Nucleic Acids and the RNA World: Structure and Function of DNA and RNA

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Chapter 4: Nucleic Acids and an RNA World

Introduction

Nucleic acids are essential biomolecules that store and transmit genetic information. The chemical evolution of life led to the production of molecules capable of self-replication, marking the beginning of biological evolution. Two key molecules, DNA and RNA, play central roles in genetic information storage and catalysis.

Chemical evolution produced self-replicating molecules.
Deoxyribonucleic acid (DNA): Stores genetic information and is replicated using proteins.
RNA world hypothesis: Proposes that RNA once both stored genetic information and catalyzed its own replication.
Once self-replicating molecules evolved, evolution began.

4.1 What is a Nucleic Acid?

Structure of Nucleic Acids

Nucleic acids are polymers made of nucleotide monomers. Each nucleotide consists of three components:

Phosphate group ()
Five-carbon sugar (pentose)
Nitrogenous base (nitrogen-containing base)

The phosphate group and nitrogenous base are bonded to the sugar molecule.

Types of Nucleotides

Ribonucleotides: Monomers of RNA; contain ribose sugar with an –OH group at the 2' carbon.
Deoxyribonucleotides: Monomers of DNA; contain deoxyribose sugar (lacking oxygen at the 2' carbon, replaced by H).
Both sugars have an –OH group at the 3' carbon.

Nitrogenous Bases

Purines: Two-ring structures (Adenine (A), Guanine (G))
Pyrimidines: One-ring structures (Cytosine (C), Uracil (U, only in RNA), Thymine (T, only in DNA))
Mnemonic: "CUT the Py" (C, U, T are pyrimidines)

General Structure of a Nucleotide

Nucleotides are the building blocks of DNA and RNA, consisting of a phosphate group, a five-carbon sugar, and a nitrogenous base. The structure determines the properties and function of nucleic acids.

How Do Nucleotides Polymerize to Form Nucleic Acids?

Polymerization and Phosphodiester Linkages

Nucleic acids are formed by condensation reactions, creating phosphodiester linkages between nucleotides:

Bond forms between the phosphate group on the 5' carbon of one nucleotide and the –OH group on the 3' carbon of another.
This linkage forms the sugar-phosphate backbone of nucleic acids.

Equation:

Directionality of DNA and RNA Strands

Strands have directionality (5' to 3').
One end has an unlinked 5' phosphate group; the other has an unlinked 3' hydroxyl group.
Primary structure is written from 5' to 3' (e.g., 5'–ATTAGC–3').

Polymerization Requires an Energy Source

Polymerization in cells requires enzymes.
Monomers are activated by adding two additional phosphate groups, forming nucleoside triphosphates (e.g., ATP).
Energy is released when activated nucleotides polymerize, making the reaction spontaneous.

Equation:

What is the Nature of DNA’s Secondary Structure?

Discovery and Features

DNA polymerizes through phosphate linkages, forming a sugar-phosphate backbone.
Chargaff’s rules: Number of purines equals number of pyrimidines (A = T, C = G).
X-ray crystallography revealed a helical structure.

Antiparallel Double Helix

Watson and Crick determined that DNA consists of two antiparallel strands held together by hydrogen bonds between complementary bases (A–T, C–G).
Sugar-phosphate backbones face the exterior; nitrogenous bases face the interior.
Hydrophobic interactions and van der Waals forces stabilize the helix.
DNA has major and minor grooves, important for protein binding.

The Tertiary Structure of DNA

DNA forms more compact three-dimensional structures in cells.
Supercoiling occurs when DNA is wound too tightly or loosely.
DNA wraps around histone proteins to form nucleosomes, further compacting DNA in chromosomes.

DNA Functions as an Information-Containing Molecule

DNA stores genetic information required for growth and reproduction.
Information is encoded in the sequence of four nitrogenous bases, analogous to letters in an alphabet.
DNA replication involves separating strands, pairing free nucleotides with complementary bases, and forming new phosphodiester linkages to create two identical daughter molecules.

The DNA Double Helix is a Stable Structure

Stability is due to phosphodiester linkages, hydrogen bonds, and hydrophobic interactions.
DNA’s stability makes it an effective information-storage molecule, resistant to degradation.

4.3 RNA Structure and Function

Primary Structure of RNA

RNA contains ribose instead of deoxyribose.
RNA contains uracil instead of thymine.
The 2'–OH group on ribose makes RNA more reactive and less stable than DNA.

Secondary Structure of RNA

RNA forms secondary structures through complementary base pairing (A–U, G–C) within the same strand.
RNA strands fold over, forming hairpin structures with antiparallel sugar-phosphate strands.

Tertiary Structure of RNA

RNA can fold into complex three-dimensional shapes, making it more diverse in size, shape, and reactivity than DNA.

Table: Comparison of DNA and RNA Structure

Level of Structure	DNA	RNA
Primary	Sequence of deoxyribonucleotides (A, T, G, C)	Sequence of ribonucleotides (A, U, G, C)
Secondary	Two antiparallel strands form a double helix, stabilized by hydrogen bonding between complementary bases	Most commonly, single-stranded; forms hairpins and other structures via complementary base pairing within the same strand
Tertiary	Double helical DNA forms compact structures by wrapping around histones and supercoiling	Secondary structures fold into more complex three-dimensional shapes

RNA's Versatility and Catalytic Function

RNA can fold into complex shapes, allowing it to perform various functions, including acting as an intermediate (mRNA) and catalyzing reactions (ribozymes).
Ribozymes are RNA molecules with catalytic activity, capable of forming phosphodiester bonds and potentially self-replicating.

Example: The Tetrahymena ribozyme is a well-known catalytic RNA molecule.