Nucleotides: Synthesis and
Degradation
Nitrogenous Bases
Planar, aromatic, and heterocyclic
Derived from purine or pyrimidine
Numbering of bases is “unprimed”
Nucleic Acid Bases
Purines
Pyrimidines
Sugars
Pentoses (5-C sugars)
Numbering of sugars is “primed”
Sugars
D-Ribose and 2’-Deoxyribose
*Lacks a 2’-OH group
Nucleosides
Result from linking one of the sugars with
a purine or pyrimidine base through an Nglycosidic linkage
– Purines bond to the C1’ carbon of the sugar at
their N9 atoms
– Pyrimidines bond to the C1’ carbon of the
sugar at their N1 atoms
Nucleosides
Phosphate Groups
Mono-, di- or triphosphates
Phosphates can be bonded to either C3 or
C5 atoms of the sugar
Nucleotides
Result from linking one or more phosphates
with a nucleoside onto the 5’ end of the
molecule through esterification
Nucleotides
RNA (ribonucleic acid) is a polymer of
ribonucleotides
DNA (deoxyribonucleic acid) is a polymer
of deoxyribonucleotides
Both deoxy- and ribonucleotides contain
Adenine, Guanine and Cytosine
– Ribonucleotides contain Uracil
– Deoxyribonucleotides contain Thymine
Nucleotides
Monomers for nucleic acid polymers
Nucleoside Triphosphates are important
energy carriers (ATP, GTP)
Important components of coenzymes
– FAD, NAD+ and Coenzyme A
Naming Conventions
Nucleosides:
– Purine nucleosides end in “-sine”
Adenosine, Guanosine
– Pyrimidine nucleosides end in “-dine”
Thymidine, Cytidine, Uridine
Nucleotides:
– Start with the nucleoside name from above
and add “mono-”, “di-”, or “triphosphate”
Adenosine Monophosphate, Cytidine Triphosphate,
Deoxythymidine Diphosphate
In-Class Activities
Look at the Nucleotide Structures
Take the Nucleotide Identification Quiz
Be prepared to identify some of these
structures on an exam. Learn some
“tricks” that help you to distinguish among
the different structures
Nucleotide Metabolism
PURINE RIBONUCLEOTIDES: formed de novo
– i.e., purines are not initially synthesized as free bases
– First purine derivative formed is Inosine Monophosphate (IMP)
The purine base is hypoxanthine
AMP and GMP are formed from IMP
Purine Nucleotides
Get broken down into Uric Acid (a purine)
Buchanan (mid 1900s) showed where purine
ring components came from:
N1: Aspartate Amine
C2, C8: Formate
N3, N9: Glutamine
C4, C5, N7: Glycine
C6: Bicarbonate Ion
Purine Nucleotide Synthesis
O
COO
OOC
2-
O3P O CH2
H
O
H

H
H
C
OH
OH
OH
Aspartate
+ ATP
CH
5
ADP
+ Pi
HC
N
H
SAICAR Synthetase
CH2
C
COO
Ribose
Phosphate
Pyrophosphokinase
AIR
Car boxylase
AMP
ADP + Pi
O3P O CH2
H

O
H
H
OH
OH
H
O
Ribose-5-Phosphate
Fumarate
O
P
O
O
P
O
C
O
C
H2N
CH
5
N
C
5-Aminoimidazole Ribotide (AIR)
ADP + Pi
N10-Formyl-
H2C
CH
NH2
O
C

