2Lecture contents Why water important to biochemistry Uses of water Physics & chemistry of waterUnique physical properties of waterMolecular structure of waterNoncovalent Bonding in waterIonic interactionsHydrogen Bondsvan der Waals ForcesThermal Properties of WaterSolvent Properties of WaterHydrophilic, hydrophobic, and amphipathic moleculesOsmotic pressure
3Ionization of WaterAcids, bases, and pHBufferstitration
4Why water is important to biochemistry More than 70% earth’s surface covered with waterThe substance that make possible life on earthSolvent & substrate for many cellular reactionTransports chemicals from place to placeHelps to maintain constant body temperatureCell components and molecules (protein, polysaccharides, nucleic acid, membranes) assume their shape in response to water
6Introduction Physic and chemistry of water Water is the chemical substance with chemical formula H2O: one molecule of water has two hydrogen atoms covalently bonded to a single oxygen atom.Water is a tasteless, odorless liquid at ambient temperature and pressure, and appears colorless in small quantities, although it has its own intrinsic very light blue hue.
7Oxygen attracts electrons much more strongly than hydrogen, resulting in a net positive charge on the hydrogen atoms, and a net negative charge on the oxygen atom.The presence of a charge on each of these atoms gives each water molecule a net dipole moment.
8Introduction Unique physical properties of water Exist in all three physical states of matter: solid, liquid, and gas.Has high specific heatWater conducts more easily than any liquid except mercuryWater has a high surface tensionWater is a universal solventWater in a pure state has a neutral pH
9Molecular Structure of Water Tetrahedral geometryThe oxygen in water is sp3 hybridized. Hydrogens are bonded to two of the orbitals. Consequently the water molecule is bent. The H-O-H angle is 104.5o.
10The bent structure indicate water is polar coz linear structure is nonpolar. Phenomenon where charge is separated to partial –ve charge and partial +ve charge is called dipoles.
11Water is a polar molecule. A polar molecule is one in which one end is partially positive and the other partially negative.Oxygen is more electronegative than hydrogen, so oxygen atom bears a partial –ve charge, hydrogen atoms are partial +ve charge
13Molecules eg water, in which charge is separated are called dipoles. Molecular dipoles will orient themselves in the direction opposite to that of the field when subjected to an electric field.
14Noncovalent Bonding Usually electrostatic They occur between the positive nucleus of one atom and the negative electron clouds of another nearby atomRelatively weak, easily disruptedLarge no. of noncovalent interactions stabilize macromolecules
15Types of noncovalent bonding : 1)Ionic interactions2)Hydrogen bonding3)Van der Waals forces-Dipole-dipole-Dipole-induced dipole-Induced dipole-induced dipole
16Typical “Bond” Strengths TypekJ/molCovalent>210NoncovalentIonic interactions4-80Hydrogen bonds12-30van der Waals0.3-9Hydrophobic interactions3-12
171) Ionic InteractionsInteraction occur between charged atoms or group.Oppositely charged ions are attracted to each other. (eg. NaCl)ions with similar charges eg K+ and Na+ will repel each other
19In proteins, certain amino acid side chains contain ionizable groups. Glutamic acid ionized as –CH2CH2COO-Lysine ionized as -CH2CH2CH2CH2NH3+Attraction between +ve and –ve charged amino acid side chains forms a salt bridge (-COO-+H3N-)Salt bridge
202) Hydrogen bondingHydrogen bonding is a weak attraction between an electronegative atom (O,N,F) in one molecule and a hydrogen atomin another molecule.*Has both electrostatic(ionic) and covalentcharacter.
21Water molecule form hydrogen bond with one another Four hydrogen bonding attraction are possible for each molecule:*2 through the hydrogen*2 through thenonbonding electronpairs
22The resulting intermolecular hydrogen bond acts as bridge between water molecules. Large no. of intermolecular bond (in liquid/solid states of water),the molecules become large, dynamic.This explain why water have high boiling & melting point.
