Notes on 4.1: Chemical Composition and Structure of DNA

4.1 Historical context: DNA as the genetic material

• Deoxyribonucleic acid (DNA) is a linear polymer of four different subunits and is the molecule by which hereditary information is transmitted from generation to generation.
• Historical perspective:
  • Prior to ~1950, many biologists believed proteins were the information-carrying molecules because of their diverse three-dimensional structures and broad range of cellular activities.
  • DNA appeared chemically simpler, yet its role as the information carrier was uncertain at first.
• Functional roles of DNA and proteins:
  • DNA stores genetic information and directs its transmission.
  • Proteins carry out most cellular activities and support replication, error correction, and readout of DNA information, but are not the primary information storage molecule.
• Griffith (1928) transformation experiment (Fig. 4.1):
  • Frederick Griffith studied pneumococcal bacteria with two strains:
  • Virulent strain: causes illness and death in mice.
  • Nonvirulent strain: does not cause illness.
  • Observations:
  • Live nonvirulent bacteria do not sickened mice (Fig. 4.1b).
  • Heat-killed virulent bacteria do not cause disease (Fig. 4.1c).
  • Mixture: live nonvirulent bacteria + heat-killed virulent bacteria transform into virulent form, causing disease (Fig. 4.1d).
  • Bacteria isolated from dead mice are virulent, even though the mice were injected with live nonvirulent bacteria.
  • Conclusion: a molecule present in debris from killed virulent bacteria carries the genetic information for virulence; the molecule was not identified.
  • Implication: the virulent trait can be transferred between strains by a transforming factor.
• Follow-up by Avery, MacLeod, and McCarty (1944) (Fig. 4.2):
  • They purified the debris from killed virulent bacteria and tested which molecule carried transformation capability by enzymatic treatments.
  • Experimental design:
  • Treat the transformation solution with DNase (destroys DNA), RNase (destroys RNA), or protease (destroys proteins).
  • If the molecule responsible is destroyed, transformation should not occur.
  • Results:
  • RNase and protease treatments left the transforming activity intact.
  • DNase treatment destroyed the transforming activity; the solution could no longer transform nonvirulent bacteria.
  • Conclusion: DNA is the molecule responsible for transformation; DNA is the genetic material.
  • Source: Avery, O., MacLeod, C., and McCarty, M. 1944. Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types.
• Follow-up by Hershey and Chase (1952):
  • Used bacteriophage experiments to confirm DNA as the genetic material (not detailed here, but acknowledged as confirming the conclusion).
• Why DNA must serve as genetic material:
  • To serve as genetic material, DNA must store genetic information, be able to replicate, and direct the synthesis of other cellular macromolecules.
  • These three capabilities were historically emerging from later work, leading to the acceptance of DNA as the genetic material.
• Emergence of the DNA structure concept:
  • James D. Watson and Francis H. C. Crick proposed the three-dimensional structure of DNA, showing how its structure relates to its function.
  • This discovery revealed how genetic information is stored, faithfully replicated, and directed toward synthesis of other macromolecules.

Nucleotides: components and basic chemistry

• A DNA strand consists of nucleotides, each containing:
  • A five‑carbon sugar (in DNA, deoxyribose).
  • A nitrogenous base (A, G, T, or C).
  • One or more phosphate groups.
• Nucleotides and related terms:
  • Nucleoside: a sugar attached to a base.
  • Nucleotide: a nucleoside with one or more phosphate groups.
  • Monophosphate (NMP), diphosphate (NDP), triphosphate (NTP) forms.
  • Nucleoside triphosphates (e.g., dNTPs) are the substrates used to synthesize DNA and RNA.
  • Nucleoside triphosphates also function as cellular energy carriers (e.g., ATP, GTP).
• Sugar component and backbone features:
  • DNA sugar: deoxyribose (2′‑H instead of 2′‑OH).
  • The phosphate groups on the sugar form the backbone, linking nucleotides together.
  • Phosphate group characteristics:
  • At cellular pH (~7), phosphate oxygens are ionized, giving negative charges on two oxygens, making DNA a mild acid.
• Base components and classification:
  • Four bases: adenine (A), guanine (G) — purines; thymine (T), cytosine (C) — pyrimidines.
  • Purines: two-ring structures; Pyrimidines: single-ring structures.
• Nucleotide structure (Fig. 4.3):
  • The five‑carbon sugar is the core with one base attached to the 1′ carbon.
  • The phosphate group attaches to the 5′ carbon of the sugar.
  • The base defines the identity of the nucleotide.
• Distinctions:
  • A nucleoside with one or more phosphate groups is a nucleotide.
  • The bond linking nucleotides in the DNA backbone is a phosphodiester bond.

