Nucleic Acids: Structure, Properties, and Biological Functions

4.1 Nucleic Acids—Informational Macromolecules

Introduction to Nucleic Acids

Nucleic acids are essential macromolecules responsible for the storage, transmission, and expression of genetic information in all living organisms. The two primary types are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

• DNA contains the genetic blueprint for cellular function and heredity.

• RNA plays various roles in gene expression and protein synthesis.

Chemical Structure of DNA and RNA

• Both are polymers of nucleotides, each consisting of a sugar, a phosphate group, and a nitrogenous base.

• DNA contains deoxyribose sugar; RNA contains ribose sugar.

• DNA uses thymine (T) as a base, while RNA uses uracil (U).

Purine and Pyrimidine Bases

• Purines: Adenine (A) and Guanine (G)

• Pyrimidines: Cytosine (C), Thymine (T, in DNA), and Uracil (U, in RNA)

Nucleosides and Nucleotides

• Nucleoside: Nitrogenous base + sugar

• Nucleotide: Nucleoside + phosphate group

Base	Nucleoside	Nucleotide
Adenine	Adenosine	Adenosine 5'-monophosphate (AMP)
Guanine	Guanosine	Guanosine 5'-monophosphate (GMP)
Cytosine	Cytidine	Cytidine 5'-monophosphate (CMP)
Uracil	Uridine	Uridine 5'-monophosphate (UMP)
Thymine	Thymidine	Thymidine 5'-monophosphate (TMP)

Properties of Nucleotides

• Tautomerization: Reversible conversion between structural forms (e.g., keto/enol, amino/imino).

• Acidity: Nucleotides are strong acids; phosphate group ionizes at low pH.

• UV Absorption: Nucleotides absorb UV light at ~260 nm, useful for detection and quantification.

Phosphodiester Linkage

Formation and Stability

• Nucleotides are joined by phosphodiester bonds between the 3'-hydroxyl and 5'-phosphate groups.

• These linkages create the backbone of DNA and RNA strands.

• Polar molecules interact via charge-dipole and dipole-dipole interactions in aqueous environments.

Alkaline Hydrolysis of RNA

• RNA is susceptible to alkaline hydrolysis via a cyclic intermediate, a process not possible in DNA due to the absence of the 2'-hydroxyl group.

4.2 Primary Structure of Nucleic Acids

Nature and Significance

The primary structure of nucleic acids refers to the linear sequence of nucleotides in a strand, which determines the genetic information carried.

• Sequences are conventionally written from the 5' to 3' direction.

• Example: 5'-ACGTT-3'

DNA as the Genetic Substance: Early Evidence

Key Experiments

• Avery et al. (1944): Demonstrated that DNA can transfer genetic traits between bacteria.

• Hershey and Chase (1952): Showed that DNA, not protein, is the genetic material in viruses.

4.3 Secondary and Tertiary Structures of Nucleic Acids

DNA Double Helix

• Secondary Structure: 3D arrangement of nucleotides, including the double helix.

• Tertiary Structure: Long-range 3D interactions, such as supercoiling and cruciforms.

Watson-Crick Base Pairing

• Adenine pairs with Thymine via two hydrogen bonds.

• Guanine pairs with Cytosine via three hydrogen bonds.

• Chargaff's rules: %A = %T, %G = %C

Major and Minor Grooves

• The double helix has alternating major and minor grooves, important for protein-DNA interactions.

Semiconservative Nature of DNA Replication

Replication Models

• Each DNA strand serves as a template for a new complementary strand.

• Three models: conservative, semiconservative, dispersive.

• Meselson-Stahl experiment (1958) proved the semiconservative model using isotopic labeling and density centrifugation.

4.4 Alternative Secondary Structures of DNA

Left-Handed DNA (Z-DNA)

• Z-DNA is a left-handed helix, with purines in syn and pyrimidines in anti conformations.

G-Quadruplexes

• G-rich sequences can form G-quartets and G-quadruplexes, structures found in telomeres.

4.5 The Helix-to-Random Coil Transition: Nucleic Acid Denaturation

Denaturation of DNA

• Double-stranded DNA can be separated into single strands by heat, alkali, or electrostatic repulsion.

• High ionic strength stabilizes the duplex structure.

4.6 The Biological Functions of Nucleic Acids: A Preview of Genetic Biochemistry

Central Dogma of Molecular Biology

• DNA stores genetic information.

• Replication: DNA is copied for cell division.

• Transcription: DNA is transcribed into messenger RNA (mRNA).

• Translation: mRNA is translated into proteins at ribosomes.

4.7 Tools of Biochemistry

Techniques for Studying Nucleic Acids

• Gene cloning

• Automated oligonucleotide synthesis

• Dideoxynucleotide sequencing

• Site-directed mutagenesis

• X-ray diffraction

Summary Table: DNA vs. RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Strands	Double-stranded	Single-stranded (mostly)
Function	Genetic information storage	Gene expression, protein synthesis

Example: Meselson-Stahl Experiment

• Used isotopic nitrogen ($^{15}N$ and $^{14}N$) to label DNA.

• Density gradient centrifugation showed intermediate DNA after one generation, confirming semiconservative replication.