Chapter 4: Nucleic Acids – Structure, Properties, and Biological Functions

Chapter 4: Nucleic Acids

Overview

Nucleic acids are essential biomolecules responsible for the storage, transmission, and expression of genetic information. This chapter covers the chemical structure, nomenclature, physical properties, and biological functions of DNA and RNA, as well as analytical techniques used to study them.

Bases, Nucleosides, and Nucleotides: Nomenclature and Structure

Basic Components

• Phosphate group: Provides negative charge and enables polymerization.

• Sugar: Ribose (RNA) or deoxyribose (DNA).

• Base: Purines (Adenine, Guanine) and Pyrimidines (Cytosine, Thymine, Uracil).

Purines and Pyrimidines

• Purines: Adenine (A), Guanine (G) – larger, double-ring structure.

• Pyrimidines: Cytosine (C), Thymine (T, DNA only), Uracil (U, RNA only) – smaller, single-ring structure.

Nomenclature Table

Base	Nucleoside	5'-Nucleotide
Adenine	Adenosine	Adenosine 5'-monophosphate
Guanine	Guanosine	Guanosine 5'-monophosphate
Cytosine	Cytidine	Cytidine 5'-monophosphate
Uracil	Uridine	Uridine 5'-monophosphate
Thymine	Thymidine (deoxythymidine)	Deoxythymidine 5'-monophosphate

Tautomeric Forms

• Bases can exist in amino/imino or keto/enol forms, affecting hydrogen bonding.

• Predominant forms: Amino (A, C), Keto (G, T).

Ionization and pKa Values

• Phosphate groups and certain base nitrogens can ionize, with characteristic pKa values.

• At physiological pH (6.5–8.5), bases are typically uncharged.

Nucleotide	pKa1 (Phosphate)	pKa2 (Phosphate)	pKa (Base)
AMP	1.0	6.1	3.8 (N1)
GMP	1.0	6.1	2.4 (N7), 9.4 (N1)
CMP	1.0	6.1	4.5 (N3)
UMP	1.0	6.1	9.5 (N3)

Additional info: pKa values determine the ionization state and net charge of nucleotides at different pH values.

DNA and RNA: Structure and Differences

Chemical Structure

• DNA: Contains deoxyribose sugar and bases A, T, G, C.

• RNA: Contains ribose sugar and bases A, U, G, C.

Key Differences

• DNA is more stable due to lack of 2'-OH group; RNA is more susceptible to hydrolysis.

• RNA's 2'-OH group prevents B-form helix and increases flexibility.

• DNA uses thymine (5-methyl-uracil) instead of uracil to facilitate repair of deaminated cytosine.

Base Pairing

• Watson-Crick base pairs: A-T (DNA), A-U (RNA), G-C.

• Distance between paired bases: 1.08 nm.

• Chargaff's rules: %A = %T, %G = %C in double-stranded DNA.

Nucleotide Functions

• Adenosine: Acts as an autacoid (local hormone), regulates sleep, blood vessel dilation, and metabolism.

• Coenzyme components: NAD+, NADP+, FMN, FAD – essential for redox reactions.

• Regulatory molecules: cAMP, cGMP – involved in signal transduction and gene regulation.

• Energy carriers: ATP, GTP, CTP, UTP – drive metabolic reactions.

• Substrates for nucleic acid synthesis: NTPs and dNTPs are building blocks for RNA and DNA.

ATP Hydrolysis Equations:

• $\text{ATP} \rightarrow \text{ADP} + P_i$

• $\text{ATP} \rightarrow \text{AMP} + PP_i$

UV Absorbance Features of DNA and Its Difference from Proteins

UV-Vis Absorbance

• Both proteins and nucleic acids absorb in the UV range.

• Beer-Lambert Law: $A = \varepsilon l c$ (Absorbance is proportional to concentration).

• DNA and RNA absorb maximally at 260 nm; proteins at 280 nm.

• Absorbance ratio (A260/A280) distinguishes nucleic acids from proteins:

  • Protein: ~0.5

  • DNA: ~1.8–2.0

Additional info: UV absorbance is used for quantification and purity assessment of nucleic acid samples.

Summary Table: Key Differences Between DNA and RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Stability	Stable	Less stable (hydrolyzed by base)
Function	Genetic information storage	Information transfer, catalysis
Helix Form	B-form (most common)	A-form (dsRNA)