!nt$%&'cti%n*t%*Meta.

%li0m*
2'$3%0e*%4*meta.%li0m*
7rocesses ten5 to spontaneousl$ achieve eAuilibrium states, in which !E is zero8
Giving organisms are far from eAuilibriumI however, living organisms must obe$
the laws of thermo5$namics, an5 therefore maintaining this 5istance from
eAuilibrium reAuires effort8 Jrganisms represent regions of or5er in a universe in
which or5er is unstable8 Jrganisms must therefore obtain energ$ !"# $%&'$(# ')*+
from their environment to allow them to maintain their or5ere5 state8

Kor most organisms, however, collecting energ$ in5iscriminatel$ is a problem8

Jrganisms must also maintain homeostasis:, in which man$ ph$sical parameters
remain constant8 Jnce a human has reache5 a5ulthoo5, the mass of the in5ivi5ual
remains fairl$ constant over time, in spite of a $earl$ ingestion of over five hun5re5
2ilograms of eLternal materials8 0aintaining this homeostatic con5ition reAuires a
high 5egree of regulation8

Jrganisms obtain the energ$ necessar$ for survival from their environment8 7lants
use photons release5 from the sun as their energ$ source8 Jther organisms consume
plants, or consume other organisms that have consume5 plants, to obtain their
energ$8 Mhe energ$ is use5 to maintain the low.entrop$, non.eAuilibrium state, to
5rive chemical processes an5 in general, to support life8

Jrganisms nee5 energ$ for chemical synthesis, because the$ nee5 to be able to
s$nthesize proteins, lipi5s, an5 nucleic aci5s8 Nll of these are ordered moleculesI
s$nthesizing large molecules from small ones reAuires energ$ to overcome the
entropic cost of the process8 Jrganisms also nee5 energ$ to generate heat Oroom
temperature is at least :-P! below human bo5$ temperatureI ambient temperature
ma$ be much lowerQ8 0aintaining a bo5$ temperature of RSP! ma$ therefore reAuire
consi5erable energ$8 Kinall$, animals nee5 energ$ for locomotion, because moving
reAuires energ$ that must be 5erive5 from chemical sources8

Tn general, heat is not useful energ$8 N human bas2ing in the sun s$nthesizes
vitamin 9, an5 eLperiences an increase5 ris2 for s2in cancer, but 5oes not 5irectl$
obtain usable energ$8 Mhe !E for the metabolism of a compoun5 is a measure of the
usable energ$ in the compoun58 Mhe !E is the energ$ available to 5o wor28

Mwo maUor t$pes of metabolic processes are use5 in biological s$stemsV catabolic an5
anabolic8

Cata.%lic*3$%ce00e0*
!atabolic processes involve the conversion of large molecules into small ones8
!atabolism has two goalsV :Q release of the energ$ reAuire5 b$ living organisms in a

: Homeostatic an5 eAuilibrium states are superficiall$ similar, in that the obvious s$stem
parameters 5o not change8 However, maintaining a homeostatic state reAuires control an5 effort8 N
river 5ownstream of a 5am is homeostatic, in that its water level remains fairl$ constant, although
the water present is in constant fluL, an5 must be continuousl$ replace58 Tn contrast, a pon5 is at
eAuilibrium, with the water having no ten5enc$ to move in an$ 5irection8

!op$right + ,---.,--/ 0ar2 3ran5t, 7h898 :

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B"@#"4>4);8 F1B( "? )(> )(%>> @1E"% 4:)%&>4) )$#>; G=&#&5;6 B1%<"($5%1)>;6 145
#%")>&4;A B14 <> B"4H>%)>5 )" <")( >4>%'$ 145 )" @>)1<"=&B &4)>%@>5&1)>;8

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I41<"=&;@ &; )(> %>H>%;> "? B1)1<"=&;@J &) &4H"=H>; )(> ;$4)(>;&; "? :;>?:= =1%'>%
@"=>B:=>; ?%"@ ;@1==>% #%>B:%;"%;8 C(> ?:4B)&"4 "? B1)1<"=&;@ &; )" B"4H>%) =1%'>
@"=>B:=>; &4)" ;@1== @"=>B:=>; 145 &4)" >4>%'$ &4 :;1<=> ?"%@J )(> ?:4B)&"4 "?
141<"=&;@ &; )" :;> )(> >4>%'$ #%"H&5>5 <$ B1)1<"=&;@ )" B"4H>%) )(>;> ;@1==>%
@"=>B:=>; &4)" =1%'>% @"=>B:=>;8

K&H&4' "%'14&;@; (1H> 1 D&5> H1%&>)$ "? 5&??>%>4) @>)1<"=&B #1)(D1$; )(1) 1=="D )(>
;$4)(>;&; "? @";) @"=>B:=>; %>L:&%>5 ?"% )(> ;:%H&H1= "? )(> "%'14&;@8 C(>;> &4B=:5>
#1)(D1$; ?"% )(> ;$4)(>;&; "? #%")>&4;6 =&#&5;6 145 B1%<"($5%1)>;8 M4 @14$ B1;>;6
)(> #%"B>;;>; ?"% <%>125"D4 145 ;$4)(>;&; "? @"=>B:=>; ;(1%> #1)(D1$;8 C(>;>

