Chapter 9: Molecular Structure of DNA and RNA

9.1 Identification of DNA as the Genetic Material

The discovery that DNA is the genetic material was a pivotal moment in genetics. Several key experiments established DNA, rather than protein, as the molecule responsible for heredity.

• Criteria for Genetic Material:

  • Information: Must contain instructions to build an organism.

  • Transmission: Must be passed from parent to offspring.

  • Replication: Must be copied accurately.

  • Variation: Must be capable of change to account for phenotypic diversity.

• Historical Context: Early geneticists recognized these properties, but the chemical identity of the genetic material was unknown. Proteins were initially favored due to their chemical diversity.

Frederick Griffith's Experiments (1928)

• Organism: Streptococcus pneumoniae (pneumococcus), with two strains:

  • Type S (Smooth): Has a polysaccharide capsule, forms smooth colonies, virulent.

  • Type R (Rough): Lacks capsule, forms rough colonies, non-virulent.

• Key Experiments:

  1. Live S injected into mice: mice die; S recovered.

  2. Live R injected: mice live; no bacteria recovered.

  3. Heat-killed S injected: mice live; no bacteria recovered.

  4. Live R + heat-killed S injected: mice die; live S recovered.

• Conclusion: A "transforming principle" from dead S transformed R into virulent S.

Avery, MacLeod, and McCarty (1944)

• Goal: Identify the chemical nature of the transforming principle.

• Experimental Design: Type R cells were mixed with extracts from heat-killed S cells, treated with enzymes to destroy DNA, RNA, or protein.

  • Only destruction of DNA (with DNase) prevented transformation.

• Conclusion: DNA is the transforming principle and thus the genetic material.

Hershey and Chase (1952)

• Organism: T2 bacteriophage (virus infecting E. coli).

• Method: Used radioactive isotopes:

  • 32P labels DNA (contains phosphorus).

  • 35S labels protein (contains sulfur).

• Results: After infection, 32P entered bacterial cells, 35S remained outside.

• Conclusion: DNA, not protein, is injected and carries genetic information.

9.2 Overview of DNA and RNA Structure

DNA and RNA are nucleic acids, first identified by Friedrich Miescher as "nuclein." They are acidic macromolecules found in the cell nucleus.

• Levels of Complexity:

  1. Nucleotides: The building blocks.

  2. Strand: Linear polymer of nucleotides.

  3. Double Helix: Two strands interact via base pairing.

  4. Chromosome: Higher-order folding with proteins.

9.3 Nucleotide Structure

Nucleotides are the monomers of nucleic acids, each consisting of three components.

• Phosphate Group: PO43−, links nucleotides together.

• Pentose Sugar:

  • Ribose (RNA): Has an OH at the 2' carbon.

  • Deoxyribose (DNA): Has an H at the 2' carbon (lacks oxygen).

• Nitrogenous Base:

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

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

• Nucleoside: Base + sugar (e.g., adenosine).

• Nucleotide: Base + sugar + phosphate(s) (e.g., ATP, ADP, AMP).

Table: Components of Nucleotides

9.4 Structure of a DNA Strand

DNA strands are polymers of nucleotides linked by phosphodiester bonds, forming a sugar-phosphate backbone with protruding bases.

• Phosphodiester Linkage: Connects 5' phosphate of one nucleotide to 3' hydroxyl of the next.

• Directionality: 5' end (free phosphate) to 3' end (free OH).

• Bases: Project outward from the backbone.

Historical Contributions to DNA Structure

• Linus Pauling: Discovered the alpha-helix in proteins using model building, inspiring similar approaches for DNA.

• Rosalind Franklin: Used X-ray diffraction to show DNA is helical, has more than one strand, and 10 base pairs per turn.

• Erwin Chargaff: Developed methods to analyze base composition, leading to Chargaff's rules.

Chargaff's Rules

• In DNA, %A ≈ %T and %G ≈ %C.

• Ratio (A+G)/(T+C) ≈ 1 for double-stranded DNA.

Table: Chargaff's Data (Selected Organisms)

Watson and Crick Model of DNA

• Double Helix: Two antiparallel strands (5'→3' and 3'→5').

• Base Pairing: A pairs with T (2 H-bonds), G pairs with C (3 H-bonds).

• Bases: Stacked perpendicular to helix axis.

• Helix: Right-handed, 10 base pairs per turn, 2 nm diameter.

Key Structural Parameters of B-DNA

• Diameter: 2 nm (20 Å)

• One turn: 3.4 nm (34 Å)

• 10 base pairs per turn

• Distance between base pairs: 0.34 nm (3.4 Å)

• Major and minor grooves present

Stabilization of the Double Helix

• Hydrogen Bonding: Between complementary bases (A-T: 2 bonds, G-C: 3 bonds).

• Base Stacking: Planar bases stack via van der Waals forces and hydrophobic interactions.

• Thermal Stability: G-C rich regions are more stable due to extra hydrogen bond.

Grooves on the DNA Double Helix

• Major Groove: Wider, exposes more base edges; common site for protein binding.

• Minor Groove: Narrower, less accessible.

• Grooves arise from the geometry of the glycosidic bonds.

Alternative Forms of DNA

• B-DNA: Standard, right-handed, 10 bp/turn, biologically significant.

• A-DNA: Right-handed, more compact, forms under dehydrating conditions.

• Z-DNA: Left-handed, 12 bp/turn, zigzag backbone, forms in high salt or with certain sequences (e.g., alternating purine/pyrimidine), may play roles in gene regulation.

Table: Comparison of DNA Forms

9.7 RNA Structure

RNA is typically single-stranded but can form complex secondary and tertiary structures.

• Differences from DNA:

  • Uses uracil (U) instead of thymine (T).

  • Ribose sugar (2' OH) instead of deoxyribose.

• Directionality: 5' to 3'.

• Classes of RNA:

  • mRNA: Messenger RNA, carries genetic code to ribosome.

  • rRNA: Ribosomal RNA, structural and catalytic component of ribosomes.

  • tRNA: Transfer RNA, brings amino acids to ribosome during translation.

RNA Secondary Structures

• Bulge Loop: Unpaired bases on one side of a double-stranded region.

• Internal Loop: Unpaired bases on both sides within a double-stranded region.

• Multibranched Loop: Junction where three or more double-stranded stems meet.

• Stem-Loop (Hairpin): Single strand folds back to form a double-stranded stem with a loop of unpaired bases.

Transfer RNA (tRNA) Structure

• Secondary Structure: Extensive base pairing forms cloverleaf pattern with stems and loops.

• Tertiary Structure: L-shaped 3D conformation stabilized by base pairing, base stacking, and interactions with ions and proteins.

• Functional Sites:

  • Acceptor Stem (3' end): Site of amino acid attachment.

  • Anticodon Loop: Recognizes codon on mRNA during translation.

Additional info: The above notes expand on the original slide content with definitions, context, and tables for clarity. All chemical structures and diagrams referenced are described in text for accessibility.