BMSC+200+Module+2+PDF

Chapter 2: Water, Weak Interactions, and Buffers

Objectives

• Dissect the structure-function relationship of water molecules.

• Characterize the importance of water to biological systems.

• Investigate the ability of water to act as a solvent.

• Explore how the structure of biomolecules is influenced by water.

• Characterize the non-covalent interactions within biomolecules.

• Determine the mechanisms, and importance, of buffers and pH.

Text Readings

• Stryer 2nd or 3rd Editions: All of Chapter 2

Water - General

• Water is the most abundant molecule in living organisms.

• Passive roles: Structure and function of biomolecules develop in response to water interactions (e.g., protein folding buries hydrophobic residues).

• Active roles: Water participates in biochemical reactions (e.g., water is released during peptide bond formation).

Water - Matrix of Life

• Critical to understanding molecular basis of life; shapes the search for life in the universe.

• Presence of water is a strong determinant of habitability on other planets.

• Consideration of alternative solvents (e.g., ammonia, formamide) for potential life forms.

Water - Structure/Function Relationship

• Water's basic structure illustrates the structure-function concept.

• Oxygen is more electronegative than hydrogen, creating a permanent dipole.

  • Oxygen carries a partial negative charge.

  • Each hydrogen bears a partial positive charge.

• The water dipole allows for:

  • Electrostatic interactions with charged molecules.

  • Hydrogen bonding with other molecules (including water itself).

Hydrogen Bonds - General

• Hydrogen bonds: electrostatic interactions between hydrogen covalently linked to one electronegative atom, interacting with another electronegative atom.

• Common donor/acceptor atoms include oxygen and nitrogen.

• Significance of hydrogen bonds surpasses any other structural features - Linus Pauling.

Hydrogen Bonds - Strength and Geometry

• Relatively weak at ~5% strength of a covalent bond; longer than covalent bonds.

• Stability of hydrogen bonds influenced by their geometric arrangement (e.g., anti-parallel vs. parallel beta sheets).

Water - Unusual Properties

• Each water molecule can donate and accept two hydrogen bonds; potential to participate in four hydrogen bonds in liquid.

• In liquid state, each water molecule is involved in an average of 3.4 hydrogen bonds, forming dynamic “flickering clusters.”

• High internal cohesion due to hydrogen bonding yields unique properties.

Water - Unusual Properties (continued)

• Large number of hydrogen bonds leads to:

  • High heat of vaporization.

  • High specific heat capacity.

• Water's boiling point, melting point, and heat of vaporization exceed those of most common solvents.

Water - Unusual Properties (continued)

• Most organisms generate heat through energy consumption; water's high specific heat aids temperature regulation.

Water - Unusual Properties (continued)

• In ice, each water molecule forms four hydrogen bonds, resulting in a less dense structure allowing ice to float.

Polywater - A New, Deadlier Form of H2O

• Investigation of water forced through quartz tubes led to discovery of polywater, exhibiting:

  • Higher boiling point, lower freezing point, higher viscosity than ordinary water.

  • Polywater: freezing temp: -40°C, boiling temp: 150°C, density: 1.4 g/cm³, viscosity: 15x greater than regular.

• Proposed structure involved unique interactions among water molecules.

Polywater - Concerns and Debunking

• Concerns arose over polywater potentially as a self-propagating weapon.

• A scientist demonstrated that similar properties could arise from impurities, deeming polywater "bad science."

Water's Ability to Act as a Solvent - Electrostatic Interactions

• Water dissolves charged solutes via hydration layers.

• Its small size and permanent dipole enhance interactions with positive and negative ions.

Water's Ability to Act as a Solvent - Hydrogen Bonds

• Biomolecules possess functional groups capable of hydrogen bonding.

• These interactions can occur intra- or intermolecularly, or with water.

• Water acts as an ideal hydrogen bonding partner due to its size and capability.

Water - Solubility of Dissolved Molecules

• Solubility in water depends on interactions with water molecules.

