CH 2 Water

Chapter 2
Water: The Solvent for

Biochemical Reactions
© 2018 Cengage Learning. All Rights Reserved.

Chapter Outline
Part 1 (S3-S17)
(2-1) Water and polarity
Part 2 (S18-S32)
(2-2) Hydrogen bonds
(2-3) Acids, bases, and pH
Part 3 (S33-S53)
(2-4) Titration curves
(2-5) Buffers

2-1 Water and Polarity
• Water is the main component
of most cells.
• The geometry of water
molecule and its properties as
a solvent play major roles in
determining the properties of
living systems.
• The tendency of an atom to
attract electrons to itself in a
chemical bond is called
Electronegativity
• Note: Oxygen and nitrogen
are more electronegative than
carbon and hydrogen.
• Table 2.1 © 2018 Cengage Learning. All Rights Reserved.
Polar Bonds. What is polarity?
• Electrons are unequally • Figure 2.1 - The Structure of
Water
shared between O & H. • The dipole moment in this figure
• More negative charge is points in the direction from
found closer to one of the positive to negative.
atoms. Water is a bent
molecule.
• Polar bond is formed
because of the
difference in
electronegativity of
atoms involved in the
bond.

Polar Bonds and Molecules
• Bonds in a molecule may be polar, but the molecule
itself can be nonpolar because of its geometry
• Molecules such as CO2 have polar bonds but given
their geometry, are nonpolar
• Nonpolar: Bond in which two atoms share electrons
evenly like between H & H.

Solvent Properties of Water
• Some important noncovalent bonds:
1. Ionic bonds (Fig. 2.2)
• Held together by positive and negative ions
2. Salt bridge
• Interaction that depends on the attraction that occurs
when oppositely charged molecules are near one
another (like between COO- and – NH3+).
3. Ion–dipole interactions
• Occur when ions in solution interact with molecules
that have dipoles (Figures 2.2 and 2.3a).
• Example - NaCl dissolved in H2O

Figure 2.2 - Ionic Bonds Become Replaced by
Ion–Dipole Interactions
• In ionic solids, ionic bonds hold the cations and anions
together. In aqueous solution, these ionic bonds are replaced
by ion–dipole interactions. The negatively charged chloride
ions are attracted to the partial positive charges on water.
• The positively charged sodium ions are attracted to the partial
negative charges on the water
• Water surrounding ions of this type are called hydration shells.

Figure 2.3 - Ion–Dipole and Dipole–Dipole
Interactions
• Ion–dipole and dipole–dipole interactions help ionic
and polar compounds dissolve in water.

Solvent Properties of Water (continued 1)
4. Van der Waals forces: Noncovalent associations
based on weak attractions of transient dipoles for one
another
• Called van der Waals interactions or van der Waals
bonds
• Included in these forces are 3-noncovalent bonds that
do not involve electrostatic interactions of a fully
charged ions.
4.1 Dipole–dipole interactions (Fig. 2.3b)
• Forces that occur between molecules that are dipoles
• Partial positive side of a molecule attracts the partial
negative side of another molecule

4.2 Dipole–induced dipole interactions (Fig. 2.4).
• Permanent dipole in one molecule can induce a
transient dipole in another molecule through
momentary distortion of electron clouds
• Weak and generally do not lead to solubility in water
4.3 Induced dipole–induced dipole interactions
Fig. 2.5 This attractive force is often referred to as
London dispersion force.
(i.e., Attraction between transient induced dipoles)

Figure 2.4 - Dipole-Induced Dipole
Bonds
• Polar water can distort the electron cloud of a
nonpolar molecule, like oxygen, creating a
momentary dipole. Once the dipole is created, water
is attracted to it.

Figure 2.5 - Induced Dipole-Induced Dipole
Interactions
• Also called London dispersion forces, these
attractions arise when otherwise nonpolar molecules
bump into each other and distort each other’s
electron shells, forming induced dipoles. Once the
dipoles are formed, the molecules are momentarily
attracted to one another.

