CHAPTER 4

1', l{L
ORGANICAND BIOCHEMISTRY

Organic chemistry is the study of compounds of carbon. Living systemsform organic

molecules but there is also an abundance of synthetic organics. Modern industry
manufactures something on the order of 10 000 new compounds per year, most of
which are organic. More than 1 100 000 organic compounds have been prepared.
Determining their behavior in the environment and methods for treatment of these
compoundspresentsa formidable task for the chemist.biologist,ecologist,and environ-
mental engineer.
In this chapter the major classesof organic compounds are described. A brief
overvierv of rnetabolism is also presented to gain some appreciation of the means of
processing foodstuffs and the complexity of ryetabolism.

4.1 CARBON
Carbon is a unique atom, with properties that account for the lirnitless compounds it
can form. The bonds between carbon atoms are stable. which allows chains to be
formed. Atoms near carbon in the periodic table can also bond to carbon to form
chains. Each carbon atom can form four bonds. The bonds are covalent in nature:
that is, electrons are shared between the participating atoms. If the atoms bonded to
carbon have an electronegativity that is significantly different from carbon, then the
D, , n bond will have a polar character,rvith the electronsbeing shared unequally between
the atoms. The degree of polarity in an organic molecule determines its solubility in
the polar solvent, water. Because of the four bonds and chaining ability of carbon,
many different configurations are possible for the same group of atoms, rvhich is
known as isomerism.
The principal atoms that form compounds with carbon are hydrogen and oxygen.
Nitrogen, phosphorus, and sulfur are the most common minor elernents found in
naturally occurring organic molecules. Carbon dioxide and its related species are
-, I i n o rg a n i c i o n s o r c o m p o unds.
.P P

,. -rrJ 4.2 PROPERTIESOF ORGANIC COMPOUNDS

There are more known compoundsofcarbon than any other element except hydrogen.
Sawyer et al. (1994) have summarized the major characteristicsof organic compounds
compared to inorganic compounds.A brief explanationis added to most of their points.

1. Organic compounds are usually combustible.

A large amount of energy is releasedas an organic compound is oxidized to CO:.
H2O, and other oxides. The energy releasepropagatesthe reacticln.
2. Org a n i c c o mp o u n d s usual l y have l ow er mcl ti ng and boi l i ng poi nts.
 (ILIA P 'tE R 4/Organi c and B i ochcuri strl

groups. The alcohol group is sirnilar in behavior to water: that is, it is neither strongly
acidic nor basic but thc bond is polar. The carboxyl group is acidic in nature. The

,9
a
t

o
H
Carboxyl gr:oup
. l- r J I I rt l l

electronegativity of the two oxygen atoms pulls electrons away from the hydrogen
atom, which then dissociatesas Ht. The carbonyl group is an extremely important
:J a ! )I ll-
group in modern synthetic organic chemistry. Because of the high electronegativity
difference between carbon and oxygen, the bond in the carbonyl group provides a
highly reactive site.
-.- : lro n t

- '. rh i c h
4.4 ALIPHATICCOMPOUNDS
: - : rl l i t r The aliphatic compounds can be broken down into alkanes,which contain only single
-., ,rrlll- carbon-carbon bonds; alkenes,which contain at least one double bond between two
carbon atoms; and alkvnes, which contain at least one triple bond between a carbon
. * rr t h c r pair. Compounds that contain double or triple carbon bonds are unsaturated com-
pounds. Double or triple carbon bonds are major reaction sites.Many synthetic reac-
tions break these multiple bonds ancl add halogensor other atoms to the carbon.
- -' : l i a l rn

TABLE 4.1 Physical Properties of n-Alkanes, CH3(CH2),-zCHro

bp,'c mp density, g/cm3
n narne at 760mm Hg at 20"C
1 Methane - 16r.5 - 183 0.424b
z Ethane 88.6 - t72 0.546b
3 Propane _ t) t - 188 0.-s01.
4 Butane il.5 - 135 0.579.
5 Pentane 36.1 - 130 0.626
6 Hex ane 68.'7 -95 0.6,59
7 Heptane 98.4 -9t 0.684
6 Octzrne 125.7 -57 0.703
9 Nonane 150.8 -54 0.718
: tl , 1JOf 10 Dc c anc 111.1 -30 0.730
r- - O. tl Undecane 19-i .9 -26 0.740
t) Dodc c ane I IO.-1 -10 0.749
15 Pentadecane 210.6 l0 0.769
20 Eicosanc - ) +_. / 37 0.7ii6d
30 Triacontane 446.4 66 0.810'r
' F r o r n Ro b cr ts e t a l. ( 1 9 7 1 )
h At th e b o ilin g p o in t.
' Un cle r p r e ssu r e .
d F o r th e su p e r co o le d liq u id
 C l l l A P 'l U t{ .1/Oruani cand B i ochenri sl r} ' tl l

:J I . t t rl c H
,i-- i u ra l ,c .
,,,H \
'.' r g\ lLl\
HCH HCH
I : t)11 1 C
. ' 1tr ri. \
' '' I -'
HCH HCH
- ,J l. -e l c 'c .
\H ,,,
H
Figure 4.3 Cyclohexane.

