BIOCHEMISTRY
MOLECULAR GENETICS
1
OUTLINE:
1. Nucleotide bases and their metabolism
2. Diseases associated with nucleotide metabolism
defect
3. Drug inhibitors of nucleotide synthesis
2
SOME TERMINOLOGY
 Genotype: The genetic makeup of an organism
 Phenotype: the physical expressed traits of an organism
 Nucleic acid: Biological molecules(RNA and DNA) that
allow organisms to reproduce;
3
MORE TERMINOLOGY
 The genome is an organism’s complete set of
DNA.
 a bacteria contains about 600,000 DNA base
pairs
 human and mouse genomes have some 3 billion.
 human genome has 23 distinct chromosomes.
 Each chromosome contains many genes.
 Gene
 basic physical and functional units of heredity.
 specific sequences of DNA bases that encode
instructions on how to make proteins.
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4
NUCLEOTIDE METABOLISM
I. Nucleotides
-Why have them?
II. Purine Biosynthesis
III. Pyrimidine Biosynthesis
IV. Nucleotide Catabolism
5
Nitrogen Bases
 There are two kinds of nitrogen-containing bases
- purines and pyrimidines.
 Purines consist of a six-membered and a five-
membered nitrogen-containing ring, fused
together.
 Pyridmidines have only a six-membered
nitrogen-containing ring.
Purines
 Adenine = 6-amino purine
 Guanine = 2-amino-6-oxy purine
 Hypoxanthine = 6-oxy purine
 Xanthine = 2,6-dioxy purine
Pyrimidines
 Uracil = 2,4-dioxy pyrimidine
 Thymine = 2,4-dioxy-5-methyl pyrimidine
 Cytosine = 2-oxy-4-amino pyrimidine
 Orotic acid = 2,4-dioxy-6-carboxy
pyrimidine
NUCLEOTIDES
WHY HAVE THEM?
8
1. nucleotides serve numerous functions in different reaction
pathways
For example, nucleotides are the activated precursors of DNA and
RNA.
2. form the structural moieties of many coenzymes (examples include
NADH, FAD, and coenzyme A).
3. are critical elements in energy metabolism (ATP, GTP).
4. Nucleotide derivatives are frequently activated intermediates in
many biosyntheses. For example, UDP-glucose and CDP-
diacylglycerol are precursors of glycogen and phosphoglycerides,
respectively.
5. nucleotides act as second messengers in intracellular signaling
(e.g., cAMP, cGMP).
6. Finally, nucleotides and nucleosides act as metabolic allosteric
regulators. Think about all of the enzymes that have been studied
that are regulated by levels of ATP, ADP, and AMP.
STRUCTURES OF NUCLEOTIDES
 A nucleoside is formed from the linkage of a sugar with
a nitrogen-containing base.
1. The bases that make up the physiologically relevant
nucleosides all have ring structures.
a. The purines adenine, guanine,
b. The pyrimidines cytosine, thymine, and uracil have six-
membered ring structures.
2. Ribose and 2-deoxyribose are the main sugars found in
nucleosides and nucleotides.
9
NOMENCLATURE
PURINES VS PYRIMIDINES
10
 Nucleotides have three characteristic
components:
(1) a nitrogenous (nitrogen-containing) base,
(2) A pentose, and
(3) a phosphate
The molecule without the phosphate group is called a
nucleoside.
 The nitrogenous bases are derivatives of two parent
compounds, pyrimidine and purine.
 The bases and pentoses of the common nucleotides are
heterocyclic compounds. 11
 The base of a nucleotide is joined covalently (at N-1 of
pyrimidines and N-9 of purines) in an N—glycosyl bond to the
1 carbon of the pentose, and the phosphate is esterified to the
5 carbon.
 The N--glycosyl bond is formed by removal of the elements of
water (a hydroxyl group from the pentose and hydrogen from
the base), as in O-glycosidic bond formation.
 Both DNA and RNA contain two major purine bases, adenine
(A) and guanine (G), and two major pyrimidines.
 In both DNA and RNA one of the pyrimidines is cytosine (C),
but the second major pyrimidine is not the same in both:
it is thymine (T) in DNA and uracil (U) in RNA.
 Only rarely does thymine occur in RNA or uracil in DNA.
12
pyrimidine purine
OR
Ribose
or
2-deoxyribose
N-b-glycosyl
bond
Structure of nucleotides
13
 Nucleic acids have two kinds of pentoses. The recurring
deoxyribonucleotide units of DNA contain 2- deoxy-D-
ribose, and the ribonucleotide units of RNA contain D-
ribose.
 In nucleotides, both types of pentoses are in their -furanose
(closed five-membered ring) form. As Figure 8–3 shows,
the pentose ring is not planar but occurs in one of a
variety of conformations generally described as “puckered.”
14
15
Nucleotide Synthesis
and Degradation
16
Nucleotide Biosynthesis
 The body requirements of nitrogenous bases are
provided by the de novo synthesis
 from low molecular weight precursors and by the
salvage pathway that recycles bases and nucleosides
into nucleotides.
 Thus, dietary requirement of nitrogenous bases is not
essential.
 In some tissues, the salvage pathways are a major
source of nucleotides for synthesis of DNA, RNA and
coenzyme
 The major control on rate of synthesis and
bioavailability of nitrogenous bases, nucleosides and
nucleotides is the body needs - controlled by cell cycle
effectors and allosteric regulation of the
products.
There are two basic mechanisms to
generate purines and pyrimidines
2. SALVAGE PATHWAYS
(the reutilization of bases from dietary
or catabolic sources)
1. DE NOVO BIOSYNTHETIC PATHWAYS
(building the bases from simple building
blocks)
18
PURINE BIOSYNTHESIS [DE NOVO ]
Isotopic labeling experiments defined the precursors.
19
 Characteristics of de novo synthesis of
purine nucleotides
1. in cytosol
2. form IMP first, then synthesize AMP
and GMP from IMP.
3. formation of purines is
based on the ribosyl
group of 5’-phosphoribose
20
The de novo pathway
 the major pathway for purine nucleotides
biosynthesis
 Site of synthesis: It takes place in liver and a
number of other tissues.
 Although all body tissues are capable of de novo
synthesis including brain and immune cells,
 The very high expenses of the process makes
salvaging bases and nucleosides - synthesized by the
liver and secreted into the blood - an easy
alternative.
 This is particularly important for the brain, resting
(non-proliferating) and HIV-infected T lymphocytes
PURINE BIOSYNTHESIS
IN THE BEGINNING THERE WAS PRPP
The purine ring is built upon ribose using PRPP
ATP AMP
Ribose 5-phosphate
PRPP Synthetase
Or
Ribose phosphate pyrophosphate kinase
The use of ribose links the pentose phosphate pathway to nucleotide
metabolism.
22
PURINE BIOSYNTHESIS ,THE FIRST COMMITTED
STEP
It is always a good idea to know the first committed step of any pathway.
Glutamine-PRPP amidotransferase
1
23
amidotransferase #1
PURINE BIOSYNTHESIS
ADDITION OF GLYCINE
24
PURINE BIOSYNTHESIS
FORMYLATION #1
25
PURINE BIOSYNTHESIS
AMIDOTRANSFERASE #2
26
PURINE BIOSYNTHESIS
IMIDAZOLE RING CLOSURE
27
Purine Biosynthesis
carboxylation
Carbon is the wrong position based on isotope labeling exp.
28
PURINE BIOSYNTHESIS
MOVE THE CARBON
Now the carbon is placed correctly.
29
PURINE BIOSYNTHESIS
ASPARTATE ADDITION
But all we need is the nitrogen.
30
PURINE BIOSYNTHESIS
FUMARATE SUBTRACTION
One more carbon.
31
PURINE BIOSYNTHESIS
FORMYLATION #2
32
INHIBITORS OF NUCLEOTIDE SYNTHESIS
 Many of these agents have been labeled =
“antimetabolites” because of their structural
similarities to naturally occurring metabolites
 . These include the antifolates (e.g., methotrexate),
pyrimidines like 5-Fluorouracil (5-FU), and
purines like 6- mercaptopurine and 6-thioguanine
 Other drugs like hydroxyurea are not
“antimetabolites
33
Folate and DNA synthesis
 The essentiality of folate for DNA (purine and
pyrimidine) synthesis, cell division and growth
 Dihydrofolate reductase activates folate - into
the tetrahydrofolate (FH4) that is active in the
transfer of one carbon moieties anabolic reaction.
 Therefore, dividing cells are most sensitive to
dihydrofolate reductase competitive
inhibitors, e.g., methotrexate, aminopterin, and
trimethoprim – all are analog of folic acid - that are
utilized as cancer chemotherapeutic and
immunosuppressant for organ transplantation
patients
PURINE BIOSYNTHESIS FINALLY PURINEA
But who needs inosinate?
35
36
Note: ATP is used
for GMP synthesis.
Note: GTP is used
for AMP
synthesis.
6-MERCAPTOPURINE (6-MP)
 6-MP is a hypoxanthine derivative antimetabolite
whose metabolites inhibit endogenous de novo
purine synthesis at several steps .
 One of the most important metabolic activation is
the formation of the nucleotide 6-MP ribose-5’-
phosphate also known as thioinosine
monophosphate (TIMP)
 It formed in the presence PRPP and the enzyme
hypoxanthine –guanin phosphoribosyltransferase
(HGPRT)
 TIMP causes a pseudo feedback inhibition
mimicking the effect of AMP or GMP.
