Biochemistry Judit Kosry (2014-1) Biogenic elements Building biomolecules: carbon (C) hydrogen (!

) o"ygen (#) nitrogen ($) (and % &s ')( )hey are in the *irst and second +eriods (high charge concentration on their sur*ace unit) their atoms are not susce+tible to de*ormation and they *orm ,ith o,n atoms and other biogenic elements strong -bonds( -lectronegati.ity can be characteri/ed the atoms connected by a -bond( )he atom ,ith higher electronegati.ity can collect a +art o* the electron density o* the -bond this causes an electron sur+lus (0) on it( )his e**ect causes an electron de*iciency () on the atom ,ith lo,er electronegati.ity( -$ 1 1 4 2 3 Columns %eriodes -$ 1 ! -$42( 1 2 C $ # -$42(2 -$45(0 -$45(2 5 % ' -$42(2 -$42(2 Position of biogenic elements in the periodical system and their electronegativity (EN) Biomolecules Biomolecules are organic molecules building u+ li.ing organisms( )y+es o* biomolecules: +roteins carbohydrates nucleic acids and li+ids (a+olar biomolecules)( %roteins carbohydrates nucleic acids are chiral bio+olymers: Type of biomolecule %roteins Carbohydrates Units -6mino acids 'im+le sugars Bonds between units %e+tide bond (a s+ecial carbo"amide bond) O-7lycosidic bond (a s+ecial acetal bond) 59 29-%hos+hodiester bond 888888888888888888888

$ucleic acids $ucleotides 888888888888888888888 888888888888888888888 8 8 :i+ids (a+olar 'im+le li+ids cannot be Com+le" li+ids can be biomolecules) hydroly/ed by $a#! hydroly/ed by $a#! haracteristic data of the structure of proteins! carbohydrates and nucleic acids" characteri#ation of lipids Rules of biochemistry at the molecular level 1( Bioa**inity ; there is at least one biological sur*ace to interact ,ith a biomolecule(

2 2( Biocatalysis ; in li.ing organisms +ractically all o* reactions are cataly/ed and the biocatalysts are called en/ymes (mostly +roteins)( 5( Bioregulation ; all o* biochemical +rocesses are regulated( Isomerism in biomolecules <hen t,o molecules ha.e some di**erences in their structure but their molecular *ormula (the com+osition o* elements) is the same they are isomers( <hen the atoms bond in di**erent order in isomers they are structural (constitutional) isomers( )here are di**erent ty+es o* structural isomers( =n biomolecules tautomerism (the di**erence bet,een t,o isomers is in the +osition o* one hydrogen atom and a double bond) can be *ound *re>uently (e(g( aldoses and ?etoses in carbohydrate chemistry)( )he stereoisomers ha.e the same molecular *ormula and se>uence o* bonded atoms (constitution) but their atoms ha.e di**erences in their three-dimensional orientation in s+ace( )here are di**erent ty+es o* stereoisomers: o+tical isomers (enantiomers and diastereomers) geometrical isomers and con*ormers( Con*ormational isomers (con*ormers) di**er by rotations around one or more single bonds (e(g( chair and so*a con*ormations o* gluco+yranoside)( Optical isomerism =n the case o* saturated carbon atoms due to hibridi/ation (s+ 5) the angle o* the bonds is 10@ 2A i(e( its geometry is tetrahedral( 6 carbon atom ,ith *our di**erent substituents (mar?ed by a star) is called a chiral carbon atom (on the basis o* the 7ree? ,ord ?heir; hand)( =n the case o* a single chiral atom t,o isomers called enantiomers are +ossible( -nantiomers (anti+odes) are related as mirror images( )he chemical and +hysical +ro+erties o* the enantiomers are the same because the microen.ironment o* the atoms is the same( )he only di**erence is in their o+tical rotation ,hich is o++osite( 6n enantiomer can be identi*ied by the direction in ,hich it rotates the +lane o* monochromatic and mono+olari/ed light( =* it rotates the light cloc?,ise that enantiomer is labeled (B) ,hile its mirror-image is labeled (C)( 7rou+ o* highest o"idation number | 'mallest *unctional grou+;C;Characteristic *unctional grou+ | #ther grou+ The application of $ischer%s convention on the &' enantiomer 7rou+ o* highest o"idation number D Characteristic *unctional grou+C'mallest *unctional grou+ D #ther grou+ The application of $ischer%s convention on the ('enantiomer

C!# !# C ! C!2#!
:-glicerinaldehid

C!# !# C ! C!2#!

C!# ! C #! C!2#!

C!# ! C #! C!2#! F-glicerinaldehid

C!2#! !# C ! C!#

)# as#immetria'centrumo* $ischer'f+le ,br,#ol,sa

COOH R C H NH2

C##! !2$ C ! E

!2$

C##! C! E

)# ('aminosava* t+rbeli! $ischer'f+le +s a speci,lis! a $ischer'f+le *onvenci-n alapul- ,br,#ol,sa The modified $ischer convention for the (''amino acids

Fistinction o* enantiomers can be carried out by a++lication o* the Gischer con.ention that is based on the sim+lest aldose glyceraldehyde( <hen the characteristic grou+ is on right side in Gischer +roHection the enantiomer is called right-handed (F ; a*ter :atin ,ord de"ter) and the other enantiomer is the le*t-handed .ariation (: ; a*ter :atin ,ord lae.us)( F and : are ty+ically ty+eset in 'I6:: C6%'( $o,adays e"ce+t *or sugars and amino acids *or the de*inition o* chirality the EJ' notation is used( )his is de*ined by the Cahn-=ngold-%relog +riority rules based on atomic number( =n the case o* glyceraldehyde the F enantiomer is the cloc?,ise (B) and :-enantiomer is the anti-cloc?,ise (;) enantiomer( Gor the :--amino acids a modi*ied Gischer con.ention is used because it is better *or illustration o* the +e+tide bond( &iastereomers contain at least t,o centers o* chirality and one o* the centers has the same and the other has the o++osite +osition( Fiastereomers are not mirror images and there*ore their chemical and +hysical +ro+erties o* are di**erent the microen.ironment o* the atoms being di**erent( )his *act can ser.e as a basis *or the se+aration o* enantiomers *rom their mi"tures (called racemic mi"tures) by *orming diastereomers( )his +rocess is called resolution( F : | | F F &iastereomers =n com+ounds containing t,o chirality centers and the carbon atoms ha.e the same substituents o* o++osite chirality there*ore the direction o* the o+tical rotation o* t,o carbon atoms is o++osite (resultant o+tical rotation is /ero) ; this .ariation is called meso *orm (e(g( meso-tartarate)(

! !# !# !

C C

#! !

C;! C;#! C##!

D L

4
C##! C C #! !

C##! C C #! #! ! !#

! !

D D

C##! me#o-bor?sa.

C##! (B)-bor?sa.

B orksav (tartart) diasztereom erek

.eso'tartarate and (/)'tartarate are diastereomers Iany biologically acti.e molecules are chiral including the naturally occurring +roteins carbohydrates and nucleic acids( 6s en/ymes are mostly +roteins and +roteins are chiral they +re*erentially cataly/e the trans*ormation o* only one o* the enantiomers o* a chiral substrate( $aturally occurring +roteins are made o* :- -amino acids carbohydrates di- oligo- and +olysaccharides are all made o* F-sugars( $ucleic acids contain also F-sugars: ribose or deo"yribose( 0eometrical isomerism =n the case o* *ree rotation in saturated hydrocarbons in eclipsed structure ; hydrogen or other atoms are in disturbing each otherK in the open structure ; hydrogen or other atoms are in the in a rotated +osition causing minimal disturbance there*ore this structure is +re*erred(
! !5C C!5 !! ! ! rotciL ! ! ! ! ! nyitott lls (?ed.e/) !

etn

! *ed lls (?ed.e/tlen) ?on*ormciL? )# et,n *onform,ci-i

onformations of ethane1eclipsed and open structures <hen there is a barrier to rotation (e(g( a ring system or a double bond) the large substituents can be on the same or on o++osite sides( <hen large substituents are on the o++osite side (trans isomer) the disturbance is less and there*ore this isomer is more ad.antageous than ,hen they are on the same side ( cis isomer)( $o, in organic chemistry E-2 notation based on the Cahn-=ngold ;%relog rules is used( ! ! ! Br C C C C Br Br Br ! trans#'1 2-dibrLm-etil&n stabilabb ) simple e3ample for geometric isomers1 cis' and trans'4!5'dibromoethylene Carbohydrates Carbohydrates (saccharides) are organic com+ounds o* the general *ormula Cn(!2#)n( )he ratio o* hydrogen and o"ygen is 2:1 as in the ,ater( Gormerly cis#'1 2-dibrLm-etil&n ?e.&sb& stabil

2 carbohydrates ,ere .ie,ed as hydrates o* carbon and this is the origin o* their name( =n sim+le sugars (monosaccharides) the general *ormula is Cn!2n#n (generally C5-CM)( )hey are +olyhydro"y carbonyl (o"o) com+ounds( )he carbonyl grou+ may be aldehyde (aldose) or ?etone (?etose)( =n ?etoses the carbonyl grou+ is al,ays at +osition 2 o* the sugar( )he sugars are named not only based on the ty+e o* their carbonyl grou+ but by the number o* the carbon atoms (on the basis o* 7ree? name o* numbers): triose (C5 ; C5!3#5) tetrose (C4 ; C4!N#4) +entose (C2 ; C2!10#2) he"ose (C3 ; C3!12#3) he+tose (CM ; CM!14#M) e(g( glyceraldehyde is an aldotriose glucose is an aldohe"ose and *ructose is a ?etohe"ose( )he secondary hydro"y grou+s o* sugars are stereocenters and the chirality o* the sugar is based on the con*iguration o* the chiral carbon atom o* highest number (e(g( C2 in he"oses)( )he di**erent aldoses and ?etoses ,ith the same number o* carbon atoms are diastereomers e"ce+t one ,hich is their enantiomer( =n the li.ing organisms sugars are generally in F- and not :enantiomer *orm =t is ?no,n that only one ?ind o* enantiomers can connect to di**erent biological sur*aces( 'ugars are usually metaboli/ed as their +hos+hate esters(
!# !# !# C! C!2#!
:-as/?orbinsa.

# #

C!# ! C #! C!2#!
F-glicerinaldehid

C!# ! C #! ! C #! C!2#!
F-eritrL/

C!# ! C #! ! C #! ! C #! C!2#!
F-ribL/

C!# ! C #! !# C ! ! C #! ! C #! C!2#!
F-glO?L/

aldL/o? C!2#! C # !# C ! ! C #! ! C #! C!2#!

F-*ru?tL/

(C-.itamin) C!2#! C # C!2#! dihidro"i-aceton C!2#! C # ! C #! ! C #! C!2#!

F-ribulL/

C!2#! C # !# C ! ! C #! C!2#!
F-"ilulL/

C!2#! C # !# C ! ! C #! ! C #! ! C #! C!2#!
F-s/eduhe+tulL/

?etL/o?

) legfontosabb egys#er cu*ro* +s a 'vitamin *+plete

The most important straight'chain simple sugars and a sugar derivative ('ascorbic acid (ascorbate! glyceraldehyde! erithrose! ribose! glucose! dihydro3yacetone! ribulose! 3ylulose! fructose! sedoheptulose =n sugars the di**erent *unctional grou+s retain their original +ro+erties there*ore aldohe"oses can be easily o"idi/ed and carbonyl grou+ can react ,ith one o* hydro"yl grou+s( &etection of sugars by o3idation: according to the condition o* chemical o"idi/ability (i(e( the +resence o* a hydrogen connected to a carbon that is in a +olari/ed bond) only aldehydes can be easily o"idi/ed to carbo"ylic acids( )he e"am+le o* acetaldehyde is +resented:

The $ehling reaction of acetaldehyde forming acetate and u5O as red precipitate Furing the reaction the o"idation o* aldehyde is combined ,ith the reduction o* the o"idi/ing reagent (on this case 2Cu2 Cu22) there*ore aldoses are called reducing sugars( Ketones cannot be o"idi/ed because o* the absence o* C! in carbonyl grou+( But in *orced conditions ?etoses can be isomeri/ed to aldoses by double o"oenol-o"o tautomerism there*ore all of simple sugars are reducing sugars(
#

! C !# C

! C !# C ! C

! C !# C ! C

# !

! C #! ! ! C #! ! C #! C!2#!

! C #! ! ! C #! C!2#! C!2#! ! !# ! #! # ! #! ! # !

! C #! ! ! C #! C!2;#! #

#! ! - F-glO?o+irano/id )# egys#er cu*ro* ci*li#,l-d,sa

ycli#ation of simple sugars )he cycli/ation o* sugars is caused by a reversible intramolecular reaction (nucleo+hilic addition) bet,een the carbonyl and one o* hydro"yl grou+ o* the straightchain (o+en *orm) sugar( )his hydro"yl grou+ is connected to the chiral carbon atom o* highest number( )he cycle that contains an o"ygen and the ne, hydro"yl grou+s is connected to chiral carbon atom can be in di**erent +ositions *orming stereoisomers( 6ldo+entoses and ?etohe"oses *orm *i.e-membered rings ,ith +lane sur*ace (*uranosides)( 6ldohe"oses *orm three dimensional si"-membered rings (+yranosides) those are generally +roHected as +lanar and F-hydro"y grou+s are under the ring and :-hydro"y grou+s are abo.e the ring( Cycli/ation generates a ne, chiral center in ,hich the F-hydro"yl grou+ is called the -anomer and the :-hydro"y grou+ is called the -anomer(

C!2#! ! !# ! ! #! ! # ! #!

#!

C!2#! # !# ! ! !# ! #! ! #! - F-glO?o+irano/id

! !# !#

C!2#! # ! ! #! #! ! !

- F-glO?o+irano/id

) gyr6s gl6*-# ,br,#ol,si lehet s+gei +s gli*o#idos *7t+s+ne* t+r,ll,sa 8epresentations of ' and '&'glucopyranoside

)he cycli/ed sugars contain a hemiacetal or hemi?etal structure (in sugars the ne, hydro"yl grou+ is called the glycosidic hydro"yl) that can be easily reacted ,ith a hydro"yl grou+ o* another sugar( )he +roduct is a disaccharide( 6 ring-*ormed sugar can be reacted ,ith a .ariety o* hydro"yl grou+sK the general name o* the +roduct is glycoside that is a s+ecial *orm o* an acetal( Because o* the re.ersibility o* this cycli/ation the disaccharides containing glycosidic hydro"yl grou+ (maltose cellobiose lactose gentiobiose) are reducing com+ounds( =n saccharose (sucrose) the glycosidic bond is *ormed bet,een t,o glycosidic hydro"yl grou+s there*ore it is not a reducing sugar( )he connection bet,een t,o sugars in disaccharides is sho,n by their names (e(g( maltose is F-gluco+yranosyl-P1 4-Q-F-gluco+yranose)(
C!2#! # ! #! ! ! #!

! !#

C!2#! # ! #! ! ! #!

!! # maltL/

C!2#! # ! #! ! ! #!

! #!

! !#

C!2#! # ! #! ! ! #!

! # ! cellobiL/

#! !

! !# !#C!2 !

C!2#! # ! #! ! !

! !# ! C!2#! # ! #! ! ! #! la?tL/ !#C!2 # ! #! ! ! #! ! # !

#! # # ! !# C!2#!

C!2#! # ! #! ! ! #!

#! !

#! ! s/aharL/ C!2#! # ! #! ! !

! !#

# C!2 ! #! !

# ! !# #! !

#! C!2#!

! ! #! !# genciobiL/

- F-*ru?to*uranL/

)# ismertebb dis#acharido* +s a ci*li#,lt fru*t-# *+plete

N The most important disaccharides and the ring'formed fructose 6mong +olysaccharides starch and cellulose are the most im+ortant( )he building unit o* starch is maltose( %lants use starch as energy reser.e( =ts *unction is similar to that o* glycogen in animals and +eo+le( )here are t,o ty+es o* starch: amilose (a linear +olymer containing only 1 4 glycosidic bonds) and amilo+ectin (a branched +olymer containing both 1 4 and 1 3 glycosidic bonds)( )he building unit o* cellulose is cellobiose( Cellulose is a structural com+onents o* +rimary cell ,alls o* green +lants and is the most ,ide-s+read organic molecule in the ,orld( )he name o* the +olysaccharides containing only F-glucose molecules is glucan ; starch is an glucan and cellulose is a -glucan( Proteins %roteins (+oly+e+tides) are bio+olymers made o* -:-amino acids connected by +e+tide bonds (a s+ecial ty+e o* carbo"amide bond)( Units of the polypeptide chain! the (''amino acids )hey are the building bloc?s o* +roteins connected by +e+tide bonds( 'tandard (+rotein +roteinogenous) amino acids build u+ +roteins non-standard (non-+rotein non-+roteinogenous) amino acids can be im+ortant metabolic intermediates( )he name o* standard amino acids is used generally in their abbre.iated *orm( )he modi*ied Gischer con.entions o* the *ormulas o* t,enty standard amino acids and their abbre.iations are +resented in schemes( )en o* amino acids (Ral :eu =le %he :ys )hr )r+ Iet 6rg !is) are called essential amino acids because the human body cannot synthesi/e them *rom other com+ounds at the le.el needed *or normal gro,th there*ore they must be obtained *rom *ood( ($otice: ,hile large >uantities o* the essential amino acids are needed there are other essential com+ounds e(g( .itamins ,hich ,e need only in small >uantities)( #*ten selenocysteine and taurine are also +ut on the list o* standard amino acids ,hile 6rg !is are classi*ied as semiessential amino acids by se.eral authors(
!2$ C!2 C##! glicin (7ly) !2$ C! C##! !2$ C! C! C!5 C!5 .alin (Ral) !2$ C! C! C!2 C!5 *enilalanin (%he) +rolin (%ro) C!5 i/oleucin (=le) C##! !2$ C! C!2 C##! C##! !2$ C! C!2 C! C!5 C!5 leucin (:eu) ! $ C##!

C!5 alanin (6la)

C##!

) hidrof-b *7lcs7nhat,sra al*almas feh+r9eal*ot- aminosava*

)mino acids of hydrophobic character

!2$

C! C!2

C##!

!2$

C!

C##!

!2$

C!

C##!

!2$

C! $!

C##!

