Download Molecular genetics of bacteria

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All living things have a genetic molecule
• In prokaryotes and eukaryotes: DNA
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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
Chromosome Structure
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• 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
Packaging of E. coli DNA
DNA is “packaged” with
proteins. Together, this is
called the nucleoid.
Note arrows: supercoiled
DNA, when ‘nicked’, does
not all unravel. Constrained
by DNA packaging proteins.
In Archaea, DNA packaging
proteins very similar to
eukaryotic histones.
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Differences in DNA organization
• Prokaryotic DNA differs from eukaryotic
• Many eukaryotes have non-coding DNA = junk
– Up to 90% junk in eukaryotes, not prokaryotes
• Eukaryotes have repeated sequences
– Few repeated sequences in prokaryotes
• Relatively little spacer (non-coding) DNA
between genes in prokaryotes
• Some Archaea have introns, but none in
Eubacteria.
• Bacteria don’t waste genetic space.
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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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Insertion sequence and
composite transposon
From Wikipedia
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Plasmids
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• Plasmids: small, usually circular, independently
replicating pieces of DNA with useful, not essential
information.
– 1% to 10% of genome
• Types of plasmids
– Fertility, resistance, catabolic,
– bacteriocin, virulence,
– tumor-inducing, and cryptic
• When is a plasmid actually part
of a complex genome?
http://www.estrellamountain.edu/faculty/farabee/biobk/14_1.jpg
About plasmids-1
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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
About plasmids-2
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• 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?
DNA is made up of genes
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• A gene is a section of DNA with the information
for making a protein (or an RNA)
– DNA codes for rRNAs and tRNAs as well
• The number of genes for different types of
proteins predicts ecology of the bacterium
– Energy metabolism: E coli has 243 genes,
Mycoplasma genitalium has only 31
• M. genitalium is a parasite, depends on host
• Many genes are grouped in operons
– Genes regulated together
Gene structure
Some sequences mark the beginning of the
information, providing binding sites for proteins.
This is followed by the information for making the
proteins.
A termination sequence signals that making mRNA
should end.
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The Genetic Code-2
http://www.biology.arizona.edu/molecular_bio/problem_sets/nucleic_acids/graphics/gencode.gif
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Transcription: making mRNA
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• RNA a polymer assembled from monomers
– Ribonucleoside triphosphates: ATP, UTP, GTP,CTP
• RNA polymerase
– Multi-component enzyme
– Needs a template, but NOT a primer
– In bacteria, a component (sigma) recognizes the
promoter as the place on DNA to start synthesis
– Synthesis proceeds 5’ to 3’, just as in DNA
• mRNA is complementary and antiparallel to the
DNA strand being copied.
Transcription-2
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• The order of nucleotides in the RNA reflects the
order in the DNA
• If RNA is complementary to one DNA strand,
then it is identical (except for T change to U) to
the other DNA strand.
Either DNA strand may
contain the gene!
Transcription just runs the
other direction.
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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/BiologyPages/S/SenseStrand.gif
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Sigma subunit recognizes promoter region of DNA
http://cats.med.uvm.edu/cats_teachingmod/microbiology/courses/gene_regulation/images/dij.tc.elong1.jpg
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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/Weaver/Chap6/Fig.0649ac.gif
Translation in bacteria:
similar to eukaryotes, Except
• First amino acid is N-formyl methionine
– Instead of methionine.
• Prokaryotic ribosomes differ in structure
– Key for effectiveness of antibiotics
• Simultaneous transcription and translation
– See below
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Ribosome schematic
http://staff.jccc.net/pdecell/proteinsynthesis/translation/elongation12.gif
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Translation-3
• Termination
– When stop codon is in A site, no tRNA binds
– GTP-dependent release factor (protein) removes
polypeptide from tRNA in P site. All done.
– Ribosomal subunits typically dissociate.
• Do a Google Search for translation animation
– Many hits. Note presence, absence of E site
– Note shape of ribosomes
– Note whether role of rRNA in catalysis is shown
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Polysomes
Multiple ribosomes attach to the
mRNA and begin translating.
Strings of ribosomes can be seen
attached to the mRNA.
http://opbs.okstate.edu/~petracek/
Chapter%2027%20Figures/Fig%2
027-29b-bottom.GIF
www.cu.lu/labext/rcms/
cppe/traducti/tpoly.html
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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/Chapter%2027%20Figures/Fig%2027-30.GIF
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