CHAPTER 4

J t o a wat cr

ric 3.-l is 7.(1.

r) l0 &1FICI.
f.)
ORGANICAND BIOCHEMISTRY
a l k a l i n ity as

dioxide at a
g/L-atm.
t this water'/
t:grtnicchemistry is the study of compounds of carbon. Living systemsform organic
librium with --.,rleculesbut there is also an abundance of synthetic organics. Modern industry
I:CO;* then .-..tnufacturessomething on the order of 10000 new compounds per year, most of
rolution and .,rr.h are organic. More than 1 100 000 organic compounds have been prepared.
lrtermining their behavior in the environment and methods for treatment of these
'. a n d K , as .:lpounds presentsa formidable task for the chemist,biologist,ecologist,and environ-
-
:'.:ntal engineer.
In this chapter the major classesof organic compounds are described. A brief
'.:r\iew of metabolism is also presented to gain some appreciation of the means of
- ,;essingfoodstuffs and the complexity of rpetabolism.

IHCO;] and
{.I CARBON
J , and h a sa 'i:bon
is a unique atom, with properties that account for the limitless compounds it
- ,: iorm. The bonds between carbon atoms are stable, which allows chains to be
::red. Atoms near carbon in the periodic table can also bond to carbon to form
-
- :ri1S.Each carbon atom can form four bonds. The bonds are covalent in nature:
,r Waterand . :. iS.electrons are shared between the participating atoms. If the atonrs bonded tcr
--:rrtrfr have an electronegativity that is significantlydifferent from carbon, then the
- :.J nill have a polar character,with the electrons being shared unequally bctween
) csley,Don
: , rtorns. The degree of polarity in an organic molecule determines its solubility in
t t ' ir on ntent uL i polar solvent, water. Because of the four bonds and chaining ability of carbon,
--.,rr different configurations are possible for the same group of atoms, rvhich is
o ron to. . '.\n as isomerism.
The principal atoms that form compounds with carbon are hydrogen and oxygen.
'. --rr!€tt, phosphorus, and sulfur are the most common minor elements found in
- . rrlllv occurring organic molecules. Carbon dioxide and its related species are
nt Floccula- :l .rn i c i o n s o r c o m p o unds.
8 2 . I l . pp.

tltrtions,3rd {.] PROPERTIESOF ORGANICCOMPOUNDS

- ::: .rremore known compounds of carbon than any other elernentexcept hydrogen.
' . .i t.ir e t al. (1994) have summarized the major characteristicsof organic compounds
-..:..i rr-d to i n o rg a n i c c o mpounds.A bri efexpl anati oni saddedtomostofthei rpoi nts.
1. ,.)rgirniccompounds are usually cornbustible.
\ lrrse amount of energy is releasedas an organic compound is oxidized to CC) .
:l O. and other oxides. The energy releasepropagatesthe reaction.
: ' );S:rn i cc o m p o u n d s usual l y have l ow er mel ti ng and boi l i ng poi nts.

-$r
 S E C I T IC) NI/Ch e m istr v

H
I
HHHHH H H H -C -H H
t lt ll tltl
H- - C- C- C- C -C -H
ltlt r rttt
HHHHH HHHH
Figure 4.1 The two possible isomersof pentane.

Covalent bonding within organic molecules reduces their bonding or attraction

tcl identical molecules or other molecules.
3. Organic compounds are usually less soluble in water.
The nonpolar nature of carbon*carbon bonds reduces solubility of these com-
pounds in the polar solvent, water.
Several isomers exist for a given formula.
The isomers are a result of different geometries for a compound or result from
changing the bonding location of atoms or groups of atorns.
Reactions of organic compounds are usually molecular rather than ionic, which
slows their rate of reaction compared to ionic compounds. \LI
The valency of carbon allows it to form multiple bonds and carbon has the ability
to form strong bonds with itself. This can result in high molecular weight com-
pounds, ofterr well over I 000.
7. Most organic compounds can serve as a source of food for bacteria and other
microorganisms.
Organic compounds are energy rich (carbon is in a reduced state) and contain
the raw materials for cell fabrication.
In general as the size of an organic molecule increases,the melting and boiling
points begin to rise (see Table 4.1). Hydrocarbons are organic compounds that onlJ' -_--4 t. I

contain hvdrogen and carbon. There are three major types of organic compounds:
aliphatic. aromatic, and heterocyclic groups. Aliphatic compounds are chained and
branchedcompounds.Examples of isomersfor a five-carboncompound are illustrated
in Fig.4.1. Because carbon atoms can be rotated about their bonds, a bend in the
compouncl does not produce a new isomer. Only changes in association of atoms
produces an isomer. As atoms are substituted for H, more isomers are possible, as
illustrared in Fig. 4.2.

4.3 FUNCTIONALGROUPS
Functional groups strongly influence {.hebehavior of organic compounds.Three major
f unc t ionalqr o l rp sa re th e a l c o h o l ,-o H : car-boxyl-cooH
. : and, carhonvl .> cl :o.

