Water, Weak Interactions and Buffers

This set of flashcards covers the biochemical properties of water, the types of weak interactions in biomolecules, and the principles of pH and buffering.

What are the passive and active roles of water in biochemistry?

The passive role involves the structure and function of biomolecules forming in response to interaction with water (e.g., protein folding), while the active role involves water as a participant in biochemical reactions (e.g., peptide bond formation).

Why does the difference in electronegativity between oxygen and hydrogen give water a permanent dipole?

Oxygen is more electronegative than hydrogen, resulting in oxygen having a partial negative charge and each hydrogen having a partial positive charge.

What constitutes a hydrogen bond in biological systems?

An electrostatic interaction between an electronegative atom with a hydrogen covalently linked (donor) and another electronegative atom with a free electron pair (acceptor).

How do the strength and length of a hydrogen bond compare to a covalent bond?

Hydrogen bonds are relatively weak, approximately $5\%$ the strength of a covalent bond, and they are about double the length of covalent bonds.

How many hydrogen bonds does a water molecule participate in on average in liquid water versus ice?

In liquid water, each molecule participates in an average of $3.4$ hydrogen bonds in dynamic 'flickering clusters,' whereas in ice, each molecule participates in hydrogen bonds with four other water molecules.

What are the definitions of Heat of Vaporization and Specific Heat Capacity?

Heat of Vaporization is the amount of heat required to vaporize a liquid at its boiling temperature; Specific Heat Capacity is the amount of heat required to raise the temperature of a substance by one degree.

Why does ice float on liquid water?

The ordered arrangement of water molecules in ice, where each molecule forms four hydrogen bonds, results in a lower density than liquid water.

What properties were reported for 'polywater' regarding its freezing point, boiling point, and density?

It was reported to have a freezing temperature of $-40\,^{\circ}C$, a boiling temperature of $150\,^{\circ}C$, and a density of $1.4\,g/cm^3$.

What was the eventual scientific conclusion regarding 'polywater'?

It was determined to be 'Bad Science' (B.S.) because the unique properties were revealed to be the influence of impurities like sweat.

What types of molecules have the greatest solubility in water?

Molecules that carry a charge (positive or negative) and those that participate in hydrogen bonds as donors or acceptors.

How do non-polar gases like $CO_2$ and $O_2$ behave in water and blood?

They have limited solubility in water and blood, requiring specialized transport proteins and strategies for movement.

Define an 'amphipathic' molecule.

A molecule containing both hydrophobic (non-polar) and hydrophilic (polar) portions, such as fatty acids.

What is the 'hydrophobic effect' in the context of molecular structure?

The drive to have polar groups interacting with water while non-polar regions cluster together and are shielded away, which increases the entropy of the associated water.

What are the four main non-covalent interactions within biomolecules?

Hydrogen bonds, ionic (electrostatic) interactions, hydrophobic interactions, and van der Waals interactions.

How does water influence the strength of ionic (electrostatic) interactions?

Water tends to shield the charged groups, which greatly diminishes the strength of the interaction.

What was the scientific consensus on the 'memory of water' hypothesis used to support homeopathy?

Nature and the scientific community concluded there is no substantial basis for the claim, calling the idea that water can be imprinted with the memory of past solutes 'fanciful.'

What is the ion product of water ($Kw$) and the equilibrium constant ($Keq$) of water?

$Kw = [H^+][OH^-] = 1.0 \times 10^{-14}\,M^2$ and $Keq = 1.8 \times 10^{-16}\,M$.

What is the formula for $pH$?

$pH = -\log([H^+]) = \log\left(\frac{1}{[H^+]}\right)$.

What is the buffering range of a weak acid relative to its $pKa$?

The buffering region extends one $pH$ unit on either side of the $pKa$ point.

State the Henderson-Hasselbalch equation.

$pH = pKa + \log\left(\frac{[A^-]}{[HA]}\right)$.

Which buffer system maintains the $pH$ of human blood?

The bicarbonate buffer system, involving compensatory respiratory alkalosis to maintain the ratio of $H_2CO_3/HCO_3^-$.

What are the $pKa$ values for the three dissociation steps of phosphoric acid?

$pKa_1 = 2.14$, $pKa_2 = 6.86$, and $pKa_3 = 12.4$.