Nucleic Acids: DNA and RNA Structures, Bonds and Functions

Nucleic Acids and Nucleotide Components

Nucleic acids: macromolecules responsible for storing, transmitting, and expressing genetic information. Examples include DNA and RNA.

Nucleotides and Nucleosides

Nucleotides: composed of a phosphate group, a pentose sugar, and a nitrogenous base.

Nucleoside: the combination of a nitrogenous base and a pentose sugar; the glycosidic bond is between C1' of the sugar and the nitrogen atom of the base: N1 for pyrimidines and N9 for purines.

Nucleotide: a nucleoside with one or more phosphate groups (nucleoside phosphate esters).

Nitrogenous Bases

Nitrogenous base: two major types:

• Pyrimidines: C, T, U — single six-membered ring (Cytosine, Thymine, Uracil).
• Purines: A, G — fused six- and five-membered rings (Adenine, Guanine).

Pentoses

Pentoses: ribose in RNA and deoxyribose in DNA.

Free Nucleotides and Cellular Roles

Nucleotides not in nucleic acids: free nucleotides can accumulate in cells and provide energy (for example ATP) or act in other functions.

Molecules with Enzymatic or Signaling Functions

Some nucleotides or nucleotide-derived molecules act as cofactors or signaling molecules:

• Coenzyme A (CoA): contains an ADP moiety and is derived from vitamin B (pantothenic acid); it carries acyl groups and participates in metabolic reactions.
• Cyclic AMP (cAMP): a second messenger that transmits and amplifies signals in the cell.

Nucleotide Polymerization and Backbone Bonds

Nucleotide binding: nucleotides polymerize by phosphodiester bonds, formed by esterification between the phosphate group at the 5' position of one nucleotide and the 3' hydroxyl group of the next nucleotide. The nitrogenous bases do not form part of the backbone bonds; they project from the backbone.

Common bases in DNA: A G T C. DNA is a polymer.

DNA Structure

Primary Structure

Primary structure: the linear sequence of nucleotides read from 5' → 3'.

Secondary Structure: Double Helix

DNA: typically comprises two antiparallel strands; the 5' end of one strand opposes the 3' end of the other. The two strands form a double helix stabilized by hydrogen bonds between base pairs:

• A — T: two hydrogen bonds.
• G — C: three hydrogen bonds.

The DNA double helix has a diameter of about 2 nm and a helical repeat (pitch) of about 3.4 nm per turn (approximately 10 base pairs per turn). The strands cannot be separated without disrupting those interactions; the helix can also supercoil under cellular conditions.

DNA Helical Forms

• Form A: base pairs are tilted relative to the helix axis (bases are inclined).
• Form Z: the two chains adopt a zig-zag backbone and form a left-handed helix; this form is narrower and longer per turn than B-form DNA.

Tertiary Structure

Tertiary structure: associated proteins (e.g., histones and other DNA-binding proteins) organize DNA into higher-order tertiary structures in the cell.

Biological Function of DNA

Function: DNA stores genetic information and has the capacity for replication — the ability to make copies of itself. DNA is found in prokaryotes, eukaryotes, mitochondria, chloroplasts, and viruses.

RNA Structure and Function

RNA: an unbranched polymer composed of the bases A, G, C, and U (adenine, guanine, cytosine, uracil).

RNA is typically single-stranded, but the chain can fold back on itself forming double-stranded regions (stems) and single-stranded loops or forks.

Function of RNA

Function: RNA extracts information from DNA and directs the synthesis of proteins.

Types of RNA and Roles

• mRNA (messenger RNA): a copy of DNA sequence that is used by ribosomes to create a protein. Transcription is the process of producing an mRNA copy from DNA.
• rRNA (ribosomal RNA): constitutes about 80% of total RNA and is involved in the assembly of amino acids and the synthesis of proteins (forming the core of the ribosome and catalyzing peptide bond formation).
• tRNA (transfer RNA): transports amino acids from the cytoplasm to the ribosome, where they come together to form proteins.

Translation

Translation: the process that converts the base sequence of mRNA into the amino acid sequence of a protein.

RNA Secondary and Higher-Order Structure

Secondary structure: consists of arms (double-stranded stretches of base pairing) and loops (unpaired regions at the ends of arms). These features allow RNA molecules to fold into complex three-dimensional shapes.

rRNA and the nucleolus: rRNA associated with proteins forms the nucleolus, the subnuclear structure where ribosome assembly begins.