C!2 C!2 C##! glutaminsa. (7lu)

(C!2)4 $!2 li/in (:ys)

(C!2)5 C4$! $!2 arginin (6rg)

C##! as/+araginsa. (6s+)

)# ionos *7lcs7nhat,sra al*almas feh+r9eal*ot- aminosava*

)mino acids with ionic character

!2$ C##! !2$ C!5 C##! !2$ C##!

C!

C! C!

C! C!2

C!2#! s/erin ('er) !2$ C! C##!

#!

treonin ()hr) !2$ C! C##! #! tiro/in ()yr)

C!2 C#$!2 as/+aragin (6sn) !2$ C##!

C!2 C!2 C#$!2 glutamin (7ln) !2$ C##!

C! C!2

C! C!2

$ ! tri+to*n ()r+)

$!

his/tidin (!is)

) hidrog+n*7t+sre al*almas feh+r9eal*ot- aminosava*

)mino acids with hydrogen bonds

10

!2$
! C! 2$ 2 Cl

C! C!2 C!2

C##!
C!2 C!2 '$i

C! #;!

C##! C!2
$a !2#

C!2 #! Cl

C!2 #

C!2'! cis/tein (Cys) etil&n-?lLrhidrin

# etil&n-o"id ';C!5 (s/Ug*es/Olts&g)

s/oms/&d-cso+ort hats metionin (Iet)

) dis#ulfid*7t+sre al*almas $a#! C!2 C! feh+r9eal*otaminosav 2 ! #

#
2

) dip-lus'dip-lus *7lcs7nhat,sra 6$ ! # feh+r9eal*otC!2 C!2 # ! al*almas aminosav

etil&ngli?ol

ysteine with disulphide and methionine with dipole'dipole interaction )#bond etil+n*l-rhidron rea*ci-9a
C!5 ' !

'

C!5

S#S !2#

C!5

'

'

C!5

metn-tiol S#S

stabil dis/ul*id hTd

C!5C!2 # C!2C!5 dietil&ter

C!5C!2

# #;C!2C!5 dietil-+ero"id

2 C!5C!2

) pero3ido* +s a dis#ulfido* stabilit,si *6l7nbs+ge

$ormation of disulphide bond and pero3ides :tructural levels of proteins %rimary structure: )he se>uence o* amino acids( #n one end o* e.ery +oly+e+tide chain called the amino terminal or N'terminal there is a *ree amino grou+( )he other end ,ith its *ree carbo"yl grou+ is called the carbo3yl terminal or 'terminal(

# !2$ C! E $ ! C!

# #!

C-terminlis ) feh+r9+* elsdleges s#er*e#ete Primary structure of proteins with the N' and 'terminals of the chain
%e+tide bonds are s+ecial carbo"amide bonds ,ith strong hydrogen bonds caused by a +artial delocali/ation in the *unctional grou+( Because o* this delocali/ation the +e+tide bond is +lanar and rigid( )his +artial delocali/ation is illustrated by the molecule acetamid(

$-terminlis

11

C!5

# $!2

acetamid # $ ! ! ?is # C!5 C $!2 $a#! nagyon nehe/en

O
C C $ ! di+olris gtolt rotciLHV s/a?as/ a sa.amidcso+ortban (a +e+tid?Ut&sben) C

O
C C $ ! C

C!5

) savamidcsoport 9ellem#+se Partial delocali#ation and hindered rotation of acetamid illustrated by mesomeric structures 'econdary structure:; 'tructures established by hydrogen bonds bet,een +e+tide bonds: righ-handed 'heli3! 'sheet ; bet,een anti+arallel chains collagen structures ; there are three o* le*t-handed e"tended heli" structures rolled into a cable *orm o* a right-handed heli" in tro+ocollagen units containing 7ly-%ro-!y+ tri+lets hydro"y+roline is synthesi/ed by a direct o"idation o* +roline in +e+tide chain by means o* :-ascorbate)(

'heli3 structure

a 'sheet structure

collagen structure

12

# $ 1J2 #2 (a/ as/?orbinsa. ?U/.etTt&s&.el) !# $

!y+ r&s/let a %ro r&s/let a *eh&rHelncban *eh&rHelncban ) hidro3i'prolin *+p#d+se a peptidl,ncban O3idation of proline to hydro3yproline in the peptide chain by ('ascorbate (vitamin ) )ertiary structure: ; Connections bet,een remote +arts o* the +e+tide chain by secondary bonds bet,een the side chains o* amino acids ; globular structures (*olded to three dimensional structures they contain all o* the secondary structures) and fibrous structures (*olded to *ibres they contain only one o* the secondary structures)( =nteractions: hydro+hobic interactions ; glycine (7ly) alanine (6la) .aline (Ral) leucine (:eu) isoleucine (=le) +henylalanine (%he) +roline (%ro) ionic interactions ; as+artic acid (6s+) glutamic acid (7lu) lysine (:ys) arginine (6rg) hydrogen bonds ; serine ('er) threonine ()hr) tyrosine ()yr) as+aragine (6sn) glutamine (7lu) try+to+han ()r+) histidine (!is) disul+hide bond ; cysteine (Cys) di+ole-di+ole interactions methionine (Iet)K Wuaternery structure:; Connection bet,een se.eral +oly+e+tide chains usually called +rotein subunits by secondary bonds bet,een the side chains o* amino acids( 'im+le +roteins contain only +rotein chains( Com+le" +roteins contain other ?inds o* biomolecules or metal ions: glyco+roteins (o*ten in membranes) nucleo+roteins (in ribosomes) li+o+roteins (e(g( :F: ; a cholesterol trans*erring li+o+rotein) metallo+roteins (e(g( some en/ymes as lactate dehydrogenase contain /inc) chromo+roteins (e(g( red hemoglobin) +hos+ho+roteins (e(g( casein) etc( Biological function of proteins -n/yme +roteins ; catalysts o* biochemical reactions they are .ital to metabolism 'tructural +roteins ; e(g( collage *ibers as *ibrin Contractile (mechanical) +roteins ; e(g( muscle +roteins )rans+ort +roteins ; e(g( hemoglobin trans+orts o"ygen %roteins *or su++ly ; e(g( myoglobin su++lies o"ygen =mmune +rotection ; etc( immunoglobulins )o"ins (+oisons) ; e(g( sna?es +oison Biuret reaction is a colorimetric +rotein assay methods that use cu+ric ions as colouring agent( Cu+ric ions *orm a com+le" o* *aint blue-.iolet color ,ith the imide tautomer o* at least t,o (according to se.eral authors *our) +e+tide bonds( )he intensity o* the color +roduced is +ro+ortional to the number o* +e+tide bonds +artici+ating in the reactionK there*ore the biuret reaction is an o*ten used analytical method *or the >uantitati.e determination the total +rotein concentration( )he reaction ,as named a*ter the organic com+ound biuret ($!2-C#-$!-C#-$!2) that is the sim+lest com+ound to gi.e a colored (light blue) com+le"(

15

# C! C E ! E

# $ C! C $ ! # C! C E

$a#! Cu #

# ! C! C E

# !

$ C! C $

Cu2B

E imid (a ntrium-hidro"iddal sLt ?&+e/het)

$ C! C $

E ibolyas/Tn ?om+le" ) biuret rea*ci-

En#ymes -n/ymes are globular +roteins generally ,ith >uaternary structure( 6s biocatalysts they gi.e an alternati.e reaction *or the +roduct synthesis ,ith lo,er acti.ity energy than the original reaction o* really high acti.ity via *orming a com+le" ,ith substrate( 'ince en/ymes are selecti.e *or their substrates and s+eed u+ only a *e, reactions *rom among many +ossibilities the set o* en/ymes made in a cell determines ,hich metabolic +ath,ays occur in that cell( -n/ymes are ?no,n to cataly/e about 4 000 biochemical reactions( 6cti.ity o* en/yme is a**ected by tem+erature chemical en.ironment (e;g; +! and salt concentration) and the concentration o* substrate(

8eaction diagram without and with en#yme -n/yme reactions are re.ersible( )he sum o* the rate o* the dissociation o* the en/yme substrate com+le" (.-1) and the rate o* the synthesis o* +roduct and regeneration o* the en/yme (.2) *rom this com+le" can be e>ual to the rate o* *orming en/yme substrate com+le" (.1) this status is called Xsteady state9( E +S .14 ?1P-Q(P'Q
v1 v-1

ES

v2

E +P .24 ?2P-'Q

.-14 ?-1P-'Q

6 saturation cur.e can be *ound ,hen the concentration o* the +roduct P%Q is +lotted against reaction time( 6lso a saturation cur.e can be *ound *or the relation bet,een the substrate concentration P'Q and rate ( v<)( )his rate (v<) is the rate o* en/yme reaction at the *irst +eriod o* the reaction( )his can be characteri/ed by the modi*ied Iichaelis-Ienten +lot that is called the e=uation of en#yme *inetics( 6s the

14 substrate concentration increases more and more o* the *ree en/yme is con.erted into the substrate-bound -' *orm( 6t the ma3imum rate (>ma3) o* the en/yme all the en/yme acti.e sites are bound to substrate and the amount o* -' com+le" is the same as the total amount o* en/yme( )he amount o* substrate needed to achie.e a gi.en rate o* reaction is also im+ortant( )his is gi.en by the .ichaelis constant (?.) ,hich is the substrate concentration re>uired *or an en/yme to reach one-hal* its ma"imum rate(

&iagrams and e=ual of en#yme *inetics #nly the active site o* an en/yme ta?es +art in the catalytic reaction ,hile other +arts o* the en/yme assure the acti.e con*ormation o* the acti.e site that contains t,o im+ortant +arts( )he substrate binding site can be characteri/ed by ?. *or a gi.en substrate and this can sho, ho, tight the binding o* the substrate is to the en/yme( )he +arameters andJor com+ounds decreasing the binding o* the substrate can increase the .alue o* ?.( Gor a gi.en substrate the catalytic site can be characteri/ed by >ma3( )he +arameters andJor com+ounds decreasing the trans*ormation o* the substrateen/yme com+le" to the +roduct can decrease the .alue o* >ma3(

The double reciprocal plot )he ?. and >ma3 .alues are the im+ortant ?inetic constants o* the ?inetics o* en/ymes *or a gi.en substrate( )he determination o* these constants is gi.en by a double reciprocal plot (:ine,ea.er-Bur? +lot) that yields a straight line ,ith an interce+t o* 1J>ma3 and a slo+e o* ?.@>ma3(

12 Certain com+ounds can alter the acti.ity o* en/ymes( -n/yme acti.ity can be decreased by .arious inhibitors or can be increased by acti.ators( )he e**ect o* such com+ounds can be re.ersible or irre.ersible( Ee.ersible inhibitors are classi*ied according to their lin?age to the acti.e site( Com+ounds o* similar structure to the substrate can bind to the substrate binding site and are called com+etiti.e inhibitors( Com+ounds ,hich disturb the *unction o* the catalytic site are called non-com+etiti.e inhibitors( Com+ounds that can disturb the *unction o* both the substrate binding and catalytic sites are called mi"ed inhibitors(

The types of reversible inhibitions1 competitive inhibition! mi3ed inhibition! non' competitive inhibition The classification of en#ymes A en/ymes can be identi*ied by their number in -n/yme $omenclature (-n/yme Catalogue -C)( -C number is a combination o* *our numbers( )he *irst number o* the combination sho,s the ty+e o* the reaction cataly/ed( 1( #"idorecuctases ; cataly/e o"idation and reduction (dehydrogenases and o"igenases) 2( )rans*erases ; cataly/e subtitutions 5( !ydrolases ; cataly/e hydrolysis 4( :yases ; cataly/e addition and elimination 2( =somerases ; cataly/e tautomerism 3( :igases ; cataly/e reactions using the energy o* macroerg bonds #"idoreductases and trans*erases need reagents (compounds with coen#yme function) *or the cataly/ed reactions( Com+ounds ,ith coen/yme *unction (hence*orth they are called as coen/ymes) are connected to en/ymes either by secondary bonds (they are really coen/ymes ; they can be regenerated also in other reactions) or by co.alent bonds (+rosthetic grou+s ; they can be regenerated only in their original +lace)( Com+ounds ,ith coen/yme *unction ha.e t,o *orms (unreacted and reacted) ; only li+oic acid has three *orms( )he starting materials *or coen/ymes are ,ater soluble .itamins and in a *e, cases essential amino acids)( =n +rimary metabolism o3idoreductases are al,ays dehydrogenases because the reo"idation o* reduced coen/ymes is connected ,ith the +roducing o* energy in *orm o* macroerg bonds( )he mechanism o* these o"idoreductase coen/ymes can be ionic (hydrogen molecules are trans+orted as hydride anions and +rotons) or radical (one hydrogen molecule is trans+orted in *orm o* t,o hydrogen atoms)( =n the o"idati.e degradati.e +rocesses o* catabolism $6F (its starting material is nicotinamide i(e( .itamin B5) ; its reduced *orm is ($6F!B!) (nicotinamide adenine dinucleotide) in.ol.e an ionic ,hile G6F (its starting material is ribo*la.ine i(e( .itamin B2) ; its reduced *orm is G6F!2 (*la.in adenine dinucteotide) and GI$ ; its reduced *orm is GI$!2 (*la.in mononucleotide) a radical mechanism(

13 GI$ ta?es +art only in terminal o"idation( =n reducti.e biosyntheses o* anabolism the coen/yme is ($6F%!B!) in both mechanisms( )he di**erence bet,een $6F $6F% is the +resence o* a +hos+horyl grou+ on the C-2 hydro"yl grou+ o* ribose in $6F%( Gla.in-containing coen/ymes are al,ays +rosthetic grou+s( ! !

!
# C#$!2 !$ $ ! (F!Y) 4 230dihidro;uracil nm !#C!2#

! #
!$ # $

! ! ! ma" 4 230 &s 540 nm ma" #! #! +s/eudo uridin (C) ) ni*otinamidot tartalma#- *oen#ime* redu*,l-d,si folyamata N+h,ny rit*a nu*leotid *+plete The process of reduction of coen#ymes containing a nicotinamide structure ! C#$!2 C!2 ! ! # ! $ 2! (! B ! ) $ $ ! # % # % # C!2 ! ! ! C!2 ! ! # ! $ ! $ $ ! ! ! C#$!2

C#$!2 $! B ! #

# % # %

! #! #! $!2 $ $ # ! !

! #! #! $!2 $ $ #

C!2

#! #E E 4 ! ($6FB ) ni?otinamid-adenin-dinu?leotid E 4 % ($6F%B )

#! #E E 4 ! ($6F! B !B ) E 4 % ($6F%! B !B )

) N)&/ +s N)&P/ *oen#ime*

oen#ymes N)& and N)&PB

1M

! $ $ $ 2! $

! ) flavint tartalma#- *oen#ime* redu*,l-d,si folyamata The process of reduction of coen#ymes containing flavines

# !5C !5C $ $ C!2 !C#! !C#! !C#! !2C # % # % # C!2 ! ! G6F (*la.in-adenin-dinu?leotid) # !5C !5C $ $ C!2 !C#! !C#! !C#! !2C #;E $ $! # $ $ # ! $ $! # 2! !5C !5C $!2 $ $

! $ $ C!2 !C#! !C#! !C#! !2C # !

# $! $ ! $!2 $ % # % # C!2 ! ! G6F!2 $ # ! $ $ #

#! #!

#! #!

E 4 % GI$ (*la.in mononu?leotid) E 4 ! (B2 .itamin) ribo*la.in

) flavint tartalma#- *oen#ime* +s pre*ur#or vitamin9u*

$lavin'containing coen#ymes and their precursor vitamin Ybi>uinone (coen/yme W) (its starting material is tyrosine and its reduced *orm is ubi>uinol) is that ?ind o* o"idoreductase coen/yme ,hich can ,or? by both ionic and radical mechanism( )he name o* the human ubi>uinone is CoW 10( )he starting material o* ubi>uinone is tyrosine(

1N

8edo3 reactions of ubi=uinone =n .arious ?inds o* cytochromes the coen/yme e**ecting electron trans*er is hem (by *errous-*erric trans*ormation)(

The structure of hem )he coen/yme o* direct o"ygenases is ascorbic acid (.itamin C)( # !# # !# !# C ! C!2#!
:-as/?orbinsa.

# o" red # # # !# C ! C!2#!

(C-.itamin)

dehidro-as/?orbinsa. (boml&?ony)

)# as#*orbinsav o3id,lt +s redu*,lt form,9a 8edo3 reactions of ('ascorbic acid $!2 $ Transferases can cataly/e se.eral$ ?inds o* substitutions( )he trans*erred grou+s can be di**erent carbon s?eletons: C1 ; C#2 (biotin that is .itamin !) only methyl grou+ ('6I ; '-adenosylmethionine its starting $ material is methionine) methyl $ grou+ aldehyde grou+ etc( ()!G ; tetrahydro*olate its starting material is *olic acid %;#;%;#;%;C! # 2 i(e( .itamin B@ ; earlier .itamin B10K C2 ; acetaldehyde ()%% ; thiamine +yro+hos+hate ! ! ! ! #! #!

1@ its staring material is aneurine i(e( .itamin B1) acetyl grou+ in a macroerg thiolester bond (coen/yme 6 its starting material is +antothenic acid i(e( .itamin B 2K and li+oic acid that is connected to the -amino grou+ o* a lysine as a +rosthetic grou+ there*ore it is o*ten called li+oamide)K and other grou+s: +hos+hate grou+ (6)% or other nucleoside tri+hos+hate molecules) amino grou+ (%6: ; +yrido"al +hos+hate its reacted *orm is %6I ; +yrido"amine +hos+hate and its starting material is +yrido"ine i(e( .itamin B3)(
# !$ C $! C!2 C!2 C#2 C##! ) biotin *elet*e#+se +s form,i ' 6)% 6F% # !##C $ C $! C!2 C!2 C!2 C!2 C##! ?arbo"i-biotin

'

C!2 biotin (!-.itamin)

C!2

Transfer coen#yme A carbon dio3ide A biotin

$!2 !2$ C! C!2 C!2 ' C!5 Iet !2$ C##! $ $ # ! ! ! C##! % # % # % ;#;C!2 ! #! # ! ! #! $ $ ! $ $ %%i %i

6)% $!2 $ $ C!5 !2$ C##! $ $ # ! ! #! ! #! $!2 $ $

C! C!2 C!2 '

C! C!2 C!2 '

!5C

C!2

C!2

#! #! '-adeno/il-metionin ('6I)

'-adeno/il-homocis/tein ('6!)

) :). *elet*e#+se +s *6l7nb7# form,i

Transfer coen#yme A methyl group A :).

