DNA

• DNA = deoxyribonucleic acid

  it consists of 2 long polynucleotide chains composed of 4 nucleotide subunits - each chain is DNA stranded
• 2 strands run anti parallel to eachother and hydrogen bonds between the base portions of the nucleotides holds the 2 strands together.
• nucleotide is composed of a 5-carbon sugar, phosphate group & a nitrogen containing base
• nucleotides are covalently linked together in a chain via the sugar & phosphates, this forms a ‘backbone’ of alternating sugar-phosphate
• to form nucleic acid polymers, nucleotides are joined together by phosphodiester bonds between 5’ & 3‘ carbon atoms of adjacent sugar rings
• the bases on one side of the helix pair with complementary bases on the other side (A pairs w/ T; G pairs w/ C)
• To create a phosphodiester bond:

  1. the 5’ group of a nucleotide triosphosphate is held close to the free 3’ hydroxyl group of a nucleotide chain
  2. the 3’ hydroxyl group forms a bond to the phosphorus atom of the free nucleotide closest to 5’ oxygen atom - bond between 1st phosphorus atom and oxygen atom linking it to the next phosphorus breaks
  3. a new phosphodiester bond now joins the 2 nucleotides and a pyrophosphate (P-O-P) group has been removed as its hydrolysed which releases a lot of energy and drives reaction forward to completion.
• in the double helix:

  nucleotides are covalently linked so are held by hydrogen bonds between base pairs.

  all bases are inside of the double helix whilst he sugar-phosphate backbone is on the outside.

  the strands run ant-parallel
• purine is paired with pyrimidine, as this is the most energetically favourable arrangement - since each base pair is of similar width.
• A and T have 2 hydrogen bonds

  C and G have 3 hydrogen bonds

  the bases can pair the polynucleotide chains that contain them are anti-parallel
• alpha helix structure maximised the efficiency of base pairing as the double stranded DNA winds into a right-handed helix.

  one complete turn per 10.4 base pairs - this creates 2 grooves (major + minor)
• in eukaryotic DNA there is 22 pairs of homologous chromosomes & 1 pair of non-homologous chromosomes
• each human cell nucleus contains 2 copies of each chromosome (except in gametes and some highly specialised cell types).

  each chromosome has a single lone linear DNA molecule along with the proteins that fold the fine DNA thread into more compact structure
• chromosomes associated with other proteins are required fro the processes of gene expression, DNA replication and DNA repair
• centromeres are attachment sites for the 2 halves of replicated chromosome (sister chromatids):

  • not always in centre of chromosome
  • keep chromosomes properly aligned during cell division
• telomeres are repetitive stretches of DNA located at ends of linear chromosomes
• telomeres protect the ends of chromosomes to keep them from unravelling
• in many types of cells, telomeres loose a bit of their DNA every time a cell divides.

  when all telomere is gone, the cell can to replicate and will die
• white blood cells and dividing cells have telomerase that prevents their chromosomes from losing telomeres so that the cells live longer.

  telomerase adds TTAGGG repeats to the ends of chromosomes
• In cancer, chromosomes of malignant cells do not lose their telomeres so have uncontrolled growth
• DNA packaging is required as it is a large molecule and it is difficult to fit into the nucleus. this is accomplished by specialised proteins that bind to the DNA and fold it - generating a series of organised coils and loops that prevent DNA from becoming an unmanageable tangle.
• the basic unit of dna packing is called a nucleosome which consists of two turns of double stranded DNA wrapped around eight histone proteins forming a bead-like structure
• DNA is accessible to enzymes in the cell that replicate it, repair it and use its genes to produce RNA molecules and proteins.
• human genome DNA length = 3.1x10^9 nucleotide pairs

  number of genes coding for proteins = ~20,000

  largest gene coding for proteins = 2.5x10^6 nucleotide pairs
• DNA at interphase is still tightly packed but can decondense to allow access to specific sequences for gene expression, DNA repair and replication then recondense.
• chromatin is the diffused mass of DNA found in interphase cells.
• heterochromatin = chromatin regions that are condensed during interphase and are transcriptionally inactive as it lacks genes so stains more densely.
• euchromatin = chromatin regions that are decondensed and DNA sequences are being transcribed into DNA, transcriptionally active so stains lightly
• proteins binding to DNA to form eukaryotic chromosomes are divided into two classes: histones and non-histones

  complex of both with nuclear DNA = chromatin
• histones are proteins that make up the core of the chromosome and are wrapped around DNA. They are responsible for most basic level of chromosome packing.
• Each individual nucleosome core particle consists of a complex of 8 histone proteins - 2 molecules each of histone H2A, H2B, H3 & H4.

  this histone o amber forms a protein core around which the double-stranded DNA is winded.

  147 nucleotide pairs wrap 1.7x around the histone core.

  each nucleosome separated from the next but linker DNA (few nucleotide pairs up to ~80)

  nucleosomes repeat as intervals of ~200 nucleotide pairs
• To pack nucleosome into a chromatin fibre (zig-zag model):

  • chromatin in a living cell probably rarely adopts the beads on a strong form
  • nucleosomes packed on top of each other - DNA more condensed
  • nucleosome or nucleosome linkages formed by histone tails, notably H4 tail
• DNA packaging:

  1. Short regions of DNA Double helix start to wind up around chromatin to form ‘beads-on-a-string’
  2. they then adopt the zig-zag model, so more DNA is compacted
  3. the chromatin fibre is the folded into loops so that it’s accessible for machinery of the cell
  4. results in each DNA molecule being packaged Into a mitotic chromosome that is 10,000 fold shorted than its fully extended length
• What’s the difference between rRNA and mRNA?

  rRNA = ribosomal RNA that creates ribosomes

  mRNA = messenger RNA that is used in translation by ribosomes as instructions for amino acids
• What’s the relevance of the nuclear organiser?

  lots of RNA polymerase are in one place, where multiple copies of rRNA genes are brought together.
• Why do we need multiple copies of genes that generate rRNA?

  We need lots of rRNA
• • DNA is wound around histone to form nucleosome which is known as chromatin
  • tightly packed chromatin is called heterochromatin and inhibits transcription
  • loosely packed chromatin is called euchromatin which enables transcription and stains lightly
• DNA is used as a template for transcription to generate RNA which include:

  • rRNA used to create ribosomes (recruits cap)which are essential for translation to generate protein
  • tRNA
  • mRNA possesses a cap