Lecture 2 - Water and pH

Water

-if not so ubiquitous on Earth, would be considered an exotic compound

-not a lot of molecules have the properties of water

properties of water

small, polar, bent structure, high physical state diversity (different properties between physical states)

water is…

-the principal component of cells and most biochemical reactions take place in aqueous environments

polarity of water

-bent and polarity plays a major role in determining the properties of living systems

polarity is apparent when

-2 atoms of different electronegativity become covalently linked

-different electronegativities cause the atoms’ electrons to be shared unequally

dipole moment

-occurs when the electronegativities between atoms in a molecule differ significantly

-often polar molecules

-dipole moment in water makes it a good solvent for polar molecules and ions

non-covalent bonds

-their nature affects the behavior of biochemicals in solution

-ionic bonds, salt bridges, ion-dipole interactions, van der waals forces, dipole-dipole interactions, dipole-induced dipole, hydrophobic interactions

ionic bonds

-strong bonds that are entirely based on charge attraction

-made of ions (Na+ , Cl-)

salt bridges

-similar to ionic bond charge interactions, but are made up of ionizable functional groups

-form bond through space based on attraction

ion-dipole interactions

-occurs when ions in solution interact with molecules that have dipoles (Na+, H2O)

-why ions dissolve in water

van der waals foces

-relatively weak interactions that are based on the weak attractions of transient dipoles

dipole-dipole interactions

-occur between molecules that have dipoles with a partial positive side attracting a partial negative side

dipole-induced dipole

-when a molecule with a permanent dipole comes into close contact with another molecule with no dipole and induces a dipole

hydrophobic interactions

-relatively weak, occur between hydrophobic molecules in aqueous environments

amphipathic molecules

-molecules with both polar and non-polar portions

-soaps, detergents and cell membrane components

-ex.) polar head and nonpolar tail

strength of bonds

covalent > ionic > ion-dipole > h-bond > van der waals

hydrogen bonds

-a type of dipole-dipole interaction

-relatively weak noncovalent electrostatic interactions

-occurs when hydrogen is bound to an electronegative atom (N, O, F)

h-bond cant occur to Carbon because

-these atoms have similar electronegativities

hydrogen bond donor

-group comprising the electronegative atom that is covalently bonded to the hydrogen atom

-usually linear

hydrogen bond acceptor

-electronegative atom that contributes the unshared pair of electrons to the interaction

-linear bond between 3 bonds

water can…

-participate in linear and nonlinear hydrogen bonds

-has a tetrahedral 3-D bonding configuration that becomes less dense as it freezes (why ice floats)

acid

-a molecule that acts as a proton donor

-also known as a Bronstead acid

base

-a molecule that acts as a proton acceptor

K_a

-used to determine acid strength

-K_a is the acid dissociation constant which is defined as the ratio of ions to protonated acid

-how easily a molecule gives up a proton

HA ⇌ H⁺ + A^-

-formula for a typical acid-base reaction

proton dissociation for HA at equilibrium

K_a = [H⁺] [A^-] / [HA]

K_a

-a fixed numerical value at a given temperature

-larger when the acid dissociates more completely

-larger the Ka the stronger the acid

-increase temp = increase energy = faster dissociation

more correct equilibrium equation

HA(aq) + H₂O(l) ⇌ H₃O⁺(aq) + A^-(aq)

pH

-a measure of H⁺ concentration

-has enormous implications on the rate and effectiveness of biochemical reactions

self-dissociation

-water to hydrogen and hydroxide ions

-occurs at low instances if pure water is

molar concentration of water

-55.5M

-large compared to additional solutes

-allows concentration of water to be treated as a constant (K_w)

K_w (ion product constant for water)

-can be determined experimentally by measuring the hydrogen ion concentration of pure water

monoprotic acid

-an acid that donates exactly one proton (H⁺) per molecule

-because water is one, the hydrogen ion concentration is equal to the hydroxide ion concentration in pure water at 25 degrees C

wide range of possible hydrogen concentrations in solutions…

-makes it desirable to define a quantity for expressing these concentrations more conveniently

pH

-a quantity that can be expressed without exponential notation

-b/c of logarithmic function of the equation, a difference in 1 pH is ten-fold difference in hydrogen ion concentration

pKa

-to avoid working with numbers that have large negative values

-lower pKa = stronger acid

-higher pKa = weaker acid

-only a few functional groups have pKas near physiological pH (7.4)

-pKa is a constant for any given acid at a given temp

Henderson-Hasselbalch (HH) equation

-connects the Ka of an acid with the pH of the solution containing that acid and its conjugate base

-useful to predict the properties of buffer solutions used to control the pH of a reaction mixture

biochemical reactions can only take place in a small pH range

6.9-7.8

-this is why it is necessary to control the pH of a solution for optimum reaction conditions using a buffer solution

Buffers

-solutions that resist change in pH when a small to moderate amount of acid or base is added to the solution

-typically contain conjugate acids, conjugate bases, and buffering salts

-components of buffers can scavenge and bind free protons in aqueous solutions

-pH of a buffer solution can be calculated if the concentrations of the acids and bases are known

phosphoric acid conjugates

-principal buffers in cells

carbonic acid conjugates

-principal buffers in blood/serum

pKas for many functional groups in biochemistry

-are far from 7.00, causing them to be ionized under normal physiological conditions (pH=7)

buffer curves

-can be used to determine optimum buffer range

-ideal pH on curve is where protons start to come on/off

-high pH = less protonated form = more hydroxyl

-low pH = more protonated