 6-MP is not taken up to any great extent into nucleic
acid itself
6-THIOGUANINE (6-TG)
 Although structurally very similar to 6-MP
 6-TG has a very different mechanism of action
from 6-MP
 6-TG is metabolized to 6-TG-deoxyribonucleotide
triphosphate (6-TdGTP), which can then be
incorporated into DNA in place of dGTP
38
summery of PURINE NUCLEOTIDE SYNTHESIS
 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 step 2, PPi is hydrolyzed to 2Pi (irreversible,
“committing” step)
39
Conversion of nucleoside monophosphates to nucleoside diphosphates and
triphosphates
Purine nucleoside diphosphates and triphosphates:
- to be incorporated into DNA and RNA, nucleoside monophosphates
(NMP’s) must be converted into nucleoside triphosphates (NTP’s)
- nucleoside monophosphate kinases (adenylate & guanylate
kinases)
- nucleoside diphosphate kinase
40
Regulation
 There are 4 key regulated reactions; namely, PRPP
synthetase, amidotransferase, adenylosuccinate
synthase, and IMP dehydrogenase.
 PRPP synthetase is simultaneously allosterically
inhibited by GDP at one site, and, by ADP at
another allosteric site.
 Although is key regulatory, PRPP synthetase is not
the committed step of purinebiosynthesis
 because PRPP is also used in de novo pyrimidine
synthesis and for both the purine and pyrimidine
salvage pathways.
 Regulatory mechanisms in the biosynthesis of adenine
and guanine
04/02/2025 42
COT’D
 GTP is involved in AMP synthesis and ATP is
involved in GMP synthesis (reciprocal control of
production)
 PRPP is a biosynthetically “central” molecule
(why?)
 Rate of AMP production increases with
increasing concentrations of GTP; rate of GMP
production increases with increasing
concentrations of ATP 43
2. SALVAGE SYNTHESIS OF PURINE
NUCLEOTIDES
 The salvage pathway; the minor pathway for purine
nucleotides:
 Salvage pathway recycles purine bases and nucleosides into
nucleotide
 s
 Material:
PRPP, purine (conjunction)
nucleosides (phosphorylation)
 Location:
brain and bone marrow
N.B; No need of synthesis of nitrogenous basis
What is the stimulus for Salvag pathway?
44
COT’D
 Purine bases created by degradation of RNA or DNA and
intermediate of purine synthesis were costly for the cell to
make, so there are pathways to recover these bases in the
form of nucleotides
 This is particularly important for the brain, resting (non-
proliferating) and HIV-infected T lymphocyte
 Two phosphoribosyl transferases are involved:
 APRT (adenine phosphoribosyl transferase) for adenine
 HGPRT (hypoxanthine guanine phosphoribosyl
transferase) for guanine or hypoxanthine
45
Two mechanisms
1. Single Step Direct Conversion ;
by phosphoribosylation activated by adenosine
phosphoribosyltransferase (APRT) giving rise to AMP
and by hypoxanthine-guanine phosphoribosyltransferase
(HGPRT)
2. Two Steps Pathway reverses the reaction of the purine
nucleotide phosphorylases to salvage guanine and
hypoxanthine from their catabolic fate
adenine+ PRPP AMP + PPi
APRT
hypoxanthine+PRPP IMP + PPi
HGPRT
guanine+ PRPP
HGPRT
GMP + PPi
adenosine
Adenylate kinase
ATP ADP
AMP
APRT: adenine phosphoribosyltransferase
HGPRT: hypoxanthine-guanine
phosphoribosyltransferase
47
COMMON PROBLEM OF SALVAGE
LESCH-NYHAN SYNDROME
 This syndrome is an recessive X-linked disorder
associated with a virtually complete deficiency of
HPRT.
 Enzyme : hypoxanthine-guanine posphoribosyl
transferase, HPRT
48
HPRT ENZYME
 Deficiency in HPRT enzyme activity results in
overproduction of hypoxanthine via the de novo pathway
and accumulation of uric acid in urine.
 The combination of decreased purine reutilization and
increased purine synthesis results in the production of large
amounts of uric acid,
 making the Lesch-Nyhan syndrome a severe, heritable form
of gout.
 characteristic neurologic features of the disorder include self-
mutilation and involuntary movements.
 Blood of Lesch-Nyhan patient has a shortage of HPRT
enzymes
 HPRT enzyme activity measured in erythrocytes is near
zero (common method)
49
three main problems that elucidate the importance of salvag
pathway particularly for the brain:
 The first is overproduction hyperuricemia
 The second problem is self-mutilation at age 2-3.
 Finally, mental retardation and severe muscle weakness.
 Study performed on brains from Lesch-Nyhan patient
showed 60%-90% decrease in dopamine and its metabolite
within the putamen, caudate, nucleus accumbens and
globus pallidus
 A decrease in enzymes involved with dopamine synthesis
was also found in brains of these patients
DEOXYRIBONUCLEOTIDE BIOSYNTHESIS
NDP
dNDP
Ribonucleotid
e reductase
dNDP + ATP
kinase dNTP + ADP 51
Biosynthetic pathways are only for ribonucleotide
production
Deoxyribonucleotides are synthesized from
corresponding ribonucleotides
Deoxyribonucleoside diphosphates
 Ribonucleoside diphosphates (ADP, GDP, CDP and
UDP) reduction at C2.-OH of the ribose gives rise to
their corresponding 2'-deoxyribonucleoside
diphosphates.
 This is activated by the one enzyme ribonucleotide
reductase complex in the actively DNA synthesizing
cells.
 The enzyme requires reduced thioredoxin that is
renewed from the protein thioredoxin by the NADPH-
thioredoxin reductase.
 The enzyme is inhibitable by the anticancer hydroxyurea.
Nucleotide  you ii.pptxsheikh abdul wadood haneef
HYDROXYUREA (HU)
 it is not a true antimetabolite, since
antimetabolites areanalogs of naturally occurring
metabolites in nucleic acid synthesis and urea is
actually an end product of metabolism
 HU has a unique affect on ribonucleotide
reductase a critical enzymatic step in the
synthesis of DNA by which the two major
pyrimidine (TDP, CDP) and two major purine
(ADP, GDP) ribonucleotide diphosphates are
converted to their corresponding
deoxyribonucleotide diphosphates (dTDP, dCDP,
dADP, dGDP). 54
METABOLISM OF PYRIMIDINE NUCLEOTIDES
 Biosynthesis of pyrimidine nucleotides
de novo synthesis
salvage pathway
55
1.DE NOVO SYNTHESIS OF
PYRIMIDINE NUCLEOTIDES
Aspartate
Glutamine
CO2
1
5
4
3
6
2
56
Characteristics of de novo synthesis of pyrimidine
nucleotides
1. mostly in cytosol
2. form UMP first, then synthesize other pyrimidine
nucleotides from UMP.
3. Unlike the synthesis of the purine ring, in which the ring is
constructed on a preexisting ribose 5-phosphate, the
pyrimidine ring is synthesized before being attached to ribose
5-phosphate, which is donated byPRPP.
4. in the synthesis of UMP, pyrimidine ring is formed first ,
then combined withPRPP.
57
PROCESS OF DE NOVO SYNTHESIS OF UMP
 1. formation of Carbamoyl phsphate (CP)
CO2 + glutamine + H2O + 2ATP
C
O
H2N O ~ PO3
2-
+ 2ADP + Pi
Carbamoylphosphat
e
Carbamoyl phosphate
synthaseII (CPSII)
58
CPS-I CPS-II
肝细胞线粒体中
氨
N-乙酰谷氨酸
胞液(所有细胞)
谷氨酰胺
无
分布
氮源
变构激活剂
功能 尿素合成 嘧啶 合成
CPS-I CPS-II
肝细胞线粒体中
氨
N-乙酰谷氨酸
胞液(所有细胞)
谷氨酰胺
无
分布
氮源
变构激活剂
功能 尿素合成 嘧啶 合成
氨基甲酰磷酸合成酶 I、II 的区别
The different between Carbamoyl phosphate
synthaseI and II
Location
Source of
nitrogen
Activator
Function
NH3 Glutamine
None
N-acetylglutamate
Mitochondria of
liver cells
cytosol of all
cells
Formation of urea Formation of
pyrimidine 59
C
O
H2N O ~ PO3
2-
carbamoyl phosphate
+
Aspartate
Carbamoyl aspartate
PRPP
Orotate
UMP
2. Formation of UMP
60
ATP ADP
UMPK
UDP
NDK
ATP ADP
UTP
CTP
synthase
Gln
ATP
Glu
ADP
3. Synthesis of CTP, dTMP or TMP
dCMP
dUDP
dUMP
dTMP
TMP synthase
61
62
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 intra-mitochondrial
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 63
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
64
The anticancer 6-azauridine l as
alternative substrates inhibit
orotidylate decarboxylase.
