DNA Structure

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DNA, or deoxyribonucleic acid, is a complex biological molecule found predominantly within the nucleus of the cells of all living organisms. There are three different types of DNA- A, B and Z. B form is by far the most abundant at neutral pH. It is the typical right-handed double helix structure found in most organisms. Type A DNA is similar in structure but much thicker than type B and with shorter distances between base pairs. Type Z is completely different to the other two types in the sense that it is a left-handed double helix rather than right-handed. The rest of this page describes the B form of DNA in more detail.

Each nucleotide within the DNA structure is composed of three subunits- a deoxyribose sugar, a phosphate and one of four organic bases: adenine (A), cytosine (C), guanine (G) and thymine (T).  Adenine and guanine are derivatives of purine and are therefore called purines, whereas cytosine and thymine are derivatives of pyrimidine and hence called pyrimidines [1]. All four of these bases are planar [2] and can be arranged in any order to create a strand of DNA. Single strands of DNA are almost never seen in natural biology as two strands can join together via hydrogen bonds between specific base pairs to form the more stable right-handed double helix structure. The two strands of DNA in a double helix run anti-parallel to one another. This essentially means they have opposite polarity (one strand runs 5' to 3', whilst the other runs 3' to 5'). The 5' carbon has a phosphate group (PO4 3-) attached to it and the 3' carbon a hydroxyl group (OH) [3]. This is what gives the DNA molecule directionality.

A hydrogen bond is a weak electrostatic force of attraction between an electronegative atom (e.g. O, N or F) and a hydrogen atom bonded to another electronegative atom. Which bases pair with one another is very specific due to their structures only being able to form hydrogen bonds in certain places. Adenine pairs with thymine by two hydrogen bonds and cytosine pairs with guanine by three hydrogen bonds (Berg et. al, 2011, pp.5). Between the G-C base pairs there are 3 hydrogen bonds which makes this bond pair stronger than the A-T base pair. This third hydrogen bond in G-C base pairs occurs between the additional exocyclic amino group on guanine and the C2 keto group on cytosine [4]. This explains why G-C rich DNA requires higher temperatures to denature it as there is greater bonding between base pairs. The pairing in DNA is highly specific- adenine only pairs with thymine and likewise, guanine only pairs with cytosine. This is because a purine can ony base pair with a pyrimidine (i.e. no purine-purine or pyrimidine-pyrimidine base pairs can occur). This is because the distance is too great for hydrogen bonds to form between two pyrimidines and there is not enough space (the diameter of the helix is just 20 Å [5]) for two purines to pair within the helix[6]

The phosphate-sugar framework/backbone is on the outside of the molecule so as to protect the organic bases on the inside. The bonds in DNA are phosphodiesterbonds. The bases are almost perpendicular to the framework and each turn of the helix is 3.4 nm [7]. With there being 10 bases within each turn, each adjacent base is separated by 0.34 nm [8]. The phosphate-sugar framework does not however completely contain the bases inside. Each molecule of DNA contains a major and minor groove- the major being deep and broad and the minor being shallow and thin. Proteins bind to the floors of these grooves specifically by hydrogen bonds and Van der Waals' forces [9]. This process is essential for many biological pathways[10]

References:

  1. Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition
  2. Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition
  3. Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition
  4. BioWiki, available at:fckLRhttp://biowiki.ucdavis.edu/Genetics/Unit_I%3A_Genes,_Nucleic_Acids,_Genomes_and_Chromosomes/Chapter_2._Structures_of_nucleic_acids/B-Form,_A-Form,_Z-Form_of_DNA fckLRlast accessed 27.11.14
  5. Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition
  6. DNA tutorial, available at: http://www.dnatutorial.com/BasePairing.shtml last accessed 27.11.14
  7. BioWiki, available at:fckLRhttp://biowiki.ucdavis.edu/Genetics/Unit_I%3A_Genes,_Nucleic_Acids,_Genomes_and_Chromosomes/Chapter_2._Structures_of_nucleic_acids/B-Form,_A-Form,_Z-Form_of_DNA fckLRlast accessed 27.11.14
  8. Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition
  9. Atlas of Genetics and Cytogenetics in Oncology and Haematology, available at: http://atlasgeneticsoncology.org/Educ/DNAEngID30001ES.html last accessed 27.11.14
  10. About Education, available at: http://chemistry.about.com/od/chemistryglossary/g/hbond.htm last accessed 27.11.14






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