1. Chapter 2b | Water

2. Water
the liquid of life

3. Water, the Liquid of Life (part 2)
Water has all sort of strange and unusual properties.
Water:
has a high boiling point and high heat of vaporization.
has high surface tension.
dissolves many salts (like sodium chloride) and polar molecules (like ethanol).
does not dissolve non-polar substances (oil and water don’t mix).
has high heat capacity.
expands when it freezes, so ice floats. The density of water decreases when it freezes.
forms compartments in the presence of amphipaths.
is often found on Earth simultaneously as a solid, liquid and gas.

4. Water is a reagent in some of the most central and ubiquitous biochemical reactions. Shown are the net reactions for formation of biopolymers - by condensation dehydration. a) Synthesis of protein. b) Synthesis of RNA. c) Synthesis of polysaccharide. Chiral centers (stars) and strand directionalities (arrows) are indicated.

5. Water Associated with Proteins Is Essential for Their Functions
FIGURE 2-9 Water binding in hemoglobin. (PDB ID 1A3N) The crystal structure of hemoglobin, shown (a) with bound water molecules (red spheres) and (b) without the water molecules. The water molecules are so firmly bound to the protein that they affect the x-ray diffraction pattern as though they were fixed parts of the crystal. The two α subunits of hemoglobin are shown in gray, the two β subunits in blue. Each subunit has a bound heme group (red stick structure), visible only in the β subunits in this view. The structure and function of hemoglobin are discussed in detail in Chapter 5.

6. Water Bound to Proteins Is Essential for Their Functions
FIGURE 2–10 Water chain in cytochrome f. Water is bound in a proton channel of the membrane protein cytochrome f, which is part of the energy-trapping machinery of photosynthesis in chloroplasts (see Fig. 19–61). Five water molecules are hydrogen-bonded to each other and to functional groups of the protein: the peptide backbone atoms of valine, proline, arginine, and alanine residues, and the side chains of three asparagine and two glutamine residues. The protein has a bound heme (see Fig. 5–1), its iron ion facilitating electron flow during photosynthesis. Electron flow is coupled to the movement of protons across the membrane, which probably involves “proton hopping” (see Fig. 2–14) through this chain of bound water molecules.

7. Water Bound to Proteins Is Essential for Their Functions
FIGURE 2–11 Hydrogen-bonded water as part of a protein's sugarbinding site. In the L-arabinose-binding protein of the bacterium E. coli, five water molecules are essential components of the hydrogen-bonded network of interactions between the sugar arabinose (center) and at least 13 amino acid residues in the sugar-binding site. Viewed in three dimensions, these interacting groups constitute two layers of binding moieties; amino acid residues in the first layer are screened in red, those in the second layer in green. Some of the hydrogen bonds are drawn longer than others for clarity; they are not actually longer than the others.

8. Fatty acid anions (soaps) are called amphiphilic (or amphipathic).

9. Structures of micelles and bilayers (idealized representation).

10. All four of these atoms commonly form hydrogen bonds.
Which atom does NOT commonly form hydrogen bonds between or within biological molecules?
oxygen
hydrogen
carbon
nitrogen
All four of these atoms commonly form hydrogen bonds.
Answer C

11. What are the top two molecular forces that drive protein folding?
ionic interactions and hydrogen bonding
van der Waals and ionic interactions
hydrophobic interactions and hydrogen bonding
hydrogen bonding and van der Waals interactions
Answer C

12. pH, pKa and pKb

13. Ionization of Water  H2O H+ + OH⎼
O-H bonds are polar and can dissociate heterolytically.
Products are a proton (H+) and a hydroxide ion (OH–).
Dissociation of water is a rapid & reversible process.
Most water molecules remain un-ionized, pure water has very low electrical conductivity (resistance: 18 M•cm).
The equilibrium is strongly to the left (small Keq).
The extent of dissociation depends on the temperature.

14. Ionization of Water: Quantitative Treatment
Concentrations of participating species in an equilibrium process
are not independent but are related via the equilibrium constant: 
[H+] • [OH⎼]
H2O H+ + OH⎼ 
Keq = __________
[H2O]
Keq can be determined experimentally, it is 1.8 • 10–16 M at 25C.
[H2O] is 55.5 M.
Ionic product of water:
In pure water, [H+] = [OH–] = 10–7 M.