H
H
OH
OH
HN
H
C
O
C
ADP
+ Pi
O
O3P O CH2
H
NH2
Ribose-5-Phosphate
5-Formaminoimidazole-4-carboxamide
ribotide (FAICAR)
ATP +
Glutamine +
H2O
H 2C
NH
O
C
N10-Formyl-THF
THF
O
IMP
Cyclohydrolase
O
C
OH
Glycinamide Ribotide (GAR)
GAR Transformylase
N
CH
HN
C
O
HC
C5
NH
H
H
N
NH
H2O
H
N
CH
5
C
H
OH
ADP +
Glutamate + Pi
FGAM
Synthetase
GAR Synthetase
H 2C
C
H
Ribose-5-Phosphate
Formylglycinamidine ribotide (FGAM)
N
C4
NH
O
Glycine
+ ATP
AICAR
Transformylase
THF
H2N
H
-5-Phosphoribosylamine (PRA)
2-
THF
O
H
N
Glutamate
+ PPi
O3P O CH2
5-Aminoimidazole-4-carboxamide
ribotide (AICAR)
ATP
Transferase
2-
N
Ribose-5-Phosphate
AIR
Synthetase
Glutamine
+ H2O
Amidophosphoribosyl
CH
5
H2N
Ribose-5-Phosphate
5-Phosphoribosyl--pyrophosphate (PRPP)
N
C4
H2N
O
Adenylosuccinate
Lyase
O
N
HC 4
N
5-Aminoimidazole-4-(N-succinylocarboxamide)
ribotide (SAICAR)
ATP
+HCO3
2-
CH
5
H2N
Ribose-5-Phosphate
Carboxyamidoimidazole Ribotide (CAIR)
N
C4
N
H2N
-D-Ribose-5-Phosphate (R5P)
ATP
C
N
C4
Ribose-5-Phosphate
Formylglycinamide ribotide (FGAR)
4
CH
N
N
2-
O3P O CH2
H
H
OH
O
H
H
OH
Inosine Monophosphate (IMP)
Purine Nucleotide Synthesis
at a Glance
ATP is involved in 6 steps
PRPP in the first step of Purine synthesis is also a precursor for
Pyrimidine Synthesis, His and Trp synthesis
– Role of ATP in first step is unique– group transfer rather than
coupling
In second step, C1 notation changes from  to  (anomers
specifying OH positioning on C1 with respect to C4 group)
In step 2, PPi is hydrolyzed to 2Pi (irreversible, “committing” step)
Coupling of Reactions
Hydrolyzing a phosphate from ATP is relatively easy
G°’= -30.5 kJ/mol
– If endergonic reaction released energy into cell as heat energy,
wouldn’t be useful
– Must be coupled to an exergonic reaction
When ATP is a reactant:
– Part of the ATP can be transferred to an acceptor: Pi, PPi, adenyl,
or adenosinyl group
– ATP hydrolysis can drive an otherwise unfavorable reaction
(synthetase; “energase”)
Purine Biosynthetic Pathway
Channeling of some reactions on pathway organizes and
controls processing of substrates to products in each step
– Increases overall rate of pathway and protects intermediates from
degradation
In animals, IMP synthesis pathway shows channeling at:
– Reactions 3, 4, 6
– Reactions 7, 8
– Reactions 10, 11
In Class Activity
***
Calculate how many ATP equivalents are needed for the de novo synthesize IMP.
Assume that all of the substrates (R5P, glutamine, etc) are available
Note: You should be able to do this calculation for the synthesis of
any of the nucleoside monophosphates
IMP Conversion to AMP
IMP Conversion to GMP
Regulatory Control of Purine
Nucleotide Biosynthesis
GTP is involved in AMP synthesis and ATP is involved in
GMP synthesis (reciprocal control of production)
PRPP is a biosynthetically “central” molecule (why?)
– ADP/GDP levels – negative feedback on Ribose Phosphate
Pyrophosphokinase
– Amidophosphoribosyl transferase is activated by PRPP levels
– APRT activity has negative feedback at two sites
ATP, ADP, AMP bound at one site
GTP,GDP AND GMP bound at the other site
Rate of AMP production increases with increasing
concentrations of GTP; rate of GMP production
increases with increasing concentrations of ATP
Regulatory Control of Purine Biosynthesis
Above the level of IMP production:
– Independent control
– Synergistic control
– Feedforward activation by PRPP
Below level of IMP production
– Reciprocal control
Total amounts of purine nucleotides controlled
Relative amounts of ATP, GTP controlled
Purine Catabolism and Salvage
All purine degradation leads to uric acid (but it might not
stop there)
