Page 19 - Color Atlas of Biochemistry

10 Basics
Biomolecules I
A. Important classes of compounds
Most biomolecules are derivatives of simple
compounds of the non-metals oxygen (O),
hydrogen (H), nitrogen (N), sulfur (S), and
phosphorus (P). The biochemically important
oxygen, nitrogen, and sulfur compounds can
be formally derived from their compounds
with hydrogen (i. e., H 2 O, NH 3 ,and H 2 S). In Carboxylic acid esters (R-O-CO-R )arise from
biological systems, phosphorus is found al-
most exclusively in derivatives of phosphoric
acid, H 3 PO 4 .
If one or more of the hydrogen atoms of a
non-metal hydride are replaced formally with
another group, R—e. g., alkyl residues—then
derived compounds of the type R-XH n–1 ,
R-XH n–2 -R, etc., are obtained. In this way,
alcohols (R-OH) and ethers (R-O-R) are de-
rived from water (H 2 O); primary amines (R-
NH 2 ), secondary amines (R-NH-R) and terti-
ary amines (R-N-R R )amines are obtained
from ammonia (NH 3 ); and thiols (R-SH) and
thioethers (R-S-R )arise from hydrogen sul-
fide (H 2 S). Polar groups such as -OH and -NH 2
are found as substituents in many organic
compounds. As such groups are much more
reactive than the hydrocarbon structures to
which they are attached, they are referred to
as functional groups.
New functional groups can arise as a result
of oxidation of the compounds mentioned
above. For example, the oxidation of a thiol
yields a disulfide (R-S-S-R). Double oxidation
of a primary alcohol (R-CH 2 -OH) gives rise
initially to an aldehyde (R-C(O)-H), and then
to a carboxylic acid (R-C(O)-OH). In contrast,
the oxidation of a secondary alcohol yields a
ketone (R-C(O)-R). The carbonyl group (C=O)
is characteristic of aldehydes and ketones.
The addition of an amine to the carbonyl
group of an aldehyde yields—after removal of
water—an aldimine (not shown; see p.178).
Aldimines are intermediates in amino acid
metabolism (see p.178) and serve to bond
aldehydes to amino groups in proteins (see
p. 62, for example). The addition of an alcohol
to the carbonyl group of an aldehyde yields a
hemiacetal (R-O-C(H)OH-R). The cyclic forms
of sugars are well-known examples of hemi-
Koolman, Color Atlas of Biochemistry, 2nd edition © 2005 Thieme
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acetals (see p. 36). The oxidation of hemiace-
tals produces carboxylic acid esters.
Very important compounds are the carbox-
ylic acids and their derivatives, which can be
formally obtained by exchanging the OH
group for another group. In fact, derivatives
of this type are formed by nucleophilic sub-
stitutions of activated intermediate com-
pounds and the release of water (see p.14).
carboxylic acids and alcohols. This group in-
cludes the fats, for example (see p. 48). Sim-
ilarly, a carboxylic acid and a thiol yield a
thioester (R-S-CO-R ). Thioesters play an ex-
tremely important role in carboxylic acid me-
tabolism. The best-known compound of this
type is acetyl-coenzyme A (see p.12).
Carboxylic acids and primary amines react
to form carboxylic acid amides (R-NH-CO-R ).
The amino acid constituents of peptides and
proteins are linked by carboxylic acid amide
bonds, which are therefore also known as
peptide bonds (see p. 66).
Phosphoric acid, H 3 PO 4 , is a tribasic (three-
protic) acid—i. e., it contains three hydroxyl
+
groups able to donate H ions. At least one
of these three groups is fully dissociated
under normal physiological conditions, while
the other two can react with alcohols. The
resulting products are phosphoric acid mono-
esters (R-O-P(O)O-OH) and diesters (R-O-
P(O)O-O-R ). Phosphoric acid monoesters are
found in carbohydrate metabolism, for exam-
ple(seep. 36),whereas phosphoric acid
diester bonds occur in phospholipids (see
p. 50) and nucleic acids (see p. 82 ).
Compounds of one acid with another are
referred to as acid anhydrides.Aparticularly
large amount of energy is required for the
formationofanacid—anhydride bond. Phos-
phoric anhydride bonds therefore play a cen-
tralrolein the storageand releaseof chemical
energy in the cell (see p.122). Mixed anhy-
drides between carboxylic acids and phos-
phoric acid are also very important “energy-
rich metabolites” in cellular metabolism.