20
C!2 #
4

! $
2 3 N M

C1 C!2;$! C#!$ C! C!2 C!2 C##! 7lu # C##! C1: C!# C!5 C!2#!

!$ 5
2

!2$

4-aminoben/oesa. tetrahidro-*olsa. ()!G)

!$ !2$ $

$ $

C!2;$!

C#!$

C! C!2 C!2

C##!

*olsa. (B10 .itamin)

4

C##! ) r+s#lete*et s#,llCt- *oen#im +s pre*oen#im vitamin9a

Transfer coen#yme A
!5C C!2 $ $ $!2 ' C!2C!2# C! % # % $ !5C $ tiamin-+iro*os/*t ()%%) !5C C!2 $ $ $!2 tiamin (aneurin) B1-.itamin '

A TB$

$ !5C

!5C C!2 $ '

C!2C!2# C

$!2 !5C C #! ! Sa?tT. acetaldehidS C!2C!2#! C!

$ !5C

)# acetaldehidet s#,llCt- *oen#im +s pre*ur#or vitamin9a

Transfer coen#yme A acetaldehyde A TPP

# !$ C $! C!2 C!2

6)%

6F%

# !##C $ C $! C!2 C!2 C!2 C!2 C##! ?arbo"i-biotin

C#2 C##! ) biotin *elet*e#+se +s form,i '

'

C!2 biotin (!-.itamin)

C!2

!5C

$ +irido"in (B3-.itamin)

!5C

$ +irido"l-*os/*t (%6:)

!5C

)# aminocsoportot s#,llCt- *oen#im +s pre*ur#or vitamin9a $!2 $ % # % $ # C!2 ! ! # % -alanin # ! #! ! C!5 $ $ # C!2 C C!5 C!;#! C4# $! C!2 C!2 C4# $! cis/teamin C!2 C!2 ';C;C!5 # C!5;C#;'Ko6 acetil ?oen/im 6 Sa?tT. ecetsa.S ) *oen#im') *6l7nb7# form,i % # % # C!2 ! ! 2 4-dihidro"i# 5 5-dimetil.aHsa. % $ $ # ! #! ! $!2

21

+irido"amin-*os/*t (%6I)

$ $

# C!2 C!5

C C!5 C!;#! C4# $! C!2 C!2 C4# $! C!2 C!2 '! Koen/im-6

C!2#! C!5 C C!5 C!;#! C4# $! C!2 C!2 C##! +antot&nsa. (r&gen B@-.itamin) (VHabban B2 .itamin)

Transfer coen#yme A acetyl group A coen#yme ) C##! !' li+onsa. !' '! dihidro-li+onsa.

C##! ' '

C##! ' C C!5 # acetil-dihidro-li+onsa. ) liponsav *oen#im *6l7nb7# form,i Transfer coen#yme A acetyl group A lipoic acid

22

C!2#! !# !5C $ +irido"in (B3-.itamin) C!2#! !# !5C

C!# C!2#; % $ +irido"l-*os/*t (%6:) !# !5C

C!2$!2 C!2#; % $

+irido"amin-*os/*t (%6I)

)# aminocsoportot s#,llCt- *oen#im +s pre*ur#or vitamin9a

Transfer coen#yme A amino group A P)( Lipids )here are t,o ty+es o* li+id (a+olar ; *atty soluble) biomolecules( 'im+le li+ids cannot be hydroly/ed by sodium hydro"ide and com+le" li+ids can be hydroly/ed by sodium hydro"ide( )he t,o main ty+es o* simple lipids are the *atty acids and the ter+enes( Gatty acids (C13 and C1N) are building bloc?s o* com+le" li+ids (neutral triglycerides and +hos+holi+ids)( 'aturated *atty acids are palmitate (C!5(C!2)14;C##!) and stearate (C!5(C!2)13;C##!)( Ynsaturated *atty acids are the unsaturated .ersions o* stearate (C1N): oleate linoleate and linolenate( )he essential linoleate (-3-*atty acid) and linolenate (-5-*atty acid) are ?no,n as %YG6 (+olyunsaturated *atty acids) or .itamins G(

$ormulas of oleate! linoleate and linolenate Terpenes can be deri.ed *rom iso+rene (methylbutadiene) C!24C(C!5); C!4C!2 (C2!N)( Ionoter+enes contain t,o (C2!N)2 (C10) diter+enes *our (C2!N)4 (C20) triter+enes si" (C2!N)3 (C50) and tetrater+enes eight iso+rene units (C 2!N)N (C40)( )he branched end o* iso+rene is called the head (*eH in !ungarian) and the other +art is called the tail (lb in !ungarian)( )here are di**erent .ariations *or connecting the iso+rene units( Iost *re>uent are head-to-tail connections ,hile and tail-to-tail and head-to-head .ariations are rare(

25

!2C

C C! C!2 C!5 i/o+r&n *eH lb *eH-*eH

*eH-lb

lb-lb )# i#opr+n egys+ge* *apcsol-d,si fa9t,i

&ifferent variations of connecting isoprene units1 head'to'head! head'to'tail and tail'to'tail #nly t,o re+resentati.es o* +olyiso+renoids are sho,n here: chloresterol as triter+ene (C50) and 'carotene as tetrater+ene (C40)( )riter+enes and tetrater+enes C!5 generally contain t,o chains C! ,ith head-to-tail connection and these chains are 5 C!5 connected in a tail-to-tail combination in the middle o* the molecule( )he chain o* the # triter+ene s>ualene is cycli/ed to cholesterol( )he ring system o* cholesterol is called C! 5 C!5 grou+s gonane s?eleton)( Cholesterol can be the the sterane s?eleton (,ithout methyl ! startingC! material *or di**erent ?inds o* steroids ; among them se"ual hormones( C!2 #! 5 Ritamin F limon&n *ormed *rom cholesterol mentol an im+ortant role in calci*ication ?m*or by u. light +lays o* cartilage and bone(
N+h,ny monterp+n *+plete C!5 C!5 C!5 C!5 C!5

C!5 C 6 B F 6 C!5 B !# ?oles/terol C F

gonn./ ci?loal?no?

s/tern./

) gon,nv,#! a s#ter,nv,# +s a *oles#terol *+plete

$ormulas of gonane and sterane s*eletons! and of cholesterol C! C!5 5 C!

C!5
5

)etrater+ene carotenoides are organic h+igments that are naturally occurring in C!5 C!5 C!and Cchromo+lasts F 5 the chloro+lasts o* +lants( )here areC! t,o classes o* carotenoides: 2 carotenes 6 are hydrocarbons and 3anthophylls contain o"ygen( Because o* B +olyconHugated double h bond system carotenoids can absorb light energy *or use in !# !# +hotosynthesis and as antio"idants they +rotect chloro+hyll *rom +hotodamage( F5-.itamin (?ole?alci*erol) 6ntio"idants can eliminate *ree radicals by reduction( =n humans -carotene and other carotenoids can be con.erted to retinol (.itamin 6) by an o"idati.e s+litting( 8etinal C!5 synthesi/ed retinol is essential *or .ision( C! C!5 C! C!5 *rom 5 5
C!5 C!5 C!5 C!5

C!5

C!5

C!5 -Honon C!5 C!5 C!5 C!5

o"( -?arotin C!5 C!2#!

-Honon C!5 C!5

C!5

C!5 C!5 retinol (6-.itamin) 11- cis#'retinl C!#

24

The con9ugated double bond system of 'carotene Com+le" li+ids ha.e generally ester grou+(s) (sometimes carbo"amides) there*ore they can be attac?ed by nucleo+hilic reagents e(g( sodium hydro"ide( )here are *our categories o* com+le" li+ids: *ruit esters ,a"es neutral triglycerides (*ats and oils) and +hos+holi+ids (membrane li+ids that can *orm the li+id bilayers o* cell membranes)( $ruit esters (synthesi/ed *rom short-chained carbo"ylic acids and short-chained alcohols) are *la.our com+onents o* *ruits e(g( aroma o* +inea++le is methyl butyrate (C!5C!2C!2;C##C!5)( Da3es (synthesi/ed *rom long-chain carbo"ylic acids and long-chain alcohols) are not only ,ater-re+ellent materials on the sur*ace o* lea.es and *ruits but bees use bees,a" (!5C(C!2)14;C##(C!2)2@C!5 myricyl +almitate) to *orm the ,alls and ca+s o* the comb( Neutral triglycerides (triacylglycerols)are triesters o* glycerol ,ith *atty acids (C13-C1N)- )hey ser.e as are highly concentrated energy stores in *at cells (adi+ose cells) as ,ater-re+ellent materials (e(g( on the s?in) and as heat-insulators in humans and animals( Gats are solid and their *atty acid +arts are +alminate stearate and oleate( #ils are li>uids and their maHor *atty acid +art is linoleate( 'ur*actant (detergent) soa+s (sodium salts o* *atty acids) can be +roduced by the hydrolysis o* *ats ,ith sodium hydro"ide(
EC##C!2 EC##C! B 5 $a#! EC##C!2 5 E C # C!2 # !

# $a s/a++an

B C! # !
C!2 # ! glicerol

) s#appanf #+s 7ss#folyamata Bydrolysis of triglycerides by sodium hydro3ide

'ur*actant molecules (o) contain both +olar (o) and a+olar ( ) +arts that are suitable *or selecti.e adsor+tion( =n this ,ay the a+olar sur*ace o* the *at (/sTr in !ungarian) can be changed to >uasi-+olar and *ats can +roduce an emulsion in ,ater( # C!5 (C!2)14;C # ntrium-+almitt a+olros $a +olros ) mos-hat,s :elective adsorption of surfactants to fat # # # # # /sTr # # # # # +olros *elOlet

22

% %

% %

)here are di**erent ty+es o* phospholipids and ty+e % is % % o* phosphoglycerides their maHor class( %hos+hoglycerols can be deri.ed *rom phosphatidate (+hos+hatidic acid) that is a +hos+hate ester o* diacylglycerols +roducing +hos+hatidyl % ethanolamines +hos+hatidyl serines and +hos+hatidyl cholines( )he acyl grou+s are *rom *atty acids (C13-C1N)( %hos+hoglycerides are sur*actants and lecitines are the maHor com+onent o* animal cell membranes (in +lants the maHor membrane li+id com+onents are glycoli+ids)( EC##C!2 EC##C! C!2;#; % *os/*atidsa.a? EC##C!2 EC##C! C!2 # $!2 % #;C!2;C! s/erin-?e*alino? C##!

EC##C!2 EC##C! EC##C!2 EC##C! C!2 # a+olros r&s/ % # ;C!2C!2 $(C!5)5 +olros r&s/ C!2 # % #;C!2C!2 $!2

?olamin-?e*alino?

lecitine? ) fos#folipide* s#,rma#tat,sa a fos#fatidsavb-l

$ormation of different *inds of phosphoglycerols1 phosphatidyl ethanolamines (s#erin'*efalino* in Bungarian)! phosphatidyl serines (s#erin'*efanino* in Bungarian) and phosphatidyl cholines (lecithines) (lecitine* in Bungarian) from phosphatidate )here many biomolecules containing +hos+hate in ester (e(g( +hos+hatidate acid) or anhydride (e(g( 6)%) *orm there*ore their abbre.iations are used(

)bbreviations of phosphates in esters and anhydrides .embrane transport processes 6 membrane is a layer o* material ,hich ser.es as a selecti.e barrier bet,een its t,o sides and remains im+ermeable to s+eci*ic +articles molecules or substances( )he structure o* membranes can be illustrated by the *luid mosaic model( )hrough the bimolecular layer sur*actant +hos+holi+ids membrane'integrated (transmembrane) proteins can ma?e +assage +ossible *or s+eci*ic molecules( :urface proteins can bind di**erent regular molecules as rece+tors(

23

thatolL *eh&rHe

*elOleti *eh&rHe irnyTtott bimole?ulris *os/*oli+id r&teg

) membr,no* fel+pCt+se $luid mosaic model of the structure of membranes A place of a transmembrane (membrane'integrated) protein (,thatol- feh+r9e in Bungarian) and a surface protein (fel6leti feh+r9e in Bungarian)

The sch e m e of an Eu*aryotic cell (fro m boo* of Ed, m and $eh+r) 'ome com+ounds are allo,ed to +ass through the membrane ,hereas others are retained( )he dri.ing *orce *or the +assage is a di**erence in the concentrations o* the molecule on the t,o sides o* the membrane and the molecules +ass *rom the higher to lo,er concentration ,ithout the in.estment o* energy (called passive diffusion)(

2M )he trans*er can be carried out in a sim+le ,ay *or small molecules (e(g( ,ater) or by a facilitated diffusion by s+ecial trans*er molecules( )here are di**erent ?inds o* +assi.e di**usion ,ith the aid o* transmembrane +roteins( =n symport trans+ort there are t,o molecules bound to the same +art o* membrane and the concentration gradient *rom higher to lo,er concentration is .alid *or the sum o* the concentrations o* both molecules( =n antiport trans+ort there are t,o molecules bound to the o++osite sides o* membrane and the concentration gradient *rom higher to lo,er concentration has to be .alid *or both o* them( =n this ,ay the +osition o* t,o molecules is e"changed during the +assi.e di**usion( )he name o* this ?ind o* +roteins is translocases( %assage *rom a lo,er to a higher concentration needs a change in the con*ormation o* the integrated +rotein by energy in.estment (by the hydrolysis o* a macroerg bond)( )he +rocess is similar to the anti+ort because generally the +osition o* t,o molecules is e"changed( Nucleic acids $ucleic acids are bio+olymers consisting o* nucleotide units connected by 59 29-+hos+hodiester bonds( 6 nucleotide unit contains a nucleic acid base either containing a +yrimidine ring (thymine ()) and cytosine (C) *or F$6 or uracil (Y) and cytosine (C) *or E$6) and or a +urine s?eleton (adenine (6) and guanine (7) *or both F$6 and E$6)( )he connection o* sugars i(e( F-29-deo"yribose *or F$6 and Fribose *or E$6 to nucleic bases is sho,n by an arro, ( )( )his +oint is 5-$ *or +yrimidine and @-$ *or +urine bases( $ucleic acids are $-glycosides( )he numbering o* sugar is distinguished *rom that o* the base ,ith comma( )he +hos+hate is connected to the 29-hydro"yl grou+ o* sugars *orming ester grou+(
# !$ #
2 5$ 1 3 2 4

# !$ # $ ! timin (F$') C!5 # $

$!2 $ $ ! cito/in
2 5 1

$!2
3 2

#
N

$ $ !

!$ !2$ $ guanin

$ $ !

! uracil (E$')

adenin

+irimidin b/iso? a ?a+csolLdsi hely (

+urin b/iso? ) *eltOntet&s&.el

!#C!2 +entL/o?

2Z 4Z 5Z

# ! !

1Z #! 2Z

!#C!2

2Z 4Z 5Z

# ! !

1Z 2Z

#! !

#! #! - F-ribo*urano/id

#! ! - F-2Z-de/o"iribo*urano/id

) nu*leinsava* +pCt elemei

The structure of nucleoside units )he unit consisting only o* a nucleic base and sugar is called nucleoside( )he name *or a nucleoside mono+hos+hate is nucleotide( )he name o* nucleosides are uridine thymidine cytidine adenosine guanosine( $ucleotides o* F$6 are

2N distinguished *rom E$6 by the abbre.iation o* Xdeo"y9: YI% d)I% CI% dCI% 6I% d6I% 7I% d7I%(
# !$ # E#C!2 ! ! #! # ! #! ! $ # E#C!2 ! ! # ! ! !$ $ # C!5 # # ! #! ! W ! $ $ $!2

E#C!2 !

#! ! E 4 ! de/o"itimidin (d)) E 4 ! uridin (Y) E 4 % uridin mono*os/*t E 4 % de/o"itimidin-mono*os/*t (d)I%) (YI%)

E 4 ! W 4 ! de/o"icitidin (dC) E 4 % # % W 4 #! citidin-di*os/*t (CF%)

N+h,ny pirimidinv,#as nu*leo#id! nu*leotid! nu*leo#id'difos#f,t +s nu*leo#id'trifos#f,t *+plete

The formulas of some nucleosides! nucleotides! nucleoside diphosphates and nucleoside triphosphates containing a pyrimidine ring

The formulas of some nucleosides! nucleotides! nucleoside diphosphates and nucleoside triphosphates containing a purine s*eleton )he nucleotide units are connected by 59 29-+hos+hodiester bonds( =n each unit there is one acidic hydrogen atom at the +hos+hate +art there*ore the bio+olymer itsel* is called nucleic acid( )he 29 terminal o* the +olymer chain (strand) contains a +hos+hate ester and its 59 terminal contains a hydro"yl grou+(

2@

The F%!G%'phosphodiester bond in the polynucleotide chain (8HB &N)! 8HOB 8N))
% # C!2 B/is # 2Z-lnc.&g ! ! ! ! 5Z # #! %
2Z

B b/is % 2Z 5Z cu?or egys&g (ribL/ de/o"iribL/)

6 nu?leo/id egys&g semati?us br/olsa B/is ! ! 2Z-lnc.&g % 2Z 6 5Z % 2Z 5Z 5Z-lnc.&g 7

# C!2

# !

# #! 5Z-lnc.&g 6 nu?leinsa.a? elsdleges s/er?e/ete (a % a meg*elel *os/*orsa. egys&get Helenti)

6 nu?leinsa. s/e?.encia semati?us br/olsa

2Z-lnc.&g 67C ((((((((( 5Z-lnc.&g 6 nu?leinsa. s/e?.enciHna? legegys/erbb br/olsa ) polinu*leotid l,nc ,br,#ol,si lehets+gei

>arious modes to represent the polynucleotide chain =n F$6 t,o o* anti+arallel +olynucleotide strands *orm a double helical structure described by the <atson - Cric? Iodel( #n the sur*ace o* heli" is the chain containing the sugar and +hos+hate( =nside the heli" t,o nucleic bases (a +yridine and a +urine base) *orm a +air connected by hydrogen bonds (t,o *or )-6 and three *or C7) and the character o* one base determines the another base there*ore they are called com+lementary base +airs(

