DNA and RNA: Molecular Structure and Biological Functions

Nucleic Acids: Fundamental Components of Life

Nucleic acids are naturally occurring substances, first discovered within the cell nucleus. They are characterized by their richness in phosphorus. Scientists later identified molecules of basic character, known as nitrogenous bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T), and Uracil (U). These are categorized into purine bases (Adenine and Guanine) and pyrimidine bases (Cytosine, Thymine, and Uracil).

They also contain a pentose sugar, which can be either ribose or 2-deoxyribose, but never both simultaneously within the same molecule. RNA typically contains Uracil (U) instead of Thymine (T).

If a nucleotide lacks its phosphate group, it is referred to as a nucleoside. A nucleoside is formed by the union of a ribose or deoxyribose sugar with a nitrogenous base, connected by an N-glycosidic bond. Examples include guanosine, cytidine, adenosine, and uridine.

A nucleotide consists of a nucleoside linked to a phosphoric acid group via a phosphoester bond.

Nucleic acids are polymers of nucleotides, characterized by two distinct ends: a 5' end and a 3' end. The nucleotides are joined together by phosphodiester bonds during synthesis.

Deoxyribonucleic Acid (DNA)

General and Structural Levels of DNA

DNA is formed by two chains of nucleotides that twist around each other to form a double helix. It is synthesized in a specific direction, from the 5' end to the 3' end.

In eukaryotic cells, DNA is primarily located in the nucleus. Here, DNA is associated with basic proteins called histones and other non-histone proteins. This association forms a complex fiber known as chromatin.

In prokaryotic cells, which lack a membrane-bound nucleus, DNA, RNA, and non-histone proteins are found in a region called the nucleoid. Basic proteins associated with viral DNA have also been observed.

DNA exhibits three main levels of structural organization: primary, secondary, and tertiary structures.

Primary Structure of DNA

The primary structure of DNA refers to the specific sequence of nucleotides within a single strand. This strand can exist as a single filament or be folded upon itself. The vast number of possible sequences is generated by combining the four types of nucleotides: Adenine (A), Cytosine (C), Guanine (G), and Thymine (T).

Secondary Structure of DNA

The secondary structure of DNA, the double helix, was deduced from observations such as the density and viscosity of aqueous DNA dispersions, which exceeded expectations, suggesting that the molecules were grouped together through hydrogen bonds.

It was also found that in all DNA samples, the amount of Adenine (A) was equal to Thymine (T), and the amount of Cytosine (C) was equal to Guanine (G). In this secondary structure, the nitrogenous bases are positioned internally within the molecule, while the pentose sugars and phosphate groups remain on the exterior, often due to their ionization.

The double helix is a very stable natural state. However, if heated to 100°C, the two strands separate, a process known as denaturation. If the denatured DNA is slowly cooled to 65°C, the complementary strands can rejoin, a process called renaturation.

Tertiary Structure of DNA

The tertiary structure involves the further coiling of the DNA fiber upon itself, forming a superhelix or 'DNA supercoil'. This supercoiling helps to shorten and compact the DNA, facilitating processes like DNA replication and gene expression.

Levels of DNA Packaging

• The first level of packaging is constituted by a succession of 100Å diameter particles called nucleosomes.
• The second level of packaging involves the coiling of the nucleosome fiber itself, forming condensed chromatin, with approximately six nucleosomes per turn.
• The third level of packaging forms a series of fiber loops, creating 'structural loop domains' that coil upon themselves.
• Higher levels of packaging achieve a reduction in the DNA fiber's length by 35 to 40 times. Many authors consider that chromosomes are organized around a central scaffold of non-histone proteins.

Ribonucleic Acid (RNA)

RNA is constituted by nucleotides containing ribose sugar and the bases Adenine (A), Guanine (G), Cytosine (C), and Uracil (U) (instead of Thymine). These nucleotides are linked by phosphodiester bonds in a 5'-3' direction. RNA is found in many viruses and in both prokaryotic and eukaryotic cells.

There are several types of RNA, including transfer RNA (tRNA), messenger RNA (mRNA), ribosomal RNA (rRNA), and nucleolar RNA (nRNA).

Types of RNA

Transfer RNA (tRNA)

Transfer RNA (tRNA) molecules are typically 70-90 nucleotides long and are found in the cytoplasm. Their function is to transport specific amino acids to the ribosomes, where proteins are synthesized. tRNA molecules are single-stranded but fold into a characteristic cloverleaf shape (secondary structure) and an L-shaped tertiary structure, featuring a D arm, T arm, anticodon arm, and an amino acid acceptor arm.

Messenger RNA (mRNA)

Messenger RNA (mRNA) is a single-stranded, linear molecule whose function is to copy genetic information contained in DNA and carry it to the ribosomes for protein synthesis. mRNA contains coding segments called exons and non-coding segments called introns. Introns are removed after transcription in a process called splicing or 'maturing,' which occurs in the nucleus.

Ribosomal RNA (rRNA)

Ribosomal RNA (rRNA) constitutes the ribosomes, the cellular machinery for protein synthesis. Its size is often expressed in Svedberg units (s), which represent its sedimentation coefficient.

Nucleolar RNA (nRNA)

Nucleolar RNA (nRNA) is found in the nucleolus and originates from specific DNA regions known as 'nucleolar organizing regions'.

Functions of Ribonucleic Acids

RNA plays several crucial roles:

• Transmission of Genetic Information: RNA transmits genetic information from DNA to the ribosomes. Enzymes involved in this process synthesize RNA by complementary base pairing, a process known as transcription.
• Conversion of mRNA Sequence into Amino Acid Sequence: This process, called translation, occurs in the ribosomes and involves mRNA, rRNA, and tRNA to synthesize proteins.
• Storage of Genetic Information: Some viruses, such as the influenza virus, lack DNA and store their biological information in the form of RNA.