Phosphodiester backbone and strand polarity

• Phosphodiester bond details:
  • The covalent linkage between nucleotides occurs between the 3′ carbon of one sugar and the 5′ phosphate of the next nucleotide.
  • Chemical representation: C−O−P−O−C (phosphodiester linkage).
  • This bond forms the backbone of a DNA strand and is relatively stable under heat and pH changes.
• Strand directionality and ends:
  • Each DNA strand has a 5′ end (free 5′ phosphate) and a 3′ end (free 3′ hydroxyl).
  • The backbone polarity runs from 5′ to 3′ along the strand.
  • Example notation: a strand with sequence AGCT can be written as 5′‑AGCT‑3′; the complementary strand would be 3′‑TCGA‑5′.
• Example orientation convention:
  • When a sequence is stated without specifying the 5′ end, the left end is conventionally the 5′ end.

DNA structure: double helix, polarity, and base pairing

• The canonical DNA structure is a double helix consisting of two strands with backbones on the outside and bases inward (the Watson–Crick model).
• Key dimensions and features:
  • The double helix has 10 base pairs per complete turn.
  • Diameter: $2 ext{ nm}$.
  • The strands are antiparallel: the 3′ end of one strand aligns opposite the 5′ end of the other strand.
• The two structural representations common in teaching:
  • Space-filling model (Fig. 4.7a): atoms shown as spheres.
  • Ribbon model (Fig. 4.7b): backbones as ribbons with base pairs in the interior.
• Major and minor grooves:
  • The outside contours create major and minor grooves.
  • These grooves are important for protein–DNA interactions, as many proteins recognize specific base sequences via contacts in the major or minor groove (or both).
• Base complementarity and sequence information:
  • The paired strands are complementary, not identical.
  • The base-by-base pairing is constrained by specific pairing rules and geometry (see below).

Base pairing rules and hydrogen bonding

• Specific base pairing:
  • Adenine pairs with thymine (A–T) and guanine pairs with cytosine (G–C).
  • This base-pairing leads to two antiparallel strands with complementary sequences.
• Why A pairs with T and G with C:
  • Base pairing is dictated by hydrogen bonding between bases:
  • A–T base pair forms two hydrogen bonds.
  • G–C base pair forms three hydrogen bonds.
  • Hydrogen bonds are relatively weak individually (roughly 5–10% of covalent bond strength) but collectively provide stability along the length of the molecule.
  • Hydrogen-bonding mechanism:
  • A hydrogen bond forms when an electronegative atom (O or N) in one base shares a hydrogen atom with an electronegative atom in the opposite base.
  • Specificity of pairing is essential to maintain the distance between backbones and the overall helical geometry.
• Consequences of pairing rules:
  • The base sequence on one strand determines the sequence on the complementary strand; the two strands are not identical but complementary: the pairs are always A with T and G with C.
• Practical implications:
  • The complementary nature allows accurate replication and transcription of genetic information.
• Visualizing base pairing with a short example:
  • If one strand has 5′‑ATGC‑3′, its partner strand is 3′‑TACG‑5′.

Stability: base stacking and helix integrity

• Base stacking (within a strand):
  • Nonpolar, planar bases tend to stack on top of one another to minimize exposure to water, contributing to the stability of the double helix.
  • Base stacking is a major stabilizing force in DNA alongside hydrogen bonding between strands.
• Together, hydrogen bonding and base stacking stabilize the DNA double helix across biological conditions.