Nucleotide  you ii.pptxsheikh abdul wadood haneef
REGULATION OF DE NOVO SYNTHESIS
OF PYRIMIDINE NUCLEOTIDES
ATP + CO2+ glutamine
Carbamoyl phosphate
UMP
Carbamoyl aspartate
UTP CTP
aspartate
ATP + 5-phosphate ribose
PRPP
Pyrimidine nucleotides
-
+
-
-
-
Purine nucleotides
-
+
1.Activated by
substrates
2.Inhibited by products
67
COT’D
 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
68
SALVAGE PATHWAY OF PYRIMIDINE NUCLEOTIDES
Uracil + PRPP UMP + PPi
Uracil phosphate
ribosyltransferase
Uridine + ATP
Uridine kinase
UMP +ADP
Uracil + 1-phosphoribose Uridine + Pi
Uridine
phosphorylase
69
Degradation of Nucleotides
Digestion:
 Plant and animal tissues taken in the diet are
formed of cells with their nuclei containing the
nucleoprotein.
 The very small amounts of nucleic acids component
of the dietary nucleoproteins is released from the
protein component by sequential digestion of the
protein by pepsin and trypsin.
 However, diet differs massive in its nucleic acid
content with the highest in the liver to the lowest
(almost zero nucleic acid content) in the milk and
dairy products and eggs.
 Tea, coffee and coca contain the methyl
purines; e.g., caffeine, theobromine and
theophylline.
 The nucleic acid part is hydrolyzed by a number
of enzymes of the pancreatic juice [the nucleases:
deoxyribonuclease (DNases) and ribonucleases
(RNases)] and those of the intestinal juice and
mucosa (the polynucleotidases, phosphatases,
nucleotidases and nucleosidases).
 The hydrolysis products include: nitrogenous
bases (purines and pyrimidines), pentoses (ribose
or deoxyribose) and inorganic phosphate.
72
DIGESTION AND ABSORPTION OF NUCLEOTIDE
Nucleoprotein
Protein Nucleic acid
Nucleases
Nucleotide
Nucleotidase
Phosphate Nucleoside
Nucleosidas
Base Ribose
Absorptio
n Blood
73
Absorption:
 Ingested purines and pyrimidines are poorly
absorbed from the small intestine and fate to be
catabolized into uric acid in the liver and intestinal
mucosa.
 Nucleosides are fairly absorbed from the small
intestine again to be catabolized or salvaged in the
mucosa and liver.
 However, the parenterally administered (injected)
nucleosides/nucleotides are readily incorporated into
DNA.
DEGRADATION OF PURINE NUCLEOTIDES
 Site: Purine catabolism occurs in liver, intestine, spleen, kidney,
pancreas, skeletal and heart muscles.
 In human and higher primates as chimpanzee, the ultimate end
product of purine catabolism is uric acid( but it might not stop
there)
 The starting metabolites are either adenosine or guanosine.
 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)
 AMP is deaminated by AMP deaminase to form IMP.
 Adenine is deaminated to inosine by the action of adenosine
deaminase.
 NOTE: MOST INGESTED NUCLEIC ACIDS ARE DEGRADED AND EXCRETED.
75
76
INTRACELLULAR PURINE
CATABOLISM
 Xanthine is the point of convergence for the metabolism of
the purine bases
 Xanthine  Uric acid
 Xanthine oxidase catalyzes two reactions
 dual specific molybdenum-requiring xanthine
dehydrogenase (oxidase)
 Purine ribonucleotide degradation pathway is same for
purine deoxyribonucleotides
77
URIC ACID EXCRETION
 Humans and highr primats – excreted into urine as insoluble
crystals
 In lower primates and other mammals, the copper-dependent
uricase enzyme converts uric acid to allantoin by oxidative
decarboxylation.
 Birds, terrestrial reptiles, some insects – excrete insoluble
crystals in paste form
Excess amino N and nucleotide converted to uric acid
(conserves water)
uricotelic , ureotelic mammals and ammonotellic,
Uric Acid  Allantoin  Allantoic Acid  Urea  Ammonia
78
DISEASES ASSOCIATED WITH DEFECTS IN
PURINE METABOLISM
 HYPERURICEMIA
 GOUT
 LESCH-NYHAN SYNDROME
 KIDNEY STONES
 SEVERE COMBINED IMMUNODEFECIENCY
(SCID) 79
HYPERURICEMIA
Characterized by plasma urate (uric acid) level
greater than 7.0 mg/dL
Normal plasma levels
Females = 2.4 - 6 mg/dL
Males = 3.4 - 7 mg/dL
80
HYPERURICEMIA
• Primary Hyperuricemia: an innate defect in
purine metabolism and/or uric acid excretion
urate saturation arising in the absence of coexisting
diseases or drugs that alter uric acid production or
excretion
• Secondary Hyperuricemia: excessive urate
production or diminished renal clearance that is the
result of another disease, drug, dietary product, or
toxin.
81
PROGRESSION OF HYPERURICEMIA TO GOUT
At a serum urate concentration greater than 6.8
mg/dL, urate crystals may start to deposit in the
joints.
serum urate concentration is elevated,
There are three major crystal deposition-related
disorders associated with hyperuricemia:
Gout
urolithiasis; and
urate nephropathy.
82
GOUT
Gout is caused by precipitation
of sodium urate crystals in the
joints resulting in inflammation
and pain.
83
CLINICAL SYNDROMES
The three classic stages of Gout
1. Acute gouty arthritis - If sufficient urate deposits develop
around joints, and if the local environment or some trauma
triggers the release of crystals into the joint space, an
inflammatory response occurs. These flares can be self-
resolving but are likely to recur.
2. Intercritical (or interval) gout - These are the intervals
between attacks. During these periods, crystals may still be
present at a low level in the synovial tissue and fluid,
resulting in future attacks.
3. Chronic recurrent and tophaceous gout - Tophaceous gout is
characterized by collections of solid urate in connective tissues
(which may occasionally be calcified)
84
GOUT - CAUSES
 Decreased/partial HGPRT activity
1) Deficiency of HGPRT = accumulation of PRPP = increased
purine synthesis = increased uric acid levels
2) Deficiency of HGPRT = decreased IMP and GMP =
decreased inhibitors for purine synthesis
 Under excretion of uric acid
 Diet rich in
 Increased purine degradation
 Increased PRPP Synthetase activity 85
 Colchicine –reduces inflammation
 Uricosuric agents – increase renal excretion of uric acid
(probenecid)
 Allopurinol – inhibits uric acid synthesis
 Low purine diet - Foods that are high in purine include:
 Red meat and organ meats (eg. liver)
 Yeasts and yeast extracts (eg. beer and alcoholic
beverages)
 Asparagus, spinach, beans, peas, lentils, oatmeal,
cauliflower and mushrooms
 Avoid caffeine and alcohol
 Keep hydrated
GOUT - Treatment
86
ALLOPURINOL IS A
XANTHINE OXIDASE
INHIBITOR
87
SEVERE COMBINED IMMUNODEFICIENCY
(SCID)
mutations in different genes whose products are crucial for
the development and function of both T and B cells
In some cases, the molecular defect prevents only T cell
function, while B cells are normal
It mainly due to Adenosine deaminase( ADA deficiency.)
 SELECTIVELY KILLS LYMPHOCYTES
 BOTH B- AND T-CELLS
 MEDIATE MUCH OF IMMUNE RESPONSE
88
ADA DEFICIENCY
 caused by mutations in the ADA gene
 ADA is an ubiquitous enzyme found in all cells, including red and WBC,
and in the serum.
 It catalyzes the deamination of adenosine and deoxyadenosine to
inosine and deoxyinosine, which are converted to waste products and
excreted
 In the absence of functional ADA, there is an intracellular accumulation of
adenosine and deoxyadenosine.
 Adenosine and deoxyadenosine are also converted to 5'-
triphosphates (dATP), which inhibit ribonucleotide reductase and
prevent de novo synthesis of nucleotides and deoxynucleotides.
 There is a decrease in DNA synthesis in replicating cells, because of
the depletion of deoxynucleotides
89
Disorders of Purine Metabolism:
Disorder Defect Comments
Gout PRPP synthase/ Hyperuricemia
HGPRT
Lesch Nyhan lack of HGPRT Hyperuricemia
syndrome
SCID ADA High levels of dAMP
von Gierke’s disease glucose -6-PTPase Hyperuricemia
90
nucleotide
nucleosides
phosphoribose pyrimidine
DEGRADATION OF PYRIMIDINE NUCLEOTIDES
Nucleotidase
Nucleoside phosphorylase
CMP and UMP degraded to bases similarly to purines
Dephosphorylation
Deamination
Glycosidic bond cleavage
91
Unlike the purine rings, which are not cleaved in human cells, the
pyrimidine ring can be opened and degraded to highly soluble
structures, such as β-alanine, and β-aminoisobutyrate, which can
serve as precursors acetyl CoA and succinyl CoA, respectively.
1. The nucleotides are initially converted to
nucleosides by nonspecific phosphatases that
remove the phosphate groups.
2. Cytidine is deaminated to uridine and
deoxycytidine is deaminated to deoxyuridine.
3. The sugars are removed from the nucleosides to
form the bases uracil and thymine.
4. These bases are then degraded to two β-amino
acids, uracil to β-alanine and thymine to β-
aminoisobutyrate.
92
CONT……
a. The same enzymes catalyze these parallel
reactions on either substrate.
b. β-Aminoisobutyrate is derived exclusively from
DNA, so the amount excreted in urine is a
measure of DNA turnover.
c. β-Alanine and β-aminoisobutyrate are converted
into malonyl-CoA and methylmalonyl-CoA for
further metabolism. 93
Cytosine
NH3
Uracil
dihydrouracil
H2O
CO2 + NH3
β-alanine
Thymine
β-ureidoisobutyrate
H2O
Acetyl CoA
TCA cycle
liver
Urea
+ +
β-aminoisobutyrate
Succinyl CoA
TCA Glucose
Excreted
in urine
94
Diseases due to defective pyrimidine metabolism
 Most of the defects in the catabolism of
pyrimidines do not cause clinical diseases because
of the water solubility of their metabolic
intermediate.
