Table of Contents
Overview
Nucleic acids are the cell’s information macromolecules. While proteins, carbohydrates, and lipids mainly build structures or provide energy, nucleic acids specialize in storing, copying, transmitting, and sometimes interpreting genetic information. Two closely related types occur in all known life:
- Deoxyribonucleic acid (DNA)
- Ribonucleic acid (RNA)
They are polymers (long chains) made from simpler building blocks called nucleotides.
Building Blocks: Nucleotides
Each nucleotide has three components:
- A nitrogenous base
- A five‑carbon sugar (pentose)
- One or more phosphate groups
In nucleic acids, nucleotides are usually present as nucleoside monophosphates (one phosphate group) when part of the chain. Free nucleotides involved in metabolism can have more phosphates (e.g., ATP is a nucleoside triphosphate).
Nitrogenous bases
Bases fall into two groups:
- Purines (two rings): adenine (A), guanine (G)
- Pyrimidines (one ring): cytosine (C), thymine (T), uracil (U)
They differ slightly between DNA and RNA:
- DNA: A, G, C, T
- RNA: A, G, C, U (U instead of T)
The sugar
The pentose defines whether the nucleic acid is DNA or RNA:
- Ribose (with an OH at the 2′ carbon) → RNA
- Deoxyribose (lacking the 2′ OH; it has just H) → DNA
This small change has big consequences:
- The extra 2′ OH in RNA makes RNA more chemically reactive and less stable.
- The missing 2′ OH in DNA makes DNA more chemically stable, better suited for long‑term information storage.
Nucleosides vs. nucleotides
- Nucleoside = base + sugar (no phosphate)
- Nucleotide = nucleoside + phosphate(s)
Examples:
- Adenosine = adenine + ribose
- Adenosine monophosphate (AMP) = adenosine + 1 phosphate
- Deoxyadenosine monophosphate (dAMP) = adenine + deoxyribose + phosphate
Polymer Structure: The Sugar–Phosphate Backbone
In both DNA and RNA, nucleotides link together via phosphodiester bonds between the 3′ carbon of one sugar and the 5′ carbon of the next:
$$
\text{3′-OH–Sugar}_1 + \text{Phosphate–5′-Sugar}_2
\rightarrow \text{3′–O–PO}_2\text{–O–5′ linkage}
$$
This creates:
- A repeating sugar–phosphate backbone
- Bases sticking out to the side
- An inherent direction: from 5′ end (with a free 5′ phosphate) to 3′ end (with a free 3′ OH)
Biological processes (e.g., DNA replication, transcription) are strongly direction‑dependent: nucleic acid chains are synthesized and “read” in specific directions (commonly 5′ → 3′).
DNA: The Stable Information Archive
Although the detailed structure of DNA is treated elsewhere, some features are specific and central when comparing nucleic acids.
Double-helical organization
In cells, DNA usually exists as a double-stranded molecule:
- Two antiparallel strands (one 5′ → 3′, the other 3′ → 5′)
- Coiled into a double helix
- The sugar–phosphate backbones form the outer “rails”
- The bases meet in the middle as “rungs” connected by hydrogen bonds
Complementary base pairing
Pairing follows strict complementarity:
- A pairs with T (in DNA) via two H-bonds
- G pairs with C via three H-bonds
Thus:
- If one strand has the sequence
5′-A T G C C A-3′ - The complementary strand is
3′-T A C G G T-5′
This complementarity gives DNA several key properties:
- Reliable copying: Each strand can serve as a template to make its partner.
- Error checking: Incorrect pairings distort the helix and can be recognized by repair systems.
- Information redundancy: Two copies of the same information are present (one in each strand).
Stability and packaging
DNA is chemically and physically stabilized by:
- The absence of the 2′ OH group in deoxyribose
- Hydrogen bonds between complementary bases
- Base stacking interactions (hydrophobic and van der Waals) inside the helix
In cells, DNA is further compacted:
- In prokaryotes: into a dense nucleoid region (often circular DNA).
- In eukaryotes: wrapped around proteins (histones) to form chromatin and chromosomes.
These packaging strategies protect DNA and help organize access to genetic information.
