Genome Organisation I

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Genome Organisation I

• Bacterial chromosome is a large (4 Mb in E coli)
  circular molecule
• Bacterial cells may also contain small circular
  chromosomes called plasmids (4kb - 100kb 1 -
  1000 copies) that code for optional functions
  such as antibiotic resistance
• Will look at circular DNA in this lecture
• The bacterial chromosome is 1000 times longer
  than the cell - it is not tangled up, but
  arranged as a series of loops (figure 24-6 in
  Lehninger)

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Supercoiling of DNA

• The tension induced in a circular DNA molecule
  (e.g. a plasmid) causes it to become supercoiled
• Supercoiling is the usual state for bacterial
  chromosomes, which consist of a number of
  independently supercoiled loops
• The process is controlled by topoisomerase
  enzymes that can cut and re-join one strand of
  the DNA
• Topoisomerases can also untangle DNA
• Refer to figures 24-9, 24-10, 24-20 in Lehninger

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Supercoiled DNA
The DNA forms coiled coils, like a telephone cable
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The topology of supercoiled circular DNA
Supercoiled form
DNA helix
Relaxed circular form
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Action of a topoisomerase
DNA topoisomerases have several functions, in all
organisms, that require DNA to be changed in
this way
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Direction of supercoiling

• Negative supercoiling is where the supercoils are
  in the opposite direction to the coiling of the
  DNA double helix
• Positive supercoiling is in the same direction as
  the helix
• Negative supercoils, when unwound, cause the
  helix to become partly strand-separated
• Positive supercoils, when unwound, cause the
  helix to become over-wound

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Linking number

• The linking number (L) is the total number of
  turns in a circular DNA
• It is made up of the number of turns in the helix
  (T) plus the number of superhelical turns (W, can
  be positive or negative)
• L T W
• L is constant for any intact circular DNA
• L can only be changed by breaking the circle
  (e.g. by a topoisomerase)

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Importance of DNA topology

• The topology (3-dimensional arrangement) of DNA
  becomes important every time DNA has to do
  something, e.g
• Replicate during cell division
• Be transcribed
• Be packaged into cell
• Be repaired if mutated
• Many of these will be discussed later in course

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Gene organisation in bacteria

• Most prokaryotic genes are arranged in units
  called operons
• These are transcribed together and allow several
  genes activities to be co-ordinated, e.g. the
  genes in a pathway responsible for the metabolism
  of a specific compound, e.g. lactose, tryptophan
• Figure 28-5 in Lehninger

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Prokaryotic gene organisationthe operon
Gene 1
RNA
Protein 1
(Polycistronic)
Promoter
Gene 1
Gene 2
RNA
Proteins 1 and 2
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The differences between prokaryotes and eukaryotes

• Eukaryotic genomes are completely different in
  their organisation compared to prokaryotic, and
  also much bigger
• Eukaryotic genes are mostly split into exons
  and introns
• Eukaryotic genomes contain a large fraction of
  non-coding (junk) DNA, prokaryotic genomes are
  nearly all coding

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Eukaryotic gene organisation
Promoter
Exon1
Intron 1
Exon2
Intron 2
Exon 3
Primary RNA transcript
splicing
mRNA
Protein