CI H CI CI
li il
H- C- C- H H -C -C --H
tl tl
CI H HH
Figure 4.2 Isomersof dichloroethane.
 C H A P TE R 4/C )rcani cand B i ochc'rni str r' 79

,rl.: -flrealcoholgroupis similarin behaviorto water;that is,it is neitherstrongl\

.jri nor basichut the bronclis polar. Thc carboxylgroup is trcidicin nuture.'I-lre

(-)
(-

0
H
.- - r r i lr o u p
rr attractlon

, ;jtrorep?tivity of the two oxygen atoms pulls electrons away from the hydrogen
.,,.,nr.uhich then dissociatesas H*. The carbonyl group is an extremely important
thes e co m-
.:,rup irl modern synthetic organic chemistry. Because of the high electronegativity
-,:ierence between carbon and oxygen, the bond in the carbonyl group provides a
..:h l v re a c ti v es i te .
result from

Ltrnic.which
{.{ ALIPHATIC COMPOUNDS
,s the a b i l i ty T re a l i p h a ti cc o mp oundscan be broken dow n i nto al kanes.w hi ch contai n onl v single
.reight com- r,lrbon-carbon bonds; alkenes,which contain at least one double bond between two
--,rbon atoms; and alkynes,which contain at least one triple bond between a carbon
,i anci other :-iir. Compounds that contain double or triple carbon bonds are unsaturated com-
:\rur1ds.Double or triple carbon bonds are major reaction sites.Many synthetic reac-
:n d c o n ta i n ::.,ns break these multiple bonds and add halogensor other atoms to the carbon.

encl boiling
J s that o n l y f.\BLE 4.1 Physical Properties of n-Alkanes, CH3(CH2),zCH;u
Jclrnpounds: bp,'c mp density, g/cm3
:h a ined a n d name aI 760mm Hg at 20'C
. - i l l ust ra te d Methane - 161.5 - 183 0.124b
b'end in the l Ethane -r.i8.6 - 172 0.546b
,n of atoms Propane -42.1 - 188 0.50t '
p r ) s s ibl e a ,s "+ Butane -0.5 - 135 0.579.
i Pent ane 36.1 -t30 0.626
Hexane 68.7 ,95 0.659
Heptane 98.4 -91 0.684
Octane t25.7 -57 0.703
Non: r ne 150.8 _<A 0.718
. h r e e ma j o r Decanc t]4.1 -30 0.710
rl . -'C : O . Undecanc l9-5.9 -26 0.740
Dodecane 216.3 -10 0.741)
Pentadecane 270.6 l0 0.769
Eicosanc 312.7 37 0.786.'
Triacontane 446.4 o(-) 0.810'
F r r r r n Ro b e r ts e t a l. ( i9 71).
\t th e b o ilin g p o in t.
I' n d e r p r cssu r e .
F o r th c su p e r co o le d liq ui d.
 nr
1i

80 SECl'ION [/Ctremistrv

The chained compounds that can occur in this group havc a fairly predictable
as an additional carbon atom is added to thc structural
gradation in phvsicalprc'rperties
berckbone.This concept is known zrshomology and the compounds form a homologous
series. The names that usc Greek prefixes and a few physical properties of sorne
chained alkanes arc given in Table 4.1. Greek prefixes are used in naming complex
organicmolecules.For instance,diethyl in the name of a long compound would indicate
two two-carbon groups.

Aldehydes and Ketones

All aldehydescontain thc-carbonyl group with a hvdrosen atom bonded to the carbon
atom in the carbonvl qroup. Their generzrlformula is

,taO
R- C:
-H

Ketones have tl-regeneral formula

l - - - t,- - .
o I

n- t -n'
The carbonyl group is the most important functional group in synthetic organic
chemistry.
The structural formulas for formaldehyde, a preservativeand a toxic compound,
and acetone (dimethyl ketone), a common household solvent, are shown below:

oo
ll
H- C- H C H 3 -C -C H ,r
Formaldehvde Acetone

Esters
Estersare compoundsformed by the reaction of acidsand alcoholsand they correspond
t o s alt s in ino rg a n i cc h e mi s try .T h e g e n e ral formul a of an ester i s R -C OO-R ' . A
typical reaction for the hydrolysis formation of an ester is

R C O -OH + H -O R ' H ,O + R C OOR '