Table 2.2 - Strengths of Bonds Found in
Biochemistry

Hydrophobic Interactions
• Hydrophobic interactions: Attractions between
molecules that are nonpolar; also called hydrophobic
bonds.
• Hydrophilic Substances (water loving)
• Tending to dissolve in water. See Table 2.3
• Examples - Ionic and polar substances
• Hydrophobic Substances (water-hating)
• Tending not to dissolve in water.
• Amphipathic Substances
• Molecules that contain both hydrophobic and
hydrophilic regions
• Example - Sodium palmitate (Fig. 2.6)
Table 2.3 - Examples of Hydrophobic and
Hydrophilic Substances

Figure 2.6 - Sodium Palmitate, an
Amphipathic Molecule
• Amphiphilic molecules are frequently symbolized by a ball
and zigzag line structure where the ball represents the
hydrophilic polar head, and the zigzag line represents the
nonpolar hydrophobic hydrocarbon tail.

Fig. 2.7 Micelle Formation by
Amphipathic Molecules
• Spherical arrangement • When micelles form, the
of organic molecules in ionized polar groups are in
contact with the water, and
water solution clustered
the nonpolar parts of the
so that their: molecule are protected from
• Hydrophobic parts are contact with the water.
buried inside the sphere
• Hydrophilic parts are on
the surface of the sphere
and in contact with the
water environment
• Formation depends on
the attraction between
temporary induced
dipoles
2-2 Hydrogen Bonds
• Another type of noncovalent attractive interactions between dipoles when
the:
• Positive end of one dipole is a hydrogen atom bonded to a highly
electronegative atom (hydrogen-bond donor)
• Negative end of the other dipole is an atom with a lone pair of electrons
(hydrogen-bond acceptor).
• Fig. 2.8 A comparison of linear and nonlinear H-bonds.
• Nonlinear bonds are weaker than bonds in which all three atoms lie in a
straight line.

Figure 2.9 - Hydrogen-Bonding Sites
• A comparison of the numbers of hydrogen-bonding sites in
HF, H2O, and NH3. (Actual geometries are not shown.) Each
HF molecule has one hydrogen-bond donor and three
hydrogen-bond acceptors. Each H2O molecule has two
donors and two acceptors. Each NH3 molecule has three
donors and one acceptor.

Interesting and Unique Properties of Water
• Each water (ice) molecule is hydrogen bonded to
four others.
• Acts as a donor in 2 and as an acceptor in the other 2
• Enabled by the tetrahedral arrangement of the water
molecule with bond angles of 104.3°
• Fig 2.10 shows:
Tetrahedral H-bonding
in water. In an array of H2O
molecules in an ice crystal,
each H2O molecule is
hydrogen-bonded to four
others.
Table 2.4 - Comparison of Properties of Water,
Ammonia, and Methane
• Even though hydrogen bonds are weaker than
covalent bonds, they have a significant effect on the
physical properties of hydrogen-bonded compounds

Figure 2.11 Hydrogen Bonding between Polar
Groups and Water
• If a polar solute can serve as a donor or an acceptor
of hydrogen bonds, it can:
• Form hydrogen bonds with water
• Participate in nonspecific dipole–dipole interactions
• R-OH, R-NH2, R-COOH, R-CHO, & ketones can form
H-bonds with water, so they are soluble in water.

Table 2.5 - Examples of Major Types of Hydrogen
Bonds Found in Biologically Important Molecules
• Hydrogen bonding is important in the stabilization of
3-D structures of biological molecules, such as DNA,
RNA, and proteins.

2-3 Acids, Bases, and pH
• The biochemical behavior of important compounds
depends on their acid-base properties.
• Acids and Bases
• Acid
• Molecule that behaves as a proton donor.
• Commonly known as a Brønsted acid.
• Base
• Molecule that behaves as a proton acceptor.
• Commonly known as a Brønsted base.

Acid Strength
• Tendency of an acid to dissociate to a hydrogen ion
and its conjugate base
• Characterized by acid dissociation constant (Ka)
• The greater the Ka, the stronger the acid.