Ingested nucleic acids are degraded to nucleotides by
pancreatic nucleases, and intestinal phosphodiesterases
in the intestine
Group-specific nucleotidases and non-specific
phosphatases degrade nucleotides into nucleosides
– Direct absorption of nucleosides
– Further degradation
Nucleoside + H2O  base + ribose (nucleosidase)
Nucleoside + Pi  base + r-1-phosphate (n. phosphorylase)
NOTE: MOST INGESTED NUCLEIC ACIDS ARE DEGRADED AND
EXCRETED.
Intracellular Purine Catabolism
Nucleotides broken into nucleosides by action of
5’-nucleotidase (hydrolysis reactions)
Purine nucleoside phosphorylase (PNP)
–
–
–
–
Inosine  Hypoxanthine
Xanthosine  Xanthine
Guanosine  Guanine
Ribose-1-phosphate splits off
Can be isomerized to ribose-5-phosphate
Adenosine is deaminated to Inosine (ADA)
Intracellular Purine Catabolism
Xanthine is the point of convergence for the
metabolism of the purine bases
Xanthine  Uric acid
– Xanthine oxidase catalyzes two reactions
Purine ribonucleotide degradation pathway
is same for purine deoxyribonucleotides
Adenosine Degradation
Xanthosine Degradation
• Ribose sugar gets recycled (Ribose-1-Phosphate  R-5-P )
– can be incorporated into PRPP (efficiency)
• Hypoxanthine is converted to Xanthine by Xanthine Oxidase
• Guanine is converted to Xanthine by Guanine Deaminase
• Xanthine gets converted to Uric Acid by Xanthine Oxidase
Xanthine Oxidase
A homodimeric protein
Contains electron transfer proteins
– FAD
– Mo-pterin complex in +4 or +6 state
– Two 2Fe-2S clusters
Transfers electrons to O2  H2O2
– H2O2 is toxic
– Disproportionated to H2O and O2 by catalase
THE PURINE NUCLEOTIDE CYCLE
AMP + H2O  IMP + NH4+
(AMP Deaminase)
IMP + Aspartate + GTP  AMP + Fumarate + GDP + Pi
(Adenylosuccinate Synthetase)
COMBINE THE TWO REACTIONS:
Aspartate + H2O + GTP  Fumarate + GDP + Pi + NH4+
The overall result of combining reactions is deamination of Aspartate to
Fumarate at the expense of a GTP
Purine Nucleotide Cycle
***
In-Class Question: Why is the purine nucleotide
cycle important in muscle metabolism during a
burst of activity?
Uric Acid Excretion
Humans – excreted into urine as insoluble
crystals
Birds, terrestrial reptiles, some insects –
excrete insoluble crystals in paste form
– Excess amino N converted to uric acid
(conserves water)
Others – further modification :
Uric Acid  Allantoin  Allantoic Acid  Urea  Ammonia
Purine Salvage
Adenine phosphoribosyl transferase (APRT)
Adenine + PRPP  AMP + PPi
Hypoxanthine-Guanine phosphoribosyl transferase
(HGPRT)
Hypoxanthine + PRPP  IMP + PPi
Guanine + PRPP  GMP + PPi
(NOTE: THESE ARE ALL REVERSIBLE REACTIONS)
AMP,IMP,GMP do not need to be resynthesized
de novo !
A CASE STUDY : GOUT
A 45 YEAR OLD MAN AWOKE FROM SLEEP WITH A PAINFUL
AND SWOLLEN RIGHT GREAT TOE. ON THE PREVIOUS NIGHT
HE HAD EATEN A MEAL OF FRIED LIVER AND ONIONS, AFTER
WHICH HE MET WITH HIS POKER GROUP AND DRANK A
NUMBER OF BEERS.
HE SAW HIS DOCTOR THAT MORNING, “GOUTY ARTHRITIS”
WAS DIAGNOSED, AND SOME TESTS WERE ORDERED. HIS
SERUM URIC ACID LEVEL WAS ELEVATED AT 8.0 mg/dL (NL <
7.0 mg/dL).
THE MAN RECALLED THAT HIS FATHER AND HIS
GRANDFATHER, BOTH OF WHOM WERE ALCOHOLICS, OFTEN
COMPLAINED OF JOINT PAIN AND SWELLING IN THEIR FEET.
A CASE STUDY : GOUT
THE DOCTOR RECOMMENDED THAT THE MAN USE
NSAIDS FOR PAIN AND SWELLING, INCREASE HIS
FLUID INTAKE (BUT NOT WITH ALCOHOL) AND REST
AND ELEVATE HIS FOOT. HE ALSO PRESCRIBED
ALLOPURINOL.
A FEW DAYS LATER THE CONDITION HAD
RESOLVED AND ALLOPURINOL HAD BEEN
STOPPED. A REPEAT URIC ACID LEVEL WAS
OBTAINED (7.1 mg/dL). THE DOCTOR GAVE THE
MAN SOME ADVICE REGARDING LIFE STYLE
CHANGES.
Gout