Chargaff, Donohue, and the foundational rules for base pairing

• Chargaff’s rules (context for DNA structure):
  • In DNA from a wide variety of organisms, the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine: [A] = [T], \[G] = [C]
  • Ratios of A vs G can vary between organisms, but A pairs with T and G pairs with C, maintaining balance within each molecule.
• Donohue and Griffith (base-pairing hypothesis):
  • They proposed that if bases pair, the most likely arrangement would be A pairing with T and G pairing with C.
  • This hypothetical pairing informed the correct model in Watson and Crick’s DNA structure.
• The Watson–Crick model (1953):
  • A double helix with backbones on the outside, bases pointing inward.
  • A pairs with T; G pairs with C.
  • The model integrated data from three sources:
  • X-ray crystallography data ( Rosalind Franklin and Maurice Wilkins).
  • Chargaff’s rules.
  • The pairing hypothesis by Donohue and Griffith.
  • Publication: Watson and Crick published the structure in 1953; this work revolutionized modern biology by explaining how genetic information is stored and replicated.
• Nobel Prize and 생명의 비밀 (historical notes):
  • Watson, Crick, and Wilkins were awarded the Nobel Prize in Physiology or Medicine in 1962 for DNA structure.
  • Rosalind Franklin died in 1958 and could not be awarded the Nobel Prize.
• Context of discovery and public anecdote:
  • The discovery day is celebrated with reminiscences, including Crick’s proclamation at the Eagle pub: “We have discovered the secret of life.”
  • The Eagle pub still honors this moment with a commemorative plaque.

Physical depiction and genomic scale

• Structural depictions:
  • Space-filling model (Fig. 4.7a) shows atoms as spheres.
  • Ribbon model (Fig. 4.7b) emphasizes the double helix with backbones as the rims and base pairs as the steps.
• Geometric scale:
  • A human egg or sperm genome has approximately $3 imes 10^9$ base pairs.
  • If scaled to a real spiral staircase, the DNA would reach from the Earth to the Moon.
• Antiparallel nature and sequence orientation:
  • The two strands run in opposite directions: one strand runs 5′ to 3′ while the other runs 3′ to 5′.
  • Knowledge of the base sequence on one strand immediately gives the sequence on the opposite strand due to complementarity.
• Practical significance of grooves:
  • The major groove allows many sequence-specific DNA–protein interactions by providing accessible base pairs for recognition.
  • The minor groove also contributes to recognition and binding in some contexts.

Summary of key concepts and implications

• DNA as the primary genetic material: stores information, replicates faithfully, and directs synthesis of other macromolecules.
• Nucleotides and the backbone: nucleotides (sugar + base + phosphate) join via phosphodiester bonds to form linear chains with 5′ to 3′ polarity.
• Double-stranded, antiparallel structure: two complementary strands form a right-handed double helix with 10 base pairs per turn and a diameter of $2 ext{ nm}$.
• Base pairing specificity: A–T (2 hydrogen bonds) and G–C (3 hydrogen bonds) provide stability and a mechanism for accurate replication.
• Complementarity and information content: Knowing one strand’s sequence determines the other; this underpins replication, transcription, and molecular recognition.
• Stability factors:
  • Hydrogen bonding between base pairs.
  • Base stacking within each strand.
  • The overall architecture is robust under physiological conditions but can be destabilized by high temperature or extreme pH.
• Historical milestones and credits:
  • Griffith (1928): transformation concept.
  • Avery, MacLeod, and McCarty (1944): DNA as the transforming molecule.
  • Hershey and Chase (1952): confirmation via phage experiments.
  • Watson and Crick (1953): double-helix structure; Nobel Prize in 1962; Franklin’s pivotal contributions acknowledged posthumously.
• Foundational numbers and conventions:
  • Base count rules: [A] = [T], \[G] = [C].
  • Base pair geometry and stability equations are empirical rather than single-number formulas, but key quantitative markers include:
  • Diameter: $2\;\text{nm}$.
  • Base pairs per turn: $10\;\text{bp/turn}$.
  • Genome size example: $3 \times 10^9\;\text{bp}$ in a human genome germ cell.
• Nucleotides and energy considerations:
  • NTPs provide energy and building blocks for DNA/RNA synthesis.
  • The term “nucleoside triphosphate” reflects both the energetic and polymerization roles in biology.

Self-Assessment prompts (referenced in the source material)

• Why is DNA considered the genetic material based on historical experiments?
• What is the significance of Chargaff’s rules for DNA structure?
• How do hydrogen bonding and base stacking contribute to DNA stability?
• What does antiparallel mean in the context of DNA strands, and why is it important for replication?
• How do the major and minor grooves influence protein–DNA interactions?
• What roles did Watson, Crick, Franklin, and Wilkins contribute to the understanding of DNA structure?
• How is the DNA sequence written, and how does complementarity relate to the sequence on the opposite strand?
• Why is the phosphodiester backbone essential for DNA integrity under physiological conditions?
• What are the key properties that allow DNA to store information, be copied, and direct synthesis in cells?