• Correct form of the equation:

Figure 2.13 – The Ionization of Water
• Let us quantitatively examine the dissociation of
water:  H +  OH - 
Ka 
H 2 O 
• Molar concentration of pure water, [H2O], is equal to
1000/18 = 55.5 M. Thus, + -
 H   OH 
Ka 
55.5
K a  55.5   H +  OH -   K w

Ion Product Constant for Water (Kw)
• The value of Kw increases with the increase of temperature, i.e., the
concentration of H+ and OH- ions increases with increase in temperature.
• A measure of the tendency of water to dissociate to give H+
and OH– ions
• The numerical value can be determined experimentally by
measuring [H+] of pure water
• In monoprotic acids, [H+] = [OH–]
• At 25°C in pure water,
+
 H  = 10
7
M = OH  
• At 25°C, the numerical value of Kw is given by:

K w =  H +  OH   = 107 107  = 10 14

pH and pKa
• Quantity for expressing [H+] and [OH–] in aqueous
solutions
pH  -log10  H 
+
• Difference of one pH unit implies a tenfold difference in

[H+]
• Neutral solutions have pH = 7, acidic solutions have
pH < 7, and basic solutions have pH > 7
• pKa
• Convenient numerical measure of acid strength
pK a =  log10 K a
• The smaller the value, the stronger the acid
Example 2.1 - pH Calculations
• In pure water, [H+] = 1×10–7 M and pH = 7.0
• Calculate the pH of the following aqueous
solutions:
a. 1×10–3 M HCl
b. 1×10–4 M NaOH
• Assume that the self-ionization of water
makes a negligible contribution to the
concentrations of hydronium ions and of
hydroxide ions, which will typically be true
unless the solutions are extremely dilute.
Example 2.1 - Solution
• The key points in the approach to this problem
are the definition of pH, which needs to be
used in both parts, and the self-dissociation of
water, needed in the second part
a. For 1×10–3 M HCl, [H3O+] = 1×10–3 M
• Therefore, pH = 3
b. For 1×10–4 M NaOH, [OH–] = 1×10–4 M
• Because [OH–] [H3O+] = 1×10–14, [H3O+] =
1×10–10 M
• Therefore, pH = 10.0
Why do we want to know the pH?
Figure 2.15 - pH versus Enzymatic Activity
Pepsin, trypsin, and lysozyme all have steep pH optimum curves.
Pepsin has maximum activity under very acidic conditions, as
would be expected for a digestive enzyme that is found in the
stomach. Lysozyme has its maximum activity near pH 5, while
trypsin is most active near pH 6.
Note how the activities of three enzymes can rapidly

change as pH leaves optimum range
Henderson–Hasselbalch Equation
• Mathematical  H    A  
relationship between the Ka 
pKa of an acid and the HA
pH of a solution  A 

containing the acid and  log K a  log  H   log
 
its conjugate base HA
• When concentrations of  A 

a weak acid and its  log  H    log K a  log
 
conjugate base are HA
equal, the pH of the
 A  
solution equals the pKa pH  pK a  log
of the weak acid HA
2-4 Titration Curves
• Titration: Experiment in which measured
amounts of standard base are added to
measured amounts of acid.
• Equivalence point: Point in an acid–base
titration at which enough base has been
added to neutralize the acid. It coincides with
the end point.
• An inflection point is reached when the pH
equals the pKa of acetic acid (Fig. 2.16).
• This is for a monoprotic weak acid.
Figure 2.16 - Titration Curve for Acetic Acid
• Note that there is a
region near the pKa at
which the titration
curve is relatively flat.
In other words, the pH
changes very little as
base is added in this
region of the titration
curve.

