Water and Biochemistry Review

Water and Hydrogen Bonding

Water is dipolar and has bent geometry.
Hydrogen atoms carry partial positive charges; oxygen carries partial negative charge.
Hydrogen bonds are weak interactions between a hydrogen atom in one molecule and an electronegative atom in another molecule.
- Energy to break a covalent O–H bond ≈ 470\ \text{kJ mol}^{-1}
Energy to break a hydrogen O…H bond ≈ 23\ \text{kJ mol}^{-1}
Hydrogen bonds are ~20 times weaker than covalent O–H bonds (470 / 23 ≈ 20).
Hydrogen bonds can be depicted as dashed lines between donor and acceptor atoms.
Hydrogen-bond donor: the functional group whose hydrogen initiates the interaction.
Hydrogen-bond acceptor: the functional group whose lone pair interacts with the donor.

Water as a solvent

Polar molecules are more soluble in water than nonpolar molecules.
Generally, charged species are more soluble than neutral species.

Water dissolves salts by hydration

Salts dissolve in water by hydrating individual ions, leading to a large increase in entropy (ΔS).
Example: NaCl (ionic lattice) dissolves with water forming hydration layers around ions.
- Hydration layer around anion Cl¯.
- Hydration layer around cation Na⁺.

Weak forces in biochemistry

Hydrogen bonds: ≈ 10-30\ \text{kJ mol}^{-1}
- Between neutral groups (e.g., OH–O, OH–N interactions)
Ionic (electrostatic) interactions: ≈ 20-80\ \text{kJ mol}^{-1}
van der Waals interactions: ≈ 1-10\ \text{kJ mol}^{-1}
Intermolecular attractions and repulsions are affected by charge distribution and proximity (as shown in examples like NH3 interacting with other groups).
Hydrophobic interactions occur when nonpolar regions cluster, influencing water structure around them.

Interaction of nonpolar molecules with water

Bulk water has high entropy (not highly ordered).
Water near a nonpolar molecule becomes highly ordered, reducing local entropy.
This drives the hydrophobic effect: nonpolar groups aggregate to release ordered water molecules to the bulk, increasing overall entropy.

Nonpolar molecules in water: examples

Glucose (a polar, uncharged molecule) can form hydrogen bonds with water; water motion is not restricted.
Limonene (uncharged and nonpolar) cannot form hydrogen bonds with water; water motion is restricted to satisfy water–water hydrogen bonds.
Diagrammatic ideas: interactions between water and polar/nonpolar groups influence solubility and mobility.

Hydrophobic effect

When nonpolar groups cluster, ordered water molecules are excluded from the interface.
Leads to a large increase in ΔS (entropy).

van der Waals interactions

Temporary and distance-dependent interactions between atoms.
Mechanism involves: temporary dipoles, induced dipoles, and distance r between atoms.
Strong repulsion when atoms are too close; weak attraction when they are farther apart.
Optimal van der Waals interactions occur at a characteristic interatomic distance r.

Ionic/electrostatic interactions and hydrogen bonds (summary)

Ionic/electrostatic interactions: charged species attracting/repelling each other.
Hydrogen bonds: specific dipole–dipole attractions involving H and electronegative atoms.
van der Waals interactions: distance-dependent, non-covalent attractions.
Hydrophobic effect: entropic driving force from water reorganization around nonpolar groups.

Organic chemistry rules: valence and hybridization (Part 3)

Carbon has four valence electrons and needs four more to satisfy the octet; always draw carbon with four bonds.
s and p orbitals can hybridize:
- For carbon:
- sp^3: four atoms attached → tetrahedral geometry
- sp^2: three atoms attached → trigonal planar geometry
- sp: two atoms attached → linear geometry

Organic chemistry rules (continued)

General valence concepts (octet rule):
- Hydrogen: 1 valence electron, typically forms 1 bond.
- Carbon: 4 valence electrons, typically forms 4 bonds.
- Nitrogen: 5 valence electrons, typically forms 3 bonds and 1 lone pair.
- Oxygen: 6 valence electrons, typically forms 2 bonds and 2 lone pairs.
- Phosphorus: 5 valence electrons, typically 5 bonds.
- Sulfur: 6 valence electrons, typically 2 bonds and 2 lone pairs.
Formal charge (FC) = (no. of valence electrons) − (no. of bonds) − (no. of lone pair electrons).
When drawing organic reaction mechanisms, include all unshared valence electrons and formal charges.