 In cases of increased purine breakdown and
hyperuricemia, there is also increased pyrimidine
breakdown.
 Orotic acidosis and orotic aciduria types I and II
are very rare genetic condition accompanied with
poor growth and hypochromic megaloplastic
anemia with defective maturation of red cells and
leukopenia.
 They are treatable by supplementing cytidine or
uridine that replenishes the deficiency by being
converted into UMP.

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Nucleotide you ii.pptxsheikh abdul wadood haneef

  • 2. OUTLINE: 1. Nucleotide bases and their metabolism 2. Diseases associated with nucleotide metabolism defect 3. Drug inhibitors of nucleotide synthesis 2
  • 3. SOME TERMINOLOGY  Genotype: The genetic makeup of an organism  Phenotype: the physical expressed traits of an organism  Nucleic acid: Biological molecules(RNA and DNA) that allow organisms to reproduce; 3
  • 4. MORE TERMINOLOGY  The genome is an organism’s complete set of DNA.  a bacteria contains about 600,000 DNA base pairs  human and mouse genomes have some 3 billion.  human genome has 23 distinct chromosomes.  Each chromosome contains many genes.  Gene  basic physical and functional units of heredity.  specific sequences of DNA bases that encode instructions on how to make proteins. . zs3x 4
  • 5. NUCLEOTIDE METABOLISM I. Nucleotides -Why have them? II. Purine Biosynthesis III. Pyrimidine Biosynthesis IV. Nucleotide Catabolism 5
  • 6. Nitrogen Bases  There are two kinds of nitrogen-containing bases - purines and pyrimidines.  Purines consist of a six-membered and a five- membered nitrogen-containing ring, fused together.  Pyridmidines have only a six-membered nitrogen-containing ring.
  • 7. Purines  Adenine = 6-amino purine  Guanine = 2-amino-6-oxy purine  Hypoxanthine = 6-oxy purine  Xanthine = 2,6-dioxy purine Pyrimidines  Uracil = 2,4-dioxy pyrimidine  Thymine = 2,4-dioxy-5-methyl pyrimidine  Cytosine = 2-oxy-4-amino pyrimidine  Orotic acid = 2,4-dioxy-6-carboxy pyrimidine
  • 8. NUCLEOTIDES WHY HAVE THEM? 8 1. nucleotides serve numerous functions in different reaction pathways For example, nucleotides are the activated precursors of DNA and RNA. 2. form the structural moieties of many coenzymes (examples include NADH, FAD, and coenzyme A). 3. are critical elements in energy metabolism (ATP, GTP). 4. Nucleotide derivatives are frequently activated intermediates in many biosyntheses. For example, UDP-glucose and CDP- diacylglycerol are precursors of glycogen and phosphoglycerides, respectively. 5. nucleotides act as second messengers in intracellular signaling (e.g., cAMP, cGMP). 6. Finally, nucleotides and nucleosides act as metabolic allosteric regulators. Think about all of the enzymes that have been studied that are regulated by levels of ATP, ADP, and AMP.
  • 9. STRUCTURES OF NUCLEOTIDES  A nucleoside is formed from the linkage of a sugar with a nitrogen-containing base. 1. The bases that make up the physiologically relevant nucleosides all have ring structures. a. The purines adenine, guanine, b. The pyrimidines cytosine, thymine, and uracil have six- membered ring structures. 2. Ribose and 2-deoxyribose are the main sugars found in nucleosides and nucleotides. 9
  • 11.  Nucleotides have three characteristic components: (1) a nitrogenous (nitrogen-containing) base, (2) A pentose, and (3) a phosphate The molecule without the phosphate group is called a nucleoside.  The nitrogenous bases are derivatives of two parent compounds, pyrimidine and purine.  The bases and pentoses of the common nucleotides are heterocyclic compounds. 11
  • 12.  The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N—glycosyl bond to the 1 carbon of the pentose, and the phosphate is esterified to the 5 carbon.  The N--glycosyl bond is formed by removal of the elements of water (a hydroxyl group from the pentose and hydrogen from the base), as in O-glycosidic bond formation.  Both DNA and RNA contain two major purine bases, adenine (A) and guanine (G), and two major pyrimidines.  In both DNA and RNA one of the pyrimidines is cytosine (C), but the second major pyrimidine is not the same in both: it is thymine (T) in DNA and uracil (U) in RNA.  Only rarely does thymine occur in RNA or uracil in DNA. 12
  • 14.  Nucleic acids have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain 2- deoxy-D- ribose, and the ribonucleotide units of RNA contain D- ribose.  In nucleotides, both types of pentoses are in their -furanose (closed five-membered ring) form. As Figure 8–3 shows, the pentose ring is not planar but occurs in one of a variety of conformations generally described as “puckered.” 14
  • 15. 15
  • 17. Nucleotide Biosynthesis  The body requirements of nitrogenous bases are provided by the de novo synthesis  from low molecular weight precursors and by the salvage pathway that recycles bases and nucleosides into nucleotides.  Thus, dietary requirement of nitrogenous bases is not essential.  In some tissues, the salvage pathways are a major source of nucleotides for synthesis of DNA, RNA and coenzyme  The major control on rate of synthesis and bioavailability of nitrogenous bases, nucleosides and nucleotides is the body needs - controlled by cell cycle effectors and allosteric regulation of the products.
  • 18. There are two basic mechanisms to generate purines and pyrimidines 2. SALVAGE PATHWAYS (the reutilization of bases from dietary or catabolic sources) 1. DE NOVO BIOSYNTHETIC PATHWAYS (building the bases from simple building blocks) 18
  • 19. PURINE BIOSYNTHESIS [DE NOVO ] Isotopic labeling experiments defined the precursors. 19
  • 20.  Characteristics of de novo synthesis of purine nucleotides 1. in cytosol 2. form IMP first, then synthesize AMP and GMP from IMP. 3. formation of purines is based on the ribosyl group of 5’-phosphoribose 20
  • 21. The de novo pathway  the major pathway for purine nucleotides biosynthesis  Site of synthesis: It takes place in liver and a number of other tissues.  Although all body tissues are capable of de novo synthesis including brain and immune cells,  The very high expenses of the process makes salvaging bases and nucleosides - synthesized by the liver and secreted into the blood - an easy alternative.  This is particularly important for the brain, resting (non-proliferating) and HIV-infected T lymphocytes
  • 22. PURINE BIOSYNTHESIS IN THE BEGINNING THERE WAS PRPP The purine ring is built upon ribose using PRPP ATP AMP Ribose 5-phosphate PRPP Synthetase Or Ribose phosphate pyrophosphate kinase The use of ribose links the pentose phosphate pathway to nucleotide metabolism. 22
  • 23. PURINE BIOSYNTHESIS ,THE FIRST COMMITTED STEP It is always a good idea to know the first committed step of any pathway. Glutamine-PRPP amidotransferase 1 23 amidotransferase #1
  • 28. Purine Biosynthesis carboxylation Carbon is the wrong position based on isotope labeling exp. 28
  • 29. PURINE BIOSYNTHESIS MOVE THE CARBON Now the carbon is placed correctly. 29
  • 30. PURINE BIOSYNTHESIS ASPARTATE ADDITION But all we need is the nitrogen. 30
  • 33. INHIBITORS OF NUCLEOTIDE SYNTHESIS  Many of these agents have been labeled = “antimetabolites” because of their structural similarities to naturally occurring metabolites  . These include the antifolates (e.g., methotrexate), pyrimidines like 5-Fluorouracil (5-FU), and purines like 6- mercaptopurine and 6-thioguanine  Other drugs like hydroxyurea are not “antimetabolites 33
  • 34. Folate and DNA synthesis  The essentiality of folate for DNA (purine and pyrimidine) synthesis, cell division and growth  Dihydrofolate reductase activates folate - into the tetrahydrofolate (FH4) that is active in the transfer of one carbon moieties anabolic reaction.  Therefore, dividing cells are most sensitive to dihydrofolate reductase competitive inhibitors, e.g., methotrexate, aminopterin, and trimethoprim – all are analog of folic acid - that are utilized as cancer chemotherapeutic and immunosuppressant for organ transplantation patients
  • 35. PURINE BIOSYNTHESIS FINALLY PURINEA But who needs inosinate? 35
  • 36. 36 Note: ATP is used for GMP synthesis. Note: GTP is used for AMP synthesis.