Example 2.2 - Calculating pH Values for Weak
Acids and Bases
• Calculate the relative amounts of acetic acid
and acetate ion present at the following points
when 1 mol of acetic acid (pKa=4.76) is titrated
with sodium hydroxide
• NaOH + CH3COOH → CH3COONa + H2O
1 mol 1 mol 1 mol 1 mol
• Also use the Henderson–Hasselbalch equation
to calculate the values of the pH at these
points: a) 0.1 mol of NaOH is added
b) 0.3 mol of NaOH is added
c) 0.5 mol of NaOH is added
Example 2.2 - Solution
• Approach this problem as an exercise in
stoichiometry
• There is a 1:1 ratio of moles of acid reacted to
moles of base added
• Difference between the original number of
moles of acid and the number reacted is the
number of moles of acid remaining
• These are the values to be used in the
numerator and denominator, respectively, of
the Henderson–Hasselbalch equation
Example 2.2 - Solution (continued 1)
a. When 0.1 mol of NaOH is added, 0.1 mol of acetic
acid reacts with it to form 0.1 mol of acetate ion,
leaving 0.9 mol of acetic acid (1.0- 0.1).
• Composition is 90% acetic acid and 10% acetate
ion 0.1
pH = pK a + log
0.9
0.1
pH = 4.76 + log
0.9
pH = 4.76  0.95
pH = 3.81

b. When 0.3 mol of NaOH is added, 0.3 mol of acetic
ion
0.3
pH = pK a + log pH = 4.39
0.7
c. When 0.5 mol of NaOH is added, 0.5 mol of acetic

ion
0.5
pH = pK a + log pH = 4.76
0.5
• Note that this one is possible without doing much
math
• We know that when the [HA] = [A–], the pH = pKa
• Therefore, the minute we saw that we added 0.5
mol of NaOH to 1 mol of acetic acid, we knew
that we had added enough NaOH to convert half
the acid to the conjugate base form
• Thus, the pH has to be equal to the pKa
Titration Curves (continued)
• Acid dissociation constants for three groups of acids
• Monoprotic acids (e.g., Pyruvic acid) release one H +
ion and have a single Ka and pKa
• Diprotic acids release two H+ ions and have two Ka
values and two pKa values (e.g., Oxalic acid).
• Polyprotic acids release more than two H + ions ( e.g.,
Phosphoric acid).
• Here is a way to keep track of protonated and deprotonated
forms of acids and their conjugate bases:
• When pH < pKa, the weak acid predominates
• H+ on, substance protonated
• When pH > pKa, the conjugate base predominates
• H+ off, substance©deprotonated
2018 Cengage Learning. All Rights Reserved.
2-5 Buffer Solutions
• Tend to resist changes in pH when small to
moderate amounts of a strong acid or strong
base are added.
• A buffer solution consists of a mixture of a
weak acid and its conjugate base.
• How do buffers work? See Fig. 2.17
• Examples of acid–base buffers are solutions
containing:
• (acetate) CH3COOH and CH3COONa
• (bicarbonate) H2CO3 and NaHCO3
Figure 2.17 - Buffering
• Acid is added to the two
beakers on the left. The pH
of unbuffered H2O drops
dramatically while that of
the buffer remains stable.
Base is added to the two
beakers on the right. The
pH of the unbuffered
water rises drastically
while that of the buffer
remains stable.

Example 2.3 Using the Henderson-
Hasselbalch Equation.
• For illustration consider a solution in which the
concentrations are [HPO42–] = 0.063 M and [H2PO4–] = 0.10
M, thus, the conjugate base/weak acid ratio is 0.63 and
pH= 7.2 + log (0.63) = 7
If 1.0 mL of 0.10 M HCl is added to 99.0 mL of the
buffer, the following reaction takes place and almost all
the added H+ is used up 2 + 
HPO 4 + H  H 2 PO 4
The concentrations of [HPO42–] and [H2PO4–] will change,
and the new concentrations can be calculated

Mechanism of Buffers - Example (continued)
• The new pH can then be calculated using the

Henderson–Hasselbalch equation and the phosphate
ion concentrations.
• The appropriate pKa is 7.20 (Table 2.6).
 HPO 24  0.062
pH = pK a + log pH = 7.20 + log = 6.99
 H 2 PO 4 
 0.101