233)Van Der Waals Forces Force between molecules Occur between permanent and/or induced dipoles3 types of van der waals forces :- Dipole-dipole interactions- Dipole-induced dipole interactions- Induced dipole-induced dipoleinteractions
24a) Dipole-dipole interaction Occur between molecules containing electronegative atoms, cause positive end of one molecule is directed toward negative end of anothereg. Hydrogen bonds are strong type of dipole-dipole interaction
25b)Dipole-induced dipole interaction A permanent dipole induces a transient dipole in a nearby molecule by distorting its electron distributioneg. Carbonyl-containing molecule is weakly attracted to hydrocarbonWeaker than dipole-dipole interaction
26c)Induced dipole-induced dipole interactions Forces between nonpolar moleculesBecause of the constant motion of electron, an atom/molecule can develop a temporary dipole (induced dipole) when the electron are distributed unevenly around nucleusNeighboring atom can be distorted by the appearance of the temporary dipole which lead to an electrostatic interaction between themAlso known as London dispersion forceseg. Stacking of base ring in DNA molecule
28Thermal Properties of Water Hydrogen bonding keeps water in the liquid phase between 0oC and 100oC.Liquid water has a high:Heat of vaporization - energy to vaporize one mole of liquid at 1 atmHeat capacity - energy to change the temperature by 1oCWater plays an important role in thermal regulation in living organisms.
29Relationship between temperature and hydrogen bond Max number of hydrogen bonds form when water has frozen into ice.Hydrogen bonds is approximately 15% break when ice is warmed.Liquid water consists of continuously breaking and forming hydrogen bonds.As the tempt rise, the broken of hydrogen bonds are accelerating.When boiling point is reached, the water molecules break free from one another and vaporize.
30Solvent properties of water Water is an ideal biological solventWater easily dissolves a wide variety of the constituents of living organisms.Water also unable to dissolve some substancesThis behavior is called hydrophilic and hydrophobic properties of water.
31Hydrophilic molecules Ionic or polar substances that has an affinity for waterIn Greek= Hydro, “water” philios, “loving”Water dipole structure and its capacity to form hydrogen bond with electronegative atoms enable water to dissolve ionic and polar substanceThese substances soluble in water due to 3 kinds of noncovalent bonding :a) ion-dipoleb) dipole-dipolec) hydrogen bonding
32Salts (KCl,NaCl) held together by ionic interactions When ionic compound eg. KCl,NaCl dissolved in water, its ions separate because the polar water molecules attract ions more than the ions attract each other. (ion-dipole interaction)Shells of water mol. cluster around the ions = solvation spheres
33Dipole-dipole Interactions Organic molecules with ionize groupThe polar water molecule interacts with carboxyl group of aldehyd & ketones (carbohyd) and hydroxyl group of alcoholDipole-dipoleinteractions
34Hydrogen Bonding hydrogen bond shown in yellow A hydrogen attached to an O or N becomes very polarized and highly partial plus. This partial positive charge interacts with the nonbonding electrons on another O or N giving rise to the very powerful hydrogen bond.hydrogen bondshown in yellow
35Hydrophobic molecules Non ionic or nonpolar substanceThese molecules do not form good attractions with the water molecule. They are insoluble and are said to be hydrophobic (water hating).eg. Hydrocarbon : CH3CH2CH2CH2CH2CH3, hexane
36Water forms hydrogen-bonded cagelike structures around hydrophobic molecules, forcing them out of solution. (droplet/into a separate layer)
37Amphipathic Molecules Amphipathic molecules contain both polar and nonpolar groups.Ionized fatty acids are amphipathic. The carboxylate group is water soluble (hydrophilic) and the long carbon chain is not (hydrophobic).Amphipathic molecules tend to form micelles when mixed with water.
38polar head – orient themselves in contact with water molecules Nonpolar tails – aggregate in the center, away from water
39Osmotic PressureOsmosis is a spontaneous process in which solvent (eg water) molecules pass through a semi permeable membrane from a solution of lower solute concentration (dilute) to a solution of higher solute concentration (concentrated).Osmotic pressure is the pressure required to stop osmosis (22.4 atm for 1M solution)
40Over time, water diffuses from side B (more dilute) to side A (concentrated)AABB
41Osmotic PressureOsmotic pressure (p) is measured using an osmometer.