  • 37. 6-MERCAPTOPURINE (6-MP)  6-MP is a hypoxanthine derivative antimetabolite whose metabolites inhibit endogenous de novo purine synthesis at several steps .  One of the most important metabolic activation is the formation of the nucleotide 6-MP ribose-5’- phosphate also known as thioinosine monophosphate (TIMP)  It formed in the presence PRPP and the enzyme hypoxanthine –guanin phosphoribosyltransferase (HGPRT)  TIMP causes a pseudo feedback inhibition mimicking the effect of AMP or GMP.  6-MP is not taken up to any great extent into nucleic acid itself
  • 38. 6-THIOGUANINE (6-TG)  Although structurally very similar to 6-MP  6-TG has a very different mechanism of action from 6-MP  6-TG is metabolized to 6-TG-deoxyribonucleotide triphosphate (6-TdGTP), which can then be incorporated into DNA in place of dGTP 38
  • 39. summery of PURINE NUCLEOTIDE SYNTHESIS  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 step 2, PPi is hydrolyzed to 2Pi (irreversible, “committing” step) 39
  • 40. Conversion of nucleoside monophosphates to nucleoside diphosphates and triphosphates Purine nucleoside diphosphates and triphosphates: - to be incorporated into DNA and RNA, nucleoside monophosphates (NMP’s) must be converted into nucleoside triphosphates (NTP’s) - nucleoside monophosphate kinases (adenylate & guanylate kinases) - nucleoside diphosphate kinase 40
  • 41. Regulation  There are 4 key regulated reactions; namely, PRPP synthetase, amidotransferase, adenylosuccinate synthase, and IMP dehydrogenase.  PRPP synthetase is simultaneously allosterically inhibited by GDP at one site, and, by ADP at another allosteric site.  Although is key regulatory, PRPP synthetase is not the committed step of purinebiosynthesis  because PRPP is also used in de novo pyrimidine synthesis and for both the purine and pyrimidine salvage pathways.
  • 42.  Regulatory mechanisms in the biosynthesis of adenine and guanine 04/02/2025 42
  • 43. COT’D  GTP is involved in AMP synthesis and ATP is involved in GMP synthesis (reciprocal control of production)  PRPP is a biosynthetically “central” molecule (why?)  Rate of AMP production increases with increasing concentrations of GTP; rate of GMP production increases with increasing concentrations of ATP 43
  • 44. 2. SALVAGE SYNTHESIS OF PURINE NUCLEOTIDES  The salvage pathway; the minor pathway for purine nucleotides:  Salvage pathway recycles purine bases and nucleosides into nucleotide  s  Material: PRPP, purine (conjunction) nucleosides (phosphorylation)  Location: brain and bone marrow N.B; No need of synthesis of nitrogenous basis What is the stimulus for Salvag pathway? 44
  • 45. COT’D  Purine bases created by degradation of RNA or DNA and intermediate of purine synthesis were costly for the cell to make, so there are pathways to recover these bases in the form of nucleotides  This is particularly important for the brain, resting (non- proliferating) and HIV-infected T lymphocyte  Two phosphoribosyl transferases are involved:  APRT (adenine phosphoribosyl transferase) for adenine  HGPRT (hypoxanthine guanine phosphoribosyl transferase) for guanine or hypoxanthine 45
  • 46. Two mechanisms 1. Single Step Direct Conversion ; by phosphoribosylation activated by adenosine phosphoribosyltransferase (APRT) giving rise to AMP and by hypoxanthine-guanine phosphoribosyltransferase (HGPRT) 2. Two Steps Pathway reverses the reaction of the purine nucleotide phosphorylases to salvage guanine and hypoxanthine from their catabolic fate
  • 47. adenine+ PRPP AMP + PPi APRT hypoxanthine+PRPP IMP + PPi HGPRT guanine+ PRPP HGPRT GMP + PPi adenosine Adenylate kinase ATP ADP AMP APRT: adenine phosphoribosyltransferase HGPRT: hypoxanthine-guanine phosphoribosyltransferase 47
  • 48. COMMON PROBLEM OF SALVAGE LESCH-NYHAN SYNDROME  This syndrome is an recessive X-linked disorder associated with a virtually complete deficiency of HPRT.  Enzyme : hypoxanthine-guanine posphoribosyl transferase, HPRT 48
  • 49. HPRT ENZYME  Deficiency in HPRT enzyme activity results in overproduction of hypoxanthine via the de novo pathway and accumulation of uric acid in urine.  The combination of decreased purine reutilization and increased purine synthesis results in the production of large amounts of uric acid,  making the Lesch-Nyhan syndrome a severe, heritable form of gout.  characteristic neurologic features of the disorder include self- mutilation and involuntary movements.  Blood of Lesch-Nyhan patient has a shortage of HPRT enzymes  HPRT enzyme activity measured in erythrocytes is near zero (common method) 49
  • 50. three main problems that elucidate the importance of salvag pathway particularly for the brain:  The first is overproduction hyperuricemia  The second problem is self-mutilation at age 2-3.  Finally, mental retardation and severe muscle weakness.  Study performed on brains from Lesch-Nyhan patient showed 60%-90% decrease in dopamine and its metabolite within the putamen, caudate, nucleus accumbens and globus pallidus  A decrease in enzymes involved with dopamine synthesis was also found in brains of these patients
  • 51. DEOXYRIBONUCLEOTIDE BIOSYNTHESIS NDP dNDP Ribonucleotid e reductase dNDP + ATP kinase dNTP + ADP 51 Biosynthetic pathways are only for ribonucleotide production Deoxyribonucleotides are synthesized from corresponding ribonucleotides
  • 52. Deoxyribonucleoside diphosphates  Ribonucleoside diphosphates (ADP, GDP, CDP and UDP) reduction at C2.-OH of the ribose gives rise to their corresponding 2'-deoxyribonucleoside diphosphates.  This is activated by the one enzyme ribonucleotide reductase complex in the actively DNA synthesizing cells.  The enzyme requires reduced thioredoxin that is renewed from the protein thioredoxin by the NADPH- thioredoxin reductase.  The enzyme is inhibitable by the anticancer hydroxyurea.
  • 54. HYDROXYUREA (HU)  it is not a true antimetabolite, since antimetabolites areanalogs of naturally occurring metabolites in nucleic acid synthesis and urea is actually an end product of metabolism  HU has a unique affect on ribonucleotide reductase a critical enzymatic step in the synthesis of DNA by which the two major pyrimidine (TDP, CDP) and two major purine (ADP, GDP) ribonucleotide diphosphates are converted to their corresponding deoxyribonucleotide diphosphates (dTDP, dCDP, dADP, dGDP). 54
  • 55. METABOLISM OF PYRIMIDINE NUCLEOTIDES  Biosynthesis of pyrimidine nucleotides de novo synthesis salvage pathway 55
  • 56. 1.DE NOVO SYNTHESIS OF PYRIMIDINE NUCLEOTIDES Aspartate Glutamine CO2 1 5 4 3 6 2 56
  • 57. Characteristics of de novo synthesis of pyrimidine nucleotides 1. mostly in cytosol 2. form UMP first, then synthesize other pyrimidine nucleotides from UMP. 3. Unlike the synthesis of the purine ring, in which the ring is constructed on a preexisting ribose 5-phosphate, the pyrimidine ring is synthesized before being attached to ribose 5-phosphate, which is donated byPRPP. 4. in the synthesis of UMP, pyrimidine ring is formed first , then combined withPRPP. 57
  • 58. PROCESS OF DE NOVO SYNTHESIS OF UMP  1. formation of Carbamoyl phsphate (CP) CO2 + glutamine + H2O + 2ATP C O H2N O ~ PO3 2- + 2ADP + Pi Carbamoylphosphat e Carbamoyl phosphate synthaseII (CPSII) 58
  • 59. CPS-I CPS-II 肝细胞线粒体中 氨 N-乙酰谷氨酸 胞液(所有细胞) 谷氨酰胺 无 分布 氮源 变构激活剂 功能 尿素合成 嘧啶 合成 CPS-I CPS-II 肝细胞线粒体中 氨 N-乙酰谷氨酸 胞液(所有细胞) 谷氨酰胺 无 分布 氮源 变构激活剂 功能 尿素合成 嘧啶 合成 氨基甲酰磷酸合成酶 I、II 的区别 The different between Carbamoyl phosphate synthaseI and II Location Source of nitrogen Activator Function NH3 Glutamine None N-acetylglutamate Mitochondria of liver cells cytosol of all cells Formation of urea Formation of pyrimidine 59
  • 60. C O H2N O ~ PO3 2- carbamoyl phosphate + Aspartate Carbamoyl aspartate PRPP Orotate UMP 2. Formation of UMP 60
  • 61. ATP ADP UMPK UDP NDK ATP ADP UTP CTP synthase Gln ATP Glu ADP 3. Synthesis of CTP, dTMP or TMP dCMP dUDP dUMP dTMP TMP synthase 61
  • 62. 62
  • 63. 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 intra-mitochondrial 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 63
  • 64. 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 64
  • 65. The anticancer 6-azauridine l as alternative substrates inhibit orotidylate decarboxylase.
  • 67. REGULATION OF DE NOVO SYNTHESIS OF PYRIMIDINE NUCLEOTIDES ATP + CO2+ glutamine Carbamoyl phosphate UMP Carbamoyl aspartate UTP CTP aspartate ATP + 5-phosphate ribose PRPP Pyrimidine nucleotides - + - - - Purine nucleotides - + 1.Activated by substrates 2.Inhibited by products 67
  • 68. COT’D  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 68
  • 69. SALVAGE PATHWAY OF PYRIMIDINE NUCLEOTIDES Uracil + PRPP UMP + PPi Uracil phosphate ribosyltransferase Uridine + ATP Uridine kinase UMP +ADP Uracil + 1-phosphoribose Uridine + Pi Uridine phosphorylase 69
  • 71. Digestion:  Plant and animal tissues taken in the diet are formed of cells with their nuclei containing the nucleoprotein.  The very small amounts of nucleic acids component of the dietary nucleoproteins is released from the protein component by sequential digestion of the protein by pepsin and trypsin.  However, diet differs massive in its nucleic acid content with the highest in the liver to the lowest (almost zero nucleic acid content) in the milk and dairy products and eggs.  Tea, coffee and coca contain the methyl purines; e.g., caffeine, theobromine and theophylline.