50

!5C

# $ $ E # ) 6 !

!2$ $ $ $ $ E $ E

$!2 $ # C

# ! $ $ !2$ 7

$ $ E

) *omplementer b,#isp,ro*

omplementary pairs of bases;) =n most o* the cases E$6 contains only one strand but it can *orm a double heli" ,ith a F$6 during its biosynthesis( )here can be a double helical section in an E$6 chain ,hen it contains an anti+arallel com+lementary se>uence ; this *olded *orm is called palindromic structure (e(g( in tE$6)( )here can be double +alindromic structures in F$6 as ,ell( $ucleic acids are in the nucleus o* the cell there*ore the double heli" needs to assume .arious more com+act *orms( )he double heli" o* F$6 is ,ra++ed around clusters o* histones (small +roteins ,ith a basic character) by le*thanded su+erhelical turns to *orm nucleosomes ,hich are coiled to *orm solenoids that are *urther com+act *ormations *or F$6( 'olenoids are able to become increasingly e.en more +ac?ed *ormations ; these are chromosomes(

:cheme of the Datson' ric* .odel of &N) )he biological *unction o* F$6 is to +reser.e genetic in*ormation *or the biosynthesis o* +roteins( Fi**erent ty+es o* E$6 include tE$6 (trans*er) mE$6 (messenger) rE$6 (ribosomal) and snE$6 (small nuclear) +ro.ide the conditions *or the biosynthesis o* +roteins (translation)( Fetails are gi.en in the section o* the metabolism o* the biomolecules o* the genetic in*ormation( mE$6 trans+orts in*ormation *rom F$6 about a +rotein se>uence to the ribosome (the site o* +rotein synthesis in the cell)K tE$6 trans+orts amino acids to the ribosome connected to its 59 terminal as estersK rE$6 is the catalytic com+onent o* the ribosome containing not only E$6 but se.eral +roteinsK

51 snE$6 ma?es ri+ening o* di**erent ty+es o* E$6 by s+licing(

.acroerg bonds )he +hos+horic acid anhydride (+yro+hos+hate) deri.ati.es o* nucleotides are the nucleotide di+hos+hates ($F%) and nucleoside tri+hos+hates ($)%)( )heir anhydride bonds (one in $F% and t,o in $)%) are called macroerg bonds (they ha.e a high +hos+horyl-trans*er +otential) because their synthesis re>uires energy ,hile their hydrolysis generates an energy o* about 50 3 ?JJmol( )he most im+ortant $)% is adenosine tri+hos+hate( )here are di**erent ty+es o* macroerg bonds( )hey are *ormed *rom an acid and a com+ound ,ith acidic character( 6nhydrates can be synthesi/ed *rom t,o molecules o* +hos+hates (+hos+horic acid anhydrides e(g( 6)%) or *rom a carbo"ylate and a +hos+hate (mi"ed anhydrides e(g( glycerate 1 5-bis+hos+hate)( )here are other com+ounds ,ith acidic character that can *orm esters ,ith an acid( 6n ester *rom +hos+hate and an enol (e(g( +hos+hoenol+yru.ate ; %-%) or a thiolester *rom a carbo"ylate and a thiol (e(g( acetyl coen/yme 6 ; acetyl-Co6) (!5C;C#'Co6) contain also macroerg bonds( $!2 $ % # % # % # C!2 ! ! $ # ! $ $

#! #! adeno/in-tri*os/*t (6)%) )# )TP *+plete )denosine triphosphate ()TP)

52

# a) sa.anhidride? ; *os/*orsa.anhidrid (+l( 6)%) ! # # .egyes sa.anhidrid # +l( # !

# # % # % # # ! # C # C!2 # %

# % # % #

C # % #

! C # ! % glicerinsa. 1 5-di*os/*t

b) ?OlUnleges &s/tere? ; enol&s/ter +l( %-% (*os/*o-enol-+iru.t)

C##! C! # % C!2 # C ' Ko6

; tiol&s/ter +l( acetil-?oen/im-6 ) ma*roerg *7t+se*

C!5

ompounds containing macroerg bonds1 phosphoric acid anhydride! mi3ed anhydrides e;g; glycerate 4!F'bisphosphate! enolester e;g; phosphoenolpyruvate! thiolester e;g; acetyl coen#yme ) Metabolism )he ,hole range o* organic reactions o* biomolecules in the li.ing organisms are called metabolism( Primary metabolism ; the metabolism o* biomolecules( Phases of primary metabolism: atabolism ; o"idati.e degradation o* biomolecules combined ,ith the generation o* energy in *orm o* macroerg bonds (e(g( 6)%)( )he intermediates o* catabolism are the starting materials o* anabolism( )he terminal +roducts o* the catabolism are C#2 and !2#( )nabolism ; reducti.e biosynthesis o* biomolecules by means o* the energy +roduced during catabolism( =n autotro+hic +lants glucose molecules are synthesi/ed *rom C#2 and !2# by the energy o* the light( )he other biomolecules are synthesi/ed *rom ammonia and the metabolites o* glucose degradation( )he starting materials o* anabolic reactions o* heterotro+hic li.ing organisms (animals and human beings) deri.e *rom the o"idati.e degradation o* the nutriti.e materials (*oods)( :econdary metabolism: the metabolism o* di**erent molecules o* the li.ing organisms ,hich are generally needed *or their *unctioning( 'econdary metabolites are synthesi/ed *rom the di**erent intermediates o* biomolecules( )he most im+ortant ty+es o* secondary metabolites are coen/ymes regulating (e(g( hormones) attracting (e(g( the s,eet sucrose the *ruit esters as scent agents etc() and re+elling agents (e(g( al?aloids and to"ins)( )he +rocesses o* basic biochemistry ta?e +lace inside the cell: in the cytosol (cyto+lasm) mitochondria and ribosomes ; and ,e are *ocused on human biochemistry (e"ce+t +hotosynthesis)( #nly the metabolism o* nutriti.e materials is discussed because the metabolism o* nucleic acids is in nucleus o* the cell and its role is +eri+heral in the nutrition(

55

:cheme of the degradation of the nutritive materials

:cheme of the biosynthesis of biomolecules Catabolism )he *irst +hase o* the degradation o* nutrients (and nucleic acids) is the hydrolysis o* the combined *unctional grou+s o* bio+olymers in the cytosol( )hen in the second +hase (at *irst in the cytosol then in the mitochondria) the o"idati.e degradation o* the intermediates (sugars ; es+ecially glucose amino acids *atty acids and glycerol) leads to a synthesis o* a common intermediate acetyl coen/yme 6 (! 5CC#'Co6 ,ith a macroerg thiolester) (the intermediates o* some amino acids are the members o* citric acid cycle)( =n the third +hase (in the mitochondria) o"idati.e degradation o* acetyl coen/yme 6 by o"ygen to C# 2 (citric acid cycle) and !2# (,ith the *orm o* macroerg bonds) (terminal o"idation ; res+iratory chain) ta?es +lace( Biomolecule %olysaccharides -n/yme 7lycosidasesJ %hos+horylases =ntermediate 'ugarsJ 'ugar +hos+hates

54 %roteins %roteasesJ%e+tidases 6mino acids $eutral triglycerides :i+ases Gatty acids and glycerol (triacylglycerols) $ucleic acids $ucleases $ucleotides The first phase of the degradation of biomolecules =n the hydrolytic +hase o* the degradation o* bio+olymers di**erent ty+es o* hydrolase en/ymes ta?e +art( -"ohydrolase en/ymes start the hydrolysis at one end o* the bio+olymers (e(g( ,ith +olysaccharose chains at the non-reducing endK in +roteins amino +e+tidase en/ymes at $-terminal and carbo"y+e+tidase en/ymes at C-terminal)( -ndohydrolase en/ymes start hydrolysis in the middle o* the bio+olymers (in +olysaccharide chains in a random ,ay in +roteins bet,een s+ecial amino acid units: +e+sin ; be*ore aromatic amino acidsK try+sin ; a*ter basic amino acidsK chymotry+sin ; a*ter aromatic amino acids)( !ydrolase en/ymes o*ten need an acti.ating ste+ (+hos+horylation or hydrolysis) be*ore action( !ydrolases o* amylose (one o* the t,o com+onents o* starch): -amylase is an endohydrolaseK -amylase an e"ohydrolaseK that starts the hydrolysis o* amylose at the non-reducing end s+litting o** maltose moleculesK maltase hydroly/es maltose to t,o glucose molecules( Cellulose is hydroly/ed by cellulase (only in certain microorganisms) to cellobiose that is hydroly/ed by -glucosidase to glucose( :actose is hydroly/ed by lactase (-galactosidase) to glucose and galactose sucrose is hydroly/ed by in.ertase to glucose and *ructose( )he addition o* a +hos+hate grou+ *rom an inorganic +hos+hate (+hos+horic acid) to a substrate can be cataly/ed by +hos+horylases( )he name X+hos+horylase9 is generally used *or glycogen +hos+horylase that cataly/es the release o* glucose-1+hos+hate *rom the reducing end o* glycogen molecule ,ith an inorganic +hos+hate (%i)( 7lucose-1-+hos+hate is con.erted to glucose-3-+hos+hate to enter glycolysis( )he details o* this reaction are gi.en in the section o* biosynthesis o* +olysaccharides( The degradation of carbohydrates to acetyl coenzyme 6*ter the hydrolysis o* carbohydrates the +roduct is mostly glucose( #ther sugars (e"ce+t *ructose) can be *ormed directly or in $F%-sugar +hase to glucose (e(g( galactose)( )he *irst +hase o* the degradation o* glucose is glycolysis *rom glucose (C3 stage) to +yru.ate (+yru.ic acid) (C 5 stage) in the cytosol( %yru.ate is a common starting material *or the t,o ?inds o* anaerobic degradations (alcoholic and lactic acid *ermentations) o* glucose in the cytosol and its aerobic degradation (at *irst to acetyl coen/yme 6 then to carbon dio"ide and ,ater) in the mitochondria( Fi**erent biochemical +rocesses are characteri/ed not only by their +artici+ants but also by their stoichiometry( :toichiometry (stoichiometry o* reactions) is the >uantitati.e relationshi+s o* the reactants and +roducts in a balanced chemical reaction( 0lycolysis )he ste+s o* glycolysis are re.ersible ; e"ce+t three o* them( )he *irst and the third reactions are cataly/ed by ?inases (he"o?inase and +hos+ho*ructo?inase ; %GK)( 6 ?inase (trans*erase) can +hos+horylate a molecule cou+led ,ith the hydrolysis o* a macroerg +hos+horic acid anhydride bond o* a $)% (mostly 6)%) but the +roduct has not a macroerg bond (in the case o* sugars the +roduct is a +hos+hate ester o* a sugar) there*ore this ?ind o* reaction is irre.ersible( )he details o* the third irre.ersible ste+ o* glycolysis ,ill be gi.en later( )he +hos+horylation o* glucose to glucose 3-+hos+hate by he"o?inase is o*ten called the Xacti.ation o* glucose9( =t is not a real acti.ation ste+ because ; as it ,as

52 mentioned earlier ; this ester does not contain a macroerg bond( But the +hos+horic acid unit o* sugars can hel+ the *ormation o* a connection bet,een sugars and en/ymes by ionic interactions( )he isomeri/ation o* glucose 3-+hos+hate to *ructose 3+hos+hate cataly/ed by an isomerase is a double o"o-enol-o"o tautomerism that ,as +resented earlier( )he last ste+ o* C3 stage o* glycolysis is the synthesis o* *ructose 1 3bis+hos+hate *rom *ructose 3-+hos+hate cataly/ed by %GK( %GK is the ?ey en/yme in the control o* glycolysis because its acti.ity can be inhibited by 6)% that is the end +roduct o* o"idati.e +hos+horylation +art o* the res+iratory chain( =n the case o* high 6)% concentration glycolysis is sto++ed but at lo, 6)% concentration glycolysis is started( )his control system is called feedbac* and its mechanism is called allosteric mechanism( )here are also other regulating agents o* %GK( =n the second stage (C5) o* glycolysis the clea.age o* *ructose 1 3-bis+hos+hate cataly/ed by aldolase results in a mi"ture o* glyceraldehyde 5-+hos+hate and dihydro"yacetone +hos+hate (F!6%)( 7lyceraldehyde 5-+hos+hate is on the direct +ath,ay o* glycolysis( )he con.ersion o* F!6% to glyceraldehyde 5-+hos+hate is cataly/ed by an isomerase( =t is noticed that at e>uilibrium @3[ o* triose +hos+hate is F!6%(

0lycolysis and the possibilities for the further degradation of pyruvate )he o"idati.e ste+ o* the glycolysis is the *ormation o* 1 5-bis+hos+hoglycerate (its earlier name is 1 5-di+hos+hoglycerate) containing a macroerg mi"ed anhydride

53 bond *rom glyceraldehyde 5-+hos+hate cataly/ed by glyceraldehyde 5-+hos+hate dehydrogenase ,ith a co.alent catalysis( )he coen/yme is $6F that is reduced to ($6F!B!)( )his ste+ is one o* the t,o energy +roducing ste+s o* glycolysis( =n the course the synthesis o* the macroerg mi"ed anhydride bond during the o"idation at *irst a macroerg thiolester intermediate is *ormed in the en/yme-substrate com+le" (-') that is attac?ed by an inorganic +hos+hate(

The stoichiometry of glycolysis )he energy o* 1 5-bis+hos+hoglycerate is con.erted to the synthesis o* an 6)% molecule *rom 6F% and an inorganic +hos+hate (%i) accom+anied by the *ormation o* 5-+hos+hoglycerate( )he rearrangement o* 5-+hos+hoglycerate to 2-+hos+hoglycerate is in *act a combination o* t,o trans*er reactions by means o* a co*actor 2 5bis+hos+hoglycerate and cataly/ed by a mutase that is a trans*erase( Furing the elimination o* a ,ater molecule *rom 2-+hos+hoglycerate to +hos+hoenol+yru.ate (%-%) a macroerg thiolester bond is *ormed (the catalyst is enolase)( )he energy o* this thiolester bond is con.erted to the energy o* a +hos+horic acid anhydride (6F%B%i6)%) and enol+yru.ate is trans*ormed immediately to pyruvate by an irre.ersible o"o-enol tautomerism (the catalyst is +yru.ate ?inase)( )his reaction is the third irre.ersible ste+ o* glycolysis because direct con.ersion o* +yru.ate to enol+yru.ate is im+ossible it can be carried out only in a roundabout ,ay (see gluconeogenesis)(

The entrance of fructose to the glycolysis

5M

Gructose can enter the glycolysis in an alternati.e ,ay called *ructose 1+hos+hate +ath,ay because the a**inity o* he"o?inase is about t,enty times lo,er than that o* glucose and the glucose concentration is generally higher in cells than that o* *ructose( )he +hos+horylation o* *ructose by 6)% to *ructose 1-+hos+hate is cataly/ed by *ructose?inase and the elimination o* *ructose 1-+hos+hate to F!6% and glyceraldehyde is cataly/ed by *ructose 1-+hos+hate aldolase( F!6% is the intermediate o* the glycolysis but glyceraldehyde can enter the glycolysis only a*ter a +hos+horylation glyceraldehyde 1-+hos+hate by 6)% cataly/ed by triose ?inase( =t is noticed that there are some tissues (e(g( adi+ose tissue) in ,hich he"o?inase can +hos+horylate *ructose to *ructose 3-+hos+hate because o* the high *ructose concentration in them( The possibilities for the further degradation of pyruvate 6ccording to the stoichiometry o* glycolysis during the degradation o* one molecule o* glucose to t,o molecules o* +yru.ate one molecule reduced coen/yme ($6F!B!) and t,o molecules o* 6)% (e"actly t,o macroerg bonds) are *ormed( =n a *ermentation +rocess only the reduced coen/yme is used *or the reduction o* +yru.ate (to ethanol and C#2 in alcoholic *ermentation and to :-lactate in lactic acid *ermentation)( )hat means that the bene*it o* the combination o* glycolysis and *ermentation (that is the anaerobic degradation o* glucose) is only 26)%Jglucose(

The stoichiometry of the lactic acid and alcoholic fermentations of glucose -thanol is *ormed *rom +yru.ate in yeast and se.eral other microorganisms in t,o ste+s( )he decarbo"ylation o* +yru.ate to acetaldehyde is cataly/ed by +yru.ate decarbo"ylase then the reduction o* acetaldehyde by ($6F!B!) *ormed in glycolysis to ethanol is cataly/ed by alcohol dehydrogenase( :-:actate *rom +yru.ate can be *ormed by the reduction o* ($6F!B!) not only in certain microorganisms but in the muscle o* animals and human beings( =t is a *ast but Xnon-economic9 method *or releasing o* energy during the degradation o* glucose( )here is another +ossibility *or the *urther degradation o* +yru.ate( )his ta?es +lace in mitochondria and the result o* this com+le" +rocess using o"ygen (3 #2Jglucose) is 53-5N6)%Jglucose( )his +rocess is called the aerobic degradation o* glucose( 6*ter the irre.ersible +enetration o* +yru.ate to the mitochondria the *irst ste+ o* this com+le" +rocess is the *ormation o* acetyl coen/yme 6 *rom +yru.ate cataly/ed by +yru.ate dehydrogenase com+le"( The structure of mitochondria Iitochondria ha.e an outer membrane (in !ungarian ?Ols\ membrn) and a highly *olded inner membrane (in !ungarian bels\ membrn) ,ith a large sur*ace( )he

5N intermembrane space is bet,een the *olds o* the membranes( )he inside o* the mitochondria is the matri3 that is bound by the inner membrane( )he outer membrane is +ermeable to small molecules and ions( =n contrast +enetration through the inner membrane is only +ossible by membrane trans+ort +rocesses o* transmembrane +roteins( )he site o* the dehydrogenation o* +yru.ate the citric acid cycle and the *atty acid o"idation occurs in the matri"( )he site o* terminal o"idation (res+iratory chain) is in the inner membrane(

.embranes of mitochondria The o3idative decarbo3ylation of pyruvate to acetyl coen#yme ) cataly#ed by pyruvate dehydrogenase multien#yme comple3 )he o"idati.e decarbo"ylation o* +yru.ate to acetyl coen/yme 6 ,ith a macroerg thiolester bond is cataly/ed by the +yru.ate dehydrogenase multien/yme com+le"( Coen/yme is $6F(

The reaction cataly#ed by pyruvate dehydrogenase )here are di**erent ste+s three en/yme subunits (+yru.ate dehydrogenase dihydroli+oyl transacetylase dihydroli+oyl dehydrogenase) three coen/ymes ()%%