Impaired excretion or overproduction of uric
acid
Uric acid crystals precipitate into joints
(Gouty Arthritis), kidneys, ureters (stones)
Lead impairs uric acid excretion – lead
poisoning from pewter drinking goblets



Fall of Roman Empire?
Xanthine oxidase inhibitors inhibit
production of uric acid, and treat gout
Allopurinol treatment – hypoxanthine
analog that binds to Xanthine Oxidase to
decrease uric acid production
ALLOPURINOL IS A XANTHINE OXIDASE
INHIBITOR
A SUBSTRATE ANALOG IS CONVERTED TO AN
INHIBITOR, IN THIS CASE A “SUICIDE-INHIBITOR”
ALCOHOL CONSUMPTION AND GOUT
Choi HK, Atkinson K, Karlson EW et al. . 2004. “Alcohol intake and risk of incident gout in men:
a prospective study”. Lancet 363: 1277-1281
Lesch-Nyhan Syndrome

A defect in production or activity of
HGPRT


Also,PRPP accumulates


Causes increased level of Hypoxanthine and
Guanine ( in degradation to uric acid)
stimulates production of purine nucleotides
(and thereby increases their degradation)
Causes gout-like symptoms, but also
neurological symptoms  spasticity,
aggressiveness, self-mutilation
 First neuropsychiatric abnormality that
was attributed to a single enzyme
Purine Autism
 25%
of autistic patients may
overproduce purines
 To diagnose, must test urine over
24 hours


Biochemical findings from this test
disappear in adolescence
Must obtain urine specimen in
infancy, but it’s difficult to do!
• Pink urine due to uric acid crystals may
be seen in diapers
IN-CLASS QUESTION
***

IN von GIERKE’S DISEASE, OVERPRODUCTION OF URIC ACID OCCURS. THIS
DISEASE IS CAUSED BY A DEFICIENCY OF
GLUCOSE-6-PHOSPHATASE.
• EXPLAIN THE BIOCHEMICAL EVENTS THAT
LEAD TO INCREASED URIC ACID
PRODUCTION?
• WHY DOES HYPOGLYCEMIA OCCUR IN THIS
DISEASE?
• WHY IS THE LIVER ENLARGED?
Pyrimidine Ribonucleotide
Synthesis

Uridine Monophosphate (UMP) is
synthesized first
• CTP is synthesized from UMP

Pyrimidine ring synthesis completed
first; then attached to ribose-5phosphate
N1, C4, C5, C6 : Aspartate
C2 : HCO3N3 : Glutamine amide Nitrogen
Pyrimidine Synthesis
O
2 ATP + HCO3- + Glutamine + H2O
C
2 ADP +
Glutamate +
Pi
O
Carbamoyl
Phosphate
Synthetase II
C
C
NH2
CH
C
N
H
PO3-2
O
PRPP
C
O
C
C
N
O
HN
O
CH
HN
PPi
2-
COO
O3P
O
Orotate Phosphoribosyl
Transferase
CH2
O
H
H
OH
OH
H

