7.1.1 Features of the double helix
7.1.2 The structure of the nucleosome.
7.1.3 Supercoiling.
7.1.4 Single-copy genes and repetitive regions of nuclear DNA.
7.1.5 Eukaryotic DNA with exons and introns.
It is assumed that the student will have read section 3.3 which contains the other necessary details.
DNA has a double stranded helix which has uniform diameter along its entire length.
Both helices are right handed which allows it to fit within a defined three dimensional space.
Two polynucleotide chains are 'anti-parallel', running in opposite directions
The polynucleotides are form around the outside of the helix with the bases extending into the centre.
Polynucleotide chains are held together by the bases (in centre) hydrogen bonding with bases on the opposite polynucleotide.
The hydrogen bonding is specific and known as complementary base pairing.
The double helix has major and minor groves on its outer diameter.
These groves expose chemical groups that can form hydrogen bonds.
These chemical groups within DNA are bonded to by proteins.
DNA is bonded to proteins called HISTONES.
The diagram to the left is of a nucleosome:
DNA is wound around and hydrogen bonded to eight histones.
146 DNA bases or 1.65 turns of the helix are associated with the 8 histones
The combination of DNA and histones is secured by the 'H1 linker' protein.
Supercoiling condenses the DNA molecule by a factor of X 15,000
Histones are responsible for the packaging of DNA at the different levels (diagram left).
The metaphase chromosome is an adaptation for mitosis and meiosis.
The fibre must be less condensed for transcription to occur during the interphase.
Condensing controls if the genes are transcribed or not.
A little extra info:-
The histones interact with the DNA structure to neutralize the acidity of this molecules. The DNA raps around the histones x 1.65 ( 146 base pairs)which means that although condensed in wrapping the DNA it is still accessible to polymerase molecules. This preserves the functionality of the DNA. This level of winding around the histones brings about a X 6.8 fold reduction in length. This is the so called 30nm fibre. However there is still a long way to go before achieving the 1600 (250 nm fibre) or the 10 000 reduction in the metaphase chromosome. Beads of histones still remain in regions being transcribed and also where there is polymerisation. It would appear that the histones of the nucleosome are just slightly displaces locally.
Remember that this common image of a chromosome is the metaphase chromosome when the condensation is at its maximum x 15-16, 000 times. This is an adaptation to moving around the chromosome (~1.8m long in humans) during mitosis and meiosis.
There can be no gene expression in this super condensed form.
The coiling that occurs however is not random and it is possible to still specify the location of the gene within this super condensed structure.
Audio reference.
Berkeley Cell Biology podcast: These are recording from Berkeley's undergraduate programme on aspects of cell biology. Subscribe to the RSS feed sit back and join the Berkeley students on your MP3 player.
The 'gene coding region' (about 1.5 % of our DNA) codes for a polypeptide (around 25, 000 proteins).
Around 3% of the human genome is regulatory coding for genetic switches which control development.
The non-coding region function remains unclear but can be as much as 5-45% of the total genome.
These regions are often made of highly repetitive sequences of bases each some 5-300 bases long. These are referred to as satellite regions. Due to the combination of bases in the repeating regions they tend to create dense and less dense DNA regions. These are the parts of DNA used in finger print technologies.
Challenge:
a) Can you work out why some repetitive sequences will be more dense than other repetitive sequences?
b) How is this density difference used in DNA finger printing?
Beyond the syllabus:
Recommended reading: Carroll, Sean.( 2005) Endless forms most beautiful . Norton: New York
This book (in itself is 'most beautiful' ) explores the new science of Evo-devo, Evolutionary developmental biology. The evolutionary and developmental significance of genetic switches, the tool kit of genes that explains the paradox that whilst many species share the same genes and proteins that there is such incredible diversity.
As the complexity of an organism increases so the size of the genome increases. In part this relationship holds true but there are many exceptions. Once it was thought that higher organisms would have more genes than lower organisms but studies of the genomes of different organism show that this relationship does NOT hold. That is unless you consider ferns and some flowering plants like Lilies to be the highest forms of living organisms! Indeed this is the whole basis of 'endless forms most beautiful' which is recommended above.
Variation in genome size is not because of the number of functional proteins encoded but as a consequence of the size of the non-coding regions. The size of the non-coding region and the proximity of the gene to that region may have an effect on the rate of expression of a gene.
Here's some ideas to think about which will challenge your understanding of the syllabus.
There are at least two hypothesis to explain this non-coding regions.
a) Development rate hypothesis.
b) Population size hypothesis.
a) Development rate hypothesis.
The size of the genome is related to the rate of development of the organism.
Large genomes can slow down the rate of development and the rate at which functional genes are expressed.
Changing the rate of expression changes the phenotype (back to Evo devo again !).
Therefore there maybe a selection pressure on retaining a large non-coding region even though it plays no direct role in the phenotype.
b) Population size hypothesis.
Non-coding sequences that have slight negative consequences will be removed by selection pressures in species which form large populations.
Small population species the effects of genetic drift in which random changes in alleles affect the allele frequency overcomes selection against the non-coding regions.
Selection will therefore eliminate non-coding regions from large populations species (e.g. E. coli ) but have less effect on small population species (Humans, Lung fish).
Alternative hypothesis:
Look at the graph above and using your understanding of the syllabus so far, suggest an alternative hypothesis. Discuss your idea with other students and suggest the types of experiment or sources of data that might allow you to test your idea.
Eukaryotic organisms have DNA which differs from prokaryotic organism
Eukaryotic organism have non-coding regions within the gene called introns.
These are copied when the gene is transcribed to produce pre-mRNA.
The intron-RNA is edited out to form mature mRNA.
