Nucleic Acids: Structure, Components, and Mutation Mechanisms

Lecture 9: Nucleic Acids – The Second Biopolymer

Introduction to Nucleic Acids

Nucleic acids are essential biopolymers responsible for the storage, transmission, and expression of genetic information. The two main types are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). This section covers their structure, components, and the mechanisms underlying genetic mutations.

Mutation Rates and Mechanisms

Mutation Rates in Genomes

• Mutation rate in humans: Approximately 1 mutation per 30 million bases per generation.

• Human haploid genome size: 3 billion bases.

• Number of mutations per generation: 100–200 new mutations per individual.

• DNA polymerase proofreading: Reduces mutation rate by correcting errors during DNA replication.

• HIV genome: ~9,500 bases; mutation rate ~1 per 100,000 bases, resulting in 1 mutation every 10 generations.

• HIV replication: In untreated AIDS, ~10 billion virus particles are produced per day, leading to ~1 billion mutations daily due to lack of proofreading by viral polymerase.

Example: The high mutation rate in HIV is a major reason for its rapid evolution and resistance to antiviral drugs.

Watson-Crick Mechanism of Mutagenesis

• Watson and Crick (1953) proposed that mutations can occur due to tautomerization of bases—a rare event where a base temporarily adopts an alternative structure (tautomer) during DNA replication, leading to incorrect base pairing.

• Other sources of DNA damage include environmental factors such as UV radiation.

Reference: Watson JD, Crick FHC (1953) Genetical implications of the structure of deoxyribonucleic acid. Nature 171:964–967.

Components and Structure of Nucleotides

Objectives

• Identify the components of a nucleotide.

• Distinguish between nucleobases, nucleosides, and nucleotides.

• Recognize the structures of purine and pyrimidine nucleobases.

• Identify one-letter and three-letter codes for nucleobases.

• Differentiate between ribose and deoxyribose sugars.

• Recognize the phosphoanhydride bond.

• Distinguish DNA nucleotides from RNA nucleotides.

• Understand the structure of ATP.

Basic Structure of Nucleotides

• Nucleotides are composed of three components:

  1. Phosphate group(s)

  2. Pentose sugar (ribose in RNA, deoxyribose in DNA)

  3. Nitrogenous base (purine or pyrimidine)

• DNA and RNA are polymers of nucleotides linked by phosphodiester bonds.

Example: The repeating unit of RNA contains ribose, while DNA contains deoxyribose (lacking an –OH group at the 2' position).

Types of Nitrogenous Bases

Purines and Pyrimidines

Nitrogenous bases are classified as either purines or pyrimidines based on their ring structure.

• Purines: Double-ring structures with 9 constituent atoms. Examples: Adenine (A) and Guanine (G).

• Pyrimidines: Single-ring structures with 6 constituent atoms. Examples: Cytosine (C), Thymine (T) (DNA only), and Uracil (U) (RNA only).

• Bases are planar, pseudoaromatic, and hydrophobic, facilitating base stacking in nucleic acid structures.

Structural Modifications

• Adenine: Modification at C6.

• Guanine: Modifications at C2 and C6.

• Cytosine: Modifications at C2 and C4.

• Thymine: Modifications at C2, C4, and C5 (methyl group at C5).

• Uracil: Similar to thymine but lacks the methyl group at C5.

pKa Values of Nitrogenous Bases

The pKa values of the N1-H in purine and pyrimidine rings influence their protonation state at physiological pH (pH 7):

Base	pKa (N1-H)	Protonation at pH 7
Adenine	3.8	Unprotonated
Guanine	9.4	Mostly protonated
Cytosine	4.5	Unprotonated
Thymine	9.9	Mostly protonated
Uracil	9.5	Mostly protonated

Additional info: The removal of a proton from these positions can affect base pairing and mutagenesis.

Pentose Sugars in Nucleic Acids

Ribose vs. Deoxyribose

• Ribose: Found in RNA; has a hydroxyl group at the 2' carbon.

• Deoxyribose: Found in DNA; lacks the 2' hydroxyl group (has only hydrogen at this position).

• The sugar is linked to the base via a glycosidic bond (N1 of pyrimidines, N9 of purines).

Nucleosides and Nucleotides

Definitions

• Nucleobase: Nitrogenous base only (A, T, G, C, U).

• Nucleoside: Base + sugar (e.g., adenosine, guanosine).

• Nucleotide: Base + sugar + phosphate group(s) (e.g., adenosine monophosphate, AMP).

Nomenclature Table

Base	Ribonucleoside	Ribonucleotide (5' monophosphate)	Deoxyribonucleoside	Deoxyribonucleotide (5' monophosphate)
Adenine	Adenosine	Adenosine 5'-monophosphate (AMP)	Deoxyadenosine	Deoxyadenosine 5'-monophosphate (dAMP)
Guanine	Guanosine	Guanosine 5'-monophosphate (GMP)	Deoxyguanosine	Deoxyguanosine 5'-monophosphate (dGMP)
Cytosine	Cytidine	Cytidine 5'-monophosphate (CMP)	Deoxycytidine	Deoxycytidine 5'-monophosphate (dCMP)
Uracil	Uridine	Uridine 5'-monophosphate (UMP)	—	—
Thymine	—	—	Deoxythymidine	Deoxythymidine 5'-monophosphate (dTMP)

Phosphate Groups and Bonds

Phosphate Chemistry

• Nucleotides can have one (monophosphate), two (diphosphate), or three (triphosphate) phosphate groups.

• Phosphates are attached to the 5' carbon of the sugar via phosphoester and phosphoanhydride bonds.

• Phosphate groups are ionizable, with pKa values around 0–2 for the first two protons and 6–7 for the third, resulting in a net charge of approximately –4 for nucleoside triphosphates (NTPs) at pH 7.

Example: The phosphoanhydride bond between the β and γ phosphates in ATP is a high-energy bond, hydrolysis of which releases energy for cellular processes.

Structure and Function of ATP

Adenosine Triphosphate (ATP)

• ATP is a ribonucleotide with three phosphate groups attached to the 5' carbon of ribose.

• ATP serves as the primary energy currency of the cell.

• Energy is released by hydrolysis of the terminal (γ) phosphoanhydride bond:

$\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

• ATP is a ribonucleotide (contains ribose, not deoxyribose).

Polymerization of Nucleotides

Formation of Nucleic Acid Polymers

• Nucleotides are joined by phosphodiester bonds between the 3' hydroxyl of one sugar and the 5' phosphate of the next.

• During DNA/RNA synthesis, nucleoside triphosphates (NTPs or dNTPs) are added to the 3' end of the growing chain, releasing pyrophosphate (PPi).

$\text{(NMP)}_n + \text{NTP} \rightarrow \text{(NMP)}_{n+1} + \text{PP}_i$

Summary Table: Key Differences Between DNA and RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Strandedness	Double-stranded (usually)	Single-stranded (usually)
Stability	More stable	Less stable

Additional info: The presence of the 2' hydroxyl group in RNA makes it more susceptible to hydrolysis, contributing to its lower stability compared to DNA.