  • 72.  The nucleic acid part is hydrolyzed by a number of enzymes of the pancreatic juice [the nucleases: deoxyribonuclease (DNases) and ribonucleases (RNases)] and those of the intestinal juice and mucosa (the polynucleotidases, phosphatases, nucleotidases and nucleosidases).  The hydrolysis products include: nitrogenous bases (purines and pyrimidines), pentoses (ribose or deoxyribose) and inorganic phosphate. 72
  • 73. DIGESTION AND ABSORPTION OF NUCLEOTIDE Nucleoprotein Protein Nucleic acid Nucleases Nucleotide Nucleotidase Phosphate Nucleoside Nucleosidas Base Ribose Absorptio n Blood 73
  • 74. Absorption:  Ingested purines and pyrimidines are poorly absorbed from the small intestine and fate to be catabolized into uric acid in the liver and intestinal mucosa.  Nucleosides are fairly absorbed from the small intestine again to be catabolized or salvaged in the mucosa and liver.  However, the parenterally administered (injected) nucleosides/nucleotides are readily incorporated into DNA.
  • 75. DEGRADATION OF PURINE NUCLEOTIDES  Site: Purine catabolism occurs in liver, intestine, spleen, kidney, pancreas, skeletal and heart muscles.  In human and higher primates as chimpanzee, the ultimate end product of purine catabolism is uric acid( but it might not stop there)  The starting metabolites are either adenosine or guanosine.  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)  AMP is deaminated by AMP deaminase to form IMP.  Adenine is deaminated to inosine by the action of adenosine deaminase.  NOTE: MOST INGESTED NUCLEIC ACIDS ARE DEGRADED AND EXCRETED. 75
  • 76. 76
  • 77. INTRACELLULAR PURINE CATABOLISM  Xanthine is the point of convergence for the metabolism of the purine bases  Xanthine  Uric acid  Xanthine oxidase catalyzes two reactions  dual specific molybdenum-requiring xanthine dehydrogenase (oxidase)  Purine ribonucleotide degradation pathway is same for purine deoxyribonucleotides 77
  • 78. URIC ACID EXCRETION  Humans and highr primats – excreted into urine as insoluble crystals  In lower primates and other mammals, the copper-dependent uricase enzyme converts uric acid to allantoin by oxidative decarboxylation.  Birds, terrestrial reptiles, some insects – excrete insoluble crystals in paste form Excess amino N and nucleotide converted to uric acid (conserves water) uricotelic , ureotelic mammals and ammonotellic, Uric Acid  Allantoin  Allantoic Acid  Urea  Ammonia 78
  • 79. DISEASES ASSOCIATED WITH DEFECTS IN PURINE METABOLISM  HYPERURICEMIA  GOUT  LESCH-NYHAN SYNDROME  KIDNEY STONES  SEVERE COMBINED IMMUNODEFECIENCY (SCID) 79
  • 80. HYPERURICEMIA Characterized by plasma urate (uric acid) level greater than 7.0 mg/dL Normal plasma levels Females = 2.4 - 6 mg/dL Males = 3.4 - 7 mg/dL 80
  • 81. HYPERURICEMIA • Primary Hyperuricemia: an innate defect in purine metabolism and/or uric acid excretion urate saturation arising in the absence of coexisting diseases or drugs that alter uric acid production or excretion • Secondary Hyperuricemia: excessive urate production or diminished renal clearance that is the result of another disease, drug, dietary product, or toxin. 81
  • 82. PROGRESSION OF HYPERURICEMIA TO GOUT At a serum urate concentration greater than 6.8 mg/dL, urate crystals may start to deposit in the joints. serum urate concentration is elevated, There are three major crystal deposition-related disorders associated with hyperuricemia: Gout urolithiasis; and urate nephropathy. 82
  • 83. GOUT Gout is caused by precipitation of sodium urate crystals in the joints resulting in inflammation and pain. 83
  • 84. CLINICAL SYNDROMES The three classic stages of Gout 1. Acute gouty arthritis - If sufficient urate deposits develop around joints, and if the local environment or some trauma triggers the release of crystals into the joint space, an inflammatory response occurs. These flares can be self- resolving but are likely to recur. 2. Intercritical (or interval) gout - These are the intervals between attacks. During these periods, crystals may still be present at a low level in the synovial tissue and fluid, resulting in future attacks. 3. Chronic recurrent and tophaceous gout - Tophaceous gout is characterized by collections of solid urate in connective tissues (which may occasionally be calcified) 84
  • 85. GOUT - CAUSES  Decreased/partial HGPRT activity 1) Deficiency of HGPRT = accumulation of PRPP = increased purine synthesis = increased uric acid levels 2) Deficiency of HGPRT = decreased IMP and GMP = decreased inhibitors for purine synthesis  Under excretion of uric acid  Diet rich in  Increased purine degradation  Increased PRPP Synthetase activity 85
  • 86.  Colchicine –reduces inflammation  Uricosuric agents – increase renal excretion of uric acid (probenecid)  Allopurinol – inhibits uric acid synthesis  Low purine diet - Foods that are high in purine include:  Red meat and organ meats (eg. liver)  Yeasts and yeast extracts (eg. beer and alcoholic beverages)  Asparagus, spinach, beans, peas, lentils, oatmeal, cauliflower and mushrooms  Avoid caffeine and alcohol  Keep hydrated GOUT - Treatment 86
  • 87. ALLOPURINOL IS A XANTHINE OXIDASE INHIBITOR 87
  • 88. SEVERE COMBINED IMMUNODEFICIENCY (SCID) mutations in different genes whose products are crucial for the development and function of both T and B cells In some cases, the molecular defect prevents only T cell function, while B cells are normal It mainly due to Adenosine deaminase( ADA deficiency.)  SELECTIVELY KILLS LYMPHOCYTES  BOTH B- AND T-CELLS  MEDIATE MUCH OF IMMUNE RESPONSE 88
  • 89. ADA DEFICIENCY  caused by mutations in the ADA gene  ADA is an ubiquitous enzyme found in all cells, including red and WBC, and in the serum.  It catalyzes the deamination of adenosine and deoxyadenosine to inosine and deoxyinosine, which are converted to waste products and excreted  In the absence of functional ADA, there is an intracellular accumulation of adenosine and deoxyadenosine.  Adenosine and deoxyadenosine are also converted to 5'- triphosphates (dATP), which inhibit ribonucleotide reductase and prevent de novo synthesis of nucleotides and deoxynucleotides.  There is a decrease in DNA synthesis in replicating cells, because of the depletion of deoxynucleotides 89
  • 90. Disorders of Purine Metabolism: Disorder Defect Comments Gout PRPP synthase/ Hyperuricemia HGPRT Lesch Nyhan lack of HGPRT Hyperuricemia syndrome SCID ADA High levels of dAMP von Gierke’s disease glucose -6-PTPase Hyperuricemia 90
  • 91. nucleotide nucleosides phosphoribose pyrimidine DEGRADATION OF PYRIMIDINE NUCLEOTIDES Nucleotidase Nucleoside phosphorylase CMP and UMP degraded to bases similarly to purines Dephosphorylation Deamination Glycosidic bond cleavage 91 Unlike the purine rings, which are not cleaved in human cells, the pyrimidine ring can be opened and degraded to highly soluble structures, such as β-alanine, and β-aminoisobutyrate, which can serve as precursors acetyl CoA and succinyl CoA, respectively.
  • 92. 1. The nucleotides are initially converted to nucleosides by nonspecific phosphatases that remove the phosphate groups. 2. Cytidine is deaminated to uridine and deoxycytidine is deaminated to deoxyuridine. 3. The sugars are removed from the nucleosides to form the bases uracil and thymine. 4. These bases are then degraded to two β-amino acids, uracil to β-alanine and thymine to β- aminoisobutyrate. 92
  • 93. CONT…… a. The same enzymes catalyze these parallel reactions on either substrate. b. β-Aminoisobutyrate is derived exclusively from DNA, so the amount excreted in urine is a measure of DNA turnover. c. β-Alanine and β-aminoisobutyrate are converted into malonyl-CoA and methylmalonyl-CoA for further metabolism. 93
  • 94. Cytosine NH3 Uracil dihydrouracil H2O CO2 + NH3 β-alanine Thymine β-ureidoisobutyrate H2O Acetyl CoA TCA cycle liver Urea + + β-aminoisobutyrate Succinyl CoA TCA Glucose Excreted in urine 94
  • 95. Diseases due to defective pyrimidine metabolism  Most of the defects in the catabolism of pyrimidines do not cause clinical diseases because of the water solubility of their metabolic intermediate.  In cases of increased purine breakdown and hyperuricemia, there is also increased pyrimidine breakdown.  Orotic acidosis and orotic aciduria types I and II are very rare genetic condition accompanied with poor growth and hypochromic megaloplastic anemia with defective maturation of red cells and leukopenia.  They are treatable by supplementing cytidine or uridine that replenishes the deficiency by being converted into UMP.

