Biochem chapter 8: Nucleic Acids

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Nucleic Acids: DNA and RNA

Overview of Nucleic Acids

Nucleic acids, including DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are polymers of nucleotides that store and transmit genetic information. Each nucleotide consists of a sugar, a nitrogenous base, and one or more phosphate groups. The sequence of nucleotides encodes biological information essential for life.

Nucleoside: A molecule composed of a nitrogenous base and a sugar.
Nucleotide: A nucleoside with one or more phosphate groups attached.
Phosphodiester linkage: The covalent bond connecting nucleotides in a nucleic acid chain.

Generic Structures of Nucleosides and Nucleotides

Sugar: Ribose in RNA; 2'-deoxyribose in DNA.
Base: Purines (adenine, guanine) and pyrimidines (cytosine, thymine in DNA, uracil in RNA).
Phosphate: Attached to the 5' carbon of the sugar.

Structures of Bases in Nucleic Acids

Pyrimidines: Single-ring structures. Cytosine (C), Thymine (T, DNA only), Uracil (U, RNA only).
Purines: Double-ring structures. Adenine (A), Guanine (G).

Table: Nucleosides and Nucleotides in DNA and RNA

	Sugar + Base (Nucleoside)	Sugar + Base + Phosphate (Nucleotide)
RNA	Purines: Adenosine (A) Guanosine (G) Pyrimidines: Cytidine (C) Uridine (U)	Purines: Adenosine-5'-monophosphate (AMP) Guanosine-5'-monophosphate (GMP) Pyrimidines: Cytidine-5'-monophosphate (CMP) Uridine-5'-monophosphate (UMP)
DNA	Purines: 2'-Deoxyadenosine (A) 2'-Deoxyguanosine (G) Pyrimidines: 2'-Deoxycytidine (C) 2'-Deoxythymidine (T)	Purines: 2'-Deoxyadenosine-5'-monophosphate (dAMP) 2'-Deoxyguanosine-5'-monophosphate (dGMP) Pyrimidines: 2'-Deoxycytidine-5'-monophosphate (dCMP) 2'-Deoxythymidine-5'-monophosphate (dTMP)

Monosaccharides and Sugar Chemistry

Structure and Stereochemistry of Sugars

Monosaccharides are polyhydroxyketones or polyhydroxyaldehydes with the general formula CnH2nOn. Ribose (in RNA) and 2'-deoxyribose (in DNA) are pentoses (5-carbon sugars) that differ at the 2' position.

D- and L- Isomers: Determined by the configuration at the chiral center farthest from the carbonyl group.
Furanose and Pyranose Forms: Sugars can cyclize to form 5-membered (furanose) or 6-membered (pyranose) rings.
Anomeric Carbon: The carbonyl carbon becomes a new chiral center upon cyclization, leading to α and β anomers.

Comparison of Ribose and Deoxyribose

Ribose: Has a hydroxyl group at the 2' position.
2'-Deoxyribose: Lacks the 2' hydroxyl group (has H instead).
Biological significance: The absence of the 2' OH in DNA increases its chemical stability compared to RNA.

Bases, Nucleosides, and Nucleotides

Nitrogenous Bases

Pyrimidines: Cytosine, Thymine (DNA), Uracil (RNA)
Purines: Adenine, Guanine

The base is attached to the C-1' of the ribose or deoxyribose via a β-N-glycosidic bond.

Nucleoside and Nucleotide Nomenclature

Nucleosides end with -osine (purines) or -idine (pyrimidines).
Nucleotides are named by adding the number and position of phosphate groups (e.g., adenosine-5'-monophosphate).

Phosphodiester Linkages and Nucleic Acid Structure

Formation of Phosphodiester Bonds

Nucleotides are joined by phosphodiester linkages between the 3' hydroxyl of one sugar and the 5' phosphate of the next. This forms the sugar-phosphate backbone of nucleic acids.

Directionality: Nucleic acid sequences are written from 5' to 3'.
Enzymatic catalysis: DNA and RNA polymerases catalyze the formation of phosphodiester bonds.

Properties of the Sugar-Phosphate Backbone

Backbone is negatively charged due to phosphate groups.
Phosphodiester bonds in RNA are less stable in alkaline conditions due to the 2' OH group.

Base Pairing and Double Helix Structure

Watson-Crick Base Pairing

A-T (DNA) or A-U (RNA): Two hydrogen bonds.
G-C: Three hydrogen bonds (stronger pairing).

Base pairing is specific due to hydrogen bonding patterns and molecular geometry.

Forces Stabilizing the Double Helix

Hydrogen bonding between complementary bases.
Base stacking interactions (van der Waals forces).
Hydrophobic interactions among bases.
Electrostatic interactions with cations (e.g., Mg2+).
Phosphate repulsion is minimized by shielding from water and cations.

Helical Structure of DNA

DNA is a right-handed double helix (B-form) with antiparallel strands.
Major and minor grooves provide access for protein binding.
Base pairs are stacked 3.4 Å apart; one turn of the helix contains about 10 base pairs.

Chargaff's Rules

In double-stranded DNA, the amount of A equals T, and G equals C.
This base composition supports the base-pairing model.

RNA Structure and Function

Single-Stranded and Secondary Structures

RNA is usually single-stranded but can form complex secondary structures (e.g., stem-loops, hairpins) via intramolecular base pairing.
RNA can form non-Watson-Crick base pairs and base triples, contributing to its structural diversity.

Stability of RNA vs. DNA

RNA is less stable than DNA due to the 2' OH group, which can participate in hydrolysis of the phosphodiester bond.
Phosphodiester bonds in RNA are more susceptible to alkaline hydrolysis.

Additional Concepts

Tautomerism in Bases

Bases can exist in different tautomeric forms (e.g., keto and enol forms), which can affect base pairing.
At physiological pH, the lactam (keto) form predominates.

Phosphoric Acid and pKa Values

Phosphoric acid is triprotic, with three pKa values: 2.15, 7.20, and 12.35.
At physiological pH, the predominant form is the hydrogen phosphate ion ().

Summary Table: Key Differences Between DNA and RNA

Feature	DNA	RNA
Sugar	2'-deoxyribose	Ribose
Pyrimidine Bases	Thymine, Cytosine	Uracil, Cytosine
Strandedness	Double-stranded (usually)	Single-stranded (usually)
Stability	More stable	Less stable (due to 2' OH)

Example: DNA Sequence and Complementarity

Given a DNA strand: 5'-ATTC TGGCATGACG-3'
Complementary strand: 3'-TAAG ACCGTACTGC-5'

Key Equations

General formula for carbohydrates:
Phosphodiester bond formation:

Additional info:

Some explanations and context were expanded for clarity and completeness.
Tables were reconstructed and summarized for study purposes.