1

Take Home Message From Lecture 1

Basic Cell Structure (Figure 1-7a, Animal Cell)
Macromolecular Building Blocks (slide 17)
Common Functional Groups (Figure 1-15)
Definitions related to DG (slide 20, text pp. 22-23)

Reading: Chapter 1 pp. 1 - 36
2
Lecture 2: Water, Molecular Interactions,
Acid-Base Chemistry
Chapter 2, pp. 43-66

Properties of water
Hydrogen bonds
Weak interactions
Ionization and Equilibrium
pH and buffers
3
Structure of Water & Hydrogen Bonding
Dipolar nature of water: Hydrogen atoms have localized
partial positive charges (d+) and the oxygen atom has a
partial negative (d-) charge
Tetrahedral arrangement of electron pairs and hydrogen
atoms around oxygen atom
Hydrogen bonds are longer and weaker than covalent
O-H bond
E (kJ/mol)
Covalent OH Bond 459
Hydrogen Bond ~ 5 - 30
4
Structure & Hydrogen Bonding in Water
Four hydrogen bonds possible per water molecule,
where in liquid water average 3.4 hydrogen bonds and
ice all 4 hydrogen bonds
Entropy effect is important for clathrate-like structures
(later)
Lifetime of hydrogen bond 1-20 ps (10
-12
s) so liquid
water is can be described as a flickering structure

http://en.wikipedia.org/wiki/Water
5
Hydrogen Bonds in Biochemistry
Hydrogen bond donors (N-H, O-H not C-H)
Hydrogen bond acceptors (N: and O: )
6
Examples of Hydrogen Bonding Between
Molecules
Water as the
hydrogen bond
acceptor
Water as the
hydrogen bond
donor
7
More Examples of Hydrogen Bonding
Between Molecules
8
Directionality and Strength of Hydrogen
Bonding
Hydrogen bonding is stronger when
3 atoms involved lie in a line
9
Weak Noncovalent
Interactions
Many weak
interactions in
biomolecules

Aggregate effect or
sum of interactions is
significant: Only 10 kJ
mol
-1
differentiates a
functional folded
protein from a
precipitated protein
10
Strengths of Noncovalent Interactions
Hydrophobic interactions (displacement of water)
0.4 4 kJ/mol
Pi stacking (aromatic ring stacking)
0.4 4 kJ/mol
Van der Waals interactions (weak but many)
0.4 4 kJ/mol
Hydrogen Bond (e.g. O-HO=C)
4 40 kJ/mol
Electrostatic (pH effects, opposites attract, likes repel)
4 40 kJ/mol
Salt bridge (hydrogen bonding plus electrostatic)
e.g. carboxylate amino acid side-chain (Asp, Glu) to basic
amino side-chain (Arg, Lys)
40 400 kJ/mol

11
Amphipathic Compounds in Aqueous Solution
Amphipathic: both
hydrophilic (likes water,
polar or charged) and
hydrophobic (dislikes
water, nonpolar)

Long-chain fatty acids
have very hydrophobic
alkyl chains, each of which
is surrounded by a layer of
highly ordered water
molecules.

12
Amphipathic Molecules in Water (cont.)
By clustering together in
micelles, the fatty acid
molecules reduce the
hydrophobic surface area
exposed to water, so fewer
water molecules are required
to form a the shell of ordered
water around a hydrophobic
surface.

The energy gained by freeing
immobilized water molecules
(entropy increase) stabilizes
the micelle.

13
Effect of Water on
Enzyme-Substrate
Interactions
Figure 2-8
Lehninger, Principles of Biochemistry, 5
th
Ed.
14
Water Dissociation at Equilibrium
Water equilibrium dissociation
In reality, no free H
+
,
instead hydronium ions, H
3
O
+
15
Ionization of Water
Equilibrium constant for water dissociation



K
eq
= 1.8 x 10
-16
M at 25 C (electrical conductivity measurements)

Ion product of water at 25 C
K
W
= K
eq
[H
2
O] = [H
+
][OH
-
] = (1.8 x 10
-16
M)(55.5 M) = 1.0 x 10
-14
M
2



At neutral pH, [H
+
] = [OH
-
] and

K
eq
=
[H
+
][OH

]
[H
2
O]
[H
+
] =[OH

] = K
W
=1.0x10
7
16
Worked Example 2-3
Question: What is the concentration of H
+
in a solution
of 0.1 M NaOH?

