BIOL 4087 : BIOL4087 Notes For Exam 1
1-16-14
Chapter 2 - Water
H20
Noncovalent interactions
• Hydrogen bonds
• Electrostatic interactions
• Van der waals interactions
Ionization of water
• pH
• buffers
• Henderson-Hasselbalch equation
H20
• 60-75% of weight of most organisms
• Is the solvent of life - it determines shape and interactions of biological molecules
• Figure 2.1 shows water is polar, oxygen is more electro negative and hydrogen is electro
positive, electrons hang out around the oxygen atom so it is slightly negative,
• Figure 2.1 b water forms hydrogen bonds, hydrogen bond is longer than covalent
bond,
▪ H-bond - .177 nm, 23 kJ/mol
▪ Covalent bond - .0965 nm, 50-500 kJ/mol
• Figure 2.2
Noncovanlent interactions (hydrogen bonds, electrostatic interactions, van der Waals
interactions)
• Are weak → 4-20 kJ/mol but bc they are so weak they are readily reversible at body
temperature which makes them dynamic
▪ Allows substrates to release enzyme without energy
• Sum of many will yield strong interactions (individually they are weak)
▪ DNA, RNA, and proteins
▪ Biological membranes
• Hydrogen bonds
▪ Hydrogen bonds are about ~20 kJ/mole
▪ They form between an O or N (acceptor) (electronegatively) and a hydrogen
which is covalently bonded to another O or N (donor)
▪ Look for O or N to tell if hydrogen bond exist
▪ Figure 2.3
▪ Figure 2.4 hydrogen bond between ketones, peptides, complementary bases of
DNA → are extremely important to the environment
▪ Figure 2.5
• Hydrogen bonds are directional → strongest hydrogen bonds are linear
and weaker hydrogen bonds are not linear
▪ Hydrogen bonds make water a good solvent for polar molecules
• Electrostatic interactions
▪ Are ~20 kJ/mol
▪ Are also called ‘salt bridges’ and ‘ionic bonds’
▪ F=Q1Q2/εr2 where ε is the dielectric constant
▪ SEE IMAGE #1 on force
• Opposite charges attract, like charges repel
• Force is strongest in vacuum (because dielectric constant is smallest)
▪ Figure 2.6
▪ Water is a good solvent for ions (“hydration shells”)
• Van der Waals interactions
▪ 2-4 kJ/mole
▪ Transient dipole-induced dipole interactions
▪ Molecules have preferred distance between one another like an energy well.
Microscopically, potential energy decreases as the molecules are pushed
together or pulled apart from the ideal state
▪ See image #2
• Gecko use van der waals interaction to climb walls (spatulae)
• Better duct tape proposed using van der Waals
▪ HIV protease – protease cuts protein to allow the virus to penetrate cell
membrane. Van der waals forces are important to enzymes because they
influence affinity that the active site has for a target molecule
Water and amphipathic molecules
• Sodium stearate – (a fatty acid, 18 Carbons) will form micelle when placed in water with
hydrophilic heads facing out and fatty chains facing in.
• See image #3
• Figure 2.7b
Ionization of water
• pH
▪ water will dissociate to a proton and hydride
▪ Keq=[H+][OH-]/[H2O]
▪ KW=[H+][OH-]
▪ see image #4
▪ pH = -log[H+] → be able to define and do calculations!
• 1 unit increase in pH is a 10 fold decrease in M (mol/liter)
• pH of 4 indicates H+ conc of 10-4 mol/liter
▪ Neutral solution → proton concentration is equal to the hydroxide
concentration – [H+]=[OH-]=10-7 M bc KW=10-14
▪ Figure 2.15
▪ Blood, sweat, and tears ~7.2 pH
▪ Milk and saliva ~6.5
Acids and Bases
➢ Strong acids and bases will completely dissociate in water
• HCl → H+ + Cl-
• NaOH → Na+ + OH-
➢ Weak acids and bases partially dissociate
• HA → H+ + A- (equilibrium)
▪ HA is the acid and A- is conjugate base
• NH4+ → H+ + NH3
• CH3COOH → H+ + CH3OO-
• Figure 2.17 titration of acidic acid, need to add base then measure base → in the
beginning of titration, you get a big increase in pH (change of ~3) as OH- equivalents are
added, going from 0 to 0.1. When the equivalents go from 0.4 to 0.5, only get a change
in pH of 0.5 (smaller than beginning so this acts as a buffer)
• Ka is constant for each acid
• Buffer – a weak acid or base that resists a change in the pH of a solution
▪ See image #5
▪ Buffer works best in the midpoint of titration: big change in titer conc = small
change in pH
▪ [CH3COOH]=[CH2COO-] → midpoint of titration
▪ Acid dissociation constant = Ka→ see image
▪ In this case, Ka=[H+], pKa=-log(Ka)=pH
▪ Buffer works best within ±1 unit of the pKa
▪ Figure 2.18 – pKa’s of different molecules
▪ Memorize the Henderson-Hasselbalch equation
Phosphate is an intracellular buffer: Three different hydrogens on phosphate, so three different pKas.
The middle pKa (7.2) is most important for biological systems.
1-21-12
Bicarbonate is an important blood buffer
• CO2 + H2O →H2CO3 (carbonic acid)→H+ + HCO3- (bicarbonate)
• Carbonic anhydrase pushes the rxn towards carbonic acid
• Ka (combined) = [H+][HCO3-]/[]
• pKa=6.1
• respiratory acidosis/alkalosis
• metabolic acidosis/alkalosis – change in blood pH because of metabolic processes
