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Advanced Level Chemistry: Organic nitrogen compounds

Part 8. 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

Part 8.8 Amine bases and the hydrogen bonding in DNA and RNA


INDEX of Organic Nitrogen Compound NOTES

All Advanced A Level Organic Chemistry Notes

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

double stranded alpha helix of DNA molecules intermolecular hydrogen bonding between base pairs of two strandsDNA (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).

structure of a nucleotide phosphate sugar pentose base that forms the molecules of DNA and RNA 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.

diagram showing the two starnds of DNA linked by hydrogen bonding between base pairs on the nucleotides


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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.

structural formula thymine cytosine uracil skeletal formula molecular structure of thymine cytosine uracil

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

The names and molecular formulae are:

Thymine C5H6N2O2cytosine C4H5N3O  and  uracil C4H4N2O2.

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

 

structural formula adenine guanine skeletal formula molecular structure of adenine guanine

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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The hydrogen bonding that holds together the double strands of the DNA helix structure

The following two diagrams show how the base pairs are linked by hydrogen bonding to hold the two strands of DNA together in the alpha helix.

 

intermolecular hydrogen bonding between thymine and adenine base pairs of two strands of DNA alpha helix molecular structure

The hydrogen bonded pair of thymine and adenine

Note

(i) There are two parallel sites of hydrogen bonding (llll) between the base pairs.

>N-Hδ+llllδ-:N<  and  O:δ-llllδ+H-N<

(ii) The lone pairs of non-bonding electrons are important because of the directional nature of the hydrogen bond, the hydrogen bond angle is ~180o.

 

intermolecular hydrogen bonding between cytosine and guannine base pairs of two strands of DNA alpha helix molecular structure

The hydrogen bonded pair of cytosine and guanine

Note

(i) There are three parallel sites of hydrogen bonding (llll) between the base pairs.

O:δ-llllδ+H-N< >N:δ-llllδ+H-N<  and  >N-Hδ+llllδ-O=C<

(ii) The lone pairs of non-bonding electrons are important because of the directional nature of the hydrogen bond, the hydrogen bond angle is ~180o.


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The base pairing in double stranded RNA

Most of RNA exists as single strands, but double stranded RNA does exist.

Like DNA, there are two base pairings that hold the strands of RNA together, cytosine ... guanine hydrogen bonding has been already described above.

Since uracil replaces thymine in RNA, the other base pair involved in hydrogen bonding is uracil ... adenine (shown below).

RNA intermolecular hydrogen bonding between uracil and adenine base pairs of two strands of double stranded RNA

The hydrogen bonded pair of uracil and adenine

Note

(i) There are two parallel sites of hydrogen bonding (llll) between the base pairs.

>N-Hδ+llllδ-:N<  and  O:δ-llllδ+H-N<

(ii) The lone pairs of non-bonding electrons are important because of the directional nature of the hydrogen bond, the hydrogen bond angle is ~180o.


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Doc Brown's Advanced Level Chemistry Revision Notes

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INDEX of Organic Nitrogen Compound NOTES

 All Advanced Organic Chemistry Notes

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