42Osmotic Pressure = iMRT i = van’t Hoff factor (degree of ionization of solute)M = molarity (concentration of solute in mole/L)R = gas constant (0.082 L.atm/K.mole)T = absolute temp (in Kelvin)Osmolarity = iM (osmol/Liter)
43i is the van't Hoff coefficient. For non-electrolytes (non ionizable solute) i=1For strong electrolytes i= the number of ions that are produced by the dissociation according to the molecular formulae.g for NaCl you have 2 ions (1 Na+ and 1 Cl-) so i=2for CaCl2, 3 ions (1 Ca+2 and 2 Cl-) so i=3For weak electrolytes i=(1-a)+nan = the number of ions coming from the 100% dissociation according to the molecular formulaa = the degree of dissociatione.g the degree of ionization of 1M CH3COOH solution is 80%a=80%/0.8 , n=2so,i=(1-0.8) + 2(0.8) =1.8
44Question 11)Estimate the osmotic pressure of a solution 1M NaCl at 25°C. Assume 100% ionization of solute. = iMRTi= 2 (1 Na+ and 1 Cl-)M= 1 mol/LR= L.atm/K.molT= 298K
45Question 2Estimate the osmotic pressure of a solution 0.2M Magnesium chloride at 25°C. Assume 70% ionization of solute.
46Osmotic pressure is an important factor affecting cells Cells contain high concentration of solutes – small organic mol., ionic salts, macromoleculeCells may gain or lose water depend on concentration of solute in their environment.
47Definitions of solutions Isotonic – solutions of equal concentration on either side of the membraneCells placed in isotonic solution no net movement of water across the membraneVolume of cells are unchanged bcoz water entering & leaving the cell at the same rate.
49Hypotonic – solution with a lower solute concentration than the solution on the other side of the membraneCells placed in hypotonic solution water moves into the cellsCause cells ruptureeg. Red blood cells swell & rupture when immersed in pure water (hemolysis)
50Hypertonic – solution with higher concentration of solutes than the solution on the other side of the membraneCells placed in hypertonic solution water moves out the cellsCause cells to shrinkeg. Red blood cells shrink when immersed in 3% NaCl solution. (crenation)
51Water ionization, pH, titration, buffer The self-ionization of water is the chemical reaction in which two water molecules react to produce a hydronium (H3O+) and a hydroxide (OH−) ion.Water ionization occurs endothermically due to electric field fluctuations between molecules caused by nearby dipole librations resulting from thermal effects, and favorable localized hydrogen bonding.
53Ions may separate but normally recombine within a few min. to seconds. Rarely (about once every eleven hours per molecule at 25°C, or less than once a week at 0°C) the localized hydrogen bonding arrangement breaks before allowing the separated ions to return, and the pair of ions (H+, OH-) hydrate independently and continue their separate existence.
54Ionization of watermay be expressed asKeq = [H3O+][OH-][H2O]2The conditions for the water dissociation equilibrium must hold under all situations at 25°C.Kw= [H3O+][OH-] = 1 x 10-14MPure water ionize into equal amount of[H3O+ ] = [OH-] = 1 x 10-7 M
55Acids, Bases and pHWhen external acids or bases are added to water, the ion product ([H3O+ ][OH-] ) must equal.Kw= [H3O+][OH-] = 1 x 10-14The effect of added acids or bases is best understood using the Bronsted-Lowry- theory of acids and bases.
56Bronstead-Lowry theory Bronsted-Lowry theory is an acid-base theoryAcid is a substance that can donate proton (ion H+ donor)acid + base = conjugate base + conjugate acidHCl + H2O = H3O+ + Cl-Asid Base CA CBC: conjugate (product) A/B
57base is a substance that can accept proton RNH2 + H2O = OH- + RNH3+B A CB CAC: conjugate (product) A/B
58Measuring Acidity Added acids, increase concentration of hydronium ion In acid solutions [H3O+] > 1 x 10-7 M[OH-] < 1 x 10-7 MAdded bases, increase concentration of hydroxide ion.In basic solutions [OH-] > 1 x 10-7 M[H3O+] < 1 x 10-7 MpH scale measures acidity without using exponential numbers.
59pH Scale Define: pH = - log(10)[H3O+] acidic basic[H3O+]=1 x 10-7 M, pH = ?
62pH Scale Questions 1) [H3O+]=2.6 x 10-5 M, pH = ?
63pH Scale pH to [H3O+]? inverse log of negative pH orange juice, pH [H3O+]=?urine, pH 6.2. [H3O+]=?
