1. 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)

3. 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

4. Supercoiled DNA The DNA forms coiled coils, like a telephone cable

6. The topology of supercoiled circular DNA Relaxed circular form DNA helix Supercoiled form

7. 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

8. 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

9. 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)

10. 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

11. 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

12. Prokaryotic gene organisation: the operon PromoterGene 1Gene 2 Gene 1 RNA Protein 1 Proteins 1 and 2 (Polycistronic)

13. 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

14. Eukaryotic gene organisation PromoterExon1Intron 1Exon2Intron 2Exon 3 mRNA Protein Primary RNA transcript splicing