA)
• AUG is the start codon (also codes for methionine)

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Translation see figure 8.9

• The mRNA must attach to the ribosome (the site of
  protein synthesis)
• The tRNA anticodon finds its complementary
  triplet codon and brings an amino acid into
  place.
• A second tRNA finds its spot, and the amino
  acids join with a peptide bond
• The first tRNA leaves the ribosome.
• The ribosome moves to the next codon, and the
  process continues until a stop codon is reached.

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Polyribosome

• As the ribosome moves along the mRNA in a 5?3
  direction, eventually the start codon will be
  exposed.
• When this happens a second ribosome will attach
  and begin processing another protein
• Lets more than one protein be created at the same
  time in prokaryotes.

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Interesting note

• In eukaryotic organisms, transcription occurs in
  the nucleus
• The mRNA must leave the nucleus and enter the
  cytoplasm to attach to the ribosome
• In eukaryotic cells, there are areas of DNA that
  dont code for proteins (introns) in between the
  areas that do code (exons)
• The red dog ate the rabbit (prokaryotic)
• The xxobored dog .oow89te7w ate kjieurio the
  akeiturabbit..suie (eukaryotic)

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Mutations

• Change in DNA
• An adaptation is a GOOD change in DNA
• The most common type is caused by a base
  substitution (point mutation)
• A single base is replaced by a substituted base
• If this causes an amino acid substitution the
  mutation is called a missense mutation
• If a stop codon is created in the middle of the
  mRNA, a nonsense mutation results

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Mutations continued

• Also have frameshift mutations where the
  nucleotide pairs are deleted or inserted
• This changes the reading frame
• Huntingtons Disease in humans is caused by extra
  bases inserted into a particular gene
• Spontaneous mutation occur because of natural
  mistakes in replication
• Mutagens can cause mutations too.

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Chemical mutations

• One example is nitrous acid which converts
  adenine to a form that no longer pairs with
  thymine, but will pair with cytosine
• Nucleotide analogs are another type of chemical
  mutagen that mimic normal bases and cause
  mistakes in base pairing

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Radiation

• X rays, gamma rays can cause serious mutations
  due to free radicals
• Ultraviolet light causes thymine dimers to form.
• Adjacent thymines link and are read as one
  thymine (this happens in humans too)
• Can repair this with special enzymes like
  photolyases (light repair enzymes).

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Genetic Transfer

• 1. Transformation-genes are transferred from one
  bacterium to another as naked DNA
• Shown by Griffiths experiment in 1928 on lab
  rats infected with 2 strains of Streptococcus
  pneumoniae
• S strain was encapsulated and deadly
• R strain was un-encapsulated and harmless

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Transfer continued

• 2. conjugation-requires direct cell to cell
  transfer
• And the conjugating cells must be the same
  species and opposite mating types
• Donor has a plasmid, recipient gets it!
• Gram negatives must use sex pili

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transduction

• Bacterial DNA is transferred from a donor cell to
  a recipient inside a virus that infects a
  bacteria (bacteriophage)
• Generalized transduction-pieces of bacteria DNA
  are mistakenly packaged inside protein coats and
  will transfer into new bacteria when infected by
  virus
• Specialized transduction-only certain bacterial
  genes are transferred (diptheria toxin)