64Strength of AcidsStrength of an acid is measured by the percent which reacts with water to form hydronium ions.Strong acids (and bases) ionize close to 100%.eg. HCl, HBr, HNO3, H2SO4eg. NaOH, KOH, CaOH
65Strength of AcidsWeak acids (or bases) ionize typically in the 1-5% rangeeg. Organic acid (contain carboxyl groups)CH3COCOOH, pyruvic acidCH3CHOHCOOH, lactic acid CH3COOH, acetic acid
66Strength of AcidsStrength of an acid is also measured by its Ka or pKa valuesDissociation of weak acid :HA + H2O = H3O+ + A-Weak acid conjugate base of HAStrength of weak acid may be determined :pKa= -log Ka
67Strength of Acids Ka pKa CH3COCOOH 3.2x10-3 2.5 CH3CHOHCOOH xCH3COOH xLarger Ka and smaller pKa values indicate stronger acids.
68Monitoring acidityThe Henderson-Hasselbalch (HH) equation is derived from the equilibrium expression for a weak acid.
69HH equationThe HH equation enables us to calculate the pH during a titration and to make predictions regarding buffer solutions.What is a titration?It is a process in which carefully measured volumes of a base are added to a solution of an acid in order to determine the acid concentration.
70When chemically equal (equivalent) amounts of acid and base are present during a titration, the equivalence point is reached.The equivalence point is detected by using an indicator chemical that changes color or by following the pH of the reaction versus added base, ie. a titration curve.
71Titration Curve (HOAc with NaOH) End pointEquivalence pointpHNaOH (equivalents added)
72Titration Curve (HOAc with NaOH) At the end point, only the salt (NaOAc) is present in solution.At the equivalence point, equal moles of salt and acid are present in solution.[HOAc] = [NaOAc]pH = pKa
73QuestionsBy using HH equation, calculate the pH of a mixture of 0.25M acetic acid and 0.1M sodium acetate. The pKa of acetic acid is 4.76pH = pKa + log [A-][HA]pH = log [acetate][acetic acid]pH = log 0.1 = 4.360.25
742) Calculate the ratio of lactic acid to lactate in a buffer at pH 5 2) Calculate the ratio of lactic acid to lactate in a buffer at pH The pKa for lactic acid is 3.86= 13.8
753) During the fermentation of wine, a buffer system consisting of tartaric acid and potassium hydrogen tartrate is produced by a chemical reaction. Assuming that at some time the concentration of potassium hydrogen tartrate is twice that of tartaric acid, calculate the pH of the wine. The pKa of tartaric acid is 2.96
77Buffer solutionBuffer : a solution that resists change in pH when small amounts of strong acid or base are added.A buffer consists of:a weak acid and its conjugate base ora weak base and its conjugate acid
78How does buffer work?Accepting hydrogen ions from the solution when they are in excessDonating hydrogen ions from the solution when they have depleted
79Buffer Solutions Maximum buffer effect occurs at the pKa for an acid. Effective buffer range is at 1 pH unit above and below the pKa value for the acid or base.eg. H2PO4-/HPO42-, pKa=7.20buffer range pH
80Buffer SolutionsHigh concentrations of acid and conjugate base give a high buffering capacity.Buffer systems are chosen to match the pH of the physiological situation, usually around pH 7.
81Physiological buffer 3 most important buffer in body: Within cells the primary buffer is the phosphate buffer: H2PO4-/HPO42-The primary blood buffer is the bicarbonate buffer: HCO3-/H2CO3.Proteins also provide buffer capacity. Side chains can accept or donate protons. (eg. Hemoglobin, serum albumins)
82A zwitterion is a compound with both positive and negative charges. Zwitterionic buffers have become common because they are less likely to cause complications with biochemical reactions.
83N-tris(hydroxymethyl)methyl-2-aminoethane sulfonate (TES) is a zwitterion buffer example. (HOCH2)3CN+H2CH2CH2SO3-
84Assignment (water)Date of submission: 30/7/10Explain how the changes in temperature give effect to hydrogen bonds in water molecule. Elaborate the situation with drawing of water molecules at every temperature level.2. Explain how the acids produced in metabolism are transported to the liver without greatly affecting the pH of the blood.