15. What Is pH?
pH is defined as the negative logarithm of the hydrogen ion concentration.
Simplifies equations
The pH and pOH add to 14.
In neutral solution, pH = pOH = 7.
pH can be negative ([H+] = 6 M).
pH = −log[H+]

16. Relationship of pH and the concentrations of H+ and OH- in water.
pH = -log[H+]

17. pH Scale Is Logarithmic:
1 unit = 10-fold
TABLE 2-6
The pH Scale
[H+] (M) pH
[OH–] (M)
pOHa
100 (1)
10–14 14
10–1 1
10–13 13
10–2 2
10–12 12
10–3 3
10–11 11
10–4 4
10–10 10
10–5 5
10–9 9
10–6 6
10–8 8
10–7 7
aThe expression pOH is sometimes used to describe the basicity, or OH– concentration, of a solution; pOH is defined by the expression pOH = 2log [OH2], which is analogous to the expression for pH. Note that in all cases, pH + pOH = 14.

18. pH of Some Common Liquids
FIGURE 2-15 The pH of some aqueous fluids.

19. Dissociation of a Weak Acid: Principle
Weak acids dissociate only partially in water.
The extent of dissociation is determined by the dissociation constant Ka.
We can calculate the pH if the Ka is known. But some algebra is needed!

20. Dissociation of a Weak Acid: Example
What is the final pH of a solution when 0.1 moles of acetic acid is added to water to a final volume of 1L?
We assume that the only source of H+ is the weak acid.
To find [H+], a quadratic equation must be solved.
0.1 – x x x
x = , pH = 2.883

21. Dissociation of a Weak Acid: Simplification
The equation can be simplified if the amounts of dissociated species are much less than the amount of undissociated acid.
Approximation works for weak acids and bases.
Check that x < [total acid].
0.1 – x x x
x x
x = , pH = 2.880

22. pKa Measures Acidity pKa = –log Ka
FIGURE 2-16 Conjugate acid-base pairs consist of a proton donor and a proton acceptor. Some compounds, such as acetic acid and ammonium ion, are monoprotic; they can give up only one proton. Others are diprotic (carbonic acid and glycine) or triprotic (phosphoric acid). The dissociation reactions for each pair are shown where they occur along a pH gradient. The equilibrium or dissociation constant (Ka) and its negative logarithm, the pKa, are shown for each reaction. *For an explanation of apparent discrepancies in pKa values for carbonic acid (H2CO3), see p. 63.

23. Buffers Are Mixtures of Weak Acids and their Conjugate Bases
Buffers resist change in pH.
At pH = pKa, there is a 50:50 mixture of acid and anion forms of the compound.
Buffering capacity of acid/anion system is greatest at pH = pKa.
Buffering capacity is lost when the pH differs from pKa by more than 1 pH unit.

24. FIGURE 2-17 The titration curve of acetic acid
FIGURE 2-17 The titration curve of acetic acid. After addition of each increment of NaOH to the acetic acid solution, the pH of the mixture is measured. This value is plotted against the amount of NaOH added, expressed as a fraction of the total NaOH required to convert all the acetic acid (CH3COOH) to its deprotonated form, acetate (CH3COO–). The points so obtained yield the titration curve. Shown in the boxes are the predominant ionic forms at the points designated. At the midpoint of the titration, the concentrations of the proton donor and proton acceptor are equal, and the pH is numerically equal to the pKa. The shaded zone is the useful region of buffering power, generally between 10% and 90% titration of the weak acid.

25. Weak Acids Have Different pKas
FIGURE 2–18 Comparison of the titration curves of three weak acids. Shown here are the titration curves for CH3COOH, H2PO⎼4, and NH+4 . The predominant ionic forms at designated points in the titration are given in boxes. The regions of buffering capacity are indicated at the right. Conjugate acid-base pairs are effective buffers between approximately 10% and 90% neutralization of the proton-donor species.

