1. Genome size increases (roughly) with evolutionary complexity of organism OrganismGenome (kb)Form Virus MS24RNA Virus 50Linear DNA Other viruses5-300Circular DNA Bacteria700-5000Circular DNA Yeast13,000Linear DNA Arabidopsis (plant)100,000arranged Fruit fly165,000as Mouse3,000,000several Human3,000,000chromosomes

2. Supercoiling of DNA The tension induced in a circular DNA molecule 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 6.1 and 6.4 in Hartl

3. Eukaryotic chromosomes In metaphase of mitosis, chromosomes can be seen under microscope - they have a compact rod-like structure The ends of chromosome are called telomeres, function is to protect the ends of the DNA Near the middle is the centromere, function is to attach to spindles during cell division and ensure correct segregation Telomeres and centromeres contain special DNA sequences and associated proteins Telomeres are replicated differently from the rest of the genome - see figure 6.27 in Hartl Different regions of the chromosome can be stained with dyes (e.g. Giemsa) giving a characteristic banding pattern See figure 6.20 in Hartl

4. Chromosome structure - packing ratio Packing ratio is the length of the DNA divided by the length into which its packaged Smallest human chromosome (21) has 4x10 7 bp of DNA, 10 times size of E. coli genome Equivalent to 14mm of extended DNA In most condensed state the chromosome is about 2 m long Packing ratio = 14000/2 = 7000 So, there must be an efficient packaging mechanism

5. Chromatin and histones The first level of DNA packing is the chromatin fibre Chromatin is formed by wrapping the DNA around complexes of the 4 histone proteins (2 molecules each of histones H2A, H2B, H3, H4) to form beads on string arrangement Chromatin is of 2 different types - euchromatin (where most of the active genes are) and heterochromatin (no active genes). Some regions of genome can switch between these 2 states (facultative heterochromatin) See figure 6.8 in Hartl

6. Higher level DNA packing To achieve packing ratio of 7000, chromatin is organised into several levels of complex folded and coiled structures See figure 6.10 in Hartl

7. Unique and repeated DNA If eukaryotic DNA is melted and allowed to re-anneal, it does so in 3 distinct phases See figure 6.18 in Hartl The explanation is that there is highly repetitive DNA (which re-anneals quickly), moderately repetitive DNA (intermediate) and unique or single copy DNA (re-anneals slowly)

8. Classes of eukaryotic DNA Highly repetitive: –Bits of old virus genomes –Simple sequence repeats e.g. CACACA…. –Special sequences such as centromeres Moderately repetitive: –Other old virus genomes –Multi-gene families, e.g. ribosomal RNA Single-copy: –Most normal genes

9. Stability of genomes Most DNA is very stable - inherited without changes from parents (except 1/10 6 mutation rate) and does not change in the lifetime of the cell Some DNA is unstable, i.e. can move about in the genome - called transposable elements or transposons First observed by Barbara McLintock in the 1940s, as different coloured segments in corn cobs (see section 6.8 in Hartl) Explanation was transposon in the maize genome that affects expression of genes controlling pigment - jumps to different locations in DNA of different segments of the corn-cob, switching colour in those segments Many other examples, in many organisms (including humans). Often they are repetitive in the genome