H
COO
Orotidine-5'-monophosphate
(OMP)
Orotate
Carbamoyl Phosphate
Aspartate
Reduced
Quinone
Aspartate
Transcarbamoylase
(ATCase)
O
O
O
C
C
O
CH
N
H
CH
O
2-
CH
N
H
COO
COO
O3P
O
CH2
CH
N
O
H2O
Dihydroorotase
Carbamoyl Aspartate
C
CH2
HN
C
C
C
HN
CH2
NH2
CO2
Quinone
Pi
HO
OMP
Decarboxylase
Dihydroorotate
Dehydrogenase
O
H
H
OH
OH
H

H
Dihydroorotate
Uridine Monophosphate
(UMP)
UMP Synthesis Overview

2 ATPs needed: both used in first step
• One transfers phosphate, the other is hydrolyzed to ADP
and Pi



2 condensation rxns: form carbamoyl aspartate
and dihydroorotate (intramolecular)
Dihydroorotate dehydrogenase is an intramitochondrial enzyme; oxidizing power comes
from quinone reduction
Attachment of base to ribose ring is catalyzed by
OPRT; PRPP provides ribose-5-P
• PPi splits off PRPP – irreversible

Channeling: enzymes 1, 2, and 3 on same chain;
5 and 6 on same chain
OMP DECARBOXYLASE : THE MOST
CATALYTICALLY PROFICIENT ENZYME





FINAL REACTION OF PYRIMIDINE PATHWAY
ANOTHER MECHANISM FOR DECARBOXYLATION
A HIGH ENERGY CARBANION INTERMEDIATE NOT
NEEDED
NO COFACTORS NEEDED !
SOME OF THE BINDING ENERGY BETWEEN OMP
AND THE ACTIVE SITE IS USED TO STABILIZE
THE TRANSITION STATE
• “PREFERENTIAL TRANSITION STATE BINDING”
UMP  UTP and CTP


Nucleoside monophosphate kinase
catalyzes transfer of Pi to UMP to form
UDP; nucleoside diphosphate kinase
catalyzes transfer of Pi from ATP to UDP to
form UTP
CTP formed from UTP via CTP Synthetase
driven by ATP hydrolysis
• Glutamine provides amide nitrogen for
C4 in animals
Regulatory Control of Pyrimidine
Synthesis

Differs between bacteria and animals
• Bacteria – regulation at ATCase rxn

Animals – regulation at carbamoyl phosphate
synthetase II
• UDP and UTP inhibit enzyme; ATP and PRPP
activate it
• UMP and CMP competitively inhibit OMP
Decarboxylase
*Purine synthesis inhibited by ADP and GDP at
ribose phosphate pyrophosphokinase step,
controlling level of PRPP  also regulates
pyrimidines
Orotic Aciduria






Caused by defect in protein chain with
enzyme activities of last two steps of
pyrimidine synthesis
Increased excretion of orotic acid in
urine
Symptoms: retarded growth; severe
anemia
Only known inherited defect in this
pathway (all others would be lethal to
fetus)
Treat with uridine/cytidine
IN-CLASS QUESTION: HOW DOES URIDINE
AND CYTIDINE ADMINISTRATION WORK TO
TREAT OROTIC ACIDURIA?
Degradation of Pyrimidines

CMP and UMP degraded to bases
similarly to purines
• Dephosphorylation
• Deamination
• Glycosidic bond cleavage

Uracil reduced in liver, forming alanine
• Converted to malonyl-CoA  fatty acid
synthesis for energy metabolism
Deoxyribonucleotide Formation



Purine/Pyrimidine degradation are the
same for ribonucleotides and
deoxyribonucleotides
Biosynthetic pathways are only for
ribonucleotide production
Deoxyribonucleotides are synthesized
from corresponding ribonucleotides
DNA vs. RNA: REVIEW



