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Nucleotides & Nucleic Acids
Nucleic acids are the biopolymers, or small biomolecules, essential to all known forms of life. The term nucleic acid is the overall name for DNA and RNA. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound ribose, the polymer is RNA (ribonucleic acid); if the sugar is derived from ribose as deoxyribose, the polymer is DNA (deoxyribonucleic acid).
Nucleic acids are the most important of all biomolecules. These Nucleic acids RNA and DNA are found in abundance in all living things, where they function to create and encode and then store information of every living cell of every life-form organism on Earth. In turn, they function to transmit and express that information inside and outside the cell nucleus to the interior operations of the cell and ultimately to the next generation of each living organism. The encoded information is contained and conveyed via the nucleic acid sequence, which provides the ‘ladder-step' ordering of nucleotides within the molecules of RNA and DNA.
Strings of nucleotides are bonded to form helical backbones-typically, one for RNA, two for DNA- and assembled into chains of base-pairs selected from the five primary,or canonical, nucleobases, which are: adenine, cytosine, guanine, thymine, and uracil. Thymine occurs only in DNA and uracil only in RNA.
Nucleotide Structure
Despite the complexity and diversity of life the structure of DNA is dependent on only 4 different nucleotides Diversity is dependent on the nucleotide sequence
All nucleotides are 2 ring structures composed of:
5-carbon sugar:
D-ribose (RNA)
D-deoxyribose (DNA)
Base : Purine and Pyrimidine
Phosphate group A nucleotide WITHOUT a phosphate group is a NUCLEOSIDE.
**1. Sugar
- Base:**
Pyrimidine Purine
Sugar
PO
Base
Molecular composition and size
Nucleic acids are generally very large molecules. Indeed, DNA molecules are probably the largest individual molecules known.
Nucleic acid structures with three or four strands can form. Nucleic acids are linear polymers (chains) of nucleotides. Each nucleotide consists of three components: a purine or pyrimidine nucleobase (sometimes termed nitrogenous base or simply base ), a pentose sugar, and a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside. Nucleic acid types differ in the structure of the sugar in their nucleotides-DNA contains 2'-deoxyribose while RNA contains ribose (where the only difference is the presence of a hydroxyl group). Also, the nucleobases found in the two nucleic acid types are different: adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids are connected to each other in an alternating chain (sugar-phosphate backbone) through phosphodiester linkages. In conventional nomenclature, the carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar. This gives nucleic acids directionality, and the ends of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N- glycosidic linkage involving a nucleobase ring nitrogen (N-1 for pyrimidines and N- 9 for purines) and the 1' carbon of the pentose sugar ring. Non-standard nucleosides are also found in both RNA and DNA and usually arise from modification of the standard nucleosides within the DNA molecule or the primary (initial) RNA transcript. Transfer RNA (tRNA) molecules contain a particularly large number of modified nucleosides.
Topology
Double-stranded nucleic acids are made up of complementary sequences, in which extensive Watson-Crick base pairing results in a highly repeated and quite uniform double-helical three-dimensional structure. In contrast, single-stranded RNA and DNA molecules are not constrained to a regular double helix, and can adopt highly complex three-dimensional structures that are based on short stretches of intramolecular base-paired sequences including both Watson-Crick and noncanonical base pairs, and a wide range of complex tertiary interactions.
Nucleic acid molecules are usually unbranched, and may occur as linear and circular molecules. For example, bacterial chromosomes, plasmids, mitochondrial DNA, and chloroplast DNA are usually circular double-stranded DNA molecules, while chromosomes of the eukaryotic nucleus are usually linear double-stranded DNA molecules. Most RNA molecules are linear, single-stranded molecules, but both circular and branched molecules can result from RNA splicing reactions. The total amount of pyrimidines is equal to the total amount of purines. The diameter of the helix is about 20Å.
Types
Deoxyribonucleic acid
Deoxyribonucleic acid (DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms. The DNA segments carrying this genetic information are called genes. Likewise, other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins,
Ribosomal RNA is a major component of the ribosome, and catalyzes peptide bond formation. Transfer RNA serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA. In addition, many other classes of RNA are now known.
Primary Structure
Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bond. It is this linear sequence of nucleotides that make up the primary structure of DNA or RNA. Nucleotides consist of 3 components:
A. Nitrogenous base
- Adenine
- Guanine
- Cytosine
- Thymine (present in DNA only)
- Uracil (present in RNA only)
B. 5-carbon sugar which is called deoxyribose (found in DNA) and ribose (found in RNA).
C. One or more phosphate groups.
Secondary Structure
Secondary structure is the set of interactions between bases, i.e., which parts of strands are bound to each other. In DNA double helix, the two strands of DNA are held together by hydrogen bonds. The nucleotides on one strand base pairs with the nucleotide on the other strand.
The secondary structure is responsible for the shape that the nucleic acid assumes. The bases in the DNA are classified as purines and pyrimidines. The purines are adenine and guanine. Purines consist of a double ring structure, a six-membered and a five-membered ring containing nitrogen. The pyrimidines are cytosine and thymine. It has a single ring structure, a six-membered ring containing nitrogen. A purine base always pairs with a pyrimidine base (guanine (G) pairs with cytosine (C) and adenine (A) pairs with thymine (T) or uracil (U)).
DNA's secondary structure is predominantly determined by base-pairing of the two polynucleotide strands wrapped around each other to form a double helix. Although the two strands are aligned by hydrogen bonds in base pairs, the stronger forces holding the two strands together are stacking interactions between the bases. These stacking interactions are stabilized by Van der Waals forces and hydrophobic interactions, and show a large amount of local structural variability. There are also two grooves in the double helix, which are called major groove and minor groove based on their relative size.
The secondary structure of RNA consists of a single polynucleotide. Base pairing in RNA occurs when RNA folds between complementarity regions. Both single- and double-stranded regions are often found in RNA molecules. The antiparallel strands form a helical shape. The four basic elements in the secondary structure of RNA are helices, loops, bulges, and junctions. Stem-loop or hairpin loop is the most common element of RNA secondary structure.
Tertiary Structure
Tertiary structure refers to the locations of the atoms in three-dimensional space, taking into consideration geometrical and steric constraints. It is a higher order than the secondary structure, in which large-scale folding in a linear polymer