5@ coen/yme 6 $6F) and t,o +rosthetic grou+s (li+oic acid G6F) +artici+ating in the o"idati.e decarbo"ylation o* +yru.ate( )he *irst ste+ is the decarbo"ylation o* +yru.ate combined ,ith the synthesis o* acti.e acetaldehyde( 6cti.e acetaldehyde is deri.ati.e o* coen/yme )%% that seems to be a secondary alcohol but really it can react as a carbonyl com+ound (it can be o"idi/ed to acyl grou+) because the carbon atom bet,een $B and ' is a reacti.e carbon atom ,ith acidic (dissociable) +roton( 6cti.e acetaldehyde is o"idi/ed by li+oic acid to an acetyl grou+ that is immediately connected to one o* the thiol grou+s o* the reduced li+oic acid (acetyl dihydroli+oic acid ,ith a macroerg thiolester bond)( )he acetyl grou+ is trans*erred to a coen/yme 6 and li+oic acid is regenerated *rom dihydroli+oic acid by a cascade reducti.e system containing G6F as +rosthetic grou+ and the coen/yme $6F +roducing ($6F!B!)( )he +roduct acetyl coen/yme 6 ,ith a macroerg thiolester bond is the starting material o* the citric acid cycle(

The stoichiometry of the reaction cataly#ed by pyruvate dehydrogenase The degradation of lipids to acetyl coenzyme &egradation in the cytosol 6*ter the hydrolysis o* com+le" li+ids by li+ases the ,ays o* the o"idati.e degradation o* *atty acids and glycerol are di**erent( )he o"idati.e degradation o* alcohols is related to the degradation o* carbo"ylic acids 7lycerol 5-+hos+hate (its earlier name is -glycerol +hos+hate) is *ormed by the +hos+horylation o* glycerol ,ith 6)% cataly/ed by a ?inase( 7lycerol 5-+hos+hate can be o"idi/ed by $6F and the +roduct is F!6% ,hich is an intermediate o* glycolysis(

The decomposition of triglycerides and glycerol

40

Gatty acids are acti.ated be*ore o"idati.e degradation by trans*ormation to acyl coen/yme 6 ,ith the aid o* a macroerg thiolester bond( )he *irst ste+ is the reaction o* the *atty acid and 6)% to acyl-6I% that contains a macroerg mi"ed acid anhydride bond( )he reaction needs the energy o* another macroerg +hos+horic acid anhydride +ro.ided by the hydrolysis o* the by-+roduct +yro+hos+hate to t,o molecules o* +hos+horic acid( 6cyl coen/yme 6 is *ormed *rom the reaction o* acyl-6I% and coen/yme 6(

The activation of fatty acids to acyl coen#yme ) 6cyl coen/yme 6 enters the matri" o* mitochondria in *orm o* acyl carnitine *ormed in a reaction cataly/ed by carnitine acyltrans*erase = at the cyto+lasmic side o* the inner membrane then it ta?es +art in an anti+ort membrane trans+ort +rocess against :-carnitine that trans*ers the acyl grou+ to coen/yme 6 in a reaction cataly/ed by carnitine acyltrans*erase == at the matri" side o* the inner membrane

The membrane transport of fatty acids from cytosol to the matri3 of mitochondria

41

'O3idation of fatty acids to acetyl coen#yme ) molecules

&egradation in the mitochondrial matri3 A 'o3idation )he o"idati.e degradation o* the saturated acyl Co6 named -o"idation contains a recurring se>uence o* *our reactions and the *irst three o* these reactions closely resembles the last reactions (*rom succinate to o"aloacetate) o* the citric acid cycle( )he coen/yme (+rosthetic grou+) o* the o"idation o* acyl Co6 to enoyl Co6 containing a trans double bond bet,een C-2 and C-5 is G6F( )he coen/yme o* the second o"idation ste+ a*ter the hydration o* enoyl Co6 to :-5-hydro"yacyl Co6 is $6F and the +roduct is 5-?etoacyl Co6 (its earlier name is -?etoacyl Co6K that is the origin o* the name o* the degradation)( )he last ste+ o* the -o"idation is the clea.age 5-?etoacyl Co6 by the thiol grou+ o* a molecule o* coen/yme 6 resulting in a molecule o* acetyl-Co6 and an acyl Co6 shortened by t,o carbon atoms( )he reaction is called thiolysis and is cataly/ed by -?etothiolase (or sim+ly thiolase)( 6t the end o* -o"idation each carbon atom o* the original *atty acids is trans*ormed to acetyl coen/yme 6( 6t the end +roduct o* the -o"idation o* *atty acids ha.ing an odd number o* carbon atoms (these are minor s+ecies) is instead o* acetyl-Co6 one molecule o* +ro+ionyl Co6( )his is con.erted to succinyl Co6 (an intermediate o* citric acid cycle) in t,o ste+s (a carbo"ylation *ollo,ed by an intramolecular rearrangement)( Ynsaturated *atty acids contain cis double bonds( =n the case o* one double bond (oleate) an isomeri/ation o* cis double bond to a trans double bond is cataly/ed by an isomerase( <hen there is another double bond in the *atty acid (linoleate and linolenate) the result o* the hydration ste+ is a F-hydro"yl deri.ati.e that is con.erted to :- hydro"yl deri.ati.e by an e+imerase( )he o"idati.e degradation o* ter+enes to acetyl-Co6 is carried out by similar +rocesses as described *or -o"idation( !egradation of L"amino acids to acetyl coenzyme or intermediates of citric acid cycle 6*ter the hydrolysis o* +roteins by di**erent ?inds o* +e+tidases and +roteases there are *our le.els o* the degradation o* amino acids( )hree o* them (transamination o"idati.e deamination o* glutamate urea cycle) are connected ,ith the remo.ing o* the -amino grou+s (the details are gi.en later) and +roduce -?eto carbo"ylic acids ,hile the *ourth le.el is the o"idati.e degradation o* -?eto carbo"ylic acids to +yru.ate (6la )hr 7ly 'er Cys )r+) acetyl-Co6 ()r+ :eu =le) acetoacetyl-Co6

42 (%he )yr )r+ :eu :ys) -?etoglutarate (7lu 7ln !is 6rg %ro) succinyl Co6 (Iet Ral =le) *umarate ()yr %he 6s+) and o"aloacetate (6s+ 6sn)( )here are also other direct degradation modes (o"idati.e deamination or elimination o* an ammonia or ,ater molecule)( Transamination =n transamination reactions (cataly/ed by aminotrans*erases) the amino grou+ o* amino acids is trans+orted to -?etoglutarate (that is an intermediate o* citric acid cycle) ; the +roducts are -?eto carbo"ylic acids (*rom the amino acid) and glutamate (*rom -?etoglutarate) by means o* the coen/yme +yrido"al +hos+hate (%6:) that is in *act a +rosthetic grou+( )he *irst ste+ o* this +rocess is the *ormation o* aldimines ('chi** bases)( )hen by the rearrangement o* aldimines ?etimines are synthesi/ed by an aldimine-?etimine tautomerism( -Keto carbo"ylic acids and +yrido"amine +hos+hate (%6I) are +roduced by the hydrolysis o* ?etimines( )he regeneration o* %6I to %6: is carried out by a trans*ormation o* -?etoglutarate to glutamate( =n this ,ay the amino grou+s *rom all o* the amino acids are trans*erred to glutamate molecules( 6ldimines are the starting materials o* biogenic amines by decarbo"ylation *ollo,ed by hydrolysis( 6ldimines *rom some amino acids (e(g( serine) trans*er their side chain to a tetrahydro*olate ()!G) coen/yme +roducing glycine *rom the amino acids(

Transamination and o3idative deamination of glutarate

45

Other reactions from aldimines derived from amino acids O3idative deamination of glutarate 7lutarate molecules +roduced *rom amino acids are o"idi/ed to an imino acid deri.ati.e ,hich is hydroly/ed to -?etoglutarate and ammonia( )he reaction is cataly/ed by glutamate dehydrogenase accom+anied by $6F ($6F!B!) con.ersion( =n +lants the re.erse +rocess (reducti.e amination) o* this reaction gi.es a +ossibility *or the assimilation o* ammonia using ($6F%!B!)( The urea cycle 6 +art o* ammonia (as $!4B) is used *or the biosynthesis o* nitrogen deri.ati.es( 'ince ammonia is a to"ic *or animals and human beings there*ore sur+lus ammonia is con.erted to urea (in !ungarian ?arbamid) in the urea cycle (another name is ornithine cycle) connected to the biosynthesis o* arginine (6rg)(

44

The urea cycle and its connection with the citric acid cycle The stoichiometry of the urea cycle Grom *i.e reactions o* the urea cycle t,o are mitochondrial and three cyto+lasmic( =n the mitochondria C#2 $!5 and 26)% +roduce carbamoyl +hos+hate 26F% and %i( )hen carbamoyl +hos+hate reacts ,ith ornithine and +roduces citrulline and %i( )he cycle is continued in the cytosol( )he second amino grou+ o* urea is deri.ed *rom as+artate that reacts ,ith citrullin by means o* con.erting an 6)% to 6I% and %%i and the +roduct is argininosuccinate( Grom argininosuccinate arginine and *umarate are *ormed in an elimination reaction( 6s+artate can be reco.ered *rom *umarate in citric acid cycle (*umarate malate o"aloacetate *ollo,ed by a transamination to as+artate)( 6rginine can be hydroly/ed to ornithine (being the *inal ste+ o* the cycle) and urea (in t,o ste+s ,ith isourea as intermediate)( 6ccording to the stoichiometry o* the urea cycle the synthesis o* an urea molecule needs the energy o* three macroerg bonds( !egradation of the common intermediate #acetyl coenzyme $ to C%& and '&% Furing the *urther degradation o* acetyl coen/yme 6 the *ormation o* carbon dio"ide and ,ater molecules ta?es +lace in se+arate reactions( )hese biochemical +rocesses are locali/ed in mitochondria( =n the citric acid cycle t,o molecules o* carbon dio"ide and a Co6 molecule are *ormed *rom one acetyl-Co6 molecule

42 mean,hile *our reduced coen/ymes: 5 ($6F!B!) G6F!2 and one macroerg bond (7F%7)%) are +roduced in the mitochondrial matri"( =n the res+iratory chain (terminal o"idation) in the inner membrane o* mitochondria the reduced coen/ymes reduce an o"ygen molecule to ,ater by electron trans+ort and at the same time the energy o* nutrients are built into macroerg bonds o* 6)% (6F% B %i 6)%)( Ginally all o* the carbon atoms o* the nutrients are o"idi/ed to C#2 at the same time the hydrogen (*ormed during the regeneration o* coen/ymes) and o"ygen atoms o* nutrients +roduce ,ater molecules(

The stoichiometry of the citric acid cycle itric acid cycle )he other names o* this cycle are: tricarbo"ylic acid cycle ()C6 cycle) Krebs cycle or sometimes '/entgyUrgyi-Krebs cycle( 6cetyl-Co6 reacts ,ith the staring material (o"aloacetate) o* the cycle in an addition reaction cataly/ed by citrate synthase *ollo,ed by the hydrolysis o* the intermediate (citryl Co6) to citrate and Co6( =n this reaction the nucleo+hilic attac? o* the acetyl grou+ at the carbonyl grou+ o* o"aloacetate is carried out by the methylen +art o* the enol tautomer that is tem+orarily *ormed in the reaction under the in*luence o* the strong hydrogen bond o* a !is o* the en/yme(

Nucleophilic attac* of the enol tautomer of acetyl' o) at the carbonyl group of o3aloacetate =t ,as +ro.ed by a labeled com+ound that in the *urther reaction citric acid reacts as an asymmetric molecule because o* the asymmetric association ,ith the en/yme( )hat is the reason ,hy the carbon dio"ide molecules are deri.ed *rom carbon atoms o* o"aloacetate and the regenerated o"aloacetate contains the carbon atoms o* acetyl-Co6( )he +roblem is sho,n by the illustration o* both *orms o* o"aloacetate in the scheme o* citric acid cycle( )he ne"t ste+ o* the citric acid cycle is a rearrangement o* citrate to :-isocitrate that is carried out by a combination o* a ,ater elimination *ollo,ed by ,ater addition( )he en/yme is a lyase (aconitase a*ter the name o* the unsaturated intermediate cis-aconitate)( )he +roducts o* the o"idation o* isocitrate combined ,ith decarbo"ylation are -?etoglutarate carbon dio"ide and ($6F!B!) in a reaction cataly/ed by isocitrate dehydrogenase( )he second carbon dio"ide molecule is +roduced in the o"idati.e decarbo"ylation o* -?etoglutarate to succinyl Co6 ,ith a macroerg thiolester bond cataly/ed by -?etoglutarate dehydrogenase multien/yme

43 com+le"( )he structure o* this en/yme is similar to that o* +yru.ate dehydrogenase using three coen/ymes ()%% coen/yme 6 $6F) and t,o +rosthetic grou+s (li+oic acid G6F)( )he reduced coen/yme is again ($6F!B!) and Co6 comes *rom the acetyl-Co6(

The citric acid cycle 'uccinyl Co6 is hydroly/ed by succinate Co6 synthetase that is a ligase( )he energy o* the macroerg bond is transmitted to a 7F%B% i 7)% con.ersion( )he ne"t three ste+s o* the cycle are similar to the *irst ste+s o* -o"idation o* *atty acids( 'uccinate is o"idi/ed to *umarate by succinate dehydrogenase accom+anied by a G6F G6F!2 con.ersion( =n a hydration reaction cataly/ed by *umarase *umarate is con.erted to :-malate ,hich is o"idi/ed to o"aloacetate (the staring material o* the cycle) by malate dehydrogenase( )he reaction is accom+anied ,ith a $6F ($6F!B!) con.ersion( )he en/ymes o* the citric acid cycle are ,or?ing as large en/yme com+le"es attached to the inner membrane o* mitochondria( )he cycle is regulated by *eedbac?( )he essential regulating e**ect is the 6)%J6F% ratio but other intermediates +lay also an im+ortant role( )he citric acid cycle is in close coo+eration ,ith other biochemical +rocesses( =ts intermediates +artici+ate as starting materials in many biochemical reactions there*ore it is o*ten called Xthe +ool o* biointermediates9( 7lycolysis can ,or? under both anaerobic and aerobic condition ,hile the citric acid cycle can ,or? only in an aerobic mode because the regeneration o* the reduced coen/ymes ta?es +lace in the terminal o"idation ,hich needs the +resence o* o"ygen( )here are many bacteria and +lants that can synthesi/e glucose *rom acetylCo6 in a biosynthetic +rocess called the glyo"ylate cycle( 6s *ar as the synthesis o*

4M isocitrate the ste+s o* glyo"ylate cycle are the same as those o* the citric acid cycle( )he details are gi.en later( Terminal o3idation (8espiratory chain) )he name Xterminal o3idation9 means that this metabolic +ath,ay is the last o"idation ste+ in the catabolic +ath,ay (in the o"idation o* the carbon atoms o* biomolecules or other organic com+ounds)( $o, this name is +re*erred( )he name Xrespiratory chain9 means that this metabolic +ath,ay can be connected directly to res+iration the direct o"ygen consum+tion o* li.ing organisms( )his name is +re*erred in medical biochemistry( )here are t,o +artial +rocesses in terminal o"idation( )he e lectron transport chain is a s+ecial chain to trans*er electrons *rom a higher-energy molecule (the donor) ,ith lo,er standard o"idation-reduction +otential (-90) to a lo,er-energy molecule (the acce+tor) ,ith higher standard o"idation-reduction +otential in order to regenerate reduced coen/ymes( O3idative phosphorylation is the metabolic +ath,ay that uses energy released by the o"idation o* nutrients to +roduce macroerg bonds (6F%B%i 6)%)( =nstead o* terminal o"idation the name Xo3idative phosphorylation9 is o*ten used *or the ,hole metabolic +ath,ay( The electron transport chain )he en/yme com+le"es o* the terminal o"idation are in the inner membrane o* mitochondria( )here are three large en/yme com+le"es ($6F!-W reductase cytochrome reductase and cytochrome o"idase) and t,o small ones (coen/yme W and cytochrome c)( Coen/yme W (ubi>uinone) can mo.e bet,een the t,o ,alls o* the inner membrane there*ore it can recei.e hydrogen atoms *rom the intermembrane s+ace through the outer +art o* the inner membrane o* mitochondria (e(g( glycerate 5+hos+hate redo" shuttle)( $6F!-W reductase contains as +rosthetic grou+ GI$( )he dri.ing *orce o* electron trans+ort is the electron-trans*er +otential o* reduced coen/ymes to o"ygen( )he direction o* the electron trans+ort is determined by the standard o"idation-reduction +otential .alues (-90) o* the +artici+ants( )he direction is *rom negati.e to +ositi.e .alues o* the standard o"idation-reduction +otentials( =t means that the direction is *rom +artici+ants ,ith high-+otential electrons to those ,ith lo,-+otential electrons( )he standard o"idation-reduction +otentials are gi.en in R (.olts)( )he standard o"idation-+otential o* !:!2 is de*ined to be 0 R( )he standard o"idation-reduction +otentials o* the coen/ymes are: ($6F!B!) (-0(52 R) and ($6F%!B!) (-0(52 R) G6F!2 (-0(22)( =* necessary ($6F%!B!) reduces $6F to ($6F!B!) cataly/ed by $6F%! dehydrogenase in this ,ay it can ta?e +art in the electron trans+ort( ($6F%!B!) B $6F $6F% B ($6F!B!) 8eaction cataly#ed by N)&PB dehydrogenase )here are three o* transitions o* electron trans+ort in.ol.ed in the energy +roducing o"idati.e +hos+horylation and in these transitions there are large di**erences bet,een the standard o"idation-reduction +otential o* electrons o* the +artici+ants( )hese di**erences result in +roton +um+s (5]5 +rotons) connected ,ith a change o* the con*ormation in the membrane +roteins( )he +roton +um+s trans*er +rotons not only *rom the inner membrane but *rom the matri" (via the dissociation o* ,ater molecules) to the intermembrane s+ace causing a signi*icant di**erence in the +! bet,een the

4N intermembrane s+ace (acidic region) and the matri" (basic region)( )his di**erence in +! starts the o"idati.e +hos+horylation to +roduce a macroerg bond by an 6F%B%i 6)% con.ersion (three 6)% molecules in the case o* $6F!B!)( )hese transitions are: $6F!-W reductase ; coen/yme W cytochrome reductase ; cytochrome c cytochrome o"idase ; o"ygen molecule( 6s the standard o"idation-reduction +otential o* G6F!2 is more +ositi.e than that o* $6F!-W reductase it can Hoin later (at coen/yme W) in the electron trans+ort there*ore it +roduces only t,o 6)% molecules by the electron trans+ort( Grom ($6F!B!) to coen/yme W hydrogen atoms (+rotons and electrons) ta?e +art together in the electron trans+ort chain( Grom coen/yme W to o"ygen molecules only electrons ta?e +art in the electron trans+ort chainK and the +rotons ta?e +art in the +roton +um+(