!"#$%&'() + ,---.,--/ 01%2 3%145)6 7(898 ,

path;ays =such as the ACA cycleD are called a"#$i&'(i), to reElect their
involvement in both catabolic and anabolic processes8

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Meta%olic path-ays
Iver the Eirst t;o sections oE this course, ;e have discussed concepts that allo; us
to understand the general concepts involved in enJymatic reactions8 In real cells,
ho;ever, the enJymatic reactions do not occur in isolationL instead they are grouped
together into path;ays8

A number oE charts have been put together to sho; the reactions that occur in living
organisms8 Ahese charts appear some;hat daunting at EirstL in Eact they are Muite
useEul, because they sho; ho; the reactions are interrelated8 Nou have probably
seen the large version oE the biochemical path;ays reMuired Eor living organisms8
Ahe chart belo; sho;s a simpliEied version8 Ahis version sho;s the maOor path;ays
and highlights the maOor important compounds and the enJymes that act as control
points in the path;ays8

A Ee; Eeatures oE the chart are ;orth mentioningP

Q8 Ahe chart lists only selected enJymesL in general, these are the maOor regulatory
control points Eor each path;ay, although some enJymes are important but non.
regulated8
28 Compounds highlighted in *+e-.&'/e0 are compounds oE particular importanceL
most oE these compounds act as branch points, and are involved in more than one
path;ay8
:8 Ahe &(a)1.a++'20 sho;n represent reactions catalyJed by one or more enJymes8
Ahe *+e-.a++'20 represent translocation oE compounds, or point out the Eact that
the same compound is present in more than one path;ay8
48 Ahe irregularly shaped grey boS represents the "i3')$'45+ia(. )'"#a+3"e43

Copyright + 2000.200/ 0ar2 Brandt, 7h898 :

within eukaryotic cells. Ahe mitochondria are somewhat functionally distinct from
the remainder of the cellD relatively few molecules can enter or leave a
mitochondrion freely.

5.70-824
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Felatively few amino acid biosynthetic pathways are shown in this chart. For

Copyright © 2000-2008 Mark Brandt, Ph.D. 4

1ni;1ls6 t(is is 1 re1son1?l$ 1ccAr1te represent1tion oB eCents6 ?ec1Ase ;ost
1ni;1ls co;pletel$ l1c2 t(e 1?ilit$ to s$nt(esiDe ei'(t oB t(e tEent$ st1n51r5
1;ino 1ci5s6 1n5 (1Ce Cer$ li;ite5 c1p1cit$ Bor t(e s$nt(esis oB BoAr ot(ers. F(e
p1t(E1$s Bor 1;ino 1ci5 s$nt(esis Bro; non.1;ino 1ci5 precArsors present in
(A;1ns 1re s(oEn in t(e 5i1'r1;.

!eta%oli)*pro)esses*are*highly*reg1late2*
Ge Eill t1l2 1?oAt re'Al1tion 1n5 re'Al1tor$ ;ec(1nis;s Bor ;et1?olis; 1s Ee
5iscAss e1c( p1t(E1$. 0et1?olis; (1s seCer1l leCels oB re'Al1tion. In so;e c1ses6
t(e ;et1?olic process onl$ occArs in so;e cell t$pesI t(e ot(er cells l1c2 t(e
reJAire5 enD$;es. In ;1n$ c1ses6 t(e p1t(E1$s 1re ti'(tl$ re'Al1te5 ?$ (or;ones6
E(ic( 1lter eit(er t(e 1;oAnt oB enD$;es or t(e 1ctiCit$ oB eKistin' enD$;es. In
;1n$ c1ses6 t(e p1t(E1$s 1re ti'(tl$ re'Al1te5 ?$ Bee5?1c2 eBBectors6 E(ic( 1re
inter;e5i1tes Bro; l1ter in t(e p1t(E1$6 or Bro; ot(er p1t(E1$s6 1lter t(e r1te oB
re1ctions in t(e p1t(E1$.

In so;e c1ses E(ere it is necess1r$ to 2eep p1t(E1$s sep1r1te56 tEo p1t(E1$s eKist
in 5iBBerent co;p1rt;ents Eit(in t(e cell. F(e ;itoc(on5ri1 1re BreJAentl$ Ase5 Bor
2eepin' so;e ;olecAles 1n5 processes sep1r1te Bro; ot(ers. Ge Eill see eK1;ples
oB 1ll oB t(ese concepts 5Arin' t(e re;1in5er oB t(e coArse.

3her4o2yna4i)s*o6*path7ays*
3ioc(e;ic1l p1t(E1$s 1ll (1Ce l1r'e o8erall*negati8e*!9*8al1es. Ls 1 resAlt6 t(e
p1t(E1$s 1re eBBectiCel$ irreCersi?le An5er p($siolo'ic1l con5itions. F(is Be1tAre is
i;port1nt Bor t(e control oB t(e BloE oB ;1teri1l t(roA'( e1c( p1t(E1$.

