Nucleic Acids: DNA and RNA Molecular Structure and Roles

Nucleic Acid Building Blocks

Nucleoside Structure

The nucleoside core is formed by a pentose sugar joined to a nucleobase via an N-glycosidic link. This bond occurs between carbon 1 (C1) of the pentose and nitrogen 1 (N1) of pyrimidine bases or nitrogen 9 (N9) of purine bases, with the loss of a water molecule.

Nucleotide Structure

A nucleotide is a nucleoside with one or more phosphate groups attached.

Phosphate Ester Bond

The phosphate ester bond links the C5 of the pentose sugar to a phosphate group (PO₄^3-).

Nucleotide Linkage: The Phosphodiester Bond

The phosphodiester bond is an esterification located between the phosphate group at position 5' of one nucleotide and the hydroxyl group on carbon 3' of another nucleotide. This forms the backbone of nucleic acid polymers.

Deoxyribonucleic Acid (DNA)

Primary Structure of DNA

The primary structure of DNA is a linear sequence of nucleotides, typically read from 5' to 3'. Each strand has a free phosphate group attached to C5' at one end and a free hydroxyl (OH) group attached to C3' at the other end.

Each DNA strand differs from another in size and nucleotide base sequence.

A polynucleotide is abbreviated with the initials of its bases (e.g., ATCAGATCGTAAAT).

Secondary Structure of DNA

• DNA consists of two polynucleotide chains linked together along their entire length.
• The two chains are antiparallel: the 3' end of one strand faces the 5' end of the other.
• The two chains spiral to form a double helix around an imaginary axis.
• The chains are joined through hydrogen bonds between complementary nitrogenous bases:
  • Adenine forms 2 hydrogen bonds with Thymine.
  • Guanine forms 3 hydrogen bonds with Cytosine.
• The two strands are complementary, not identical.
• Nitrogenous bases are located within the double helix, while the pentose-phosphate backbone is on the outside.
• The planes of the nitrogenous bases are parallel to each other and perpendicular to the helix axis.
• The double helix is plectonemic, meaning the chains cannot be separated without unwinding.
• The double helix turn is dextrorotatory: the coiling rotates clockwise.

Tertiary Structure of DNA

The tertiary structure involves DNA organized with associated proteins (a complex and not fully understood process).

The double helix undergoes further folding. This is necessary for:

• Reduced space available inside the cell.
• Regulation of activity, which depends on the folding.

The final result of DNA packaging is chromatin or chromosomes.

Ribonucleic Acid (RNA)

RNA consists of linear polymers formed by ribonucleotides of Adenine (A), Guanine (G), Cytosine (C), and Uracil (U), linked by phosphodiester bonds from 5' to 3'.

In RNA, Adenine pairs with Uracil.

RNA can form secondary structures when the chain folds on itself, resulting in intramolecular base pairing. This forms loops (non-complementary regions) and hairpins (areas of complementary bases that establish hydrogen bonds).

Role of RNA

RNA extracts genetic information from DNA and directs the synthesis of proteins from the genetic message encoded by the DNA.

Messenger RNA (mRNA)

• A copy of the DNA (a gene or group of genes) used by ribosomes as information to synthesize a protein.
• Comprises between 3% and 5% of total cellular RNA.

Ribosomal RNA (rRNA)

• Comprises approximately 80% of cellular RNA.
• Forms part of ribosomes and participates in the joining of amino acids for protein synthesis.

Transfer RNA (tRNA)

• Transports amino acids (AAs) present in the cytoplasm to the ribosomes, where they will join to form proteins.

Nucleolar RNA (snoRNA)

• Associated with proteins, it forms the nucleolus.