Page 15 - Color Atlas of Biochemistry
P. 15
6 Basics
Molecular structure
B. Bond lengths and angles
The physical and chemical behavior of mole- Atomic radii and distances are now usually
cules is largely determined by their constitu- expressed in picometers (pm; 1 pm =
tion (the type and number of the atoms they 10 –12 m). The old angstrom unit (Å,
contain and their bonding). Structural formu- Å = 100 pm) is now obsolete. The length of
las can therefore be used to predict not only single bonds approximately corresponds to
the chemical reactivity of a molecule, but also thesum of what areknown as the covalent
its size and shape, and to some extent its radii of the atoms involved (see inside front
conformation (the spatial arrangement of cover). Double bonds are around 10–20%
3
the atoms). Some data providing the basis shorter thansingle bonds. Insp -hybridized
for such predictions are summarized here atoms, the angle between the individual
2
and onthe facing page. Inaddition, L-dihy- bondsisapprox. 110°; in sp -hybridized
droxyphenylalanine (L-dopa; see p. 352), is atomsitisapprox. 120°.
used as an example to show the way in which
molecules are illustrated in this book.
C. Bond polarity
A. Molecule illustrations Depending on the position of the element in
the periodic table (see p. 2), atoms have
In traditional two-dimensional structural
formulas (A1), atoms are represented as letter different electronegativity—i. e., a different
tendency to take up extra electrons. The val-
symbols and electron pairs are shown as lines.
Lines between two atomic symbols symbolize ues given in C2 areon a scalebetween 2and 4.
The higher the value, the more electronega-
two bonding electrons (see p. 4), and all of the tive the atom. When two atoms with very
other lines represent free electron pairs,such different electronegativities are bound to
as those that occur in O and N atoms. Free one another, the bonding electrons are drawn
electrons are usually not represented explic-
itly (and this is the convention used in this toward the more electronegative atom, and
the bond is polarized. The atoms involved
book as well). Dashed or continuous circles or
arcs are used to emphasize delocalized elec- then carry positive or negative partial
trons. charges. In C1,the van der Waals surface is
colored according to the different charge con-
Ball-and-stick models (A2) are used to illus-
trate the spatial structure of molecules. Atoms ditions (red = negative, blue = positive). Oxy-
gen is the most strongly electronegative of the
are represented as colored balls (for the color biochemically important elements, with C=O
coding, see the inside front cover) and bonds double bonds being especially highly polar.
(including multiple bonds) as gray cylinders.
Although the relative bond lengths and angles
correspond to actual conditions, the size at
which the atomsare representedistoo small D. Hydrogen bonds
to make the model more comprehensible. The hydrogen bond,a specialtype of nonco-
Space-filling van der Waals models (A3)are valent bond, is extremely important in bio-
useful for illustrating the actual shape and chemistry. In this type of bond, hydrogen
size of molecules. These models represent atomsof OH, NH, or SH groups(known as
atoms as truncated balls. Their effective ex- hydrogen bond donors)interactwithfree
tent is determined by what is known as the electrons of acceptor atoms (for example, O,
van der Waals radius. This is calculated from N, or S). The bonding energies of hydrogen
–1
the energetically most favorable distance be- bonds (10–40 kJ mol )are much lower
tween atoms that are not chemically bonded than those of covalent bonds (approx.
–1
to one another. 400 kJ mol ). However, as hydrogen bonds
can be very numerous in proteins and DNA,
they play a key role in the stabilization of
these molecules (see pp. 68, 84). The impor-
tance of hydrogen bonds for the properties of
water is discussed on p. 26.
Koolman, Color Atlas of Biochemistry, 2nd edition © 2005 Thieme
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