)he direction o* electron trans+ort: - .alues -90 B .alues $6F!-W reductase (-0(50 R) coen/yme W (B0(04 R) cytochrome reductase (cytochrome b B 0(0M R and cytochrome c1 B0(25 R) cytochrome c (B0(22 R) cytochrome o"idase (cytochrome a B0(2@ R and cytochrome aa5 B0(22 R) o"ygen (B0(N2 R)( The terminal o3idation pathway and the participants of the electron transport with their standard o3idation'reduction potentials (E%<) )o a.oid *orming *ree radicals *our electrons and *our +rotons are connected to o"ygen molecules almost simultaneously +roducing t,o molecules o* ,ater( )here are s+ecial en/ymes to eliminate the to"ic by+roducts i(e( the su+ero"ide anion by su+ero"ide dismutase and hydrogen +ero"ide by catalase( Gormation o* the su+ero"ide anion: #2 B e #2Gormation o* the +ero"ide anion: #2 B 2e #22Gormation o* hydrogen +ero"ide: 2 ! B #220 !2#2 -limination o* su+ero"ide anion by su+ero"ide dismutase: 2 #20 #220 B #2 -limination o* hydrogen +ero"ide by catalase: 2 !2#2 !2# B #2 Elimination of to3ic o3ygen'containing byproducts O3idative phosphorylation 6ccording the Iitchell9s chemiosmotic hy+othesis in the o"idati.e +hos+horylation the di**erence in the +! bet,een the intermembrane s+ace (acidic region) and the matri" (basic region) acti.ates the 6)%-synthesi/ing en/yme com+le" 6)% synthase also ?no,n as G#G1-6)%ase( )he +roduction o* macroerg bonds by 6F%B%i 6)% con.ersions is cataly/ed by the G1 subunit o* G#G1-6)%ase and at the same time the di**erence in the +! .alues bet,een the intermembrane s+ace and the matri" is eliminated by the contribution o* the G# subunit(

4@

The stoichiometry of the terminal o3idation )here are so called uncoupling materials eliminating the connection bet,een electron trans+ort and o"idati.e +hos+horylation( 'uch com+ounds (e(g( 2 4nitro+henol) are able to trans*er +rotons bac? to the matri" ,ithout *orming macroerg bonds( )he G# subunit o* G#G1-6)%ase is in.ol.ed in this uncou+ling acti.ity( )he # letter in G# subunit means that the antibiotic oligomycin is also an uncou+ling agent( Yncou+ling agents are to"ic materials because they eliminate the energy +roducing *unction o* terminal o"idation(

O3idative phosphorylation and uncoupling agents Connection bet(een the catabolic processes )here are com+le" systems regulating connections bet,een catabolic and anabolic +ath,ays as ,ell as ,ithin the catabolic +rocesses( $o, some +rocesses su++orting the ,ell-balanced metabolism are +resented( )naplerotic reactions )here are s+ecial reactions named ana+lerotic reactions ser.ing to maintain the le.el o* o"aloacetate not only *or the citrate acid cycle in mitochondria but also *or other metabolic +ath,ays (e(g( gluconeogenesis) in the cytosol( )he acti.ity o* the en/ymes in these reactions can be regulated by the *eedbac? o* acetyl-Co6( )he +rocesses are acti.ated by a lo, acetyl-Co6 concentration( =n the cytosol +hos+hoenol+yru.ate (in a re.ersible reaction) and in the mitochondria +yru.ate (in an irre.ersible reaction) can be carbo"ylated by carbon dio"ide to o"aloacetate( =t ,as mentioned earlier that both membranes o* the mitochondria are +ermeable *or +yru.ate( Gor the acti.ation o* carbon dio"ide direct carbo"ylation reactions al,ays need the energy o* a macroerg +hos+horic acid anhydride bond (6)% *or +yru.ate and 7)% *or +hos+hoenol+yru.ate) and the coen/yme biotin to trans*er the carbo"ylic grou+( Carbo"ylation o* the biotin-en/yme com+le" al,ays needs the +resence o* magnesium

20 ions( )he reaction o* carbo"ybiotin-en/yme com+le" ,ith +yru.ate needs the +resence o* manganese ions( 'ince the membranes o* mitochondria are not +ermeable *or o"aloacetate it can +ass through only in its reduced *orm (:-malate)( )here e"ist cyto+lasmic and mitochondrial malate dehydrogenase (IF!) en/ymes to hel+ the trans*er and regenerate o"aloacetate( )hese reactions +lay an im+ortant role in glucose biosynthesis *rom +yru.ate (gluconeogenesis)( )he details o* this +rocess are gi.en later(

O3aloacetate synthesis from pyruvate cataly#ed by pyruvate carbo3ylase

O3aloacetate synthesis from phosphoenolpyruvate cataly#ed by PEP carbo3y*inase and its passing through the membranes of mitochondria )here are other mechanisms ,hich regulate the le.el o* acetyl-Co6 in mitochondria( =n the case o* a lo, o"aloacetate le.el o* so-called *etone bodies (e(g( in the li.er in illness diabetes mellitus) can be *ormed *rom acetyl-Co6 molecules( Grom t,o molecules o* acetyl-Co6 acetoacetyl-Co6 is synthesi/ed( )his com+ound ta?es +art in an addition reaction ,ith the third acetyl-Co6 to +roduce 5-hydro"y-5methylgutaryl Co6 (its earlier name is -hydro"y--methylgutaryl Co6)( )his com+ound is the starting material o* the biosynthesis o* ter+enes ; (details see later)( =n the synthesis o* ?etone bodies acetoacetate is *ormed by the elimination o* acetylCo6 *rom 5-hydro"y-5-methylgutaryl Co6( )he ?etone bodies are: acetoacetate acetone (+roduced by the irre.ersible decarbo"ylation o* acetoacetate) and F-5hydro"ybutyrate that is +roduced by the re.ersible reduction o* acetoacetate accom+anied ,ith a $6F ($6F!B!) con.ersion(

21

The biosynthesis of *etone bodies =n the case o* a lo, concentration o* acetyl-Co6 ?etone bodies can be a source o* acetyl-Co6( =n this ,ay they can be used as energy sources (by means o* the citrate acid cycle and terminal o"idation)( )he macroerg thiolester bond o* acetoacetyl-Co6 is deri.ed *rom a succinyl Co6succinate con.ersion( 6cetoacetyl-Co6 can react ,ith acetyl-Co6 according to the last ste+ o* -o"idation o* *atty acids cataly/ed by thiolase +roducing t,o molecules o* acetyl-Co6(

8egeneration of acetyl' o) from acetoacetate 8edo3 shuttles Eedo" shuttles can regenerate coen/yme $6F *rom the reduced ($6F!B!) *ormed in the cytosol (e(g( in glycolysis)( )hese hydrogen atoms can be trans+orted to the mitochondria to the terminal o"idation *or +roducing energy by redo" shuttles( )hese cyto+lasmic (cytosolic) coen/ymes reduced in this ,ay are o*ten called e"tra mitochondrial ($6F!B!) molecules( )here are t,o redo" shuttles *or trans*erring the e"tra mitochondrial ($6F!B!) molecules: the glycerol 5-+hos+hate (its earlier name is -glycerol+hos+hate) and the malate-as+artate redo" shuttle(

The glycerol F'phosphate shuttle

22 )he starting material o* glycerol F'phosphate shuttle is dihydro"yacetone +hos+hate (F!6%) that is an intermediate o* the glycolysis( )his com+ound is reduced by ($6F!B!) in a reaction cataly/ed by cyto+lasmic glycerol 5-+hos+hate dehydrogenase to glycerol-5-+hos+hate that can +ass the outer membrane o* mitochondria( =n the intermembrane s+ace glycerol-5-+hos+hate is o"idi/ed by mitochondrial glycerol 5-+hos+hate dehydrogenase to F!6% but the coen/yme o* this reaction is G6F( F!6% returns to the cytosol and can re+eat this +rocess( 6t the outer side o* the inner membrane the hydrogen atoms o* the reduced G6F!2 coen/yme enter the electron trans+ort by coen/yme W ; that means the *ormation o* only t,o instead o* three 6)% molecules *rom 6F%( )his seems to be a loss in trans+orting o* reducing e>ui.alents but in reality it is an acti.e membrane trans+ort since the hydrogen atoms o* the reduced G6F!2 coen/yme can enter the electron trans+ort e.en at high mitochondrial concentration o* reduced coen/yme ($6F!B!)(

.alate'aspartate redo3 shuttle =n the case o* the malate'aspartate redo3 shuttle o"aloacetate is reduced by e"tra mitochondrial ($6F!B!) to :-malate by cyto+lasmic malate dehydrogenase (IF!) *or ,hich the membranes o* mitochondria are +ermeable( =n the matri" mitochondrial IF! regenerates o"aloacetate *orming reduced ($6F!B!)( =t means that there is no loss in trans+orting o* reducing e>ui.alents in this case( 'ince the inner membrane o* mitochondria is not +ermeable *or o"aloacetate only *or as+artate and ?etoglutarate there*ore o"aloacetate lea.es the mitochondria in a roundabout ,ay( #"aloacetate and glutamate gi.e -?etoglutarate and as+artate in a transamination reaction( )hey lea.e the mitochondria by anti+ort membrane trans+ort +rocesses by the hel+ o* translocases( #"aloacetate is regenerated by the transamination reaction o* ?etoglutarate and as+artate +roducing glutamate *or ,hich membranes o* mitochondria is +ermeable by an anti+ort membrane trans+ort +rocess( )he +airs in the anti+ort membrane +rocesses are as+artate and glutamate as ,ell as -?etoglutarate and o"aloacetate( )his re.ersible redo" shuttle can ,or? only in ,hen the ($6F!B!)J$6F ratio is higher in the cytosol than in the mitochondrial matri" (e(g( in tissues o* high ca+acity as the human heart and li.er)( The stoichiometry of aerobic o3idative degradation of glucose

25 Furing the o"idati.e degradation o* glucose ,hen the glycerol 5-+hos+hate shuttle is used the o.erall reaction is: C3!12#3 B 3 #2 3 C#2 B 3 !2# accom+anied by the reaction: 53 6F% B 53 %i 53 6)% B 53 !2#( =n the case o* the malateas+artate shuttle the number o* 6)% molecules is 5N( The pentose phosphate pathway )he +entose +hos+hate +ath,ay (earlier called the direct o"idation o* glucose or the +hos+hogluconate +ath,ay or the he"ose mono+hos+hate shunt) is an alternati.e cyto+lasmic o"idati.e degradation o* glucose resulting in ($6F%!B!) *rom $6F% as ,ell as di**erent intermediates (e(g( ribose 2-+os+hate ribulose 2+hos+hate erythrose-4-+hos+hate)( )he reduced coen/yme ($6F%!B!) is the coen/yme o* reducti.e biosyntheses *or all ?inds o* li.ing organisms( -"ce+t +lants (using the energy o* +hotons *or glucose biosynthesis) and some microorganisms (using other chemical energy) the li.ing organisms use +entose +hos+hate +ath,ay *or the biosynthesis o* ($6F%!B!)( Ioreo.er ($6F%!B!) is an antio"idant reducing agent in li.ing organisms (e(g( it can regenerate hemoglobin containing *errous ion *rom methemoglobin containing *erric ion by reduction)( Eibose 2-+os+hate is one o* the starting materials o* the biosynthesis o* nucleic acids( Eibulose 2-+os+hate is the starting material o* the synthesis o* ribulose 1 2-bis+os+hate being the starting material o* Cal.in cycle( -rythrose-4-+hos+hate is used in the synthesis o* aromatic amino acids(

8eactions cataly#ed by trans*etolases and transaldolases )he starting material o* the +entose +hos+hate +ath,ay is glucose 3-+hos+hate that is o"idi/ed to 3-+hos+hoglucono- -lactone (the coen/yme is $6F% reduced to $6F%!B!) cataly/ed by glucose 3-+hos+hate dehydrogenase( 6*ter the hydrolysis o* this lactone to 3-+hos+hogluconate this molecule is o"idi/ed by $6F% (,hich is reduced to $6F%!B!) and ribulose 2-+hos+hate and carbon dio"ide are +roduced( Grom ribulose 2-+hos+hate by isomerisation ribose 2-+hos+hate and "ylulose 2+hos+hate (by e+imeri/ation that is a change in the chirality) are *ormed( =n the ne"t ste+s o* the +ath,ay by means o* trans*erase en/ymes trans?etolases and a transaldolase *rom si" ribulose 2-+hos+hate molecules *i.e glucose 3-+hos+hate molecules are *ormed in a com+licated system( Both transaldolase and trans?etolases can +er*orm trans*ormations o* aldoses to ?etoses and in.ersely by trans*erring C-2

24 (trans?etolases) or C-5 (transaldolase) *ragments *rom a ?etose to an aldose( )he chirality o* the ne, hydro"yl grou+ *rom the aldehyde grou+ is : in the case o* trans?etolases and F in the case o* transaldolase( )he +entose +hos+hate +ath,ay is regulated by the le.el o* $6F%(

The pentose phosphate pathway The stoichiometry of the pentose phosphate cycle

22 =n the +entose +hos+hate cycle during the degradation o* one glucose molecule t,el.e reduced coen/ymes ($6F%!B!) (e>ui.alent to 53 6)% molecules) and si" carbon dio"ide molecules are +roduced( #n the basis o* e>ui.alents bet,een reduced coen/yme ($6F%!B!) and macroerg +hos+horic acid anhydride bond o* 6)% the +entose +hos+hate cycle is e>ui.alent to the aerobic o"idati.e degradation o* glucose .ia the glycerol 5-+hos+hate shuttle( Grom si" glucose 3-+hos+hate molecules t,el.e reduced coen/ymes ($6F%!B!) si" carbon dio"ide molecules and si" ribose 2+hos+hate molecules are +roduced( Grom si" ribose 2-+hos+hate molecules (C 2) *i.e glucose 3-+hos+hate molecules (C3) ,ere *ormed by sugar trans*ormation reactions(

:toichiometry of the pentose phosphate cycle Anabolism =n the *ollo,ing the reducti.e biosynthetic +ath,ays o* di**erent biomolecules are +resented at *irst the anabolic reactions o* glucose( Biosynthesis of glucose =n animals the maintenance o* glucose le.el can be maintained (beyond the direct use o* the glucose content o* *oods) by the biosynthesis glucose *rom noncarbohydrate +recursors called gluconeogenesis( =n +lants glucose is synthesi/ed by +hotosynthesis( Furing the germination o* seeds glucose can be synthesi/ed by di**erent ,ays( 0luconeogenesis 7luconeogenesis (or Xde no.o9 synthesis o* glucose) is a glucose biosynthesis *rom non-carbohydrate +recursors (+yru.ate :-lactate F!6% glycerol some amino acids degradation o* ,hich gi.es +yru.ate or an intermediate o* the citric acid cycle ; these are glucogenic amino acids)( 6nimals cannot synthesi/e glucose *rom *atty acids( =n the li.er glucose is synthesi/ed *rom lactate *ormed by glycolysis and lactic acid *ermentation in s?eletal muscles ,hen the rate o* glycolysis e"ceeds the metabolic rate o* the citric acid cycle and the terminal o"idation (res+iratory chain) (anaerobe +eriod o* muscle acti.ity)( )his regeneration o* glucose used u+ by muscles is called the Cori cycle( 7luconeogenesis hel+s to maintain the glucose le.el in blood and brain( )he gluconeogenesis is not a sim+le re.ersal o* glycolysis( =t ,as sho,n earlier that there are three irre.ersible ste+s o* glycolysis: )he glucose glucose 3+hos+hate and *ructose 3-+hos+hate *ructose 1 3-bis+hos+hate reactions cataly/ed by ?inase en/ymes( )hese reactions utili/e the energy o* a macroerg +hos+horic acid anhydride bond o* an 6)% molecule but sugar +hos+hates do not contain macroerg bonds( )he re.erse reactions are hydrolyses cataly/ed by +hos+hatases (glucose 3+hos+hatase and *ructose 1 3-bis+hos+hatase) to glucose and *ructose 3-+hos+hate and %i( )he third irre.ersible ste+ o* glycolysis is the +hos+hoenol+yru.ate +yru.ate con.ersion because o* the irre.ersibility o* o"o-enol tautomerism( %yru.ate *ormed in the cyto+lasm and entered to the mitochondria is carbo"ylated to o"aloacetate (by

23 +yru.ate carbo"ylase) as it ,as described in the section *or ana+lerotic reactions( )he +ass o* o"aloacetate *rom mitochondria to the cytosol in *orm o* malate and the con.ersion o* the regenerated o"aloacetate to %-% is the re.erse +rocess cataly/ed by %-% carbo"y?inase ,hich ,ere also described earlier( )his reaction is re.ersible because during the decarbo"ylation o* o"aloacetate *irst enol+yru.ate is *ormed that is immediately (be*ore the irre.ersible tautomerism) +hos+horylated by 7)%( =n the scheme o* gluconeogenesis the mitochondrial reactions are in a *rame(

0luconeogenesis )he summary o* the +rocess o* gluconeogenesis is gi.en in a se+arate scheme ,ith the names o* intermediates (lactate in !ungarian is teHsa.)(

2M

The process of gluconeogenesis Photosynthesis %ractically all energy consumed by li.ing organisms arises *rom solar energy that is tra++ed by the +rocess o* +hotosynthesis( #nly a *e, microorganisms can use other chemical energy( Gor the biosynthesis o* one glucose molecule the energy o* t,el.e +hotons is used: 3 !2# B 3 C#2 12 h C3!12#3 B 3 #2 <ater and carbon dio"ide molecules are incor+orated in se+arate +rocesses( 6s a result o* +hotolysis the hydrogen atoms o* ,ater are trans+orted se+arately as +rotons and electrons in the light +hase (electron trans+ort) o* +hotosynthesis to $6F% molecules to +roduce reduced ($6F%!B!) molecules by the energy o* absorbed light( %hotosynthesis in green +lants ta?es +lace in the chloro+lasts( )he absor+tion o* *our +hotons is accom+anied by the synthesis o* t,o macroerg +hos+horic acid anhydride bonds o* t,o 6)% molecules and the *ormation o* one o"ygen molecule(

