Nucleic Acid Metabolism

Nucleic Acid Metabolism

1. UNIT-IV
Nucleic Acid Metabolism
ANKUSH GOYAL
ASSISTANT PROFESSOR
MAHARAJA AGRASEN SCHOOL OF PHARMACY
MAHARAJA AGRASEN UNIVERSITY, BADDI (H.P.)

2. Nucleic Acids (Polymer of Nucleotides)
Nucleicacidsarethepolymersofnucleotides(polynucleotides)heldby3’and5’phosphate
bridges.Inotherwords,nucleicacidsarebuiltupbythemonomericunits—nucleotides
Nucleotidesconsistoffollowingcomponents:
•NitrogenousBase
•APentoseSugar
•APhosphateGroup
Therearetwotypesofnucleicacids,namelydeoxyribonucleicacid(DNA)andribonucleic
acid(RNA).
ThepentosesugarisD-riboseinribonucleotidesofRNAwhileindeoxyribonucleotides
(deoxynucleotides)ofDNA,thesugaris2-deoxyD-ribose.
Nucleotidesparticipateinalmostallthebiochemicalprocesses,eitherdirectlyorindirectly.
Theyarethestructuralcomponentsofnucleicacids(DNA,RNA),coenzymes,andare
involvedintheregulationofseveralmetabolicreactions.

3. •Nitrogenous bases
•Thenitrogenousbasesfoundinnucleotides(and,therefore,nucleicacids)are
aromaticheterocycliccompounds.Thebasesareoftwotypes—purinesand
pyrimidines.
•Theirgeneralstructuresare:
Purines Pyrimidines
Purinesarenumberedintheanticlockwisedirectionwhilepyrimidinesarenumberedin
theclockwisedirection.MajorPurinebasesareAdenine(A)andGuanine(G)while
PyrimidinebasesareCytosine(C),Thymine(T)andUracil(U).

4. The structures of these nitrogen bases are given below:
DNAcontains
Adenine,
Guanine,
Cytosine and Thymine.
RNA contains
Adenine,
Guanine,
Cytosine and Uracil.

5. •Pentose Sugar
Thefivecarbonmonosaccharides(pentoses)arefoundinthenucleicacidstructure.
RNAcontainsD-ribosewhileDNAcontainsD-2-deoxyribose.Riboseanddeoxyribose
differinstructureatC2.DeoxyribosehasoneoxygenlessatC2comparedtoribose.
Theadditionofapentosesugartobaseproducesanucleoside.Ifthesugarisribose,
ribonucleosidesareformed.Adenosine,guanosine,cytidineanduridinearethe
ribonucleosidesofA,G,CandUrespectively.Ifthesugarisadeoxyribose,
deoxyribonucleosidesareproduced.

6. •Phosphate Group
Thetermmononucleotideisusedwhenasinglephosphatemoietyisaddedtoa
nucleoside.Thusadenosinemonophosphate(AMP)containsadenine+ribose+
phosphate.
Nucleosidemonophosphatespossessonlyonephosphatemoiety(AMP,TMP).
Theadditionofsecondorthirdphosphatestothenucleosideresultsinnucleoside
diphosphate(e.g.ADP)ornucleosidetriphosphate(e.g.ATP)respectively.

7. Biosynthesis of Purine Ribonucleotides
•Manycompoundscontributetothepurineringof
thenucleotides:
1.N
1ofpurineisderivedfromaminogroupof
aspartate.
2.C
2andC
8arisefromformateofN
10
-formylTHF.
3.N
3andN
9areobtainedfromamidegroupof
glutamine.
4.C
4,C
5andN
7arecontributedbyglycine.
5.C
6directlycomesfromCO
2.
•Itshouldberememberedthatpurinebasesarenot
synthesizedassuch,buttheyareformedas
ribonucleotides.Thepurinesarebuiltuponapre-
existingribose5-phosphate.Liveristhemajor
siteforpurinenucleotidesynthesis.
Purine Ring

8. Synthesis of Purine Ribonucleotides(AMP and GMP)
Inosinemonophosphateis the immediate
precursor for the formation of AMP and
GMP. Aspartatecondenses with IMP in
the presence of GTP to produce
adenylsuccinatewhich, on cleavage,
forms AMP.
For the synthesis of GMP, IMP
undergoes NAD
+
dependent
dehydrogenation to form xanthosine
monophosphate(XMP). Glutamine then
transfers amide nitrogen to XMP to
produce GMP.