-

Alcohols and Ethers

A lc ohols have th e fu n c ti o n a l g ro u p , -OH . and general formul a R OH ; ethers are

c om poundst h a t h a v e th e c h a ra c te ri s ti cfo rmul a R -O-R ' . I' hey can be regarcl edas
substitution procluctsof water. Alcohols tend to be very weakly acidic, up the
-qiving
H* ion fron'r t[.re-OH group becauseof the electronegertivityof oxygen.
One rva1,of preparing ethers is to dehydrate two moleculesof alcohol. Ethers are
relativelv lorv in chemical reactivitv except in the prcsenceof free molecular oxvger-r,
r v hic hc aus c st h e fo rma ti o n o f u n s ta b l e .e x pl osi ve-proneperoxi des.E thers are rvi cl el v
us ed indus t r ia ls o l v e n ts .L o w mo l e c u l a r w e i sht ethers are hi ehl v fl ammabl e.
 C IIA P l 'E IL .l l Oruani c and FJi or:l temi sl l r 8l

.l i c t abl e H
-r-rctltral ,C .
,,,H \
.rl ogou s HCH HCH
rf sonrc
rlmplex HCH HCH
ndicate \H //
.C
H
Figure 4.3 Cyclohexane.

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

Reactions of Aliphatic Compounds

In general, aliphatic compounds can be oxidked by oxygen or other oxiciizingaqents.
Halogenswill substitutethemselvesfor hydrogen,forming haloorganics,many of rvhich
are toxic or carcinogenic.Aerobic bacteria have enzymesthat catalyzethe oxidation
r)rqanlC
of hydrocarbonsto alcoholsand then further to carbon dioxide and water. The bacteria
rvork on the terminal carbon atom and carrv this on until the whole molecnleis oxidized.
)p ound,
t\ \ ':

4.5 NITROGEN-CONTAININGCOMPOUNDS
Amines are derivatives of ammonia, NH3. Primary, secondary, and tertiary amines
have one, two, or three of the hydrogen atoms. respectively,substituted with alkyl
groups. Tertiary amines combine witlr alkyl halides to form quarternary ammtrnium
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 group of i nterest to synthetic or -
: s p ond ganic chemists.
R'. A Amino acids have at least one amine (-NHr) and one carboxvlic group per
molecule. Becauseof the presenceof the amino group and the carboxylic acid group
these molecules have both acidic and basic properties.The general structural formula
for an amino acid is shown at the marsin.

H
I
R -C - C O OH
3 r s are
rrled as
I
NH,
uP t he
Am in o a cid

. c ' I S ille
)\) gcn . T h e h y d ro l y s i so f trvo ami no aci ds.w hi ch i nvol vesthe reacti on of thc carl .,''. '. -
ir idely g ro u p o n o n e a c i d w i th the ami ne group on the other w i th a mol ecul eof rr atr' r l .' . , '.: : ' -
re s u l tsi n th e fo rrn a ti on of a pepti de bond. A mi no aci dscan thl s be chai ne.li -- : '-
 82 SECITION I/Clhcnristrv

COOH COOH
tt
H, N- C -H H ,N -C -H
rl
C H :-----S -S_ = -C H ,
Figure 4.4 An isomer of cysteine.

in an infinite number of ways to form proteins. The 20 or so amlno acids

that are
essentialto life have both carboxylic and amino groups bonded to the same
carbon
atom. The formula for glutamic acid, which is an amino acid. is
Ci-
H02C (C H ,)2 C H C O:H ''''I:

I ::l.l
NH,
Some amino acids.such as cysteineand methionine, contain sulfui. One
of the isomers
of cysteineis shown in Fig. 4.4.
Amino acids are degradedto pyruvate, acetyl-coenzymeA (acetyl-coA),
or other {.7 (
interrnediatesof the rricarboxylic acict(TCA) c1'cle(Section 4.ll). which
is'a primary S: nr illr l
m et abol i c p a th w a v .
, _r st it u
,'.,mf ou
:.fU u-tU [i
4,6 AROMATIC COMPOUNDS
Aromatic compounds contain the benzene ring (Fig. 4.5) Many of c
the compounds
containing the benzene ring exhibit a characteristicodor. rvhich is why
this class of
compounds is termed aromatic. C.H.- s
Benzeneis a compound that exhibitsresonance,rvhichis a very stableconfiguration
, C)
becauseof the sharing of the electronsin the bond among the six participating
carbon D i phc ,n..
atoms.These compounds are'difficult to degradebecauseof this p.op"rty.
Reionance
in the benzene ring is often indicated by drawing a circle within the
rine

o A carbon atom in the ring may have an - oll group attached to it, in
which case
A nt,
pctundsa
disagreca
low conc,
iorrnula (
the compound is referred to as a phenol; an - ooH g.oup, which
makes the ring an
ac id: or a -c H o o r a , -(c o )-R g r oup, w hi ch mal e, trr" .o-pound an al deh]rde
or a k et . n e . re s p e c ti v e l yIt
. i s p o s s i b l eto attach carbon chai nsto benzeneri nes.
and

4.8 N/
H H Organism
,,C tC,r compoun(
,,/ ,/ \\
HC CH HC CH classesof
I ll or rl and oils.
HC CH HCt,. CH
\^ ,l'
( C
H H Carbohl
Figure 4.5 Benzene Carbohvcl
The sim pl,
 C IH A P TE R 4/Organi c and B i ocherni strv

polyring aromatic hydrocarbons exist. There are many naturally occurring uromatics
as well as svnthetic aromatics.