The stoichiometry of the light phase of photosynthesis )he assimilation o* carbon dio"ide molecules to ribulose 1 2-bis+hos+hate by the contribution o* ($6F%!B!) and 6)% molecules ta?e +lace in the dar? +hase o* the +hotosynthesis (Cal.in cycle)( )his +hase can be carried out ,ithout the +resence o* light(

2N

The stoichiometry of the dar* phase of photosynthesis %hotosynthesis in green +lants ta?es +lace in chloro+lasts in ,hich there is a socalled thyla?oid membrane system the structure o* ,hich resembles to that o* the o* mitochondria( )here are t,o +hotosystems in chloro+lasts that can tra+ the energy o* +hotons in a com+licated system containing chloro+hylls (molecules containing a +or+hyrin s?eleton and a coordinated magnesium ion)( )he stroma that is similar to the matri" o* mitochondria contains all o* the en/ymes o* the dar? +hase o* the +hotosynthesis(

hlorophyll a and b The light phase of the photosynthesis )he light +hase o* +hotosynthesis can be illustrated by a ^-scheme that sho,s the standard o"idation-reduction +otentials o* the +artici+ants o* the electron trans+ort *rom ,ater to the coen/yme $6F%( 6s it ,as mentioned earlier the direction o* the electron trans+ort is determined by the standard o"idation-reduction +otential (-90) o* the +artici+ants (*rom the negati.e to the +ositi.e .alues) the ^-scheme illustrates that the standard o"idation-reduction +otential o* +hotosystems can be changed to the negati.e region by the energy o* the +hotons absorbed( )he energy o* absorbed

2@ +hotons is the dri.ing *orce *or the electron trans+ort *rom ,ater molecules (-9 0 B0(N0) to $6F% (-90 -0(52)(

The 2'scheme of photosynthesis 6t *irst +hotosystem = (%'-=) absorbs light o* M00 nm ,a.elength (%-M00)( 6**ected by the +hoton the standard o"idation-reduction +otential o* %'-= changes *rom about B0(2 R to about -1(5 R( #ne o* the electrons o* chloro+hyll o* %'-= *rom e"cited %'-M00_ enters the electron trans+ort cascade and through di**erent com+le" iron-sul+hur +roteins (clusters)( #ne o* them is the *erredo"in reducing system (GE') and the other is *erredo"in (Gd) *erredo"in-$6F% reductase (Gd-$-#")( Ginally the electron reduces $6F% to ($6F%!B!)( Clusters are +roteins containing sul+hur both in co.alent (in cysteine) and ionic (bet,een inorganic sul+hur and iron) bonds( )he electron de*iciency o* %'-= is eliminated by e"citation o* +hotosystem == (%'-==) by light o* 3N0 nm ,a.elength (%-3N0)( )he standard o"idation-reduction +otential o* %'-== is changed *rom about B1(0 R to about -0(N0 R by the second +hoton( #ne o* electrons o* chloro+hyll in %'-== enters electron trans+ort bet,een e"cited %-3N0_ and %-M00 and through se.eral com+le"es: a +rimary electron acce+tor that contains +heo+hytin (%-6) di**erent +lasto>uinones W6 WB W!2 ; (this reduced +lasto>uinone is called +lasto>uinone +ool %W) then to the cytochrome b* com+le" and +lastocyanin (%C)( Because o* the +roton +um+ bet,een cytochrome b and cytochrome f this electron trans+ort is accom+anied by yielding one macroerg bond in an 6F%B%i 6)% con.ersion( )his reaction is cataly/ed by CG#CG1-6)%ase( -lectron de*iciency in %'-== is sto++ed by e"citing the +hotolysis o* ,ater to +rotons electrons and o"ygen( )he electrons enter %'-== by the mediation o* a cluster com+le" containing manganese( )his cluster can +re.ent the *ormation o* o"ygen molecules *rom the generating o* dangerous o"ygen radicals( %rotons o* ,ater can reach the coen/yme reduced by electrons ,ith the hel+ o* a +roton gradient( )his last +art o* the light +hase o* the +hotosynthesis is called the !ill reaction( <hen the reduced coen/yme le.el is high there is an alternati.e +ath,ay *or electrons *rom %-M00_ through another *erredo"in to the cytochrome b* com+le"( =n this ,ay the energy o* one +hoton leads to a *ormation one macroerg bond o* 6)%:

30 h 6)%( )his +rocess is the cyclic photophosphorylation( Furing the light +hase *rom t,o +hotons one reduced coen/yme (e>ui.alent to the energy o* three macroerg bond o* 6)%) and one macroerg bond o* 6)% is *ormed: 2 h 4 6)% that means: h 2 6)%( Cyclic +hoto+hos+horylation +ro.ides the synthesis o* only a hal* o* 6)% molecules but it is an easy ,ay to +roduce e"tra 6)% molecules( The dar* phase of the photosynthesis ( alvin cycle) =n the dar? +hase o* +hotosynthesis the *i"ation (assimilation) o* carbon dio"ide to ribulose 1 2-bis+hos+hate by the contribution o* ($6F%!B!) and 6)% molecules leads to the biosynthesis o* glucose and this +rocess is connected ,ith the regeneration o* ribulose 2-+hos+hate: it is +hos+horylated by the e"tra 6)% o* cyclic +hoto+hos+horylation to restore ribulose 1 2-bis+hos+hate(

The alvin cycle )he en/yme *or carbon dio"ide assimilation to ribulose 1 2-bis+hos+hate is ribulose 1 2-bis+hos+hate carbo"ylase (its short name is Eubisco) ,hich is also an o"ygenase( )he addition o* C#2 is (through an enediol intermediate) bet,een C-2 and C-5 results in t,o glycerate 5-+hos+hate molecules but only one o* them contains the assimilated carbon dio"ide as a carbo"ylic grou+( 'imilarly to the glycolysis only glycerate 1 5-bis+hos+hate is able to ta?e +art in a o"idation-reduction reaction( =n this case glycerate 5-+hos+hate is +hos+horylated by 6)% (*ormed in the light +hase) cataly/ed by a ?inase then glycerate 1 5-bis+hos+hate containing a macroerg mi"ed acid anhydride bond is reduced by ($6F%!B!) (*ormed in the light +hase) to glyceraldehyde 5-+hos+hate( 7lucose is synthesi/ed by the ste+s o* gluconeogenesis but only in the ratio o* the absorbed carbon dio"ide( Grom the other glyceraldehyde 5+hos+hate molecules ribulose 2-+hos+hate is regenerated by similar trans*ormations cataly/ed by trans?etolases and a s+ecial aldolase +resented earlier in the +entose

31 +hos+hate +ath,ay( Eibulose 1 2-bis+hos+hate is synthesi/ed by the +hos+horylation by 6)% (*ormed in the cyclic +hoto+hos+horylation in the light +hase)( )he traditional +hotosynthesis is called C5 +hotosynthesis because the intermediates o* the assimilation o* carbon dio"ide contain three carbon atoms( Eubisco is also an o"ygenaseK there*ore it cataly/es the addition o* an o"ygen molecule to ribulose 1 2-bis+hos+hate resulting in glycerate 5-+hos+hate and +hos+hoglycolate (!2#5%-#-C!2;C##!)( Grom +hos+hoglycolate glycine can be synthesi/ed( 7enerally the rate o* carbo"ylase reaction is *our times that o* o"ygenase reaction( )he name o* this disad.antageous reaction is photorespiration( )here is another .ariation o* +hotosynthesis in tro+ical +lans because o* the e"treme circumstances( )he light and dar? +hases are ,or?ing se+arately and carbon dio"ide is stored tem+orarily in :-malate +roduced by the carbo"ylation o* %-% *ollo,ed by reduction( Because malate contains *our carbon atoms this .ariation is called I photosynthesis( 0lucose biosynthesis in different seedlings )he seedlings in the ground are unable to +hotosynthesi/e there*ore they use the stored biomolecules o* the seeds *or glucose biosynthesis( )here are di**erent ?inds o* seeds( Cereals are rich in +olysaccharides (e(g( starch) and glucose is +roduced by their hydrolysis( Grom the seeds that are rich in +roteins (e(g( bean) a*ter the hydrolysis o* +roteins glucose can be synthesi/ed *rom glucogenic amino acids by gluconeogenesis( Grom oilseeds (e(g( sun*lo,er seeds) that are rich in oil glucose can be synthesi/ed a*ter the o"idati.e degradation o* *atty acids *rom acetyl-Co6 molecules by the glyo"ylate cycle( The glyo3ylate cycle )here are many bacteria and +lants that can synthesi/e glucose *rom acetylCo6 in a biosynthetic +rocess called the glyo"ylate cycle( =n +lants the glyo"ylate cycle occurs in organelles called glyo"ysomes( Yntil the synthesis o* isocitrate the ste+s o* glyo"ylate cycle are the same that o* the citric acid cycle that is degradation +rocess (the addition o* acetyl-Co6 to the starting material o"aloacetate rearrangement o* citric acid to isocitrate)( =n the glyo"ylate cycle isocitrate ta?es +art in an elimination reaction +roducing succinate and glyo"ylate( Grom succinate o"aloacetate can be synthesi/ed in three ste+s *ollo,ing the citric acid cycle ,hich can be then ser.e as starting material *or the biosynthesis o* glucose by gluconeogenesis( Grom glyo"ylate o"aloacetate (the starting material o* glyo"ylate cycle) is regenerated by the addition o* another molecule o* acetyl-Co6 *ollo,ed by the o"idation o* the +roduct :-malate( )hese reactions are cataly/ed *irst by malate synthase that resembles citrate synthase in the citric acid cycle then by malate dehydrogenase similarly to the last ste+ o* the citric acid cycle accom+anied by a $6F ($6F!B!) con.ersion( =n the glyo"ylate cycle succinate (C 4) can be deri.ed *rom t,o molecules o* acetyl-Co6 (C2)(

32

The glyo3ylate cycle

The scheme of the biosynthesis of glucose by the glyo3ylate cycle The biosynthesis of polysaccharides 6*ter the acti.ation o* the glycosidic hydro"yl grou+ o* sugars O-glycosides can be synthesi/ed in the cytosol( =t is illustrated by the e"am+le o* glucose( 7lucose 3+hos+hate (the *irst intermediate o* glycolysis) is con.erted to glucose 1-+hos+hate by means o* a combination o* t,o trans*er reactions assisted by the co*actor glucose 1 3bis+hos+hate( )he reaction is cataly/ed by a mutase (glucose-+hos+hate mutase or +hos+hoglucose mutase) a trans*erase( 6 re.erse +rocess is carried out a*ter the degradation o* glycogen by +hos+horylase(

35

Thee reaction cataly#ed by glucose'phosphate mutase )he acti.e $F%-sugar deri.ati.es (that are sugar donors *or the biosynthesis o* O-glycosides) are +roduced *rom sugar 1-+hos+hate and nucleoside tri+hos+hate ($)%) molecules( $F%- sugars contain a +hos+horic acid anhydride macroerg bond and the energy o* the other macroerg bond o* $)% is used *or the biosynthesis o* the acti.e sugar deri.ati.e( )he hydro"yl com+onent can be an alcoholic or glycosidic hydro"yl grou+ o* another sugar or an aglycon molecule( )he *ormation o* the glycosidic bond does not need e"tra energyK the by+roduct o* the reaction is $F%(

Biosynthesis of O'glycosides of glucose =n the case o* glucose the starting material is $F%-glucose( Gor sucrose biosynthesis YF%-glucose is the starting material( Gor the biosynthesis o* glucans the starting material *or amylose is 6F%-glucose and *or cellulose that is 7F%-glucose(

34 Biosynthesis of glucans The biosynthesis of lipids )he staring material o* both *atty acids and ter+enes is acetyl-Co6( The biosynthesis of fatty acids )he biosynthesis o* *atty acids till the C13 stage is ta?es +lace in the cytosol( 6cetyl-Co6 is trans+orted *rom mitochondria to cytosol by a combination o* reactions +resented earlier(

The way of acetyl' o) from the mitochondria to the cytosol )he biosynthesis is cataly/ed by a multien/yme com+le" (*atty acid synthase) that contains si" acti.e sites and an acyl carrier +rotein (6C%)( 6C% binds the acyl grou+ o* the *atty acid o* increasing number o* carbon atoms by a macroerg thiolester( )here are t,o acetyl-Co6 molecules at the start o* the biosynthesis( #ne o* the acetylCo6 molecules is Hoined to the 6C% to the site o* the +ros+ecti.e long *atty acid (cataly/ed by acetyl transacylase)( )he other acetyl-Co6 is connected to the site o* the ne, acetyl-Co6 units and carbo"ylated to malonyl-Co6 by the coen/yme biotin (as +rosthetic grou+) aided by the energy o* 6)% 6F% con.ersion (cataly/ed by acetylCo6 carbo"ylase) *ollo,ed by a transacylation reaction *rom coen/yme 6 to 6C%( 6)% +lays role in the *ormation o* carbo"ybiotin( )he *ormation o* malonyl-Co6 is o*ten named the Xacti.ation o* acetyl-Co69( =n *act it is not a real acti.ation ste+ because the number o* macroerg bonds does not increase( But the electron distribution o* malonyl-Co6 can hel+ its connection to an acyl-6C% accom+anied by a decarbo"ylation cataly/ed by -acyl-6C%-synthase (acylmalonyl-6C% condensing en/yme)( )he dri.ing *orce o* the synthesis o* acetoacetyl6C% is the elimination o* carbon dio"ide(

32 )he ne"t three ste+s (reduction o* the -?eto grou+ dehydration and reduction o* the unsaturated double bond) o* *atty acid biosynthesis are similar to the ste+s o* the -o"idati.e degradation o* *atty acids in the o++osite direction but ,ith se.eral di**erences: the ste+s o* the biosynthesis are in a chain connected to 6C% (instead o* Co6)K the coen/yme o* both reducti.e reactions is ($6F%!B! ) (instead o* $6F and G6F)K in hydration the F-e+imer (enantiomer) is *ormed instead o* the :-enantiomer there*ore an e+imeri/ation is also needed( )he end +roduct o* the *irst elongation cycle is butyryl-6C% that reacts ,ith a second malonyl-Co6( -longation may continue until +almitoyl-6C% that is hydroly/ed to 6C% and +almitate *rom ,hich +almitoyl-Co6 is synthesi/ed in t,o ste+s( Gurther C 2 units can be attached to the chain by the *atty acid elongation system in the endo+lasmic reticulum membrane (in closed .esicles called microsomes) ,ith reactions similar to those o* cyto+lasmic 6C%(

Biosynthesis of fatty acids Ynsaturated *atty acids are synthesi/ed *rom the saturated *atty acids in microsomes cataly/ed by a monoo"ygenase( Ionoo"ygenases can use molecular o"ygen *or the o"idation but only one o* o"ygen atoms o"idi/es the saturated C;C bonds to double bonds the other o"ygen is reduced by ($6F%!B!) using an electron trans+ort chain containing $6F!-cytochrome b2 reductase (,ith G6FJG6F!2 content) cytochrome b2 reductase (,ith Ge2JGe5 content) and desaturase (,ith Ge2JGe5 content)( )his +rocess cannot be carried out in mammals there*ore linoleate and linolenate are essential *atty acids( =n mammals these *atty acids are the starting materials *or other unsaturated *atty acids o* biological im+ortance (e(g( arachidonate *or the biosynthesis o* +rostaglandin hormones)

33

$ormation of unsaturated fatty acids The biosynthesis of triacylglycerols and phosphoglycerides )riacylglycerols (triglycerides) and +hos+hoglycerides are synthesi/ed in the endo+lasmic reticulum membrane and their common intermediates are +hos+hatidates (+hos+hatidic acids) containing di**erent *atty acid com+onents( )he starting material o* +hos+hatidates is glycerol 5-+hos+hate that is synthesi/ed by the reduction o* F!6%( )his reaction in the o++osite ,ay described in the section o* redo" shuttles( =n the biosynthetic +rocess the +hos+horic acid unit o* glycerol 5-+hos+hate can hel+ the *ormation o* a lin? bet,een the substrate and en/yme by ionic interactions( )he hydro"yl grou+s o* glycerol 5-+hos+hate can react ,ith di**erent acyl-Co6 molecules to +roduce +hos+hatidates( =n the case o* the biosynthesis o* triacylglycerols +hos+hatidates are hydroly/ed by s+ecial +hos+hatases to +roduce diacylglycerols that react ,ith a third acyl-Co6( )he en/ymes o* this +rocess are associated in a triacylglycerol synthetase com+le"(

The biosynthesis of triglycerides =n the case o* the biosynthesis o* +hos+hoglycerides there are di**erent +ossibilities to introduce another ester grou+ to +hos+hatidates( #ne o* these +ossibilities is the acti.ation +hos+hatidates by *orming a macroerg +hos+horic acid anhydride bond by the reaction ,ith C)%( )his reaction is similar to the acti.ation o* glucose 1-+hos+hate to $F%-glucose that ,as described in the section o* the biosynthesis o* +olysaccharides( CF%-diacylglycerols can +roduce +hos+hatidyl ethanolamines ,ith ethanolamine +hos+hatidyl serines ,ith serine and +hos+hatidyl cholines ,ith choline (lecitines)( )he by+roduct o* the reactions is CF%( 6nother .ariation is that the hydro"yl com+ound is acti.ated by +hos+horylation *ollo,ed by a reaction ,ith C)%( =n this case the CF% deri.ati.e o* the hydro"yl com+ounds is reacted ,ith diacylglycerols (e(g( in the synthesis o* lecitines diacylglycerols are reacted ,ith CF%-choline)(

