As a class, the nucleotides may be considered one of the most important metabolites of the cell. Nucleotides are found primarily as the monomeric units comprising the major nucleic acids of the cell, RNA and DNA. However, they also are required for numerous other important functions within the cell. These functions include:
- Serving as energy stores for future use in phosphate transfer reactions. These reactions are predominantly carried out by a chemical called Adenosine Triphosphate (ATP).
- Forming a portion of several important coenzymes such as NAD+, NADP+, FAD and coenzyme A that act as catalysts for cellular activities.
- Serving as mediators of numerous important cellular processes such as second messengers in signal transduction (cellular communication) events. The predominant second messenger is called cyclic-AMP (cAMP), which is a cyclic derivative of Adenosine Monophosphate (AMP) formed from ATP.
- Controlling numerous enzymatic reactions through allosteric (structural) effects on enzyme activity.
- Serving as activated intermediates in numerous biosynthetic reactions.
Nucleoside and Nucleotide Structure and Nomenclature
The nucleotides found in cells are derivatives of the heterocyclic highly basic, compounds, purine and pyrimidine.
It is the chemical basicity of the nucleotides that has given them the common term "bases" as they are associated with nucleotides present in DNA and RNA.
There are five major bases found in cells. The bases derived from purine are called adenine and guanine, and the derivatives of pyrimidine are called thymine, cytosine and uracil. The common abbreviations used for these five bases are, A, G, T, C and U.
The purine and pyrimidine bases in cells are linked to carbohydrate (sugar) and in this form are termed, nucleosides.
Nucleosides are found in the cell primarily in their phosphorylated form. These are termed nucleotides. The most common site of phosphorylation of nucleotides found in cells is the hydroxyl group attached to the 5'-carbon of the ribose The carbon atoms of the ribose present in nucleotides are designated with a prime (') mark to distinguish them from the backbone numbering in the bases. Nucleotides can exist in the mono-, di-, or tri-phosphorylated forms.
The monophosphorylated form of adenosine (adenosine-5'-monophosphate) is written as, AMP. The di- and tri-phosphorylated forms are written as, ADP and ATP, respectively.
The nucleotides found in DNA are unique from those of RNA in that the ribose exists in the 2'-deoxy form and the abbreviations of the nucleotides contain a d designation. The mono-phosphorylated form of adenosine found in DNA (deoxyadenosine-5'-monophosphate) is written as dAMP.
Phosphodiester bond:
- Links nucleotide monomers into nucleic acid polymer chain
- Formed between 5' phosphate and 3' hydroxyl
- Gives directionality to chain (5' to 3')
Experimental determination has shown that, in any given molecule of DNA, the concentration of adenine (A) is equal to thymine (T) and the concentration of cytidine (C) is equal to guanine (G). This means that A will only base-pair with T, and C with G. According to this pattern, known as Watson-Crick base-pairing, the base-pairs composed of G and C contain three hydrogen bonds, whereas those of A and T contain two hydrogen bonds. This makes G-C base-pairs more stable than A-T base-pairs.
Utilizing X-ray diffraction data obtained from crystals of DNA, James Watson and Francis Crick proposed a model for the structure of DNA. This model (subsequently verified by additional data) predicted that DNA would exist as a helix of two complementary antiparallel strands, wound around each other in a rightward direction and stabilized by hydrogen bonding between bases in adjacent strands. In the Watson-Crick model, the bases are in the interior of the helix aligned at a nearly 90 degree angle relative to the axis of the helix. Purine bases form hydrogen bonds with pyrimidines, in the crucial phenomenon of base pairing.
The antiparallel nature of the helix stems from the orientation of the individual strands. From any fixed position in the helix, one strand is oriented in the 5' ---> 3' direction and the other in the 3' ---> 5' direction. On its exterior surface, the double helix of DNA contains two deep grooves between the ribose-phosphate chains. These two grooves are of unequal size and termed the major and minor grooves. The difference in their size is due to the asymmetry of the deoxyribose rings and the structurally distinct nature of the upper surface of a base-pair relative to the bottom surface.
If a solution of DNA is subjected to high temperature, the hydrogen bonds between bases become unstable and the strands of the helix separate in a process called thermal denaturation. Regions of the duplex that have predominantly A-T base-pairs will separate first.. In the process of thermal denaturation, a point is reached at which 50% of the DNA molecule exists as single strands. This point is the melting temperature (TM), and is characteristic of the base composition of that DNA molecule. The TM depends upon several factors in addition to the base composition. These include the chemical nature of the solvent and the identities and concentrations of ions in the solution. When thermally melted DNA is cooled, the complementary strands will again re-form the correct base pairs, in a process is termed annealing or hybridization. The rate of annealing is dependent upon the nucleotide sequence of the two strands of DNA.
DNA Structure
DNA Molecule: DNA Unzip
Cold Spring Harbor Laboratory
- Primary structure: sequence of nucleotides
- Secondary structure: path of strands - double helix
- Tertiary structure: path helix takes in space - supercoiling
The Primary Structure of DNA is its sequence of nucleosides. Nucleosides are link together by phosphodiester linkages to form a single strand as shown in the figure below. The phosphate ester links the 3' and 5' oxygens of two sugars.
The DNA secondary structure is a double helix formed by 2 anti-parallel DNA strands bind together by hydrogen bonding between bases on opposite strands.
The tertiary structure of DNA is described as supercoiling. In addition to the a-helix of DNA there is an additional level of twisting = Supercoiling. Discovered by Jerome Vinograd (1963) at Caltech; noticed multiple bands of DNA in preparations of circular DNA (plasmids). Circular DNA with no superhelical turns = relaxed (takes energy to supertwist)
Superhelical turns serve two purposes:
- yield a more compact shape
- can result in unwinding of DNA helix (aids in replication)
Two enzymes work to maintain supercoiling in DNA. Topoisomerases relax supercoiled DNA, and DNA gyrase introduces supercoiling.
