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Unformatted text preview: Bio 20A-M. Dalbey Assigned Reading: 3.1 Chapter 3: WATER NOTES Chapter 3 (all) 1/2/08 The polarity of water molecules results in hydrogen bonding p. 47 The structure of the water molecule: 2-D R esen ion o the W r M cul epr tat s f ate ole e
~105o [theoretical = ~110o] H HO
X X +0.33 H H O +0.33
-0.33 -0.33 Therepr sen on o th le d notshowthe2 e tron inthe1sorbialof e tati n e ft oes lec s t Oxyg n b usetheyare no " enceEl ctr ns"(ie. t eydo notpar patein e eca t Val e o h tici bonding ). Theserep resen onsobscu t e rue 3 te tati re h t D trahe str ctur ofwat r. dral u e e HYDROGEN BONDING Linus Pauling developed concept of H-bonding to explain the unusual properties of liquid H2O. H bonds are 10X stronger than VDW interactions in ordinary liquids, 10X weaker than covalent bonds. Note that in a H2O dimer, both molecules are free to rotate about the axis of the H bond. ICE
Association of 2 Water Molecules by Intermolecular Hydrogen Bo nding ~0.10 nm 460 kJ / m ole ~0 nm .18 20 kJ / mo le O H H O H 0.2 nm 8 H In an iso lated, H-bon dedpa of wat r mol cu , bot ir e e les arefreeto rot abo theH b ate ut ondaxi . s A CPK model of 5 water molecules H-bonded in the typical tetrahedral lattice structure of ice. 1 of 5 Bio 20A-M. Dalbey 3.2 Chapter 3: WATER NOTES 1/2/08 p. 48 Four emergent properties of water contribute to Earth's fitness for life Cohesion, Adhesion ("Surface Tension"; "Capillary Action") and Elasticity Specific Heat Heat of Vaporization Expansion on Freezing *Solvent Properties *Ionization pH Buffering + + High Electrical Conductivty by H hopping rather than H diffusion *Reactivity (hydrolysis / dehydration; oxidation / reduction) Supercooling (not mentioned in the text) * Denotes those properties most important for Bio 20A. Other properties are more germane to ecology and physiology. The properties listed above should be understood as manifestations of the difference in electronegativities between Hydrogen and Oxygen, leading to polarity of the water molecule and to intermolecular Hydrogen Bonding. The structure of liquid water is sometimes said to contain "flickering microclusters" of ice. Liquid water is somewhere between ideal liquid and ideal crystal in that it has about 30-40% of the H bonds of ice at 25C. WATER AS A SOLVENT ions and polar molecules = hydrophilic non-polar molecules = hydrophobic If a non-polar molecule is surrounded by water molecules, the ability of the water molecules to form hydrogen bonds to each other is diminished, and not compensated by their ability to interact with the solute molecule (as would be the case if the solute were polar or ionic). This amounts to forcing the water molecules into a more highly structured arrangement; i.e. causes a decrease in entropy for the system. To minimize the entropy decrease non-polar molecules tend to associate with each other rather then with the water molecules. This is the physical basis of the so-called hydrophobic effect. A nonpolar molecule in an aqueous environment decreases entropy. Consider the relative solubilities of methane (CH4) and ammonia (NH3). 2 of 5 Bio 20A-M. Dalbey Chapter 3: WATER NOTES 1/2/08 3.3 Dissociation of water molecules leads to acidic and basic conditions that affect living organisms p. 53 DISSOCIATION OF WATER MOLECULES Ionization of the water molecule can be viewed as an extreme manifestation of its polarity. This can be written as: or abbreviated to: H 2O + H 2O H 2O H3O+ + OHH+ + OH- although this is misleading because free protons (H+) are rarely present. H + OH - 10-7 10-7 = = 1.8X10-16 Keq = H 2O 55.5 The equilibrium constant shows that the tendency of water to ionize is very slight (though the 7 biochemcal implications are profound). Only one water molecule in 55 X 10 (555 million) is ionized at -12 any given moment. Moreover, the average lifetime of a hydronium ion is only 10 second (a thousand times less than the average lifetime of a hydrogen bond between two water molecules at 25C). Note that pure water is [55.5 M]. K eq H 2O = H + OH - = 10-14 M 2 = K w Thus, if [H+] is known, [OH-] can easily be calculated, and vice versa. In absolutely pure water:
-7 [H+] = [OH-] = [10 M] This is the basis for defining pH values. 3 of 5 Bio 20A-M. Dalbey Chapter 3: WATER NOTES 1/2/08 pH = log 1 H+ = - log H + " Neutral " pH = log 1 10-7 =7 ACID/BASE CONCEPTS Arrhenius 1880's Brnstead-Lowry 1923 Lewis Acid H+ Donor H+ Donor 2 e- Acceptor Base OH- Donor H+ Acceptor 2 e- Donor The Arrhenius concept is too limited because it fails to account for the properties of some important functional groups , notably the amino group. NH3 Acid NH2 + H+ Base The Lewis Acid/Base concept is useful in evaluating non-aqueous systems. This is not often necessary in biochemistry. H+ + A- For any acid/base dissociation: Buffers HA TheCar ate - Bic ona Buf er Sy bon arb te f stem CO 2
Air pKa= 3.8 10. 2 Wa ter CO + H2O 2
Carbon Dioxide H2CO 3
Carbonic Ac id HCO3+ H+
Bicarbonate CO -2 3 + H+
Carbonate Can you use this to explain why rainwater usually has a pH of between 5 and 6? 4 of 5 Bio 20A-M. Dalbey TEXT/SELF-QUIZ (p.57) 2. 5.b. 8. Chapter 3: WATER NOTES 1/2/08 In other words by "evaporative cooling". ie. Hydrogen bonds (not covalent bonds) between water molecules. The molecular weight of acetic acid is: 2(12) + 4(1) + 2(16) = 60 g/mole 60 g/mole X 0.1 mole/L X 10 L = 60 g 9. pH = -log [H+] [H+] = antilog -pH [H+] = antilog -4.0 [H+] = 10-4 M 10. [H+] [OH-] = 10-14 M [OH-] = 10-14 M / [H+] [OH-] = 10-14 M / 10-4 M [OH-] =10-10 M REFERENCES Ball, Philip (2001) Life's Matrix: A biography of Water Univ. Calif Press A popular account. Liu, K. et al. (1996) Water Clusters Science 271, 929. 5 of 5 ...
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