OH
Cl.,'\Cl

Cl\.--Cl
CI
PCP
rat are
J ar b on
Chlorinated benzene derivativesare often quite toxic. Pentachlorophenol(PCP),
shown above, is one of the most widely used pesticidesand is one of the most toxic
compounds becauseof its high number of chlorine atoms.

iomers
4.7 COMPOUNDSOF SULR]R
r other
n mary Similarly to ammonia, sulfuric acid may have either one or both H or OH atoms
substituted with organic chains to form vario[s compounds. Two examples of these
compounds are diphenyl sulfone and methane sulfonic acid, with the follorving
structures.

o o
rounds
II
l as sof cuHr- fi-cuH, cH,- fi-oH
lt il
rration o o
.-arbon Diphenyl sulfone Methane sullbnic acid
ln a nc e

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

pounds are also known as mercaptans.Like hydrogen sulficJe,the mercaptans lrave
disagreeableodors. The odors from many of these compounds are noticeable at very
lorv concentrations. An example of a mercaptan is diethyl sulfide, lvhich has the
:h c ase formula C2H.SC:H,.
- lng an
l ehy de
:s . and
4.8 NATURALLY OCCURRINGORGANIC COMPOUNDS
Organismsfrom the smallestto the largest require certain compounds to exist. These
compounds are found in all organisms to varying degrees. There are three major
c l a s s e so f n a tu ra l l v o c c u rri ng organi c compounds:carbohydrates,protei ns, and fa t s
and oils.

Carbohydrates
C a rb o h y d ra te sc o n ta i n Cl . H , and O excl usi vel y.Thei r qeneral formul a i s (C H IO),.
The simplest carbohydratesor sugarsare monosaccharidesof which glucose.C"H -O
 SECTION I/Chernistry

C H ,OH Fat
energy
H
OH H 4.9 B
G iven t l
H OH machine
Figure 4.6 Glucose. sum t ot a
accordan
obtain tl
(Fig. a.6) is a typical example. Disaccharidescontain two monosaccharidesbonded Meta
together (common householdsugar,sucrose,is a disaccharideof glucoseand fructose) usethis e
and polysaccharides are chains of monosaccharides.Two main classesof polysaccha- rlation or
rides are energy storage compounds and structural compounds. Energy storage com- energy. A
pounds are readily degraded.They are used by the cell in energy-demandingsituations. trom siml
Starch is an example of an energy storage carbohydrate. Aerol
Structural compounds serve to maintain the integrity of the cell and as such they Respirat.i
are resistantto degradation.Cellulose is a good example of a structural carbohydrate. not use o
o.ridized a
Proteins sotne ener
t he absen
Proteins are complex molecules with no general formula that contain C, H, O, N, P,
and S along with trace occurrencesof other elements. N, P, and S are contained in M et ab
ttf enzyme
lesser amounts than C, H, and O on a molar basis.The building blocks of proteins
knorvn as i
are amino acids. There are 20 amino acids that form the building blocks of proteins.
.lppreciatio
There are other amino acids that perform other functions. Amino acids have acidic
here. Ther,
and basic properties and may be polar or nonpolar, among other characteristics.The
portant ene
properties of amino acids and their sequencein a protein give the protein four levels
of structure. which is critical to the function of the protein. The en.
in synt hesi
The biological functions of proteins are multivariate. The main classesof proteins
r cell. The s
are enzymes, structural compounds, and transport compounds. Enzymes catalyze reac-
tions, acceleratingthem 10 to 100 000 or more times. Structural elements keep the
cell intact. Transport proteins serve to move compounds within the cell and between
the cell and its environment.
In metabolism, proteins are broken down into amino acids and amino acids are
resvnthesizedinto proteins, but the pathways for each processare not the reverse of
t he ot h e r.
o
Fats and Oils I
Fats and oils have the general formula C,H:,,*rCOOH. Lightweight compounds are
o- .P- o-
oilr and high rveight compounds are waxlike. Many of these compounds are sparingly o
soluble in rlater. rvhich can be a treatment problem becausemicroorganismslack the
abilitr to secreteemulsifying agents to keep the fatty acids in suspension.Many are
odoriferous. Fornlulas for two typical fatty acids are given in Fig. 4.7.

CH.r(CH. ) r ^CO O H St c ar ic ac it l I
I
l A c l en
CHr(CH. )-CH : C'HrCH. r COOH Oleicacid(anunsarurared
acid)
tri ph
-,renos rne
Figure 4.7 Typical fattl' acids. Figure 4.8 1
 C H A P T'E R 4/Organi c and B i ochcrni stry

Fatty acids play an important rc'rlein metabolism as energy-rich fuels with nrore
rnergy per unit weight than carbohydrates.