Editor's Notes

  • #7: Adenine and guanine are found in both DNA and RNA. Hypoxanthine and xanthine are not incorporated into the nucleic acids as they are being synthesized but are important intermediates in the synthesis and degradation of the purine nucleotides. Cytosine is found in both DNA and RNA. Uracil is found only in RNA. Thymine is normally found in DNA. Sometimes tRNA will contain some thymine as well as uracil.
  • #8: Ribonucleoside NAD+, NADP+. In pyrimidine NucleotideMetabolism OVERVIEW Ribonuclosid and deoxyribonucleoside phosphates (nucleotides) are essential for all cells. Without them, neither DNA nor RNA can be produced and, therefore, proteins cannot be synthesized or cells proliferate. Nucleotides also serve as carriers of activated intermediates in the synthesis of some carbohydrates, lipids, and proteins, and are structural components of several essential coenzymes, for example, coenzyme A, FAD, NAD+,NADP+ and Nucleotides, such as cyclic AMP (cAMP) and cyclic GMP (cGMP), serve as second messengers in signal transduction pathways. In addition, nucleotides play an important role as "energy currency" in the cell. Finally, nucleotides are important regulatory compounds for many of the pathways of intermediary metabolism, inhibiting or activating key enzymes. The purine and prymidin bases found in nucleotides can be synthesized de novo, or can be obtained through salvage pathways that allow the reuse of the preformed bases resulting from normal cell turnover or from the diet.
  • #16: 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.
  • #17: DNA synthesis and its precursor nucleotides are coordinately regulated with the cell cycle progression before and during the S-phase and inhibitors of nucleotide synthesis are utilized to inhibit cell proliferation as in cancer treatment and immunosuppression for organ transplantation patients. Nucleotides are not only essential for DNA and RNA synthesis, but also, for energy metabolism (e.g., ATP and GTP), coenzyme formation (e.g., NAD and FAD), synthesis of active intermediates (e.g., Sadenosylmethionine); signal transduction (e.g., cAMP and cGMP); allosteric enzyme regulation (e.g., ATP and cAMP); and in their modified form are used as chemotherapy for cancer, immunosuppression and viral infection.
  • #18: High PRPP – denovo Low PRPP – salvage of purine synthesis
  • #19: 3aas for purine synthesis; Glycine Glutamate and Aspartate And also co2 and THF
  • #22: A. The cell maintains an important pool of purine nucleotides for synthesis of coenzymes and precursors for DNA and RNA and to support reactions that are coupled to ATP hydrolysis. B. Purine nucleotides can be synthesized de novo from amphibolic or dual-purpose intermediates, which may be derived either from anabolic or catabolic pathways.
  • #23: Amidophosphoribosyl transferase is an important regulatory enzyme in purine biosynthesis. It is strongly inhibited by the end products IMP, AMP, and GMP. This type of inhibition is called FEEDBACK INHIBITION.
  • #24: 1. Ribose 5-phosphate derived from the pentose phosphate pathway or from dietary sources is the starting material that eventually gives rise to inosine monophosphate (IMP) (Figure 10–1). 2. The overall strategy is to build the carbon-nitrogen skeleton of a purine ring system in a 12-step process directly on the sugar-phosphate starting material. a. The first step creates the multi-purpose intermediate 5-phosphoribosyl-1- pyrophosphate (PRPP). b. Then, PRPP glutamyl amidotransferase, the key regulatory enzyme, acts upon PRPP to begin making the purine ring; this is the committed step of purine synthesis.
  • #25: c. Carbons are added to the growing ring in several ways: (1) By one-carbon transfer by enzymes that use tetrahydrofolate (THF) coenzymes. (2) By incorporation of glycine in the structure. (3) By addition of CO2 in the form of bicarbonate.
  • #26: d. Nitrogens are added by the following: (1) Aminotransfer reactions with glutamine as donor. (2) In a two-step mechanism with aspartic acid as donor.
  • #34: Inhibitors of human purine synthesis are extremely toxicto tissues, especially to developing structures such as in a fetus, or to cell types that normally replicate rapidly, including those of bone marrow, skin, gastrointestinal tract, immune system, or hair follicles. Nucleotide Triphosphate Inhibitors Historically there have been several approaches in developing cancer therapeutics that bear chemical similarity to the various “building blocks” of nucleic acids and inhibit the formation of functional nucleotide triphosphates needed to synthesize either DNA or RNA. Many of these agents have been labeled “antimetabolites” because of their structural similarities to naturally occurring metabolites (Daher et al. 1994; Pizzorno et al. 2003). These include the antifolates (e.g., methotrexate), pyrimidines like 5-Fluorouracil (5-FU), and purines like 6- mercaptopurine and 6-thioguanine (Fig. 2). Other drugs like hydroxyurea are not “antimetabolites” from the perspective of mimicking nucleic acid “building blocks”, but have unique inhibitory effects on important steps in the conversion of nucleotides (Fig. 2-J and K). Some of these agents like hydroxyurea are relatively pure S-phase inhibitors, while others like 5-FU have activities extending beyond S-phase itself. As a class, all of the agents inhibit DNA synthesis and affect the S-phase of the cell cycle. Thus rapidly growing cancers theoretically should be potentially the most responsive. They also share toxicities toward the most rapidly growing normal “host” cells (e.g., hematopoietic cells - white blood cells, red Chapter 26, Pharmacological agents that target DNA replication, p. 3 of 28 blood cells, and platelets; gastrointestinal mucosal cells and hair) such that common side effects are produced (e.g. myelosuppression, anemia, thrombocytopenia, diarrhea, and
  • #35: e. Conversion of the main product of de novo synthesis, IMP, to GMP or AMP, occurs in two reactions, both of which are inhibited by feedback regulation by the end products. f. Overall flux through the purine synthetic pathways is regulated primarily by feedback inhibition of PRPP glutamyl amidotransferase, by IMP, AMP, and GMP (Figure 10–2).
  • #36: Cross-regulation Is the only time in biochemistry, we use ATP to synthesise GMP and vice versaAfter the branch point, addition of the amino group of aspartate onto IMP in two reactions activated by the 3rd key regulatory adenylosuccinate synthetase and adenylosuccinase, respectively release fumarate and gives AMP. IMP dehydrogenation into XMP (xanthosine monophosphate) is activated by the 4th key regulatory IMP dehydrogenase. XMP transamidination by glutamine to give GMP is activated by the transamidinase (or GMP synthetase). IMP conversion into AMP is activated by GTP as energy deriver, or into GMP is activated by ATP as energy deriver . through the aforementioned two distinct reaction pathways. Such inter-dependence of AMP on GTP and GMP on ATP provides controlling tool to balance AMP and GMP ratio to near equivalence. The substrate-specific nucleoside monophosphate and the non-specific nucleoside diphosphate kinases convert AMP into ADP and ATP; and, GMP into GDP and GTP, respectively.
  • #37: 6-Mercaptopurine (6-MP): 6-MP is a hypoxanthine derivative antimetabolite (see Fig. 2F) whose metabolites inhibit endogenous de novo purine synthesis at several steps (Fig. 2G) (Pizzorno et al. 2003). One of the most important metabolic activation is the formation of the nucleotide 6-MP ribose-5’- Chapter 26, Pharmacological agents that target DNA replication, p. 5 of 28 phosphate also known as thioinosine monophosphate (TIMP) in the presence phosphoribosylpyrophosphate (PRPP) and the enzyme hypoxanthine –guanine phosphoribosyltransferase (HGPRT). Once formed TIMP can inhibit several steps in de novo purine synthesis. The most important of these inhibited steps is the formation of phosphoribosylamine from PRPP and glutamine (Fig. 2G). This step however is under feedback control being naturally inhibited by adenine or guanine nucleotides (AMP or GMP). TIMP causes a pseudo feedback inhibition mimicking the effect of AMP or GMP. TIMP is thought to inhibit de novo purine synthesis at two other steps (Fig. 2G): the conversion of IMP to GMP and the conversion of GMP to AMP. 6-MP is not taken up to any great extent into nucleic acid itself but rather affects the synthesis of purine nucleotides needed for both RNA and DNA synthesis. Thus, while S-phase may be primarily affected, 6- MP is not a pure S-phase inhibitor. 6-MP is used mainly in acute leukemias. As might be expected because of the affect mainly on rapidly proliferating cells, toxicities are seen in rapidly growing normal host cells in particular hematopoietic cells.
  • #38: 6-Thioguanine (6-TG): Although structurally very similar to 6-MP (see Fig. 2H), 6-TG has a very different mechanism of action from 6-MP (Pizzorno et al. 2003). As is shown in Fig. 2I, 6-TG is metabolized to 6-TG-deoxyribonucleotide triphosphate (6-TdGTP), which can then be incorporated into DNA in place of dGTP. Futile mismatch repair and DNA fragmentation occur as the cell attempts to excise 6-TG from the DNA. As a result 6-TG affects S-phase cells primarily. 6-TG is mainly used in acute leukemias with toxicities being observed in rapidly growing host tissues like hematopoietic and mucosal cells.
  • #39: 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”)
  • #40: The active forms of nucleotides in biosynthesis and energy conversions are di-and tri-phosphates Nucleoside diphosphates (NDP) are synthesized from the corresponding nucleoside monophosphates (NMP) by base-specific nucleoside monophosphate kinases (Figure 22.9). [Note: These kinases do not discriminate between ribose or deoxyribose in the substrate.] ATP is generally the source of the transferred phosphate, because it is present in higher concentrations than the other nucleoside triphosphates. Adenylate kinase is particularly active in liver and muscle, where the turnover of energy from ATP is high. function is to maintain an equilibrium among AMP, ADP, and ATP. Nucleoside diphosphates and triphosphates are interconverted by nucleoside diphosphate enzyme that, unlike the monophosphate kinases, has broad specificity.
