Chapter 5 Part C: (Nucleic Acids: Structure, Function, and Gene Expression)

Nucleic Acids: Structure and Function

Overview of Nucleic Acids

Nucleic acids are essential macromolecules that store, transmit, and help express hereditary information in all living organisms. The sequence of amino acids in a polypeptide is encoded by genes, which are units of inheritance made of DNA. Nucleic acids are polymers composed of nucleotide monomers.

• Types of Nucleic Acids:

  • Deoxyribonucleic acid (DNA): The genetic material in most organisms.

  • Ribonucleic acid (RNA): Functions in gene expression and protein synthesis.

• Origin of Name: Nucleic acids are acidic molecules first identified in the nucleus of eukaryotic cells.

Roles of Nucleic Acids in Cells

Nucleic acids play critical roles in the storage and expression of genetic information. DNA contains information for its own replication and for the synthesis of RNA through transcription. RNA, particularly messenger RNA (mRNA), carries information for protein synthesis (translation) on ribosomes.

• Replication: Copying of DNA for cell division (not part of gene expression).

• Transcription: Synthesis of RNA from DNA template.

• Translation: Synthesis of proteins from mRNA template.

• Central Dogma of Molecular Biology: The flow of genetic information is summarized as DNA → RNA → Protein.

Diagram: DNA (transcription) → RNA (translation) → Protein

Gene Expression

Definition and Process

Gene expression is the process by which information from a gene is used to synthesize a functional gene product, typically a protein. Chromosomes contain hundreds or thousands of genes, each encoding instructions for making a specific RNA molecule. If the RNA is mRNA, it provides instructions for synthesizing a particular protein.

• Gene: A segment of DNA that contains information for making an RNA molecule.

• mRNA: Messenger RNA that carries genetic instructions from DNA to ribosomes for protein synthesis.

Gene Expression in Eukaryotes

In eukaryotic cells, gene expression involves several steps and cellular compartments:

1. Synthesis of mRNA: DNA is transcribed into mRNA in the nucleus.

2. Movement of mRNA: mRNA exits the nucleus and enters the cytoplasm.

3. Synthesis of Protein: Ribosomes in the cytoplasm translate mRNA into polypeptides (proteins).

Example: The process of gene expression in eukaryotes involves transcription in the nucleus and translation in the cytoplasm.

Important Terminology

Transcription and Translation

It is crucial to use correct terminology when describing gene expression:

• DNA is transcribed to produce RNA.

• mRNA is translated to produce protein.

• Incorrect Usage: Do not say "RNA is transcribed" or "proteins are translated"; the correct terms are "DNA transcription" and "mRNA translation."

Chemical Structure of DNA and RNA

Nucleotides and Nucleosides

Nucleic acids are polymers of nucleotides, also called polynucleotides. Each nucleotide consists of three components:

• Nitrogenous base

• Pentose sugar (5-carbon sugar)

• One or more phosphate groups

A nucleoside is a pentose sugar linked to a nitrogenous base (no phosphate group).

Nitrogenous Bases

There are two families of nitrogenous bases:

• Pyrimidines: Cytosine (C), Thymine (T), and Uracil (U); single six-membered ring.

• Purines: Adenine (A) and Guanine (G); fused double ring (six-membered and five-membered).

• Uracil: Found only in RNA.

• Thymine: Found only in DNA.

Pentose Sugars in Nucleic Acids

• DNA: Contains deoxyribose (lacks a hydroxyl group on the 2' carbon).

• RNA: Contains ribose (has a hydroxyl group on the 2' carbon).

Structural Difference: The only difference between ribose and deoxyribose is the presence or absence of the 2' hydroxyl group.

Polynucleotides and Phosphodiester Bonds

Nucleotides are covalently linked by phosphodiester bonds to form polynucleotides. The bond forms between the 3' hydroxyl group of one sugar and the 5' phosphate group of the next sugar.

• Phosphodiester bond: The linkage between nucleotides in a nucleic acid chain.

$\text{Phosphodiester bond:} \quad \text{3'-OH (sugar)} + \text{5'-phosphate (next sugar)}$

Polarity of Polynucleotides

Polynucleotides have directionality, defined by the orientation of the 5' and 3' carbon atoms in the pentose sugar. Nitrogenous bases extend from the sugar-phosphate backbone.

• 5' end: Has a free phosphate group.

• 3' end: Has a free hydroxyl group.

Complementary Base Pairing in DNA

DNA consists of two polynucleotide strands joined by complementary base pairing:

• Adenine (A) pairs with Thymine (T): 2 hydrogen bonds.

• Guanine (G) pairs with Cytosine (C): 3 hydrogen bonds.

Double-stranded DNA forms a stable double helix, with the two strands running in opposite (antiparallel) directions.

Antiparallel Strands in DNA

The two strands of DNA are antiparallel, meaning they run in opposite directions (one 5' to 3', the other 3' to 5'). This orientation is essential for the structure and function of DNA.

Structure of RNA Molecules

RNA molecules are usually single-stranded but can fold into complex shapes by forming hydrogen bonds between complementary bases in different regions. In RNA, uracil (U) replaces thymine (T), so A pairs with U.

• RNA: Single-stranded, contains uracil instead of thymine.

• Base pairing: Adenine (A) pairs with Uracil (U).

Complementarity and Antiparallel Nature of RNA

RNA molecules are synthesized from one DNA strand and are complementary and antiparallel to the DNA template strand.

Example:

• DNA template: 3'-GAGGCTTCAGGA-5'

• RNA transcript: 5'-CUCCGAAGUCCU-3'

Summary Table: Key Features of Nucleic Acids

Feature	DNA	RNA
Pentose Sugar	Deoxyribose	Ribose
Strandedness	Double-stranded (helix)	Single-stranded
Nitrogenous Bases	A, T, G, C	A, U, G, C
Base Pairing	A-T (2 H-bonds), G-C (3 H-bonds)	A-U (2 H-bonds), G-C (3 H-bonds)
Function	Genetic information storage	Gene expression, protein synthesis

Chapter 5 Key Concepts

• Nucleic acids (DNA, RNA): Structure, function, and role in heredity.

• Nucleotide: Composed of sugar, phosphate, and nitrogenous base.

• Nitrogenous bases: Five types, classified as purines or pyrimidines.

• Phosphodiester bond: Covalent linkage between nucleotides.

• DNA: Double helix, antiparallel strands, complementary base pairing.

• RNA: Usually single-stranded, contains uracil, complementary and antiparallel to DNA template.

Additional info:

• Other macromolecules in living things include polysaccharides, lipids, and proteins. Each has unique monomers, bonds, and functions.

• Hydration and hydrolysis reactions are important in the synthesis and breakdown of macromolecules.