4.9 BIOCHEMISTRY
Giien the diversity of species,there is a remarkable similarity among the metabolic
nrachineriesof all life forms, from the smallest to the largest. Metabolisrn is the
\urn toterlof all chemical reactions within the organism. These reactions proceed in
.rccordancewith thermodynamic principles. All heterotropltic organisms ultimatelv
r)btain their energy from oxidation-reduction reactions.
le s bond e d Metabolism is broken down into processesto obtain energv and processesthat
,l:e this energy to synthesizenew cell componentsand pertbrm other functions.Dissim-
rd fructose)
polysaccha- Llationor catabolismis the breakdown of energy-rich (reduced) compounds to obtain
orage com- Assimilation, anabolism,or synthesisis the fabrication of complex molecules
-nergy.
irom simpler ones.
r situations.
Aerobic organisms use oxygen as the ultimate electron acceptor in catabolisnt.
rs such they Respiration is the oxidation of fuels with molecular oxygen. Anaerobic organismsdo
rbohydrate. not use oxygen and essentially break organic molecules into a component that is
trridized and another component that becomes reduced while the organism derives
some energy from the process.The extraction of.chemical energy from substratesin
the absenceof molecular oxygen is knolvn as fermentation.
H . O , N , P, Metabolic processesoccur through a series of steps depending on the presence
ontained in of enzymes and the substanceto be degraded or fabricated. The series of steps is
of proteins knorvn as a metabolic pathway. The study of metabolism is involved. To obtain an
trf proteins. appreciation of metabolic pathways two major pathways are presented summarilv
have acidic here. There are manv other pathways. Before the pathways are examined. two im-
:ristics.The portant energy carriers are discussed.
four levels The energv obtained from oxidation is stored in energy carriersthat releaseenergv
in synthesisreactions.Adenosine triphosphate (ATP) is the primary energy carrier in
trf proteins a cell. The structure of the molecule is shown in Fig. 4.8. As adenosinemonophosphate
I.(rlvzereac-
ts keep the
nd between NH'
I
Adenine
ro acids are ZC-'- --N".
I reverse of NC\
ttl CH
o-o-o HCs"-d-'-r"
l tl
o-P -o-P -o-P -o-c H.
pounds a re ililil
re sparingly
ms lack the
r. llany are
i6"D+
H C _C H
D 'R i bose

ioHoH
I Adenosine

monophosphatc
1A N {P )
i ' Ad e n o sin e
(A D P .t
I Acle n o sine lip h o sp h ate
( AT P)
' Atle n o sin etr ip h o sp h a te
Figure 4.8 The structure of ATP
I
i S E CT ION l/Ch e m istr v

(AMP) adds successivelyone (forming adenosine diphosphate, ADp) and another

e lect r ons
inorganic phosphate group, the bonds holcling these phosphate uroups become more
as a r esul
energy rich. 'l'hese high-energy bonds are indicated by "-" in Fig. 4.8. ADp-ATp
The c
transformations arc involved in oxidation-reduction reactions, the energy-rich ATP
of act ir it r
being formed in oxidation reactions (ctrtabolism)and thc lower energy ADP being
formed with the release of inorganic phosphorus in reduction (synthesis)reactions.
This cornpound is representativeof a wide variety of energy carriers. There is no
electron transf'erinvolved in the formation of ATP, ADP, or AMp.
The ATP content of microorganismsis variable (Levin et al., 1975) but for both
aerobic and anaerobic microorganismsthat are found in sewagetreatment processes,
ATP content of viable cells is in the range of l-2 pg ATp/mg cell (weddle ancl CH. (
Jenkins, 1971; Chung and Neethling, 1990).
Another important classof compounds involved in metabolism is dehyclrogenase
enzymes.T'hesecompounds participate in reactions by being reversibly reduced and
oxidized in transferringelectronsfrom the substrateto oxygen or the ultimate electron
acceptorin a generallylong seriesof steps.Nicotinamide adenihe dinucleotide (NAD.)
(its structure is shown in Fig. 4.9) is a common electron carrier representative of those
that are associatedwith enzymesof this class.
The oxidized form of NAD is symbolized as NAD' and the reduced form is
symbolizedas NADH. In fact, two hydrogen 4toms are involved in the transtbrmation
from NAD" to NADH. one H atom is released as H' and the other H atom is
transferred along with two electrons to NAD+. The transformation of NADH to
NAD' directly or indirectly involves the formation of an energy carrier such as ATP
in aerobic respiration. In an anaerobic fermentation, the H atom and the associated

o fYcoNH'
ll \N-,

tri
-o-P-o-CH,
i

OH OH

o NH, -l

I
.L
ZC-'' ',-N
NC
tll CH fr
HC\^r-ct''*

o - P- o- cH,
ii { ' 1*

c)
-:
CI

OH OH
_-i ..
Figure 4.9 The structure of NAD. :::u r e 1 .1 0
 C H ,A P TE R .l /Organi c ancl B rochcrni strl ' 87

