Composition and Structure of DNA


Conserved through evolution, nucleic acids store and transmit hereditary information. They’re
are the most important macromolecules for the continuity of life, carrying a cell’s genetic blueprint and all the instructions for proper function. 


There are two main types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It’s stored in the nucleus of eukaryotes and is made from nucleotides that join together to form a strand.


TL; DR

  • Nucleotides are the ‘building blocks’ of DNA and are composed of three components: a deoxyribose sugar, phosphate, and nitrogen base.
  • Nitrogen bases can be either pyrimidines or purines which is a classification of their structure.
  • DNA is a two stranded molecule whose shapes resembles a double helix.


DNA double helix illustration
 Author: Genome Research Limited | Sourceyour genome  | License: CC BY 4.0

Nucleotides are the Building Blocks


DNA (and RNA) are made up of monomers called nucleotides. Each individual nucleotide is made up of three components (i) a nitrogenous base (ii) a pentose (five-carbon) sugar, and (iii) a phosphate group.


Sugars


Deoxyribose
 and ribose are the two sugars that are found in DNA and RNA, respectively. On the ribose sugar, a hydroxyl group (-OH) is attached at the second carbon position. For deoxyribose, the second carbon is missing an oxygen (O), hence de-oxy-ribose.


The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′–3′ phosphodiester linkage.


Phosphate Groups


The phosphate group of one nucleotide bonds covalently with the sugar molecule of the next nucleotide, forming a polymer. Since these phosphate groups line the ‘outside’ of DNA, the sugar–phosphate groups are considered the “backbone” of the molecule. The phosphate group is attached to the 5′ carbon of one nucleotide and the 3′ carbon of the next nucleotide. In its natural state, each DNA molecule is actually composed of two single strands held together along their length with hydrogen bonds between the bases.


Nitrogen Bases


Nitrogen bases are bases because they contain an amino group. Amino groups have the potential of binding an extra hydrogen, and doing so decreases the hydrogen ion concentration in its environment making the environment more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).


Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, the nitrogenous bases are simply known by their symbols A, T, G, C, and U. DNA contains A, T, G, and C whereas RNA contains A, U, G, and C.

Purines


Adenine and guanine are classified as purines. The primary structure of a purine is two carbon-nitrogen rings.  

Purine Nitrogen Bases in DNA

Pyrimidiness


Cytosine, thymine, and uracil are classified as pyrimidines which have a single carbon-nitrogen ring as their primary structure.

Pyrimidine Nitrogen Bases in DNA
Nucleotide
 Author/Source: OpenStax | License: CC BY 4.0
 Author/Source: OpenStax | License: CC BY 4.0

Key Terms

  1. Nucelotide – structural monomer of nucleic acid; composed of a phosphate group, pentose sugar, and nitrogen base.
  2. Amino Group – nitrogen functional group
  3. Purine – structural classification of nitrogen bases that have two carbon-nitrogen rings
  4. Pyrimidine – structural classification of nitrogen bases that have a single carbon-nitrogen rings

Base Pairing between Nucleotides


Only certain types of base pairing are allowed. For example, a certain purine can only pair with a certain pyrimidine. This means A can pair with T, and G can pair with C. This is the base complementary rule. In other words, the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG. During DNA replication, each strand copies itself, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.

Discovery of the Double Helix


The DNA double-helix resembles a structure where the two DNA strands ‘twist’ around one another. The sugar and phosphate lie on the outside of the helix, forming the backbone of the DNA. The nitrogenous bases are stacked in pairs, like the steps of a staircase. The pairs are bound to each other by hydrogen bonds. Every base pair in the double helix is separated from the next base pair by 0.34 nm. Importantly, the two strands of the helix run antiparallel to each other. This means that the direction of each each strand is in opposite directions. We view the directionality of a DNA strand by looking at the 5′ and 3′ ends. When we say DNA is antiparallel, we mean that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. This orientation is important for DNA replication as well as many nucleic acid interactions.


James Watson and Francis Crick proposed that the DNA is made up of two strands that are twisted around each other to form a right-handed helix, called a double helix. Purines and pyramidines form base-pairs through hydrogen bonding which keep the two DNA stands stable. However, the nucleotides form base pairs with a specific partner. Adedine only base-pairs with thymine and guanine only base-pairs with cytosine.

DNA double helix illustration
  1. Fowler, Samantha, Rebecca Roush, and James Wise. “Molecular Biology.” Concepts of Biology. OpenStax, 2013. Houston, TX. https://openstax.org/books/concepts-biology/pages/9-1-the-structure-of-dnaLicense: CC BY 4.0 | License TermsEdited & Adapted | Access for free https://openstax.org/books/concepts-biology/pages/1-introduction
  2. Zedalis, Julianne, and John Eggebrecht. “3.5 Nucleic Acids.” Biology for AP® Courses, p. OpenStax, 2018. Houston, TX. https://openstax.org/books/biology-ap-courses/pages/3-5-nucleic-acidsLicense: CC BY 4.0 | License TermsEdited & Adapted | Access for free https://openstax.org/books/biology-ap-courses/pages/1-introduction
  3. Clark MA, Douglas M, Choi J. “3.5 Nucleic Acids.” Biology 2e. OpenStax, 2018. Houston, TX. https://openstax.org/books/biology-2e/pages/3-5-nucleic-acids. License: CC BY 4.0 | License TermsEdited & Adapted | Access for free https://openstax.org/books/biology-2e/pages/1-introduction.
  4. MiTx Bio. “The Structure of DNA.” YouTube, 5 2015, https://www.youtube.com/watch?v=o_-6JXLYS-k.