HOME PAGE * SEARCH * basic Chemistry age ~14-16 * Advanced Chemistry age ~16-19

Advanced Level Chemistry: Organic nitrogen compounds - amine bases in DNA and RNA

Organic Chemistry Part 8. Chemistry of organo-nitrogen compounds

Part 8.7 The structure of amine bases and their role in the hydrogen bonding of DNA (double helix) and RNA molecules

[Author ©  Dr Phil Brown PhD: Doc Brown's exam revision notes suitable for A level chemistry students of advanced pre-university/college level organic chemistry courses:  revision notes on organo-nitrogen compounds [page updated April 12th 2026 *]

 email doc brown - comments - query? * [privacy, cookies and disclaimer]

 All my advanced level organo-nitrogen compound chemistry notes

 All my advanced A level organic chemistry notes

 Index of GCSE level oil and basic organic chemistry notes

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

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

TOP OF PAGE 

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 C5H6N2O2,  cytosine 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.

TOP OF PAGE 

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.

TOP OF PAGE 

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.

Website content © Dr Phil Brown 2000+. All copyrights reserved on Doc Brown's Chemistry revision notes, images, quizzes, worksheets etc. Copying of website material is NOT permitted.

[SEARCH BOX]

All my advanced level organo-nitrogen chemistry

All my advanced level organic chemistry notes

All my advanced level inorganic chemistry notes

All my advanced level theoretical chemistry notes

Website content © Dr Phil Brown 2000+. All copyrights reserved on revision notes, images, quizzes, worksheets etc. Copying of website material is NOT permitted. Exam revision summaries & references to A level chemistry course specifications are unofficial. Website content © Dr Phil Brown 2000+. All copyrights reserved on these organic chemistry exam revision notes on the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules, these A level chemistry revision notes are suitable for use of pre-university students studying AQA advanced level organic chemistry revision notes on molecular structure of the bases in DNA & RNA, Edexcel advanced level organic chemistry revision notes on the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules, OCR advanced level organic chemistry revision notes on molecular structure of the bases in DNA & RNA, IB advanced level organic chemistry revision notes on the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules, WJEC (Eduqas) advanced level organic chemistry revision notes on the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules, CIE Cambridge advanced level organic chemistry revision notes on molecular structure of the bases in DNA & RNA, CCEA advanced level organic chemistry revision notes on the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules, and useful for US grade 11 grade 12 AP honors organic chemistry courses involving molecular structure of the bases in DNA & RNA Explaining the importance of the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules in organic chemistry, What you need to know about molecular structure of the bases in DNA & RNA for organic chemistry, Explaining the use of the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules knowledge in organic chemistry, Examples of molecular structure of the bases in DNA & RNA explained when studying organic chemistry, What is the significance of the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules in organic chemistry, What is the use of molecular structure of the bases in DNA & RNA in organic chemistry  Describing and explaining the theory of the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules when studying organic chemistry, exam revision notes for molecular structure of the bases in DNA & RNA in exams, online help for the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules, revision notes for molecular structure of the bases in DNA & RNA, what do I need to learn for the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules in exams? revision summary for molecular structure of the bases in DNA & RNA, help in teaching the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules, learning notes for molecular structure of the bases in DNA & RNA, help to pass the roles of bases in the hydrogen bonding in DNA & RNA polymer molecules exam, how to prepare for examination questions on molecular structure of the bases in DNA & RNA?

TOP OF PAGE