BIOSCI 106 Lecture 3

Extra video covers the portion of Lecture 2 that ran out of time in class.
All preliminary concepts (charge–charge, charge–dipole, dipole–dipole, charge-induced dipole, dipole-induced dipole) have already been demonstrated on the document camera and appear in Worksheet 2.8.
Remaining key interactions discussed today:
• van der Waals (a.k.a. dispersion; “neutrally-induced dipoles”)
• Hydrogen bonds (handled almost entirely in worksheets)
Worksheets referenced
• 2.6 → step-by-step drawing of mutually induced dipoles in aromatics
• 2.1 → calculation involving van der Waals radii and inter-base distance in DNA
• 2.11 → hydrogen-bond analysis relevant to post-weekly quiz
Post-weekly quiz is unlimited-attempt; worksheets strongly recommended before attempting.
Slido polls: (1) Why some people have curly hair (molecular-interaction basis) and (2) general engagement questions.
Pre-reading assigned: detailed article on water–water interactions (essential for Monday’s “Buffer Me” lecture on aqueous chemistry & clinical pH manipulation).

Interaction types already mastered and needed for Worksheet 2.8:
• Charge–charge (full ionic)
• Charge–dipole (ion–permanent dipole)
• Dipole–dipole (Keesom)
• Charge–induced dipole (ion-induced, Debye)
• Dipole–induced dipole (permanent dipole induces temporary dipole)
Comparative abundance inside macromolecules (approximate):
• Thousands of van der Waals contacts ≫ Hundreds of H-bonds ≫ Tens of charge–charge contacts.

Alternative names: dispersion forces, London forces, neutrally induced dipole–dipole.
Most general, weakest category but extremely numerous.
In proteins (e.g., glucagon receptor) they provide bulk stabilization despite individual weakness.

Two non-polar molecules approach; fluctuating electron clouds create instantaneous dipoles.
Each instantaneous dipole induces an opposite dipole in the neighbour → net attraction.
Visualization with benzene rings (π orbitals above & below plane):
1. Electrons are delocalized and mobile in π-systems.
2. Time-snapshot t_1: Slight excess electron density on one side of Ring A (δ-) induces complementary δ+ on that side of Ring B.
3. Time-snapshot t_2: Fluctuation shifts; dipole orientation flips but remains complementary; attraction persists.
Stacking tendency (π–π stacking) therefore favoured, especially in planar aromatics like phenylalanine side chains.

Consecutive bases in duplex DNA separated by 0.34\,\text{nm} = 3.4\,\text{Å}.
Minimum approach distance governed by additive van der Waals radii:
d{\min}=r{\text{vdW},1}+r_{\text{vdW},2}
Stacking dispersion contributes substantial stabilisation energy to the double helix, complementary to inter-strand hydrogen bonds.

Strong, directional interaction involving donor–H···acceptor geometry.
In DNA:
• A···T base pair: 2 H-bonds
• C···G base pair: 3 H-bonds
Roles discussed
• Base-pair fidelity (replication, transcription, proofreading)
• Protection of genetic information (to be revisited in Lecture 4 “Mad Cows & Cannibals”).
Worksheet 2.11 explores how H-bonds plus dispersion jointly stabilise base pairs and how they defend against certain forms of damage.

Observation: Gecko can suspend its entire body weight from a smooth glass surface by a single toe.
Hierarchical foot anatomy maximises contact surface:
• Lamellae → setae → spatulae (nanoscopic hairs)
As creature size increases, spatulae diameters decrease to retain adequate total surface area.
Molecular surface of spatulae is largely non-polar → adhesion dominated by van der Waals contacts with any substrate (glass, metal, etc.).

Engineers reproduced spatulae-like microstructures in a non-polar polymer film.
Key attributes:
• Adhesion without chemical glue (clean, residue-free)
• Re-usable \approx10\text{–}20 stick/peel cycles before dust contamination lowers performance
• Load capacity demonstrated: full human weight supported with modest tape area (publicity stunts with “Spider-Man” figurines, professor hanging from glass).
Potential/real uses:
• Astronaut tools & suit components inside ISS (no glue-mess, reusable in micro-g)
• Robotics & gripping devices where temporary, clean adhesion required.
Limitations: susceptible to fouling by dust; practical large-scale wall-crawling by humans remains engineering challenge.

Scientific naming differences: “van der Waals/dispersion” usage varies between physics, chemistry, biochemistry; explicit standardisation recommended when communicating across fields.
Bio-inspiration / biomimicry emphasised: learning from organisms (gecko, spider) to design sustainable technologies (e.g., avoiding petroleum-based glues).
Humorous reflection on legacy, safety, and sensationalism (lecturer’s fantasy of Spider-Man wall-lecture & consequent newspaper headline “Legend Lecturer Leads Secret Life as Superhero—Falls to Death Mid Lecture, Gecko Tape Blamed”). Highlights need for risk assessment even when inspired by science.

Complete Worksheets 2.1, 2.6, 2.11 before attempting the post-weekly quiz (unlimited retries).
Engage with Slido polls (curly-hair molecular basis, interaction questions).
Read assigned section on water–water hydrogen bonding and structure; foundation for Monday’s “Buffer Me” lecture on aqueous chemistry, pH, and clinical manipulation of urine pH.
Think ahead: Monday will explore equilibria & buffering; might involve life-saving scenarios via controlled pH adjustments.

van der Waals minimum contact distance:
d{\min}=r{\text{vdW},1}+r_{\text{vdW},2}
Base stacking distance in B-DNA:
0.34\,\text{nm}=3.4\,\text{Å}
Relative frequency in proteins (qualitative): N{\text{vdW}} \gg N{\text{H-bond}} \gg N_{\text{ionic}}
Re-use limit of commercial gecko tape: \approx10\text{–}20 cycles.

van der Waals interactions, though individually weak, dominate total contact count inside macromolecules and in some bio-adhesion phenomena.
Hydrogen bonds supply directionality and stronger stabilisation; their cooperative action with dispersion underpins nucleic-acid structure and fidelity.
Nature’s solutions (gecko foot) can be reverse-engineered into high-value materials (gecko tape) that solve engineering challenges without traditional adhesives.
Mastery of weak interactions is essential groundwork for understanding aqueous chemistry, buffering, and later biochemical mechanisms.