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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) 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