BSCI 1510L Literature and Stats Guide: Basic nucleotide structure

An individual DNA molecule can be extremely long: the longest human chromosome (chromosome 1) has a molecular weight of 263 000 000 base pairs (bp). Despite its enormous size, a DNA molecule is a relatively simple polymer of deoxyribonucleotide units.   Each of those deoxyribonucleotides is made up of three basic units:

• a heterocyclic nitrogenous base

• deoxyribose, a pentose sugar with a five-member ring

• a phosphate group which can confer a negative charge on the molecule

In subsequent sections of this part, we will examine each of these units in detail.

Each nucleotide contains one of four possible bases: adenine (A), thymine (T), guanine (G), or cytosine (C).  The bases can be categorized as either pyrimidines (T and C) or purines (A and G).  Both categories are heterocyclic aromatic organic compounds.  "Heterocyclic" means that the ring structure contains other kinds of atoms besides carbon (in this case nitrogen) and "aromatic" means that the ring structure is stabilized by delocalized electrons shared among the atoms forming the ring.  Pyrimidines contain a single aromatic ring, while purines contain double aromatic rings (a trait shared with another popular organic molecule, caffeine!). 

In the figures of this page, the following color key is used for identifying the elements:

black=carbon

blue=nitrogen

red=oxygen

yellow=phosphorus

white=hydrogen

Fig. 1  Structure of thymine (T), a pyrimidine.  The white lines show location of hydrogen bonds that form between bases in a DNA molecule.

Fig. 2  Structure of cytosine (C), a pyrimidine.  The white lines show location of hydrogen bonds that form between bases in a DNA molecule.

Fig. 3  Structure of adenine (A), a purine.  The white lines show location of hydrogen bonds that form between bases in a DNA molecule.

Fig. 4  Structure of guanine (G), a purine.  The white lines show location of hydrogen bonds that form between bases in a DNA molecule.

Fig. 5  Structure of deoxyribose.  In the ball-and-stick representation on the left, OH groups have been omitted in the locations where the deoxyribose attaches to other units in the DNA molecule.  Those OH groups are shown in the space-filling diagram on the right.  However, these OH groups are lost during the hydrolysis reaction in which the sugar binds to the nucleotide and phosphate groups.  So they will not be present in your final model. 

Fig. 5 shows the structure of deoxyribose.  After constructing a model of it, it can be attached to the base as shown in Fig. 6 to form a nucleoside.

Fig. 6  Attachment of deoxyribose to a base (in this case adenine) to form a nucleoside

Fig. 7  Attachment of phosphate group to deoxyribose (left: ball-and-stick, right: spacefill)

Four oxygen atoms attach to a phosphorus atom to form a phosphate group (Fig. 7).  The phosphate group can be joined to the deoxyribose units of a nucleoside by an ester bond to form a nucleotide (Fig. 8).

Fig. 8  Relationship between units making up a nucleotide; adeninosine monophosphate (AMP) in this case.  Top and bottom diagrams show the nucleotide from two angles.

Click on the following link (Java and appropriate security settings required):

http://higheredbcs.wiley.com/legacy/college/boyer/0471661791/structure/dna/dna.htm

Scroll the right frame down to the fourth paragraph where you will see links to each of the four nucleotides.  Click on the link for one of the nucleotides.  You can change the way that the nucleotide is displayed by right clicking on the modeling window and selecting "Render", then "Scheme", then either "Ball and Stick" or "CPK Spacefill".