n ot her electronsare transferredto another organic molecule.Al'P is also formed irt anaerobcs
I nlore as a result of these electron transfers.
, - AT P
The concentrationsof ATP and dehvdrogenaseenzymcscan be used as it mcasure
h ATP of activity tlf cultures.
' b eing
r c t ions.
:' is no

r r b ot h
)ces se s. cHroH
lle and
9H,o@
o. ATP eop H o cHzoH
H H -,----)
) genas e H
:e d and HO OH OH
lectron H H OH H OH
( \ AD ) Glucose Fructose
Glucose6-phosphate 6-phosphate
rf t hose

form is
in lat ion
:ttom is
CH.O(D CF
QHro@
K"",
rD H t o
:rs ATP
Glyceraldehyde
cHoH
rl <-
qH,o@
3-phosphate
rtrciated KOH
6"o H\ OH
OH
II
Onictose1.6-diphosphate
I
cH,oH
Dihydroxyacetone I
phosphate O
9:
I
CH,O@

P'-.--1,,
la*^o
3-Phosphoglycerate J ) N.qou,

CH,O(o CH,O(o
I '---z--=-- |
CHOH .iO .)'O CHOH
ll
coo- coo@

I'
CH,OH
3-Diphosphoglycerate

CH.-
ADP .{rr)
o
ll
l '^ il\ \.- -/
CHO(P) coG) H rC t-C --C OO-
t- l- Pyruvate
coo coo
2-Phosphoglycerate Phosphoenolpyruvate
Figure 4.10 Glycolysis.
 wi
il

S E Cl' l( ) N [/C- h e n r istr l

4.IO GLYCOLYSIS
Glycolysis is a ferrnentation processwhereby glucose is broken down to lactic acid.
The ability to use this pathway (also known as the E,mbden-Meyerhof-Parnas path-
rvay) exists in, of course, anaerobic organisms,ancl many aerobic organisms,which
may use this pathway in preparation for aerobiccompletion of the oxiclationof glucose.
The pathway is shown in Fig. 4. t0.
(ilycolysis is catalyzedby the action of L1 enzymes.It is seen from the figure that
the first step, in which phosphate is added to glucose (phosphorylation), requires an
iuitial expenditure of energy by the use of one ATP molecule.The net releaseof ATP
from the processis 2 ATP moleculesper molecule of glucose.As noted on the figure,
other monosaccharidescan also enter the cycle. Other fermentations proceed in a
similar fashion, although the final products vary. For instance, ethanol is a major
product of organismsused in the brewerv industry. The changeoccurs in the last step,
where pyruvate is converted to acetaldehyde,rvhich is then converted to ethanol.
The tiee energy change associatedwith the conversion of glucose to 2 lactate f l- ,
moleculesis -47.0 kcal/mol.

4.II THE TRICARBOXYLICACID CYCLE

Glvcolvsis onlv releasesa small amount of the chemical energy contained within
glucose.Complete oxidation of glucoseto CO: and HrO magnifiesthe yield of energy
considerably.The theoretical free energy changefor complete oxidation of one mole-
cule of slucose to CO2 and H2O is -686.0 kcal/mol.
The TCA cycle (Fig.4.11) is sometimesreferred to as the Krebs cycle after the
rnan who first postulated its existence. It is almost universally present in aerobic
organismsand is a primary pathwav. In catabolism the cycle proceedsclockwise as it
is r epr es e n te di n F i g . 4 .1 1 .
In an aerobic organism the NADH formed in glycolysis can ultimately transfer
its electronsto oxygen and form six rnoleculesof ATP in addition to the two molecllles
of ATP formed from the original glucose molecule. Thus glycolysiswill yield a net
gain of eight ATP moleculesin aerobic organisms.The pyruvate formed in glycolysis
entersthe TCA cvcle.As shown on the figure,GTP (guanosinetriphosphate)is forrned
in the TCA cycle. This compound is similar to ATP. Also, NADPH1 (nicotinamide
adeninedinucleotidephosphate)and FADHl (flavin adeninedinucleotide) are formed.
Their roles are essentiallythe same as NADH.
Because I mole of glucoseyields 2 moles of pyruvate and 8 moles of ATP and 1
mole of pyruvate vields 1-5moles of ATP. the aerobicbiooxidation of I mole of glucose
to carbon dioxide and water yields 38 moles of ATP. About 737oof the theoretical
Figure
cnergv vield of oxidation of glucoseis capturedin ATP. There are 10 enzymesinvolved
in the TCA cycle and other enzymesare involved in the ultimate transport of electrons
t o ox v ge n .