DNA composed of deoxyribonucleotides
Ribose sugar in DNA lacks hydroxyl group
at 2’ Carbon
Uracil doesn’t (normally) appear in DNA
• Thymine (5-methyluracil) appears instead
Formation of Deoxyribonucleotides

Reduction of 2’ carbon done via a free
radical mechanism catalyzed by
“Ribonucleotide Reductases”
• E. coli RNR reduces ribonucleoside
diphosphates (NDPs) to deoxyribonucleoside
diphosphates (dNDPs)

Two subunits: R1 and R2
• A Heterotetramer: (R1)2 and (R2)2 in vitro
RIBONUCLEOTIDE REDUCTASE

R1 SUBUNIT
• Three allosteric sites



Specificity Site
Hexamerization site
Activity Site
• Five redox-active –SH groups from cysteines

R2 SUBUNIT
• Tyr 122 radical
• Binuclear Fe(III) complex
Ribonucleotide Reductase R2
Subunit

Fe prosthetic group– binuclear, with each
Fe octahedrally coordinated
• Fe’s are bridged by O-2 and carboxyl gp of Glu
115
• Tyr 122 is close to the Fe(III) complex 
stabilization of a tyrosyl free-radical

During the overall process, a pair of –SH
groups provides the reducing equivalents
• A protein disulfide group is formed
• Gets reduced by two other sulfhydryl gps of
Cys residues in R1
Chime Exercise
E. coli Ribonucleotide Reductase:
3R1R and 4R1R: R1 subunit
1RIB and 1AV8: R2 subunit
•
Explore 1AV8: Ribonucleotide Reductase in detail.This is the R2
subunit of E. coli Ribonucleotide Reductase. The biological molecule
consists of a heterotetramer of 2 R1 and two R2 chains.
•
Identify the following structures:
–
–
–
–
8 long -helices in one unit of R2
Tyr 122 residue
The binuclear Fe (III) complex
The ligands of the Fe (III) complex
Mechanism of Ribonucleotide Reductase
Reaction



Free Radical
Involvement of multiple –SH groups
RR is left with a disulfide group that
must be reduced to return to the
original enzyme
RIBONUCLEOTIDE REDUCTASE

ACTIVITY IS RESPONSIVE TO LEVEL OF
CELLULAR NUCLEOTIDES:
• ATP ACTIVATES REDUCTION OF


CDP
UDP
• dTTP


INDUCES GDP REDUCTION
INHIBITS REDUCTION OF CDP. UDP
• dATP INHIBITS REDUCTION OF ALL NUCLEOTIDES
• dGTP


STIMULATES ADP REDUCTION
INHIBITS CDP,UDP,GDP REDUCTION
RIBONUCLEOTIDE REDUCTASE

CATALYTIC ACTIVITY VARIES WITH STATE OF
OLIGOMERIZATION:
• WHEN ATP, dATP, dGTP, dTTP BIND TO SPECIFICITY SITE
OF R1 (CATALYTICALLY INACTIVE MONOMER)

 CATALYTICALLY ACTIVE (R1)2
• WHEN dATP OR ATP BIND TO ACTIVITY SITE OF DIMERS


 TETRAMER FORMATION
(R1)4a (ACTIVE STATE) == (R1)4b (INACTIVE)
• WHEN ATP BINDS TO HEXAMERIZATION SITE

 CATALYTICALLY ACTIVE HEXAMERS (R1)6
Thioredoxin


Physiologic reducing agent of RNR
Cys pair can swap H atoms with disulfide
formed regenerate original enzyme
• Thioredoxin gets oxidized to disulfide
Oxidized Thioredoxin gets reduced by NADPH ( final electron acceptor)
mediated by thioredoxin reductase
Thymine Formation


Formed by methylating deoxyuridine
monophosphate (dUMP)
UTP is needed for RNA production, but
dUTP not needed for DNA
• If dUTP produced excessively, would cause
substitution errors (dUTP for dTTP)

dUTP hydrolyzed by dUTPase
(dUTP diphosphohydrolase) to dUMP 
methylated at C5 to form dTMP
rephosphorylate to form dTTP
CHIME EXERCISE: dUTPase