Hydrocarbons

Saturated hydrocarbons have no double bonds.
Unsaturated hydrocarbons have at least one C=C double bond.
Conjugated molecules have alternating single and double bonds.
Cis geometric isomers have bulky groups on the same side of a double bond (illustrated by examples with substituents).

Functional groups in nucleic acids

Methyl
Hydroxyl
Amine
Carbonyl
Amide
Ether
Phosphoryl
Alkene

Arrows matter in organic mechanisms

Use arrows carefully: choose the correct type of arrow for the process.
Chemical equilibrium: two arrows with full heads pointing in the same direction in the context of equilibrium.
Resonance structures: one arrow with a double-headed arrow between forms.
Pushing an electron pair: curved arrow with a full-headed arrow.
Pushing a single electron: curved arrow with a half-headed arrow.

Nucleophiles and electrophiles

Nucleophiles: electron-rich; the best nucleophiles have a negative charge; many have partial negative charge.
Electrophiles: electron-poor; the best electrophiles have a positive charge; many have partial positive charge.

Biochemistry is really, really small

An average adult human has around 30–40 trillion human cells and ~40 trillion bacteria cells (mostly in gut).
Biological macromolecules types within a cell:
- Proteins: around 10 trillion molecules per human cell; 2–4 million per E. coli cell; 42 million per yeast cell.
- Nucleic acids, carbohydrates, and lipids also form the major macromolecule classes.
These macromolecules are the fundamental building blocks of life and perform a wide array of functions.
Protein Data Bank (PDB): biomolecular structures are freely available online at rcsb.org; the PDB is the central storehouse of biomolecular structures.
About 100,000 structures are stored in the PDB, illustrated by examples of molecules across a spectrum of sizes (from water to large ribosomal subunits).
Examples of molecular machines and roles include:
- Digestive enzymes: breaking food into small nutrient molecules.
- Blood plasma proteins: transporting nutrients and defending against injury.
- Viruses and antibodies: engaging in ongoing interactions in the bloodstream.
- Hormones: carrying molecular messages through the blood.
- Channels, pumps, and receptors: mediating transport and signaling across membranes.
- Energy production complexes: powering cellular processes.
- Storage proteins: containing nutrients for future use.
- Infrastructure proteins: supporting and moving cells.
- Protein synthesis machinery: building new proteins.
- DNA: storing and reading genetic information.
- Photosynthesis complexes: harvesting light energy.
The scale is illustrated by the diversity of biomolecular structures and their atomic-level detail.

Time scales and numbers (differences by time)

1,000,000 seconds ≈ 11 days 14 hours
1,000,000,000 seconds ≈ 31 years 8 months
1,000,000,000,000 seconds ≈ 31,710 years

Large-scale perspectives

What $1 trillion dollars looks like (illustrative graphic): shows denominations and how large a sum is in real-world terms.
Historical note: in 2010, the U.S. government borrowed about $1.7 trillion; scale is often conveyed via everyday analogies (e.g., pallets of $100 bills).
Practical takeaway: large numerical scales help contextualize scientific and economic problems.

Microscopy and scale in biology

Zooming in: 35 × 13 micron violin example illustrates the scale of microscopic features.
Width of a human hair: ~ 100 µm (100,000 nm).

PDB and biomolecular machinery (revisited)

The Protein Data Bank contains 3D structures of biomolecules at atomic resolution.
Visualization examples show the range from simple water to large ribosome subunits.
The PDB enables researchers to study molecular architecture, interactions, and functions across life processes.