4.I2 ENZYMEKINETICS
rvhere
E.nzvmescatalvzc rearctionsby forming an intermediate compound with the reactants E
(substrate).The intermediate compound is metastableand normally breaks down to Si
vielcl thc- uncliauqeclcnzyme and the products of the overall reaction. As with ail PJ
chentical reactions.each step is reversible (the principle of microscopicreversibility). ES
'I'he reaction sequcncecan be representedas follows.
k
 C I'l A P 'IE R 4/()rgani c and B i ochcnl i stry

Acetyl-CirA

ac id. II coou
r a t h-
c:o *\
, h ic h
-^";L: -\r
lr,
c0se. COOH k"- CH. I
I i"' Ho-c-cooH
: t hat H-C-OH COOH I
es itn ,/ I Malate oxaloacetare
rrraluducr.rLtr 9H, \
,/ C_H" Citrate I \
ATP
gure,
/l co o H \
/ cooH cooH
li na
c.rsaconrtate I
-naJor cots cH.
s t ep, |
C C-CooH
ol. Fumarat"
ll ll
.l c tat e H-C CH
r
COOH
I'^
COOH
FADilr(\
1
II
,rr t hin
,oo1 t
COOH COOH
ner g\
ll 'ot".tt"
rnole-
!'H, ^
StlcclDate
tt,
I
I
:r t he H-C-CooH
9H, Succinl'l-CoA
: ru'rbic I H -C -OH
C OOH C O OH
J I lS I I
rl
\ cH, cooH
.ln s f e r ctr\ | /
:.-u les \ CH, ct-oxoglutarate Oxalosuccinate ,l-xsot'
r net ,,n.' \ | CooH COOH
c -s co A 4^ror,
'.rIvs'is i- " ' l. -
' rm e d [o \ >" - CH, 9H'
r n r i de nnn', r- |
:n r ed. "\l---->-, ' ', *--T-'
\AD 1". j,
H-c-cooH
'.t lJ , I
c:o O:COOH
. in d I
',taose
I
COOH
:t icai Figure 4.11 The tricarboxylic acid cycle.
.' i \ C! l
I I1lI I S

t' tr
E+SEES?2P+E (4 l)
k: (+

w h e re
-- -1l t i \ E, is enzyme
.i: ', t rl S i s s u b s tra tc
-:- r li P is product
.ii" r. ES is the intermecliateenzyme-substratecomplex
k; are rate constants
 SECTION I/Chcrnistry

If the reaction is proceeding at a uniform rate, the rates of formation ancldestrri.

tion of the intermediate are equal, although the concentrationsof reactants?nd prtr.
ucts are continuously changing. This situation often occurs, particularly rvhen rl:.
enzyme concentrationis low compared to the concentrationsof the reactants.Assun:.
ing normal first-order reactionswith respectto eachentity apply, the following equatir :-
describesthe balance for [ES].

4lEllt: ft,[E ][S] - k ,[E S ] + k.[E ][p] - k4[E S ] :0 (l _

,tt
Figure 4.12 I
The rate of formation of ES from product atrd enzyme is normally negligible.r..
k t - 0.
The overall velocity of the reaction depends on the rate of product formation
, lt er t ypes ol
dtPl - , t t hat \ \ 'hen
k4[ESl (-l -:
':T : . : s lou. t hc r
- J: \ \ 'een0 ut n
where
The rate tr
u is the overall velocity of the reaction . . r ichiom et n
c
The following mass balance also applies at any time , r bsor bedint r

lElo: [E] t [ES] (i ; Pl L, - , I, SI

where . it K+[ S
[E]u is the initial concentration of enzyme
It is difficult to measure the amount of ES present for use in Eq. (4.4); theref.. . [P] and [S]
Eqs. (4.2) and (4.4) are used to develop a formula in terms of more readily &SSCSi:-
parameters. The following expression for [ES] will be found. -I Erample 4.1

IE S 1:,,{llE ll,[S ] , : [E]'[S] r-. . . r ar is t he t im :

t--f k r[S ] + k t + k4 ,., +, kr + kr i - - iat ionwhen t
tsl k, ' : 1. 5 m g/ L. ,

The determination of the individual rate constants involved is difflcult an,l ..- The concen
overall constant,K, known as the Michaelis-Menten (they made the original der el : . I nt egr at ine
ment) constant or half-velocity constant (see Problem 15), is defined as (1
K frsl
K _ k l +k4
J lsl I
k2
a- - 4
Substituting Eqs. (4.5) and (4.6) into Eq. (4.3) yields

k4[E]ols1
: _!.
.. _
" - l (+ [s]
The maximum rate of reaction (u^,*) will occur when [ES] : [E]q,.Therefor. The two con
'- . i. - t ionvelocit i.
u : k a [E]n: u," ,
: det er m iningt
Substituting Eq. (a.8) into Eq. (4.7) results in - ,t rs knolvn
as
,. _ u..,[S]
"-1( L s l
E quat ion (4 .9 ) i s k n o w n a s th e M i c h ael i s-Menten equati on. It rvas ori si i --, The slope an
developed bv them to describeenzyme kinetics but has been fo"undto applv to n: , : r at lower sub
 C FTA P 'fE R 4/Organi c antl B i ochcnri str\' 9l