1DUD: Deoxyuridine-5'-Nucleotide Hydrolase in a
complex with a bound substrate analog,
Deoxyuridine-5'-Diphosphate (dUDP).
Explore dUTPase as follows:
• Find the substrate in its binding site
• Find C5 on the Uracil group. Is there enough room to
attach a methyl group to C5?
• Locate the ribose 2’ C. What protein group sterically
prevents an –OH group from being attached to the 2’ C
atom?
• Find the H-bond donors and acceptors (to the uracil
base) from the protein. What would be the effect on the
H-bonding if the base was changed to cytosine?
Tetrahydrofolate (THF)

Methylation of dUMP catalyzed by
thymidylate synthase
• Cofactor: N5,N10-methylene THF



Oxidized to dihydrofolate
Only known rxn where net oxidation state
of THF changes
THF Regeneration:
DHF + NADPH + H+  THF + NADP+ (enzyme: dihydrofolate
reductase)
THF + Serine  N5,N10-methylene-THF + Glycine
(enzyme: serine hydroxymethyl transferase)
REGENERATION OF N5,N10 METHYLENETETRAHYDROFOLATE
dUMP
dTMP
thymidylate synthase
DHF
N5,N10 – METHYLENE-THF
NADPH + H+
GLYCINE
dihydrofolate reductase
serine hydroxymethyl
transferase
NADP+
SERINE
THF
INHIBITORS OF N5,N10 METHYLENETETRAHYDROFOLATE
REGENERATION
dUMP
dTMP
thymidylate synthase
DHF
N5,N10 – METHYLENE-THF
X
GLYCINE
FdUMP
NADPH + H+
dihydrofolate reductase
serine hydroxymethyl
transferase
NADP+
SERINE
X
THF
METHOTREXATE
AMINOPTERIN
TRIMETHOPRIM
Anti-Folate Drugs

Cancer cells consume dTMP quickly for
DNA replication
• Interfere with thymidylate synthase rxn to
decrease dTMP production


(fluorodeoxyuridylate – irreversible inhibitor) – also
affects rapidly growing normal cells (hair follicles,
bone marrow, immune system, intestinal mucosa)
Dihydrofolate reductase step can be
stopped competitively (DHF analogs)
• Anti-Folates: Aminopterin, methotrexate,
trimethoprim
ADENOSINE DEAMINASE DEFICIENCY

IN PURINE DEGRADATION, ADENOSINE 
INOSINE
• ENZYME IS ADA
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ADA DEFICIENCY RESULTS IN SCID
• “SEVERE COMBINED IMMUNODEFICIENCY”
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SELECTIVELY KILLS LYMPHOCYTES
• BOTH B- AND T-CELLS
• MEDIATE MUCH OF IMMUNE RESPONSE

ALL KNOWN ADA MUTANTS STRUCTURALLY
PERTURB ACTIVE SITE
Adenosine Deaminase
CHIME Exercise: 2ADA
Enzyme catalyzing deamination of Adenosine to Inosine
/ barrel domain structure
– “TIM Barrel” – central barrel structure with 8 twisted
parallel -strands connected by 8
-helical loops
– Active site is at bottom of funnel-shaped pocket
formed by loops
– Found in all glycolytic enzymes
– Found in proteins that bind and transport metabolites
ADA DEFICIENCY
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

IN-CLASS QUESTION: EXPLAIN THE
BIOCHEMISTRY THAT RESULTS WHEN A PERSON
HAS ADA DEFICIENCY
(HINT: LYMPHOID TISSUE IS VERY ACTIVE IN
DEOXYADENOSINE PHOSPHORYLATION)
ADA DEFICIENCY



ONE OF FIRST DISEASES TO BE TREATED WITH
GENE THERAPY
ADA GENE INSERTED INTO LYMPHOCYTES; THEN
LYMPHOCYTES RETURNED TO PATIENT
PEG-ADA TREATMENTS
• ACTIVITY LASTS 1-2 WEEKS