27. Henderson–Hasselbalch Equation: Derivation
HA H+ + A- 

28. Henderson–Hasselbalch Equation: Example

29. Biological Buffer Systems
Maintenance of intracellular pH is vital to all cells.
Enzyme-catalyzed reactions have optimal pH.
Solubility of polar molecules depends on H-bond donors and acceptors.
Equilibrium between CO2 gas and dissolved HCO3– depends on pH.
Buffer systems in vivo are mainly based on:
phosphate, concentration in millimolar range
bicarbonate, important for blood plasma
histidine, efficient buffer at neutral pH
Buffer systems in vitro are often based on sulfonic acids of cyclic amines.
HEPES
PIPES
CHES

30. Proton Hydration Protons do not exist free in solution.
They are immediately hydrated to form hydronium ions (H3O+).
A hydronium ion is a water molecule with a proton associated with one of the nonbonding electron pairs.
Hydronium ions are solvated by nearby water molecules.
The covalent and hydrogen bonds are interchangeable. This allows for an extremely fast mobility of protons in water via “proton hopping.”

31. Answer A

32. What is the pH of a 0.1 mM solution of hydrochloric acid at 37°C? 0.1 4
It cannot be determined with the information provided.
Answer D

33. in the area about 1 pH unit higher than the pKa
In what area of the titration curve for carbonic acid (H2CO3) is the molecule fully deprotonated?
the far left
the far right
at the center, at the pKa
in the area about 1 pH unit higher than the pKa
at the second pKa value, given that there are two deprotonations
Answer B

34. Osmotic Pressure

35. Solutes Can Change the Properties of Water
Colligative properties:
boiling point elevation, melting point depression, and osmotic pressure.
do not depend on the nature of the solute, just the concentration
Noncolligative properties:
viscosity, surface tension, taste, and color
depend on the chemical nature of the solute
Cytoplasm of cells are highly concentrated solutions and have high osmotic pressure due to dissolved solutes.

36. Osmotic Pressure
Water moves from areas of high water concentration (low solute concentration) to areas of low water concentration (high solute concentration).
Osmotic pressure (π) is the force necessary to resist the movement.
Osmotic pressure is influenced by the concentration of each solute in solution.
Dissociated components of a solute individually influence the osmotic pressure.

37. Osmotic pressure.
Osmosis and the measurement of osmotic pressure. (a) The initial state. The tube contains an aqueous solution, the beaker contains pure water, and the semipermeable membrane allows the passage of water but not solute. Water flows from the beaker into the tube to equalize its concentration across the membrane. (b) The final state. Water has moved into the solution of the nonpermeant compound, diluting it and raising the column of water within the tube. At equilibrium, the force of gravity operating on the solution in the tube exactly balances the tendency of water to move into the tube, where its concentration is lower. (c) Osmotic pressure (Π) is measured as the force that must be applied to return the solution in the tube to the level of that in the beaker. This force is proportional to the height, h, of the column in (b).
Water tends to move into the solution in order to equalize its concentration on both sides of the membrane. (b) As water moves into the solution by osmosis the height of solution in the tube increases. (c) The pressure that prevents the influx of water is the “osmotic pressure”.

38. Dialysis
Molecules smaller than the membrane “cutoff” approach an equilibrium concentration across the membrane.

39. Effect of Osmotic Pressure on Cells
FIGURE 2-13 Effect of extracellular osmolarity on water movement across a plasma membrane. When a cell in osmotic balance with its surrounding medium—that is, a cell in (a) an isotonic medium—is transferred into (b) a hypertonic solution or (c) a hypotonic solution, water moves across the plasma membrane in the direction that tends to equalize osmolarity outside and inside the cell.

40. placing them in a solution of amphipathic molecules
Which condition would cause red blood cells to burst due to excess water passing through the plasma membrane?
placing them in a solution of higher osmolarity than is present within the cells
placing them in a solution of amphipathic molecules
adding an isotonic solution to the cell suspension
placing them in a hypotonic solution
adding a charged solute, such as NaCl
Answer D

41. increase in enthalpy as heat moves into the sugar.
Dissolving table sugar into iced tea is an energetically favorable reaction due to a(n):
increase in enthalpy as heat moves into the sugar.
decrease in free energy due to broken weak interactions between sugar molecules.
increase in entropy as the sugar dissolves.
increase in free energy because there is no longer a solvation layer around the sugar crystal.
negative value for ΔS because the solute is more random.
Answer C

42. Chapter 2: Summary In this chapter, we learned about the:
nature of intermolecular interactions
properties and structure of water
behavior of acids and bases in water
participation of water in biochemical reactions