Solution: Begin with the equation for the ion water
product.
K
W
= [H
+
][OH
-
] = 1.0 x 10
-14
M
2

With the [OH
-
] concentration of 0.1 M, solving for [H
+
]
gives:





[H
+
] =
K
W
[OH

]
=
1.0x10
14
M
2
0.1M
=1x10
13
M
17
Worked Example 2-4
Question: What is the concentration of OH
-
in a solution
with an H
+
concentration of 1.3x10
-4
M?

Solution: Begin with the equation for the ion water
product.
K
W
= [H
+
][OH
-
] = 1.0 x 10
-14
M
2

With the H+ concentration given in the question, solving
for [OH-] gives:




In all calculations, be sure to round the answer to the
correct number of significant figures.

[OH
-
] =
K
W
[H
+
]
=
1.0x10
14
M
2
1.3x10
4
M
= 7.7x10
11
M
18
Acid-Base Reaction in Aqueous Solution
Equibrium reaction of a Bronsted Acid (H+ donor, HA) in
water


Acid dissociation equilibrium constant

In dilute aqueous solution, the water concentration is
essentially constant
[H
2
O] = (1000 g/L)/(18.0153 g/mol) = 55.5 mol/L = 55.5 M

Customarily for dilute solutions, the water
concentration is combined with the equilibrium
constant
acid dissociation constant, K
a
K
a
= K[H
2
O] =
[H
+
][ A

]
[HA]
K =
[H
3
O
+
][ A

]
[HA][H
2
O]
19
pH Scale
pH= log
1
[H
+
]
= log[H
+
]
20
Acid-Base Titration and pK
a
pK
a
= log
1
K
a
= log K
a
pH = pK
a

when [HA] = [A
-
]
21
Henderson-Hasselbalch Equation
Equilibrium reaction
Acid dissociation constant, at equilibrium, for an
idealized acid, HA:

Derivation of Henderson-Hasselbalch equation
K
a
=
[H
+
][A
-
]
[HA]
log K
a
= log[H
+
]+log
[A
-
]
[HA]
log[H
+
] = log K
a
+log
[A
-
]
[HA]
pH= pK
a
+log
[A
-
]
[HA]
When [A
-
]=[HA], pH = pK
a
pH= log[H
+
];pK
a
= logK
a
22
Uses for Henderson-Hasselbalch Eq.
Calculate pK
a
, given pH and the molar ratio of H
+
donor
and acceptor
Calculate pH, given the pK
a
and the molar ratio of H
+

donor and acceptor
Calculate the molar ratio of H
+
donor and acceptor,
given the pH and pK
a
With these molar ratios, calculate the net charge of a
molecule in solution
See worked examples 2-5 and 2-6

pH= pK
a
+log
[A
-
]
[HA]
23
Worked Example 2-5
Question: Calculate the fraction of histidine that has a imidazole
side chain protonated at pH 7.3. The pKa values for histidine are
pK
1
= 1.82, pK
2
(imidazole) = 6.00, and pK
3
= 9.17 (see Fig. 3-12b).

Solution: The Henderson-Hasselbalch equation shows that a weak
acid goes from 1% ionization at 2 pH units below its pK
a
to 99%
ionized at 2 pH units above its pK
a
. Therefore at pH 7.3, only the
imidazole group with a pK
2
= 6.0 is partially dissociated/protonated.
Substituting pK
2
= 6.0 and pH = 7.3 into the Henderson-Hasselbalch
equation:



Solve for the ratio of non-protonated to protonated histidine
[His]/[HisH
+
] = antilog(7.3 - 6.0) = 20

So 1 part HisH
+
and 20 parts His, so the fraction protonated is
fraction HisH
+
= 1/(1+20)=0.048 or 4.8%
7.3= 6.0+log
[His]
[HisH
+
]
pH= pK
a
+log
[A
-
]
[HA]

24
pH in the body and enzyme activity
Pepsin is a digestive
enzyme secreted into
gastric juice, which has a
pH of ~1.5, allowing pepsin
to act optimally.

Trypsin is a digestive
enzyme that acts in the
small intestine, and has a
pH optimum that matches
the neutral pH in the lumen
of the small intestine.

Alkaline phosphatase of
bone tissue is a hydrolytic
enzyme thought to aid in
bone mineralization.