9. Formation of deoxyribonucleotidesfrom ribonucleotides
ReductionattheC2ofribosemoiety:Thisreactioniscatalysedbyaenzyme,
ribonucleotidereductase.TheenzymeribonucleotidereductaseitselfprovidestheH-
atomsneededforreductionfromitssulfhydrylgroups.Thereducingequivalents,in
turn,aresuppliedbythioredoxin,amonomericproteinwithtwocysteineresidues.
NADPH-dependentthioredoxinreductaseconvertstheoxidizedthioredoxintoreduced
formwhichcanberecycledagainandagain.
DeoxyribonucleotidesaremostlyrequiredforthesynthesisofDNA.

10. Degradation of Purine Nucleotides
Theendproductofpurinemetabolisminhumansisuricacid.Thesequenceof
reactionsinpurinenucleotidedegradationisgivenbelow:
1.Thenucleotidemonophosphates(AMP,IMPandGMP)areconvertedtotheir
respectivenucleosideforms(adenosine,inosineandguanosine)bytheactionof
nucleotidase.
2.Theaminogroup,eitherfromAMPoradenosine,canberemovedtoproduceIMPor
inosine,respectively.
3.Inosineandguanosineare,respectively,convertedtohypoxanthineandguanine
(purinebases)bypurinenucleosidephosphorylase.Adenosineisnotdegradedbythis
enzyme,henceithastobeconvertedtoinosine.
4.Guanineundergoesdeaminationbyguanasetoformxanthine.

11. 5.Xanthineoxidaseisanimportant
enzymethatconvertshypoxanthineto
xanthine,andxanthinetouricacid.
ThisenzymecontainsFAD,
molybdenumandiron,andis
exclusivelyfoundinliverandsmall
intestine.Xanthineoxidaseliberates
H
2O
2whichisharmfultothetissues.
CatalasecleavesH
2O
2toH
2OandO
2.
Uricacid(2,6,8-trioxypurine)isthe
finalexcretoryproductofpurine
metabolisminhumans.

12. Biosynthesis of Pyrimidine Ribonucleotides
The synthesis of pyrimidinesis a much simpler process compared to that of purines.
Aspartate, glutamine (amide group) and CO
2contribute to atoms in the formation of
pyrimidine ring .
Pyrimidine ring is first synthesized and then attached to ribose 5-phosphate.

13. 1.FormationofCarbamoylPhosphate:
GlutaminetransfersitsamidonitrogentoCO
2toproduce
carbamoylphosphate.ThisreactionisATP-dependentandis
catalysedbycytosomalenzymecarbamoylphosphate
synthetaseII(CPSII).
2.ConversionofCarbamoylphosphatetoDihydroorotate:
Carbamoylphosphatecondenseswithaspartatetoform
carbamoylaspartate.Thisreactioniscatalysedbyaspartate
transcarbamoylase.Dihydroorotasecatalysesthepyrimidine
ringclosurewithalossofH
2O.
3. Formation of orotate:
The next step in pyrimidine synthesis is an NAD
+
dependent
dehydrogenation catalysedby dihydroorotatedehydrogenase,
leading to the formation of orotate.

14. 4.Conversionoforotatetoorotidinemonophosphate(OMP):
Ribose5-phosphateisnowaddedtoorotatetoproduceorotidine
monophosphate(OMP).Thisreactioniscatalysedbyorotate
phosphoribosyltransferase.
5.FormationofUridineMonophosphate(UMP):
OMPundergoesdecarboxylationtouridinemono-phosphate(UMP).
ThisreactioniscatalysedbyOMPdecarboxylase.
6. Conversion of UMP to UDP:
By an ATP-dependent kinasereaction, UMP is converted to
UDP which serves as a precursor for the synthesis of dUMP,
dTMP, UTP and CTP.
7.FinalStep:
RibonucleotidereductaseconvertsUDPtodUDPbya
thioredoxin-dependentreaction.Thymidylatesynthetase
catalysesthetransferofamethylgroupfromN
5
,N
10
-
methylenetetrahydrofolatetoproducedeoxythymidine
monophosphate(dTMP).
UDPundergoesanATP-dependentkinasereactionto
produceUTP.Cytidinetriphosphate(CTP)issynthesized
fromUTPbyamination.CTPsynthetaseistheenzyme
andglutamineprovidesthenitrogen.

