All living things have a genetic molecule

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All living things have a genetic molecule

• In prokaryotes and eukaryotes DNA
• Even in viruses, genetic material is DNA or RNA
• Directs day to day operations of the cell
• Provides instructions for making a new individual
• passed on to daughter cells during cell division
• Eubacteria and Archaea differ in genome structure
• Focus is on Eubacteria

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Chromosome Organization

• Most bacteria genomes are single, covalently
  closed, circular DNA molecule
• Others may have a linear molecule or several
  pieces
• DNA is negatively supercoiled
• DNA is slightly underwound
• Underwinding carried out by DNA gyrases
• Makes separation of strands easier during
  transcription
• Supercoiling creates twisted loops
• A section of supercoiled DNA is a domain
• About 50 domains estimated to exist

3
Packaging of E. coli DNA
Note arrows one shows where the DNA has been
nicked, relaxing the supercoiling. The other
points to a supercoiled region. That supercoiling
can be relaxed in ONE PLACE means that the DNA is
constrained in places.
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Whats in the DNA

• Genes. Lots of genes.
• Many eukaryotes have non-coding DNA junk
• Up to 90 or more of DNA is junk in eukaryotes
• Relatively little spacer DNA between genes in
  prokaryotes
• Some Archaea have introns, otherwise, no.

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Bacteria have transposons

• A bacterial genome has a dozen or so
• jumping genes, pieces of DNA that copy
  themselves
• DNA either cuts out, inserts elsewhere or
• Copies itself and copy inserts elsewhere
• Simple Insertion sequences
• Code for transposase and repressor
• Composite transposons
• Insertion sequences which flank other DNA
• Typically antibiotic resistance genes

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Plasmids

• Plasmids small, circular, independently
  replicating pieces of DNA with useful, not
  essential info.
• 1 to 10 of genome
• Types of plasmids
• Fertility,
• resistance,
• catabolic,
• bacteriocin,
• virulence,
• tumor-inducing, and
• cryptic

http//www.estrellamountain.edu/faculty/farabee/bi
obk/14_1.jpg
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About plasmids-1
Fertility plasmid genes to make a sex pilus
replicates, and a copy is passed to another
cell. Resistance plasmid genes that make the
cell resistant to antibiotics, heavy
metals. Catabolic plasmid example, tol plasmid
with genes for breaking down and using toluene,
an organic solvent.
www.science.siu.edu/.../ micr302/transfer.html
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About plasmids-2

• Bacteriocin plasmid codes for bacteriocins,
  proteins that kill related bacteria.
• Virulence plasmid has genes needed for the
  bacterium to infect the host.
• Tumor-inducing plasmid The Ti plasmid found in
  Agrobacterium tumefaciens. Codes for plant
  growth hormones. When the bacterium infects the
  plant cell, the plasmid is passed to the plant
  cell and the genes are expressed, causing local
  overgrowth of plant tissue gall. Very useful
  plasmid for cloning genes into plants.
• Cryptic who knows?

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DNA replication figures
Because of requirement for 5to 3 synthesis,
lagging strand must repeatedly top and start
needs an RNA primer each time.
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When youre small, you need to be stingy and quick

• Look for many ways that bacteria can save energy
  and respond quickly to changes in environment.
• E. coli needs 30 minutes to replicate its DNA,
  but only 20 minutes to divide into two. How? It
  gets a head start.

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Sigma subunit recognizes promoter region of DNA
http//cats.med.uvm.edu/cats_teachingmod/microbiol
ogy/courses/gene_regulation/images/dij.tc.elong1.j
pg
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Sense, antisense
Compare the sense strand of the DNA to the
mRNA. Note that mRNA synthesis will be 5 to 3
and antiparallel.
http//users.rcn.com/jkimball.ma.ultranet/BiologyP
ages/S/SenseStrand.gif
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The Process of Transcription-2

• RNA synthesis continues (Elongation), only one
  DNA strand (template) is transcribed.
• RNA nucleotides, complementary to bases on DNA
  strand, are connected to make mRNA
• Termination must be a stop sign, right?
• In bacteria, hairpin loop followed by run of Us
  in the RNA. Of course, the DNA must code for
  complementary bases and a run of As. See next.
  Most common. OR
• Termination factor rho. Enzyme. Forces RNA
  polymerase off the DNA.

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Termination of Transcription in Bacteria
The hairpin loop destabilizes the interactions
between the DNA, mRNA, and polymerase U-A
basepairs are very weak, and the complex falls
apart.
http//www.blc.arizona.edu/marty/411/Modules/Weave
r/Chap6/Fig.0649ac.gif
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Transcription in prokaryotes

• As mRNA is made, it is ready to use.
• Info from more than one gene is typically found
  on one mRNA molecule.
• Simpler process than in eukaryotes
• no introns to remove
• no cap or poly-A tail
• no nuclear membrane to transport through
• Transcription is expensive each NTP leaves
  behind 2 Pi like spending 2 ATP for every base
  used.

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Simultaneous transcription and translation

• No processing, no nucleus mRNA already where the
  ribosomes are, so they get started quickly.

http//opbs.okstate.edu/petracek/Chapter202720F
igures/Fig2027-30.GIF