Download E coli

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)
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
Supercoiled DNA
The DNA forms coiled coils, like a telephone cable
The topology of supercoiled
circular DNA
Supercoiled
form
DNA helix
Relaxed circular form
Action of a topoisomerase
DNA gyrase cuts DNA,
passes ends through
and re-joins them
DNA topoisomerases have several functions, in all organisms,
that require DNA to be changed in this way
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
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)
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
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
Prokaryotic gene organisation:
the operon
Gene 1
RNA
Promoter
RNA
Protein 1
Gene 1
Gene 2
(Polycistronic)
Proteins 1 and 2
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
Eukaryotic gene organisation
Promoter
Exon1
Intron 1
Exon2
Intron 2
Exon 3
Primary RNA transcript
splicing
mRNA
Protein