The Structural Basis of Cellular Information: DNA, Chromosomes, and the Nucleus

Chapter 16: The Structural Basis of Cellular Information

Introduction

This chapter explores the molecular structure of DNA, the evidence leading to its discovery, and the key scientists involved. Understanding DNA's structure is fundamental to cell biology, as it underpins genetic inheritance, replication, and cellular function.

DNA Structure

Historical Evidence and Key Scientists

• Watson and Crick: Developed the double helix model of DNA structure in 1953, integrating available chemical and physical data.

• Rosalind Franklin: Provided critical X-ray diffraction images that revealed DNA's helical structure.

• Erwin Chargaff: Discovered base composition rules (Chargaff's rules) that guided the understanding of base pairing.

Example: Franklin's X-ray diffraction data (Photo 51) was pivotal in confirming the helical nature of DNA.

Key Terms and Definitions

• Chargaff's Rules: In any DNA sample, the amount of adenine (A) equals thymine (T), and the amount of guanine (G) equals cytosine (C).

• Base Pairs (bp): Pairs of nucleotides (A-T and G-C) that form the rungs of the DNA double helix.

• Purine: Nitrogenous bases with a double-ring structure (adenine and guanine).

• Pyrimidine: Nitrogenous bases with a single-ring structure (cytosine and thymine).

• Complementary Pairing: Specific hydrogen bonding between A-T and G-C.

• Antiparallel: The two DNA strands run in opposite 5' to 3' directions.

• Supercoiled DNA: DNA that is further twisted to compact its structure.

• Denature: Separation of DNA strands by breaking hydrogen bonds (e.g., by heat or pH change).

• Renature: Reannealing of separated DNA strands under suitable conditions.

• Topoisomerase: Enzymes that induce or relax supercoiling in DNA.

Chargaff's Rules and Base Composition

Chargaff's experiments showed that DNA from different cells of a given species has the same percentage of each of the four bases, but the base composition varies among species. The most striking observation was:

• Number of A = Number of T

• Number of G = Number of C

These findings are summarized as Chargaff's rules and were crucial for the double helix model.

Table: DNA Base Composition Data (Selected)

Source of DNA	A (%)	T (%)	G (%)	C (%)	A/T	G/C
Human thymus	28.4	28.2	21.1	22.1	1.01	0.95
Calf thymus	28.1	28.1	21.2	22.0	1.00	0.96
Yeast	31.3	32.9	18.7	17.1	0.95	1.09
Escherichia coli	24.7	23.6	26.0	25.7	1.05	1.01
Additional info: Table shows that A ≈ T and G ≈ C for all species, but the overall percentages differ between species.

Watson and Crick's Double Helix Model

• DNA is a double helix with sugar-phosphate backbones on the outside and nitrogenous bases on the inside.

• Bases form "steps" in a "spiral staircase"; there are ten nucleotide pairs per complete turn.

• The helix has a diameter of 2 nm, suitable for purine-pyrimidine pairing.

• Strands are held together by hydrogen bonds: A pairs with T (2 bonds), G pairs with C (3 bonds).

• The two strands are complementary and antiparallel.

Example: The sequence 5'-ATGC-3' on one strand pairs with 3'-TACG-5' on the other.

Features of DNA Structure

• DNA strands twist to form major and minor grooves, important for protein binding.

• Phosphodiester bonds link the 5' carbon of one nucleotide to the 3' carbon of the next.

• DNA length is measured in base pairs (bp), kilobases (kb = 1,000 bp), or megabases (Mb = 1,000,000 bp).

DNA Supercoiling and Topoisomerases

Supercoiling '

• DNA can be twisted upon itself to form supercoiled DNA.

• Positive supercoiling: Twisting in the same direction as the helix.

• Negative supercoiling: Twisting in the opposite direction.

• Supercoiling is important for compacting DNA, especially in circular DNA (e.g., bacterial chromosomes).

Topoisomerases

• Type I topoisomerases: Introduce transient single-strand breaks to relax supercoils.

• Type II topoisomerases: Introduce double-strand breaks; in bacteria, DNA gyrase is a type II topoisomerase that can induce negative supercoiling and relax positive supercoiling.

Example: DNA gyrase is essential for bacterial DNA replication.

DNA Denaturation and Renaturation

Denaturation (Melting)

• DNA strands can be separated (denatured) by heat or high pH, breaking hydrogen bonds.

• Denatured DNA absorbs more light at 260 nm (hyperchromic effect).

• The melting temperature ($T_m$) is the temperature at which half the DNA is denatured.

• $T_m$ reflects the stability of the DNA helix; higher GC content increases $T_m$ due to three hydrogen bonds per GC pair.

$T_m \propto \text{GC content}$

Renaturation (Reannealing)

• Separated DNA strands can re-form a double helix under suitable conditions (lower temperature, neutral pH).

• Renaturation is used in molecular biology techniques such as nucleic acid hybridization.

Nucleic Acid Hybridization

• Hybridization involves the binding of complementary nucleic acid strands (DNA-DNA, DNA-RNA, or RNA-RNA).

• Used in techniques like fluorescence in situ hybridization (FISH) to detect specific DNA sequences.

Summary Table: Key Features of DNA Structure

Feature	Description
Double Helix	Two antiparallel strands forming a right-handed helix
Base Pairing	A-T (2 H-bonds), G-C (3 H-bonds)
Major/Minor Grooves	Grooves formed by twisting, important for protein binding
Supercoiling	Additional twisting for compaction
Topoisomerases	Enzymes that manage DNA supercoiling
Denaturation/Renaturation	Strand separation and reannealing, basis for hybridization techniques

Additional info: This summary integrates textbook content and lecture notes to provide a comprehensive overview of DNA structure, its discovery, and its physical properties relevant to cell biology.