15. Hyperuricemiaand Gout disease
Thenormalconcentrationofuricacidintheserumofadultsisintherangeof3-7
mg/dl.Inwomen,itisslightlylower(byabout1mg)thaninmen.Thedaily
excretionofuricacidisabout500-700mg.
Hyperuricemiareferstoanelevationintheserumuricacidconcentration.
Goutisametabolicdiseaseassociatedwithoverproductionofuricacid.Atthe
physiologicalpH,uricacidisfoundinamoresolubleformassodiumurate.In
severehyperuricemia,crystalsofsodiumurategetdepositedinthesofttissues,
particularlyinthejoints.Suchdepositsarecommonlyknownastophi.Thiscauses
inflammationinthejointsresultinginapainfulgoutyarthritis.Sodiumurateand/or
uricacidmayalsoprecipitateinkidneysanduretersthatresultsinrenaldamageand
stoneformation.

16. Structure of DNA
DNA is a polymer of deoxyribonucleotides(or simply deoxynucleotides).
It is composed of monomericunits namely
Deoxyadenylate(dAMP)
Deoxyguanylate(dGMP)
Deoxycytidylate(dCMP)
Deoxythymidylate(dTMP)
Schematic representation of polynucleotides:
The monomericdeoxynucleotidesin DNA are held
together by 3’,5’-phosphodiester bridges.

17. Chargaff’s rule of DNA composition
Erwin Chargaff observed that in all the species he studied, DNA had equal numbers of
adenine and thymine residues (A = T) and equal numbers of guanine and cytosine
residues (G = C). This is known as Chargaff’s rule of molar equivalence between the
purinesand pyrimidinesin DNA structure.
Single-stranded DNA, and RNAs which are usually single-stranded, do not obey
Chargaff’s rule. However, double-stranded RNA which is the genetic material in certain
viruses satisfies Chargaff’s rule.

18. DNA Double Helix
ThedoublehelicalstructureofDNAwasproposedbyJamesWatsonandFrancis
Crickin1953(NobelPrize,1962).
ThesalientfeaturesofWatson-CrickmodelofDNA:
1.TheDNAisarighthandeddoublehelix.Itconsistsoftwo
polydeoxyribonucleotidechains(strands)twistedaround
eachotheronacommonaxis.
2.Thetwostrandsareantiparallel,i.e.,onestrandrunsinthe
5’to3’directionwhiletheotherin3’to5’direction.Thisis
comparabletotwoparalleladjacentroadscarryingtrafficin
oppositedirection.
3.Thewidth(ordiameter)ofadoublehelixis20A°(2nm).
4.Eachturn(pitch)ofthehelixis34A°(3.4nm)with10
pairsofnucleotides,eachpairplacedatadistanceofabout
3.4A°.

19. 5.EachstrandofDNAhasahydrophilicdeoxyribosephosphatebackbone(3’-5’
phosphodiesterbonds)ontheoutside(periphery)ofthemoleculewhilethe
hydrophobicbasesarestackedinside(core).
6.Thetwopolynucleotidechainsarenotidenticalbutcomplementarytoeachotherdue
tobasepairing.
7.Thetwostrandsareheldtogetherbyhydrogen
bondsformedbycomplementarybasepairs.TheA-T
pairhas2hydrogenbondswhileG-Cpairhas3
hydrogenbonds.TheG-Cisstrongerbyabout50%
thanA=T.

20. 8.Thehydrogenbondsareformedbetweenapurineandapyrimidineonly.Iftwo
purinesfaceeachother,theywouldnotfitintotheallowablespace.Andtwo
pyrimidineswouldbetoofartoformhydrogenbonds.Theonlybasearrangement
possibleinDNAstructure,fromspatialconsiderationsisA-T,T-A,G-CandC-G.
9.ThecomplementarybasepairinginDNAhelixprovesChargaff’srule.Thecontentof
adenineequalstothatofthymine(A=T)andguanineequalstothatofcytosine
(G=C).
10.Thegeneticinformationresidesononeofthetwostrandsknownastemplatestrand
orsensestrand.Theoppositestrandisantisensestrand.Thedoublehelixhas(wide)
majorgroovesand(narrow)minorgroovesalongthephosphodiesterbackbone.
ProteinsinteractwithDNAatthesegrooves,withoutdisruptingthebasepairsand
doublehelix.