Lrbrrn
Cyclic Aliphatic Compounds
Cyclic aliphaticcompounds,as the name implies,consistof carbon atoms singly bonded
together to form a ring conrpound. They may contain functional groups. There is no
resonancein these compounds and their behavior is similar to the chained aliphatics.
Cyclohexane is shown in Fig. 4.3.

Reactions of Aliphatic Compounds

In general, aliphatic compounds can be oxid'i.zedby oxygen or other oxidizing agents.
Halogenswill substitutethemselvesfor hydrogen,forrning haloorganics.mzinyof rvhich
are toxic or carcinogenic.Aerobic bacteria have enzymesthat catalyze the oxidation
,: giInlC
of hydrocarbonsto alcoholsand then further to carbon dioxide and water. The bacteriit
work on the terminal carbon atom and carrv this orr until the whole moleculeis oxidized.
'--rr LlOd.

4.5 NITROGEN.CONTAININGCOMPOUNDS
Amines are derivatives of ammonia, NH-,. Primary. secondar\',and tertiary arniues
have one, two, or three of the hydrogen atoms. respectively,substituted with alkyl
groups. Tertiary amines combine with alkyl halides to form quartcrnary ammoniurn
salts.These saltshave bactericidalpropertiesthat make them useful disinfectingagents.
An amide is another functional group consisting of a primary amine-carbonyl
c o mb i n a ti o n : -(C :O )-N H ,. It i s a reacti ve sroup of i nterest to synthet ic or -
: : pOI1 d ganic chemists.
R,{ Amino acids have at least one amine (-NHr) and one carboxylic group pel
molecule. Becauseof the presenceof the amino group and the carboxylic acid group
these moleculeshave both acidic and basic properties.The general structural formula
for an amino acid is shown at the marsin.

H
I
R -C - C OOH
r Is itre
I
: . iad as NH.
, r f t he
Am in o a cid

if S af e
\^ \qe n . The hydrotysisof trvo amino acids,which involves the reaction clf thc carboxvlic
.'.rtlelv g ro u p o n o n e a c i d rv ith the ami ne group on the other rvi th a mol ecul eof rvaterl e avinq.
results ir-rthe formation of a peptide bond. Amino acids can thirs be chained togetlter'
 C H A P TE R 4/C )rgani cand B i ochemi stry

polyringaromatichyclrocarbons exist There are many naturally occurring arornatlcs

as well as syntheticaromatics.

OH
cl.--"\ct
tl
II
Cl\---Cl
CI
PCP
1i a re
,irbon
Chlorinated benzene derivatives are often quite toxic. Pentachlorophenol(PCP),
shown above, is one of the most widely used pesticidesand is one of the most toxic
compounds becauseof its hieh number of chlorine atoms.

rnt e r s

4.7 COMPOUNDSOF SULFTJR

rrther
:n trr t Similarly to ammonia, sulfuric acid may have either one or both H or OH atons
substituted with organic chains to form varioils cornpounds.Two examples of these
compounds are diphenyl sulfone and methane sulfonic acid, with the following
structures.

I Und s
o o
ll
i: \ ut CuH,- CH,-;-OH
fi-Cot{,
il tl
'-r t i o n oo
rrb o n Dip h e n vlsu lfo n e M e thanesul tbni caci d
I .i nce

A more interestinq group of compounds is the derivatives of H2S. These com-

pounds are zrlsoknorvn as mercaptans.Like hydrogen sulfide, the mercaptans have
disagreeableodors. The odors from many of these compounds are noticeable at very
low concentrations. An erample of a mercaptan is diethyl sulfide, which has the
) c-3Se formula C:HrSC:H..
nq a n
.h vd e
,. i r n d

4.8 NATURALLY OCCURRINGORGANIC COMPOUNDS

Organisms from the smallest to the largestrequire certain compounds to exist. These
compounds are found in all organisms to varying degrees. There are three major
classesof naturallv occurring organic compounds: carbohydrates,proteins, and fats
and oils.

Carbohydrates

Carbohydrates contain C. H, and O exclusively.Their general formula is (CH1O),,.

The simplestcarbohydratesor sugarsare monosaccharidesof which glucose,C6H11O,,.