RNA: The Versatile Worker Molecule
RNA differs structurally and functionally from DNA in several consistent ways.
Structural differences
Compared with DNA, RNA typically:
- Contains ribose instead of deoxyribose.
- Uses uracil (U) instead of thymine (T).
- Exists mainly as single-stranded molecules.
RNA can still form base pairs:
- A–U and G–C are common Watson–Crick pairs.
- Non-standard pairings (e.g., G–U wobble) can also occur.
Folding and three-dimensional shapes
Because RNA is single-stranded, it can fold back on itself, forming:
- Short helical segments (where internal complements base‑pair)
- Loops, hairpins, bulges, and more complex three-dimensional structures
These shapes allow certain RNAs to act somewhat like proteins:
- Binding specific molecules or regions of other nucleic acids
- Catalyzing chemical reactions (these catalytic RNAs are called ribozymes)
Major functional classes of RNA
Without going into the full details of gene expression, several major roles are specific to RNA:
- Messenger RNA (mRNA):
Carries genetic instructions from DNA to the sites of protein synthesis. Its sequence of bases encodes the amino acid order via the genetic code. - Ribosomal RNA (rRNA):
A structural and catalytic component of ribosomes. rRNA helps position mRNA and transfer RNAs and catalyzes peptide bond formation. - Transfer RNA (tRNA):
Adapter molecules that match amino acids to specific codons on the mRNA. Each tRNA carries a particular amino acid and has an anticodon region that base‑pairs with a codon. - Regulatory and other RNAs (small RNAs, long non‑coding RNAs, etc.):
Many RNA molecules do not code for proteins at all. They can regulate gene expression, modify other RNAs, or help organize chromatin structure. Their existence underscores that nucleic acids are not only information “storage” but also active regulators.
Directionality and Information
The order of bases in nucleic acids is a linear code. For DNA and mRNA, reading this code in the proper direction is essential.
5′ to 3′ direction
Nucleotide sequences are conventionally written from the 5′ end to the 3′ end:
- DNA strand:
5′-A G C T-3′ - RNA strand:
5′-A G C U-3′
Most biological polymerases (enzymes that make DNA or RNA) can only add nucleotides to the 3′ end, so synthesis proceeds in the 5′ → 3′ direction. Many recognition events (binding of proteins, processing enzymes) also depend on orientation.
Base sequence as information
The sequence of bases in nucleic acids encodes:
- The composition and order of amino acids in proteins (via codons in mRNA)
- Signals for starting and stopping transcription and translation
- Signals for splicing, transport, and stability of RNA
- Binding sites for regulatory proteins and RNAs
Thus, nucleic acids carry both structural information (“build this protein”) and regulatory information (“when and where to build it”).
Nucleotides Beyond DNA and RNA
Although nucleic acids themselves are polymers of nucleotides, free nucleotides and related molecules have additional roles in cells:
- Energy currency:
ATP (adenosine triphosphate) is a nucleotide that stores and transfers energy. - Coenzymes:
Several coenzymes contain nucleotide components, e.g. - NAD\(^+\) (nicotinamide adenine dinucleotide)
- FAD (flavin adenine dinucleotide)
- Coenzyme A (via a nucleotide-derived part)
- Signaling molecules:
Cyclic AMP (cAMP) and cyclic GMP (cGMP) are nucleotides that act as intracellular “second messengers.”
These roles highlight that the same basic building blocks used in nucleic acids integrate information processing with energy management and signaling in cells.
Key Differences Between DNA and RNA (Summary)
- Sugar
- DNA: deoxyribose
- RNA: ribose
- Bases
- DNA: A, G, C, T
- RNA: A, G, C, U
- Strandedness
- DNA: typically double‑stranded
- RNA: typically single‑stranded
- Main role
- DNA: long‑term information storage and inheritance
- RNA: various roles in information transfer, decoding, catalysis, and regulation
- Stability
- DNA: more chemically stable, ideal for archives
- RNA: less stable, but more flexible for temporary and catalytic functions
Together, DNA and RNA form the core of the cell’s information system, linking genetic storage to functional molecules and enabling the continuity and diversity of life.