Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

THE CHEMICAL COMPONENTS OF A CELL
45
Figure 2–3 Schematic indicating how two macromolecules with
complementary surfaces can bind tightly to one another through
noncovalent interactions. Noncovalent chemical bonds have less than
1/20 the strength of a covalent bond. They are able to produce tight
binding only when many of them are formed simultaneously. Although only
electrostatic attractions are illustrated here, in reality all four noncovalent
forces often contribute to holding two macromolecules together (Movie 2.1).
individual noncovalent attraction would be much too weak to be effective in the
face of thermal motions, their energies can sum to create a strong force between
two separate molecules. Thus sets of noncovalent attractions often allow the complementary
surfaces of two macromolecules to hold those two macromolecules
together (Figure 2–3).
Table 2–1 compares noncovalent bond strengths to that of a typical covalent
bond, both in the presence and in the absence of water. Note that, by forming
competing interactions with the involved molecules, water greatly reduces the
strength of both electrostatic attractions and hydrogen bonds.
The structure of a typical hydrogen bond is illustrated in Figure 2–4. This bond
represents a special form of polar interaction in which an electropositive hydrogen
atom is shared by two electronegative atoms. Its hydrogen can be viewed as a
proton that has partially dissociated from a donor atom, allowing it to be shared
by a second acceptor atom. Unlike a typical electrostatic interaction, this bond is
highly directional—being strongest when a straight line can be drawn between all
three of the involved atoms.
The fourth effect that often brings molecules together in water is not, strictly
speaking, a bond at all. However, a very important hydrophobic force is caused by
a pushing of nonpolar surfaces out of the hydrogen-bonded water network, where
they would otherwise physically interfere with the highly favorable interactions
between water molecules. Bringing any two nonpolar surfaces together reduces
their contact with water; in this sense, the force is nonspecific. Nevertheless, we
shall see in Chapter 3 that hydrophobic forces are central to the proper folding of
protein molecules.
Some Polar Molecules Form Acids and Bases in Water
One of the simplest kinds of chemical reaction, and one that has profound significance
in cells, takes place when a molecule containing a highly polar covalent
bond between a hydrogen and another atom dissolves in water. The hydrogen
atom in such a molecule has given up its electron almost entirely to the companion
atom, and so exists as an almost naked positively charged hydrogen nucleus—in
Table 2–1 Covalent and Noncovalent Chemical Bonds
Bond type
Length (nm)
in vacuum
Strength kJ/mole**
in water
Covalent 0.15 377 (90) 377 (90)
Noncovalent ionic* 0.25 335 (80) 12.6 (3)
hydrogen 0.30 16.7 (4) 4.2 (1)
van der Waals
attraction (per
atom)
0.35 0.4 (0.1) 0.4 (0.1)
*An ionic bond is an electrostatic attraction between two fully charged atoms. **Values in
parentheses are kcal/mole. 1 kJ = 0.239 kcal and 1 kcal = 4.18 kJ.
(A)
(B)
donor
atom
hydrogen bond ~0.3 nm long
MBoC6 m2.16/2.03
N H
covalent bond
~0.1 nm long
O
O
O
N
N
N
+
donor
atom
H
H
H
H
H
H
acceptor
atom
O
O
N
O
O
N
O
acceptor
atom
Figure 2–4 Hydrogen bonds. (A) Ball-andstick
model of a typical hydrogen bond.
The distance between the hydrogen and
the oxygen atom here is less than the sum
of their van der Waals radii, indicating a
partial sharing of electrons. (B) The most
common hydrogen bonds in cells.