Part 8.7 The chemistry of organic nitrogen (organonitrogen) compounds

Doc Brown's Chemistry Advanced Level Pre-University Chemistry Revision Study Notes for UK KS5 A/AS GCE IB advanced level organic chemistry students US K12 grade 11 grade 12 organic chemistry

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Part 8.7 Amine bases and the hydrogen bonding in DNA and RNA

The context - the structure of DNA, the carrier of genetic code

DNA (deoxyribonucleic acid) is a large molecule essential for life and cell replication and is another example of a natural polymer.

It is the natural polymer found in all living organisms and viruses too.

DNA encodes genetic instructions for the development and functioning of living organisms and viruses e.g. every protein molecule is synthesised by other molecules reading the genetic code and combining the right amino acids in the right order.

Most DNA molecules consist of two polymer chains, made from four different monomers called nucleotides, connected in the form of a double helix (right diagram).

RNA (ribonucleic acid) is mainly single stranded.

Nucleotides form the building blocks of DNA or RNA and an individual nucleotide consists of three molecular bits combined together - (i) a phosphate group, (ii) an organic base (adenine, cytosine, guanine, thymine and uracil replaces thymine in RNA), and a cyclo-pentose sugar (simplified diagram on left).

In DNA the sugar unit is based the pentose molecule, deoxyribose, and in RNA the sugar unit is on the pentose molecule, ribose

A DNA molecule consists of two 'molecular' strands coiled together to form a double helix, but how is this helix held together?

The strands are linked by a series of complementary base pairs joined together by weak hydrogen bonds (base-pairing H bonds shown here as ):

There four bases in DNA holding the structure together (the two molecular strands) always form the same pairing.

(i) adenine (A) with thymine (T) i.e. AT, and (ii) cytosine (C) with guanine (G) i.e. CG whererepresents the weak (but crucial) intermolecular attractive force between pairs of bases, called the hydrogen bond.

It is these cross-links of hydrogen bonds that holds the two DNA strands together as a double helix.

Part of the double helix structure is shown in the diagram below, illustrating how the DNA is held together by the llll hydrogen bonds.

The molecular structure of the five crucial bases involved in the structure and coding of DNA and RNA

The following two diagrams show the molecular structure of the five bases that hold the strands of DNA and RNA together.

Three of them are based on one hexagonal ring of carbon and nitrogen atoms.

The names and molecular formulae are:

Thymine C₅H₆N₂O₂,  cytosine C₄H₅N₃O  and  uracil C₄H₄N₂O₂.

The molecular structures are shown as both structural formulae and skeletal formulae.

 

The other two bases are based on one hexagonal ring fused with a pentagonal ring, both of carbon and nitrogen atoms.

The names and molecular formulae are:

Adenine C₅H₅N₅, and guanine C₅H₅N₅O.

The molecular structures are shown as both structural formulae and skeletal formulae.

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