Fundamentals of Molecular Biology. Part 1: Molecular Biology of the Cell - A. N. Oagurtsov 2011

Nucleic Acids and Proteins
Nucleotides

All information regarding the Structure and functioning of any living Organism is stored in encoded form within its genetic material, primarily composed of deoxyribonucleic acid (DNA). In most organisms, DNA is a long, double-stranded polymer molecule. Genes are individual genetic elements with strictly specific nucleotide sequences that encode specific products. Some encode Proteins, while others encode RNA molecules only.

The information contained in genes that encode proteins (structural genes) is decoded through two successive processes: RNA Synthesis (METABOLISM/31.html">Transcription) and Protein Synthesis (Translation). First, Messenger RNA (mRNA) is synthesized on a specific region of DNA acting as a template. Then, through the coordinated action of a multicomponent system involving Transfer RNA (tRNA), mRNA, Enzymes, and various protein factors, the protein molecule is assembled. All these processes ensure the accurate Introduction/27.html">Translation of the Genetic information encoded in DNA from the language of NUCLEOTIDES to the language of Amino Acids.

Nucleic Acids (both DNA and RNA) are non-regular polymers whose monomers are called nucleotides.

Nucleic acids contain mainly five nucleic (nitrogenous) bases: three Pyrimidines — uracil, thymine, and cytosine — and two Purines — adenine and guanine (Figure 60).

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Figure 60 - Structure of nitrogenous bases

Nucleosides are Glycosides in which either D-ribofuranose (in ribonucleosides) or deoxy-D-ribofuranose (in deoxyribonucleosides) is linked via a glycosidic bond to the N1 atom of pyrimidine bases or the N9 atom of purine bases (Figure 61).

Ribonucleosides are components of Ribonucleic Acids (RNA), whereas deoxyribonucleosides are components of Deoxyribonucleic Acids (DNA).

Nucleotides are phosphate esters of nucleosides. Phosphoric acid is attached to one of the hydroxyl groups of the ribose (or deoxyribose) residue.

Figure 61 - Structure of Nucleotides: a - adenosine 5'-monophosphate (AMP), b - ribose, c - deoxyribose

Depending on the attachment site, 2'-, 3'-, and 5'-nucleotides are distinguished. The symbol "'" (pronounced as "prime") indicates that the corresponding number refers to the atoms of the pentose ring; the atoms of the nitrogenous base are numbered without primes.

Mononucleotides are esters of orthophosphoric acid and, consequently, contain one phosphorus atom per molecule.

Nucleotide = nucleoside + phosphoric acid =

= nitrogenous base + pentose +

+ phosphoric acid,

where the pentose is ribose in RNA and deoxyribose in DNA.

Mono- and diesters of pyrophosphoric (diphosphoric) and triphosphoric acids are widely distributed in nature (Figure 62).

Figure 62 - Structure of di- and triphosphates

Figure 63 illustrates The structure of another important molecule derived from adenosine. Here, adenosine and nicotinamide nucleotide are linked through a phosphate group, forming nicotinamide adenine dinucleotide (NAD), which plays a key role in bioenergetic processes.

Molecules with multiple hydroxyl groups can attach several phosphate groups (become phosphorylated). Figure 63 shows the Inositol trisphosphate (IP₃) molecule, which acts as one of the intracellular messengers in Cell signaling pathways.

Both molecules — ATP (Figure 62) and IP₃ (Figure 63) — contain three phosphate groups; however, to emphasize that these three phosphate groups form a chain in ATP, whereas in IP₃ they are attached to different carbon atoms, different prefixes are used: "tri-" in the case of adenosine triphosphate, but "tris-" in the case of inositol trisphosphate.

Figure 63 - Schemes of nicotinamide adenine dinucleotide (NAD) and inositol trisphosphate (IP3) molecules

In the exact same manner, a molecule with a chain of two phosphates is called a diphosphate, whereas a molecule possessing two phosphate groups attached to different carbon atoms is called a bisphosphate.