Understanding DNA and RNA: From Nucleotides to Double Helix

Posted on Dec 1, 2024 in Biology

Nucleic Acids: Polymers of Nucleotides

Nucleic acids, DNA and RNA, are polymers formed by the union of nucleotide subunits.

Composition

Nucleic acids are composed of:

  • A nitrogenous base
  • A pentose (sugar)
  • Phosphoric acid (phosphate)

Nitrogenous Bases

These are nitrogen-containing heterocyclic compounds. There are two types:

Purine Bases

Purine derivatives with a double ring structure. The most important are adenine (A) and guanine (G), found in both DNA and RNA.

Pyrimidine Bases

Pyrimidine derivatives with a single ring structure. There are three: cytosine (C), thymine (T), and uracil (U). Cytosine is found in both DNA and RNA. Thymine is specific to DNA, and uracil is specific to RNA.

Pentose

The pentose in nucleic acids has a cyclic structure with an intramolecular hemiacetal link.

Phosphoric Acid

Phosphoric acid (H3PO4) is found as the phosphate ion (PO43-).

N-Glycosidic Bond

The union of a pentose and a nitrogenous base through an N-glycosidic bond forms a nucleoside. This bond forms between carbon 1′ of the pentose and nitrogen 1 of pyrimidine bases or nitrogen 9 of purine bases.

Phosphodiester Bond

Nucleotides are formed by the esterification of a nucleoside with phosphoric acid. This reaction involves the hydroxyl group of the pentose and the phosphate, releasing a water molecule. The bond is between any hydroxyl of the pentose (generally positions 3′ and 5′) and the phosphate, forming a phosphodiester linkage.

DNA: The Carrier of Genetic Information

DNA carries genetic information, which is transmitted from generation to generation. It is a linear polymer composed of nucleotides containing deoxyribose as the pentose and the bases A, T, G, and C.

DNA Structure

Primary Structure

The primary structure is the sequence of deoxyribonucleotides joined by phosphodiester bonds. The phosphodiester bond forms between the phosphate group at the 5′ carbon of one nucleotide and the hydroxyl group at the 3′ carbon of the next nucleotide. A DNA strand has two free ends: a 5′ phosphate group and a 3′ hydroxyl group. DNA chains differ in size, composition, and base sequence.

Secondary Structure

The secondary structure was determined by Watson and Crick based on their own data and that of other scientists:

  • The DNA molecule is long and rigid.
  • There is an equivalence of bases: for a given species, the amount of purines equals the amount of pyrimidines (A=T and C=G).
Watson and Crick Model
  • DNA consists of two polynucleotide chains that twist around each other, forming a double helix. The strands cannot be separated without unwinding.
  • The nitrogenous bases are located inside the double helix, resembling a spiral staircase with the bases as steps and the sugar-phosphate backbones as railings.
  • Each complete turn of the double helix contains 10 pairs of nucleotides.
  • The spatial arrangement of the two strands creates a major groove and a minor groove in the double helix.
  • The two polynucleotide chains are antiparallel.
  • There is complementarity between the two chains: bases face each other and form hydrogen bonds (A with T, and C with G).

DNA Condensation Levels

Both eukaryotic and prokaryotic cells face the challenge of storing large amounts of DNA in a small volume. To solve this, DNA adopts condensed structures. The level of condensation is associated with different phases of the cell cycle.

  • In bacteria and generally in all prokaryotes, as well as in mitochondria and chloroplasts of eukaryotes, DNA is a circular double helix associated with a small number of proteins that maintain its structure.
  • In eukaryotes, with more DNA (up to 1 meter per cell), the challenge is to package this DNA into the nucleus.

10 nm Fiber (Nucleosomes)

In eukaryotes, DNA is associated with basic proteins called histones to form nucleosomes. A nucleosome consists of eight histone molecules (four different types) and a segment of DNA wrapped around them. Between nucleosomes is a linker DNA segment, giving the structure the appearance of a “pearl necklace.”

30 nm Fiber (Solenoid)

The 10 nm fiber can further coil into a more condensed 30 nm fiber, called a solenoid.

Loop Domains, Rosettes, and Chromosomes

The 30 nm fiber is folded into large radial loops (70 nm). These structures are further compacted to form rosettes and spirals of rosettes, ultimately giving rise to chromosome chromatids.

DNA Denaturation

DNA denaturation is the loss of the double helix structure. It can be caused by changes in temperature and pH.

  • When the temperature reaches a certain point (DNA melting point), the two strands separate, resulting in denaturation. This process is reversible if the two strands are complementary.
  • Abrupt changes in pH can also denature DNA. Renaturation can occur when pH values are returned to biological parameters. If renaturation is performed with DNA from another organism, it is possible to study the similarity of sequences, as pairing only occurs if the base sequences are complementary.