3M

>ariations for the biosynthesis of phosphatidyl cholines (lecitines) The biosynthesis of lecitine The biosynthesis of terpenes )he starting material o* the cyto+lasmic biosynthesis o* ter+enes is acetyl-Co6 and the *irst +hase is the synthesis o* iso+entenyl +yro+hos+hate *rom three acetyl-Co6 molecules( 6s it ,as mentioned in connection ,ith the synthesis o* ?etone bodies acetoacetyl-Co6 is synthesi/ed *rom t,o molecules o* acetyl-Co6( )his com+ound ta?es +art in an addition reaction ,ith a third acetyl-Co6 to +roduce 5-hydro"y-5methylgutaryl Co6 (its earlier name is -hydro"y--methylgutaryl Co6)( =n an addition reaction a nucleo+hilic attac? o* acetyl grou+ on the carbonyl grou+ o* acetoacetyl-Co6 is carried out by the methylene +art o* the enol tautomer that is tem+orarily *ormed in the reaction under the in*luence o* the strong hydrogen bond o* a !is o* the en/yme( 6cetyl-Co6 reacted ,ith o"aloacetate similarly in the *irst ste+ o* the citric acid cycle( =n the mitochondrial synthesis o* ?etone bodies 5-hydro"y-5-methylgutaryl Co6 ta?es +art in an elimination reaction( =n the cyto+lasmic synthesis o* ter+enes 5hydro"y-5-methylgutaryl Co6 is reduced by a reductase to me.alonate accom+anied by 2 ($6F%!B!) 2 $6F% con.ersion in an irre.ersible reaction( 6*ter +hos+horylation to 2-+yro+hos+home.alonate by 2 6)% molecules accom+anied by a decarbo"ylation iso+entenyl +yro+hos+hate is *ormed( =so+entenyl +yro+hos+hate and its isomer dimethylallyl +yro+hos+hate condense to *orm the monoter+ene geranyl +yro+hos+hate (C 10)( )he intermediate o* this reaction is an allylic carbonium ion (named acti.e iso+rene) *ormed *rom dimethylallyl +yro+hos+hate( 7eranyl +yro+hos+hate can then be trans*ormed to other ter+enes(

3N

Biosynthesis of the monoterpene geranyl pyrophosphate

Biosynthesis of amino acids )he biosynthesis o* +roteins *rom :--amino acids is connected ,ith the metabolism o* nucleic acids( )here are di**erent +ath,ays *or the biosynthesis o* amino acids but some common *eatures can be *ound( )he starting materials o* the carbon s?eletons o* amino acids are the intermediates o* glycolysis +entose +hos+hate +ath,ay and citric acid cycle( #n the basis o* the starting materials *i.e biosynthetic *amilies o* amino acids can be distinguished( )he name o* these *amilies is based on the

3@ com+ound (generally amino acid) ,hich can be the starting material o* the other members o* the *amily( )he starting material o* the glutamate amino acid family (7lu 7ln %ro 6rg) is -?etoglutarate (*rom the citric acid cycle)( )he starting material o* the aspartate amino acid family (6s+ 6sn Iet :ys )hr =le) is o"aloacetate (*rom the citric acid cycle)( )he starting material o* the serine amino acid family ('er Cys 7ly) is 5+hos+hoglycerate (*rom the glycolysis)( )he starting material o* the pyruvate amino acid family (6la Ral :eu) is +yru.ate (*rom the glycolysis)( )he starting materials o* the aromatic amino acid family (%he )yr )r+) are +hos+hoenol+yru.ate (*rom the glycolysis) and erythrose 4-+hos+hate (*rom the +entose +hos+hate +ath,ay)( )he starting material o* histidine is ribose 2-+hos+hate (*rom the +entose +hos+hate +ath,ay)( 7enerally the last ste+ o* the biosynthesis o* amino acids is the transamination reaction o* an -?eto carbo"ylic acids but there are se.eral e"ce+tions( The metabolism of the biomolecules of genetic information 6s it ,as mentioned earlier the metabolism o* nucleic acids is in se+arated +lace *rom the metabolism o* other biomolecules in the nucleus o* the cell( )he metabolism o* nucleic acids is the subHect o* another science (genetics) there*ore no, only a short summary is gi.en( Bydrolysis of nucleic acids $ucleases (F$ase an E$ase en/ymes) hydroly/e nucleic acids (F$6 and E$6) to nucleotides( )here are e"onucleases and endonucleases( -"onucleases can be s+eci*ic *or the 5Z or 2Z end o* the strand( Grom F$ase en/ymes restriction endonucleases (that clea.e F$6 chain at s+eci*ic sites) are o*ten used in genetic engineering( Furing *urther hydrolytic +rocesses nucleosides then nucleic bases are *ormed( O3idative degradation of pyrimidine nucleic bases Furing the o"idati.e degradation o* +yrimidine nucleic bases (through the intermediates uracil and then dihydrouracil) ammonia and succinate are *ormed(

O3idative degradation of pyrimidine nucleic bases O3idative degradation of purine nucleic bases 6s *irst intermediates "anthines (hy+o"anthine and "anthine) then uric acid (in !ungarian hugysa.) are *ormed by o"idati.e deamination o* +urine nucleic bases *ollo,ed by an o"idati.e degradation to urea and glyo"ylate(

M0

O3idative degradation of purine nucleic bases Biosynthesis of pyrimidine nucleotides )he +yrimidine ring is synthesi/ed *rom carbamoyl +hos+hate (*ormed in the urea cycle) and as+artate through the intermediate orotate (orotic acid) that reacts ,ith %E%% (2-+hos+horibosyl 1-+yro+hos+hate) to *orm the starting material o* +yrimidine nucleotides (orotate mono+hos+hate)( )he amino grou+ o* C)% is synthesi/ed *rom Y)% and glutamine accom+anied by an 6)% 6F% B %i con.ersion( )hymine is synthesi/ed by the methylation o* uracil (coen/yme is )!G) in their nucleoside mono+hos+hate *orm(

The scheme of the biosynthesis of pyrimidine nucleotides

M1

Biosynthesis of purine nucleotides )he starting material o* +urine nucleotides is %E%% synthesi/ed *rom ribose 2+hos+hate (*ormed in the +entose +hos+hate +ath,ay)( )he *irst ste+ o* this com+licated +rocess is the synthesis o* 29-+hos+horibosylamine (a -glycoside)( =t is the amino grou+ o* 29-+hos+horibosylamine ,hich is incor+orated into the +urine s?eleton( )he sources o* the di**erent atoms o* the +urine s?eleton are sho,n belo,(

The scheme of the biosynthesis of purine nucleotides Biosynthesis of the precursors of &N) )he reduction o* ribose deri.ati.es to 29-deo"yribose deri.ati.es +roceeds in their nucleoside di+hos+hate *orm by ($6F%!B!)(

The formation of 5%'deo3yribose from ribose The biosynthesis of &N) (replication) )he genetic in*ormation is stored and e"+ressed by F$6( Furing the semiconser.ati.e biosynthesis o* F$6 a ne, +olynucleotide chain in a 29 to 59 direction is synthesi/ed *rom +recursor d$)% molecules (d6)% d7)% d))% dC)%) ,ith the hydrolysis o* t,o macroerg +hos+horic acid anhydride bonds to the anti+arallel com+lementary original +olynucleotide chain (tem+late strand) in the course o* di.iding o* the cell( ),o identical F$6 molecules are +roduced *rom a single double-stranded helical F$6 molecule( F$6 re+lication begins at s+eci*ic locations in the genome called origins(

M2

Building a new nucleotide unit in replication )he +rocess o* re+lication is more or less di**erent in +ro?aryotes and eu?aryotes but common *eatures can be *ound( )he brea?-do,n o* the su+erhelical structure o* F$6 is carried out by the en/yme F$6 gyrase (to+oisomerase =) and un,inding o* the double heli" is cataly/ed by helicase( #+ening o* the helical structure demands the energy o* +hos+horic acid anhydride macroerg bonds (6)% 6F% B %i)( )he construct *ormed by t,o se+arated strands is named the replication for* and *i"ed by single strand binding ('sb) +roteins( 6t *irst a short E$6 +rimer is created on the tem+late strand cataly/ed by an E$6 +olymerase (+rimase)( -longation o* the F$6 chain is continued by F$6 +olymerase === holoen/yme( 6t the end o* elongation instead o* F$6 +olymerase === another en/yme (F$6 +olymerase =) continues the biosynthesis o* F$6 strand by remo.ing the E$6 +rimer and re+lacing it by a F$6 section( )his is one o* the 59 (29-`59) e"onuclease acti.ities o* F$6 +olymerase =( 6t the end o* the +rocess the end o* t,o F$6 chains are connected by F$6 ligase using the energy o* +hos+horic acid anhydride macroerg bond (*ormed *rom $6F in +ro?aryo t e s and 6)% in eu? aryo t e s ) (

The scheme of the replication 6s the direction o* the biosynthesis is 2959 it can be carried out directly only along the 5929 tem+late strand (called leading strand)( #n the other strand (called lagging strand 2959) the direction o* biosynthesis is the o++osite to the direction o*

M5 the se>uence there*ore the synthesis o* E$6 +rimers are started at se.eral +laces to the o++osite direction (2959) *ollo,ed by elongation o* F$6( <hen the short F$6 chains (called #?a/a?i *ragments) reach the ne"t E$6 +rimers the elimination o* +rimers they re+lace them by F$6 sections and the connection o* F$6 sections is re+eated se.eral times( =n the double heli" there are double re+lication *or?s *orming a bubble(

The reaction cataly#ed by &N)'ligase Furing the re+lication all o* the ne, nucleotide units is controlled (and corrected i* it is necessary) by F$6 +olymerase =( )his is the other 59 (29-`59) e"onuclease acti.ity o* F$6 +olymerase =( )he 29 terminal nucleotide unit is also controlled (and corrected i* it is necessary)( )his is the 29 (59-`29) e"onuclease acti.ity o* F$6 +olymerase =( )here are also other +ossibilities *or the correction o* the F$6 strands a*ter re+lication( The biosynthesis of 8N) (transcription) )he biosynthesis o* E$6 ,ith the +artici+ation o* F$6 is called transcription and consists o* the co+ying o* F$6 into messenger E$6 during gene e"+ression( )he techni>ue o* transcri+tion is similar to the re+lication but the ne, strand is E$6( )he +recursor molecules are 6)% 7)% Y)% and C)%( 6s only one o* the strands o* F$6 is used as tem+late (leading strand 5929) the direction o* the biosynthesis and the se>uence o* the strand is the same( )he se>uence o* ne, E$6 is anti+arallel and com+lementary to the original F$6( <hen the gene transcribed encodes *or a +rotein the result o* transcri+tion is an mE$6 ,hich is used *or the biosynthesis o* a +rotein in the +rocess o* translation( 6lternati.ely the transcribed gene can encode other E$6 ty+es (rE$6 tE$6 snE$6)( =n transcri+tion only a +art o* the F$6 ta?es +art there*ore there are se.eral +otential starting sites on it( =n eu?aryotes transcri+tion is cataly/ed by 8N) polymerase( =nitiation o* transcri+tion re>uires the +resence o* a core promoter se=uence on the F$6 that is recogni/ed by the subunit o* the en/yme( )he transcri+tion is continued to the terminal signal se>uence on the F$6 that is a palindrome se=uence *ollo,ed by a +oly6 se>uence there*ore the ne, E$6 contains a +alindrome *olded structure and a tail o* +olyY at 59 terminal( '+eci*ic +roteins called transcri+tion *actors +lay im+ortant roles in the transcri+tion( =n most o*ten the +roducts o* transcri+tion are E$6 +recursors (+re-E$6 molecules) that are modi*ied later( )he only e"ce+tions are the +ro?aryotic mE$6 molecules on ,hich the translation (the +rotein biosynthesis) can be started be*ore the termination o* transcri+tion( )here are di**erent changes in the +re-mE$6 structure o* eu?aryotes( 6 poly) tail is attached to the 59 terminal cataly/ed by +olyadenylate

M4 +olymerase using 6)% molecules( 6nother reaction is ,hen a cap (M-methylguanosine +yro+hos+hate) is connected to the 29 terminal o* +re-mE$6 to +re.ent the molecule *rom the hydrolis by E$ases( )hen a splicing is carried out that is the remo.al o* not to be translated sections called introns *rom the +re-mE$6 strand and connecting the remaining *ragments called e"ons by the hel+ o* snE$6 molecules)( )he terminals o* both +re-tE$6 and +re-rE$6 molecules in eu?aryotes are hydroly/ed to tE$6 molecules( )he +re-rE$6 molecules can also hydroly/e themsel.es (this is ribo/yme *unction that is some ?ind o* en/yme *unction)( The biosynthesis of proteins (translation) )he sites o* +rotein biosynthesis are ribosomses that contain both rE$6 molecules and +roteins( )he in*ormation o* the amino acid se>uence contains the mE$6 that *orms a com+le" ,ith ribosome( )he in*ormation is in the se>uence o* nucleotide tri+lets (called codons)( 6 codon is the se>uence o* three nucleotide units starting *rom a *i"ed +oint( )he genetic codon is uni.ersal (it can be used in all ?inds o* li.ing organisms) and there are no commas and no o.erla++ing in it( )he genetic codon is degenerate ,hat means that *or most o* amino acids ha.e not only one codon( )he codon 6Y7 is both the start codon and the codon o* methionine (Iet)( 'to+ codons are YY6 Y76 and Y67( 6mino acids are trans*erred to the ribosome in ester *orm that can react ,ith an amino grou+ (aminoacyl tE$6)( 6t *irst an amino acid is connected to 6I% by a +hos+horic acid anhydride macroerg bond o* 6)% and cataly/ed by aminoacyl tE$6 synthetase( )hen aminoacyl 6I% is reacted ,ith the 59 hydro"yl grou+ (,ith CC6 terminus) o* tE$6 to +roduce aminoacyl tE$6( )he F!Y loo+ o* tE$6 is connected to the en/yme aminoacyl tE$6 synthetase( )he anticodon section o* tE$6 contains an anti+arallel and com+lementary se>uence o* the genetic codon o* the amino acid to be trans*erredK there*ore it is the tem+late recogni/ing site o* tE$6( )he third nucleotide member o* the anticodon can be di**erent ne.ertheless tE$6 molecules can recogni/e such a codon( )he +henomenon is called wobble in base pairing(

$ormation of aminoacyl t8N)

M2

The structure of t8N) )here are t,o sites in the initiation com+le" o* ribosome and mE$6: site % (*or the gro,ing +e+tide chain connected to tE$6) and site 6 (*or the ne, amino acid unit in aminoacyl tE$6 *orm)( 6t the start o* the +rotein biosynthesis (initiation ste+) a Iet-tE$6 (in +ro?aryotes *ormylIet-tE$6) is connected to site % and the ne"t aminoacyl tE$6 to the 6 site (on the basis o* the ne"t codon)( )he connection o* the aminoacyl tE$6 to the site needs the energy o* a +hos+horic acid anhydride macroerg bond (hydrolysis o* 7)% to 7F% and an inorganic +hos+hate) cataly/ed by a 7)%ase(

$ormation of peptide bond (O'N acyl transfer reaction) )he ne"t ste+ is elongation o* the chain that is the *ormation o* a carbo"amide (+e+tide) bond bet,een the ester grou+ o* aminoacyl tE$6 connected to site % and the amino grou+ o* aminoacyl tE$6 connected to the 6 site( )his ste+ is o*ten called O'N acyl transfer reaction( )he *ree tE$6 lea.es site % and tE$6 containing di+e+tide chain is mo.ed *rom site 6 to % site by +rotein elongation *actors using the energy o* a +hos+horic acid anhydride macroerg bond o* the hydrolysis o* 7)% (to 7F% and an inorganic +hos+hate) cataly/ed by a 7)%ase( 6t the same time the +osition o* mE$6 is changed in the com+le" in this ,ay the ne"t codon is mo.ed to site 6 and the elongation can be continued( -ach ne, amino acid unit in the +e+tide chain is controlled (and corrected i* it is necessary) by a s+ecial mechanism during translation( <hen a sto+ codon is *ound at site 6 elongation sto+s and the ne, +e+tide chain is hydroly/ed *rom the tE$6 by the hel+ by release *actors( %roteins biosynthesis

M3 is regulated in di**erent ,ays in +ro?aryotes and eu?aryotes( %arallel ,ith translation the *ormation o* secondary tertiary and >uaternary structures o* +roteins +roceeds( )here can be di**erent +ost-translational modi*ications on the +rotein structure e(g( clea.age the $-terminal methionine di**erent changes in the side chains o* amino acid units (e(g( the o"idation o* +roline to hydro"y+roline described earlier) etc( (iteratur e 1( 'tryer :(: Bioche mi s tr y (5rd -dition) <(!( Gree m a n a Com+ a n y $e, bor? 1@NN( 2( cdm 7( and Geh&r #( (-ds): dletta n biolLgu s o? n a ? (%hysiology *or biologists)( )an?Uny.?ia d L Buda + e s t 1@@0 ++ 20( Topics in Biochemistry 1( Fe*inition o* biomolecules( %roteins ; structures biochemical *unctions and *igures o* some re+resentati.es( 2( Fe*inition o* biomolecules( Carbohydrates ; structures biochemical *unctions and *igures o* some re+resentati.es( 5( Fe*inition o* biomolecules( 'im+le li+ids ; structures biochemical *unctions and *igures o* some re+resentati.es( 4( Fe*inition o* biomolecules( Com+le" li+ids ; structures biochemical *unctions and *igures o* some re+resentati.es( 2( Fe*inition o* biomolecules( $ucleic acids ; structures biochemical *unctions and *igures o* some re+resentati.es( 3( -n/ymes ; structure and *unction (e>uations) M( Fegradation o* biomolecules( )he *irst ste+ ; hydrolysis( N( Fegradation o* biomolecules( 7lucose to the general intermediate (scheme)( @( Fegradation o* biomolecules( Gatty acids to the general intermediate (scheme)( 10( Fegradation o* biomolecules( 6mino acids to the general intermediate (scheme)( 11( Fegradation o* biomolecules( Gormation o* C#2 during the degradation o* the general intermediate (scheme)( 12( Fegradation o* biomolecules( Gormation o* !2# during the degradation o* the general intermediate (scheme)( 15( Fegradation o* biomolecules( )he alternati.e degradation o* glucose ; biological *unctions in autotro+hic and heterotro+hic li.ing organisms (scheme o* some starting ste+s and the stoichiometry o* the reaction)( 14( )he +rinci+le o* redo" shuttles and gluconeogenesis (discussion on the scheme o* glycolysis)( 12( %hotosynthesis( )he role o* +hotons (^-scheme)( 13( %hotosynthesis( 6ssimilation o* C#2 (scheme o* some starting ste+s and the stoichiometry o* the reaction)( 1M( Biosynthesis o* glucose in seeds (,heat bean sun*lo,er)( )he glyo"ylate cycle( 1N( Biosynthesis o* the glycosidic bond( 1@( Biosynthesis o* *atty acids and triglycerides( 20( Biosynthesis o* F$6 and E$6 21( Biosynthesis o* +roteins(