DNA Structure

3.3.1 The Chemical Composition of DNA DNA is made of 3 different components: a deoxyribose sugar, a phosphate group, and a nitrogenous base

Deoxyribose Sugar – sugar molecule containing 5 carbons that lose the OH (hydroxyl group) on its 2’ carbon Phosphate group – group of 4 oxygen atoms surrounding a central phosphorus atom found in the backbone of DNA Nitrogenous base – an alkaline, cyclic molecule containing nitrogen

The source of variation in DNA is found in the nitrogenous bases. 4 nitrogenous bases exist: Purines: Adenine (A) and Guanine (G) – both are double-ringed structures Pyrimidines: Thymine (T) and Cytosine(C) – single-ringed structures

3.3.2 DNA Bases

Structure of Nucleotides Each of DNA’s 4 NT’s comprises a deoxyribose sugar attached to a phosphate group and a nitrogenous base The nitrogenous base is attached to the 1’ C of the sugar by a glycosyl bond – a bond between a sugar and another organic molecule by way of an intervening nitrogen or oxygen atom. The phosphate group is attached to a 5’ C by an ester bond  phosphodiester bond

RNA is usually single-stranded and generally does not form double helices. The carbon atoms in the five-carbon sugar are numbered clockwise, starting with the carbon atom to the right of the oxygen. The first one is known as the one prime (1’). In DNA, the nitrogenous base is attached to the 1’ carbon by a glycosyl bond

Building a Model for DNA Structure Many scientists were working on the structure: Linus Pauling (California), Rosalind Franklin and Maurice Wilkins (London), and James Watson and Francis Crick (Cambridge University). Franklin and Maurice were using X-ray diffraction analysis of DNA to determine its structure. The X-rays are deflected by the atoms in the molecule, producing a pattern of lighter and darker lines on photographic film. The pattern that is produced is analyzed and the 3-D structure is determined using mathematics.

The pattern revealed that DNA has the shape of a helix or corkscrew, is about 2nm in diameter, and has a complete helical turn every 3.4nm (1nm = m). Animations HHMI's BioInteractive - Watson constructing base pair models

DNA Structure: The Double Helix DNA consists of 2 antiparallel strands of nucleotides. Antiparallel – parallel, but running in opposite directions; the 5’end of one strand of DNA aligns with the 3’end of the other strand in a double helix.

Complementary Base Pairing – pairing of the nitrogenous base of one strand of DNA with the nitrogenous base of another strand; AT & GC Proposed by Erwin Chargaff (1949)Erwin Chargaff HHMI's BioInteractive - Building blocks of DNA

Purines are nitrogenous bases that have 2 rings of carbon: adenine and guanine Pyrimidines are nitrogenous bases that have only 1 ring of carbon: thymine and cytosine. One purine must combine with one pyrimidine for the complementary base pairing, otherwise the DNA structure would look “wonky”. Nucleotides are 0.34nm apart To complete one turn of the helix, you need 10 nucleotides

The bases of the two DNA strands are bound by hydrogen bonds. Hydrogen bonds on their own are relatively weak, but multiple hydrogen bonds stronger. There are 2 hydrogen bonds between A and T, and 3 hydrogen bonds between G and C. This is why A cannot bind with C and G cannot bind with T.

The 2 strands of DNA run anti-parallel. One strand runs in the 5’ to 3’ direction, the other runs n the 3’ to 5’ direction. The 3’ end terminates with the hydroxyl group of the deoxyribose sugar. The 5’ end terminates with a phosphate group. 5’ – ATGCCGTTA – 3’ 3’ – TACGGCAAT – 5’ 3.3.3/4: DNA nucleotides and covalent bonds HHMI's BioInteractive - DNA packaging

DNA structure

7.1.2 Nucleosomes DNA is bonded to proteins called HISTONES. 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.

7.1.3 Chromosomes Nucleosomes help to supercoil chromosomes and help to regulate transcription (the process of converting DNA  RNA) 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.

7.1.4 Gene Sequences 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.

7.1.5 Exons and Introns 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 (next section).