• Charged molecules and those capable of hydrogen bonding exhibit greater solubility (e.g., hydrophilic molecules are polar, hydrophobic molecules are non-polar, amphipathic molecules have both functional parts).

Water - Behavior of Amphipathic Substances

• Amphipathic molecules favorably interact with water's hydrophilic regions while clustering hydrophobic parts.

• Forces holding non-polar regions together: hydrophobic interactions.

• Most biomolecules exhibit amphipathic characteristics; hydrophobic drive is significant in stabilizing biomolecular structures.

Weak Interactions - Crucial to Molecular Structure and Function

• Biomolecules comprise stable polymers with structures influenced by non-covalent interactions.

• Often transient and dynamic, these interactions grant flexibility in structure and function.

Weak Interactions - Types

• Non-covalent interactions include:

  • Hydrogen bonds

  • Ionic (electrostatic) interactions

  • Hydrophobic interactions

  • Van der Waals interactions

Weak Interactions - Hydrogen Bonds

• Functional groups in biomolecules can form hydrogen bonds with:

  • Water molecules

  • Other groups within the same molecule

  • Other molecules

• Hydrogen bonds confer specificity but do not primarily define structural formation.

Weak Interactions - Ionic (Electrostatic) Interactions

• Charged groups interact attractively or repulsively.

• Water shields ionic interactions, diminishing their strength; effectiveness relies on atom distance and medium nature.

Weak Interactions - van der Waals Forces

• Interactions between dipoles occur at short range and low magnitude.

• Maximal attraction occurs when two atoms approach their van der Waals radii.

• Crucial in protein folding core.

Weak Interactions - Hydrophobic Effect

• Non-polar regions tend to cluster, shielded from water, while polar groups interact with it.

• Protein folding involves non-polar side chains clustering interiorly and polar/charged on the exterior.

• In contrast to the Second Law of Thermodynamics, protein folding creates a more ordered state.

Weak Interactions - Thermodynamics of the Hydrophobic Effect

• Surrounding water molecules become more ordered around hydrophobic regions, lowering water entropy.

• Clustering of non-polar areas releases ordered water, elevating the system’s entropy.

Does Water Have a Memory?

• An extreme dilution of biomolecules purported to maintain biological activity despite no molecules remaining.

• Initially published in a reputable journal, this claim faced backlash, with a subsequent issue contradicting it, citing lack of scientific basis.

Homeopathy and Water's Memory

• Homeopathic remedies involve excessive dilutions, raising skepticism over effectiveness.

• Claims suggest water can "remember" previous solute structures; subjected investigations yield no scientific support, yet homeopathy remains a profitable industry.

Ionization of Water

• Water can ionize into hydrogen (H+) and hydroxide ions (OH-).

• Ion product of water (Kw): [H+][OH-] = 1.0 x 10^-14 M².

The pH scale

• Represents the concentration of hydrogen ions: pH = -log [H+].

• pH is logarithmic, meaning a variance of 1 pH unit reflects a 10-fold difference in hydrogen ion concentration.

Weak Acids and Bases Characteristics

• Strong acids and bases dissociate completely; weak acids and bases do not.

• Dissociation quantified by the constant: Ka = [H+][A-]/[HA].

• Often expressed as pKa = -log Ka.

Titration Curves Reveal the pKa of Weak Acids

• Titration curve enables observation of acid to conjugate base ratio.

• At pH = pKa, [A-] = [HA], maximizing buffering capacity.

Multiple Ionizing Groups in Molecules

• Monoprotic, diprotic, and triprotic acids exhibit distinctive pKa values corresponding to their ionizable protons.

Buffers in Biological Systems

• Essential for maintaining constant pH; fluctuations may alter biomolecule structure/function.

• Weak acids, such as bicarbonate, serve as buffers in biological contexts.

The Henderson-Hasselbalch Equation

• Relates pH, pKa of weak acid, and their respective concentrations, facilitating calculation of missing variable.

Sample Calculations with Henderson-Hasselbalch Equation

• Example for acetic acid and sodium acetate mixture yields a calculated pH.

• Calculation example for lactic acid yield results in pKa.