Ln eK1;ple oB t(is is t(e conCersion oB 'lAcose to p$rAC1te6 1n5 t(e conCersion oB

p$rAC1te to 'lAcose. 3ot( p1t(E1$s (1Ce ne'1tiCe !M. IB t(e p1t(E1$s Eere
i5entic1l6 t(is EoAl5 Ciol1te t(e l1Es oB t(er;o5$n1;ics. !le1rl$6 t(e p1t(E1$ Bor
'lAcose s$nt(esis Bro; p$rAC1te ;Ast 5iBBer Bro; t(e p1t(E1$ Bor t(e ?re125oEn oB
'lAcose to p$rAC1te. F(is is 1 'ener1l principleN t(e p1t(E1$ Bor t(e s$nt(esis oB 1
co;poAn5 1lE1$s 5iBBers in 1t le1st one step Bro; t(e p1t(E1$ Bor t(e ?re125oEn oB
t(e co;poAn5.

:;peri4ental*4etho2s**
0et1?olic p1t(E1$s Eere Eor2e5 oAt Asin' 1 C1riet$ oB ;et(o5s. 01n$ oB t(ese
p1t(E1$s6 sAc( 1s 'l$col$sis6 Eere Eor2e5 oAt Asin' t(e rel1tiCel$ crA5e ;et(o5s
1C1il1?le in t(e OP,-s 1n5 OPQ-s.

It is 5iBBicAlt to Ase pAriBie5 enD$;es to Eor2 oAt 1 p1t(E1$6 ?ec1Ase it is not

1lE1$s cle1r E(1t t(e cellAl1r sA?str1te 1n5 pro5Act concentr1tions Eill ?e6 1n5 in
so;e c1ses6 is not cle1r E(1t t(e p($siolo'ic1l sA?str1te Bor 1 'iCen enD$;e 1ctA1ll$
is. 0ost stA5ies t(ereBore ;Ast ?e perBor;e5 in cellAl1r eKtr1cts or in tissAes6 E(ic(
1ct 1s soArces oB 1ll oB t(e releC1nt enD$;es.

F(ese s$ste;s ;Ast t(en ?e ;1nipAl1te5 in C1rioAs E1$s to 1lloE t(e isol1tion oB
speciBic inter;e5i1tes R1s oppose5 to ;erel$ t(e isol1tion oB t(e Bin1l pro5Act oB t(e
p1t(E1$S. In so;e c1ses6 t(e ;1nipAl1tion inColCes t(e Ase oB nor;1l ;et1?olic
re'Al1tor$ ;olecAles. In ;ost c1ses6 (oEeCer6 t(e ;1nipAl1tion inColCes t(e Ase oB

!op$ri'(t + ,---.,--/ 01r2 3r1n5t6 7(.9. :

inhibitors o= en?ymes that cataly?e reactions proposed to be involved in pathDay8
Additional in=ormation Das derived =rom studies on naturally occurring mutations
in both eGperimental animals and genetic disorders in humans8 0ore recently,
eGperiments per=ormed in genetically manipulated animals have been used to
eGplore the role o= di==erent en?ymes in the pathDays8

Hhe use o= labeled versions o= biological molecules has an important role in

metabolic studies8 Hhe must commonly used labels are radioactive isotopes o=
hydrogen, carbon, and phosphorus8 Hhese isotopes are chemically identical to the
normal non.radioactive isotopes o= these elements, but are readily detectable in very
small amounts8 Using synthetic =orms o= biological molecules Dith labels at speci=ic
locations ma2es it possible to =olloD the processes that occur Dithin the pathDay8
!
!
!
"#$$a&'!
Jrganisms reKuire energy =rom their environment to maintain their non.
eKuilibrium state8 Lor animals, this energy must be obtained in the =orm o=
molecules that can be oGidi?ed to obtain =ree energy8

0etabolism has =our =unctionsM

NO to obtain chemical energy =rom =ood
2O to convert nutrients to the precursors o= biologically important molecules
PO to synthesi?e the biologically important molecules
4O to degrade previously =ormed molecules no longer needed8

Catabolic processes are the degradative processes8 Catabolic processes result in

oGidation o= the starting material, and result in net release o= use=ul energy8

Anabolic processes are the synthetic processes8 Anabolic processes result in

reduction o= the substrate molecules, and reKuire the input o= energy8

In general, catabolic processes start Dith a Dide variety o= molecules Smany

di==erent types o= proteins, many di==erent types o= carbohydrates, and many
di==erent types o= lipidsO, and produce a small number o= molecules SDater, carbon
dioGide, and nitrogen Daste products Dhen carried to completion, or =ree amino
acids, glucose, lactate, and acetyl.CoA Dhen the purpose is to produce
intermediatesO8

Anabolic processes, in contrast, begin Dith a =eD types o= small molecules, and
produce the Dide variety o= biological molecules reKuired by living organisms8

Hhe anabolic and catabolic pathDays are tightly regulatedT this regulation is in part
due to the =act that the pathDays all have signi=icant overall negative !U under
physiological conditions8

Copyright + 2000.200/ 0ar2 Brandt, 7h898 :