Mechanism of Buffers
• Buffers follow Le Chatelier’s principle
• If stress is applied to a system in equilibrium, the
equilibrium will shift in the direction that relieves the
stress
• When H+ ion is added to a buffer system, stress is
added to the reaction
HA  H+ + A
• To relieve the stress, H+ reacts with A– to maintain
equilibrium.
• See example 2.4 on p.50

Buffer Selection
• A consideration of titration curves can give insight
into how buffers work (Fig. 2.18a) next slide.
• pH changes little in the vicinity of the inflection point of
a titration curve
• At the inflection point, half the amount of acid originally
present has been converted to the conjugate base
• The second stage of ionization of phosphoric acid, was
the basis of the buffer used in this example.
2 + 
HPO + H 
4 H 2 PO 4
• When the pH is one unit higher than pKa, the ratio of
conjugate base form to the conjugate acid form is 10
• When pH is two units higher than pKa, the ratio is 100,
and so on. Table 2.7 shows this.
Figure 2.18 - Relationship between the Titration Curve
and Buffering Action in H2PO4–

Table 2.7 - pH Values and Base/Acid Ratios for
Buffers

Buffer Selection
• A buffer solution can maintain a relatively constant
pH value, which is met at values at or near the pKa of
the acid.
• The buffer is effective within a range of about 2 pH
units (Fig. 2.18b). The buffer is effective at range of
pH = pKa ±1.
• Buffering Capacity is a measure of the amount of
acid or base that can be absorbed by a given buffer
solution
• Related to the concentrations of the weak acid and its
conjugate base. The greater the concentration of the
weak acid and its conjugate base, the greater the
buffering capacity..
How do we make buffers in the laboratory?
• Start with the HA form and add NaOH until the pH is
correct, as determined by a pH meter or start with A –
and add HCl until the pH is correct.
• Figure 2.19 - Two Ways of Looking at Buffers. In the titration curve, we see that the pH
varies only slightly near the region in which [HA] = [A–]. In the circle of buffers, we see that
adding OH– to the buffer converts HA to A−. Adding H+ converts A− to HA.

Biological Buffers
• What naturally occurring pH buffers are present in living organisms?
• The H2PO4–/HPO42– pair is the principal buffer in cells.
• The buffering system in blood is based on the dissociation of carbonic acid
(H2CO3) H2CO3 ↔ HCO3– + H+
• Where the pKa = 6.37. The pH of the blood, 7.4, is near the end of the
buffering range of this system, but another factor enters the situation.
• CO2 can dissolve in water and water-based fluids such as blood.
• The dissolved CO2 forms H2CO3, which reacts to produce bicarbonate
ion. The conversion is catalyzed by carbonic anhydrase. This is one of
the most efficient enzymes in biochemistry.
CO 2 ( g )  CO 2 ( aq)
CO 2 ( g )  H 2 O(l )  H 2CO3 ( aq)
H 2 CO3 ( aq)  H + ( aq)  HCO3- ( aq)
Net equation: CO 2 ( g )  H 2O(l )  H  ( aq)  HCO3 ( aq)
Naturally Occurring Buffers (continued)
• The phosphate buffer system is common in the lab.
• It can be:
• In vitro (outside the living body)
• Example - Buffer system based on tris (hydroxymethyl)
aminomethane (TRIS)
• In vivo (inside the living body)
• Example - Phosphate buffer system
• Other buffers that are used widely are zwitterions,
• Which are:
. compounds that have both a positive and negative charge.
. considered less likely to interfere with biochemical reactions
than some of the earlier buffers. See (Table 2.8).

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Chapter 2

Water: The Solvent for

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

• The greater the Ka, the stronger the acid.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

• At 25°C, the numerical value of Kw is given by:

© 2018 Cengage Learning. All Rights Reserved.

• Difference of one pH unit implies a tenfold difference in

Note how the activities of three enzymes can rapidly

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

c. When 0.5 mol of NaOH is added, 0.5 mol of acetic

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

• The new pH can then be calculated using the

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.

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