BackChapter 4: Nucleic Acids – Structure, Properties, and Biological Functions
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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:
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: (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) |