Figure 4.12 The Michaelis-Mentenequation.

crther tvpes of reactions.The equation is plotted in Fig. 4.12. It is observed from the
plot that when substrateconcentrationis high, the rate of reaction is zero order; when
it is lorv the velocity is first order. In between, the reaction velocity has an order
b e tw e e n (l a n d [.
The rate of product formation is related to the rate of substrateremoval and the
stoichiornetryof the overall reaction.The constantrelating moles (or mass)of substrate
is absorbedinto un,u*. If mass,l of substrateis required to form l mass unit of product,

{-+.-:. dlP l u;,,-[S ]

-ttt
dls l 4 M: _ (u , " , / rn
)[ S l: _ u , n " , [ S l{ 4 t o }
/<+[Sl \"'/
or
t( i N d- dt / (+ [ S l
where
[P] and [S] are in mass or molar concentration units
- , . thcrL -f r)I e.
,: r l ! asse sse d
I Example 4.1 Application of the Michaelis-Menten Equation

(1 .,i) What is the time for 901ccornpletion of a reaction describedby the Michaelis-Menten
equation when the initial substrateconcentration is 32mglL, u.", = 4.3 mg/L-h. and
K - 1 .-smg l L .'
The concentration at 90c/acornpletion rvill be 0.10(32 mg/L) = 3.2 mglL.
.-'ult a n d a n
Integrating Eq. (a.10),
:: l deve l o p -
+ : -U,n", + - -u.",,
(16)
"li:iffi /ij],arst- l',,,t,-r'"ffi[s] [S]u:
r(ln ([s]/[s]o)
+ [s] [s]o
,_ _
U .n*

_ _ (1.5mg/L) ln (0.10)+ 3.2mg/L - 32mg/L =7.5h

4.3mg/L-h
(1t)

fherefore, The two constantsin the equation, K and u.n,, may be readily determined when
reaction velocitv and substrateconcentration data are available. A common nethocl
(4 8)
to r d e te rmi n i n gth e c o n stantsi s to i nvert the equati on and pl ot 1/u agai nst l /[S j . This
plot is known as a Lineweaver-Burke plot.

l_ I K1
+' _ -
(4e) U n,r. un'",[Sl
(J. l I r
U

, s o r iqi n a rl l y The slope and intercept define the constants.A Lineweaver-Burke plot ueiuht-
:rl r t o ma n y clataat lclrversubstratcconcentrationsmore than data taken at liigh substrat!-con..:r-
 SEC'IION I/Chemistrv

l -:

f-i

Figure 4.13 Eadie-Hofsteeplot.

trations. Furthermore. lower substrateconcentrationsare deteirnined with less accu-

racy than high substrate concentrations.There are other methods of algebraicallr
manipulating Eq. (4.9) to obtain una*andK from the measureddata. Rearranging Eq.
(-1.9)into the form of Eq. (a.12)and plotting u againstu/[S] resultsin an Eadie-Hoftsee li
plot (Fig. 21.13).The Eadie-Hoftsee plot magn.ifiesdepartures from linearity that mav
not be apparent in a doublc reciprocal (Lineweaver-Burke) plot.

u:_Kfr*r.". (4.12')
1v

Inhibitory substanceslimit the action of enzymesby binding with a substrateor

the enzyme. It can be demonstratedthat inhibitory substanceseffectively increasethe
half-velocity constant.Toxic substancesdestroy the enzyme. It can be seen from Eqs.
(4.7) and (4.8) that a decreasein [E]o decreasesthe maximum velocity of the reaction.

QUESTIONSAND PROBTEMS
L. Compare tbe amount of oxvgen required to oxidize methane and ethane completelv in
terms of g O2lg of compound and g O2lg C.
2. Define isomerism and illustratewith structural formulas for the compoundswith molecular
formula C6H1a.
3. What are the major functional groups and how do they affect organic molecules/ What
are the general chemical formulas for alcohols,aldehydes,ketones, esters,and ethers'l
4. In general. how do organic compounds differ from inorganic compounds?
5. Why does the carboxyl group behave as an acid?
6. Write the chemical reaction for the formation of an ether from ethanol (C,H.OH) and
methanol (CHTOH).
7. What are the three major classesof naturally occurrinq organicsand generalcharacteristics REFET
of compounds in each group? | :J \'

8. What is necessaryto saturate oleic acid (Fig. a.6)? Write the formula ot the saturated E,
comp<>und.
9. The ceneric chemical formulas for carbohydrates ancl fatty acids are (CF{.O),, and Ti t
C,,Hr,,-rCOOH, respectively.Consult a reference on organic chernistry ancl list three or ti, ,

four carbohvdratesand three or four fatty acids (not found in this text) and their chemical \\.r o n :,
formulas to prove that these formulas are generally correct. R.i