  • #43: 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 Rate of AMP production increases with increasing concentrations of GTP; rate of GMP production increases with increasing concentrations of ATP 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 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
  • #44: Stimulus – low PRPP Salvage pathway recycles purine bases and nucleosides into nucleotide. It is the sole source for purine nucleotides in some parasites (e.g., Mycoplasma, Borrelia, and Chlamydia). It is a significant source of purine nucleotides because hypoxanthine accumulation inhibits the de novo synthesis at the 2nd rate limiting amidotransferase step. In mammals, every cell is capable to salvage purines - particularly lymphocytes - through the following two mechanisms:
  • #46: i. Single Step Direct Conversion by phosphoribosylation activated by adenosine phosphoribosyltransferase (APRT) giving rise to AMP and by hypoxanthine-guanine phosphoribosyltransferase (HGPRT) that gives either IMP or GMP. Accumulation of AMP inhibits APRT and accumulation of GMP inhibits HGPRT; see the reaction below.
  • #47: Salvage is needed to maintain the purine pool (biosynthesis is not completely adequate, especially in neural tissue) Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) Hypoxanthine + PRPP IMP + Ppi Guanine + PRPP GMP + Ppi Lack of HGPRT leads to Lesch-Nyhan syndrome. Lack of enzyme leads to overproduction of purines which are metabolized to uric acid, which damages cells
  • #49: disorder associated with a virtually complete deficiency of HPRT. This deficiency results in an inability to salvage hypoxanthine or guanine, from which excessive amounts of uric acid are produced. addition, the lack of this salvage pathway causes increased PRPP levels and decreased and GMP levels. As a result, glutamine:phosphoribosylpyrophosphate amidotransferase (the committed step in purine synthesis) has excess substrate and decreased inhibitors available, and de novo purine synthesis is increased. The combination of decreased purine reutilization and increased purine synthesis results in the production of large amounts of uric acid, making the Lesch-Nyhan syndrome a severe, heritable form of gout. Patients with Lesch-Nyhan syndrome tend to produce urate kidney stones. addition, characteristic neurologic features of the disorder include self-mutilation (Figure 22.11) and involuntary movements.
  • #52: The enzyme has allosterically regulated binding sites for all nucleotides (oxy- and deoxy-) to modulate the substrate specificity and the overall reaction rate that ensures balanced production of deoxyribonucleotides for synthesis of DNA. There are two major allosteric sites; one controls the overall activity of the enzyme, whereas, the other determines the substrate specificity of the enzyme. ATP binds the overall activity site to activate the enzyme, whereas, dATP binding to this site inhibits the enzyme; detailed as follows. For the substrate specificity, ATP binding to the substrate site activates the reduction of pyrimidines (CDP and UDP) to form dCDP and dUDP. The dUDP is converted into dTTP. Accumulated dTTP binds to the substrate site and induces the reduction of GDP. Accumulated dGTP displaces dTTP to allow ADP to be reduced to dADP. Accumulated dATP inhibits the overall activity of the enzyme. The enzyme is inhibitable by the anticancer hydroxyurea.
  • #53: Regulation of deoxyribonucleotide synthesis Ribonucleotide reductase is responsible for maintaining a balanced supply of the deoxyribonucleotides required for DNA synthesis. To achieve this, the regulation of the enzyme is complex. addition to the single active site, there are two sites on the enzyme involved in regulating its activity (Figure 22.13). Activity site: The binding of dATP to an allosteric site (known as the activity site) on the enzyme inhibits the overall catalytic activity of the enzyme and, therefore, prevents the reduction of any of the four nucleoside diphosphates. This effectively prevents DNA synthesis, and explains the toxicity of increased levels of dATP seen in conditions such as adenosine deaminase deficiency (see p. 299). Substrate specificity site: The binding of nucleoside triphosphates to an additional allosteric site (known as the substrate specificity site) on the enzyme regulates substrate specificity, causing an increase in the conversion of different species of ribonucleotides to deoxyribonucleotides as they are required for DNA synthesis.
  • #63: Channeling: enzymes 1, 2, and 3 on same chain; 5 and 6 on same chain
  • #64: 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”
  • #65: Pyrimidine Antimetabolites5-Fluorouracil (5-FU) also blocks thymidylate synthesis as MTX, but works specifically on TS (Fig. 2D-E). TS converts deoxyuridine monophosphate (dUMP) to thymidine monophosphate (dTMP). TS is inhibited non-competitively by the 5-FU-deoxyuridine Chapter 26, Pharmacological agents that target DNA replication, p. 4 of 28 monophosphate (5-fluorodeoxyuridylate; FdUMP) (Fig. 2E). The resultant depletion of dTMP inhibits DNA synthesis and cell division. In addition, the accumulation of dUMP as well as the FdUMP pool formed from 5-FU can be incorporated into DNA. The repair enzymes (e.g., uracil glycosylase) can remove the incorporated uracil or 5-FU from the DNA resulting in DNA breaks, which further contribute to the S-phase directed cytotoxicity of 5- FU. Lastly, the ribonucleotide of 5-FU (FUMP) can be mis-incorporated into RNA. Because RNA dysfunction is not cell cycle specific, the resultant cytotoxicity effect is not confined only to the S-phase (Daher et al. 1994; Pizzorno et al. 2003). There have been many attempts over the years to design a better drug than 5-FU. In particular has been the desire to develop a 5-FU that could be administered orally, motivated by studies demonstrating that prolonged infusion of 5-FU had therapeutic advantages. A number of oral fluoropyrimidines have been synthesized (Diasio 1999). Capecitabine is the only oral 5-FU drug approved for use in the US, although several other analogs or prodrugs are available elsewhere. This prodrug has an added biochemical benefit in that the final step of activation to 5-FU occurs within the tumor thereby lessening release of 5-FU into the general circulation, where it potentially can affect sensitive host tissues like bone marrow, gastrointestinal mucosa, or the integument (skin, hair, and mucosal membranes). 5-FU has enjoyed extensive use in the treatment of a number of solid malignancies over the past 45 yrs (Table VIII). Today it is the major agent for advanced colorectal cancer and continues to be used in other gastrointestinal malignancies, such as stomach, esophageal and pancreatic cancer. 5-FU is also used in advanced breast and skin cancers. The deoxyribonucleoside of 5-FU, 5-fluorodeoxyuridine (FUDR or FdUrd) has been used for hepatic arterial infusion to treat liver metastases particularly from colorectal cancer. As noted above, Capecitabine has now been approved for advanced breast cancer and for both advanced and adjuvant treatment of colorectal cancer.: 5-Fluorouracil and Related Drugs
  • #67: The synthesis is largely controlled through product feedback allosteric regulation. The key regulatory carbamoyl phosphate synthetase II in humans is inhibited by UTP (and by purine nucleotides) and activated by PRPP. The sensitivity to activating effect of PRPP ismaximized close to S-phase of the cell cycle, where sensitivity to the inhibitory effect of UTP is minimized; i.e., the enzyme is more readily activated. The opposite happens at the end of the S-phase. This alteration in the sensitivity of the enzyme is due to its activating phosphorylation by the Mitogen Activated Protein Kinase (MAPK) in cells committed to cell division. But phosphorylation at a different site by the cAMP-dependent protein kinase makes carbamoyl phosphate synthetase II more readily inhibitable. CTP inhibits and ATP activates aspartate transcarbamoylase leading to a strict balance between thymine and cytosine nucleotides. This also reflects coordinate regulation of purine and pyrimidine biosynthesis mole for mole and accumulation of both type of nucleotides allosterically inhibit PRPP synthase, a key regulatory step for both. Coordinated repression and derepression control the first 3 steps into dihydroorotic acid and 5th and 6th steps into UMP. The anticancer 6-azauridine and allopurinol as alternative substrates inhibit orotidylate decarboxylase.
  • #69: INHIBITORS OF dTMP SYNTHESIS AS ANTICANCER AGENTS • Several drugs that interfere with production of dTMP by blocking the reaction catalyzed by thymidylate synthetase are inhibitors of DNA synthesis and cell proliferation. • Methotrexate is a folate analog that acts as a potent competitive inhibitor of dihydrofolate reductase, causing a decreased supply of THF coenzymes needed by thymidylate synthetase. • The thymine analog 5-fluorouracil (5-FU) is converted to 5-fluoro-dUMP, which acts as a suicide inhibitor of thymidylate synthetase.
  • #72: Dietary uptake of purine and pyrimidine bases is minimal. The diet contains nucleic acids and the exocrine pancreas secretes deoxyribonuclease and ribonuclease, along with the proteolytic and lipolytic enzymes. This enables digested nucleic acids to be converted to nucleotides. The intestinal epithelial cells contain alkaline phosphatase activity, which will convert nucleotides to nucleosides. Other enzymes within the epithelial cells tend to metabolize the nucleosides to uric acid, or to salvage them for their own needs. Dietary uptake of purine and pyrimidine bases is minimal. The diet contains nucleic acids and the exocrine pancreas secretes deoxyribonuclease and ribonuclease, along with the proteolytic and lipolytic enzymes. This enables digested nucleic acids to be converted to nucleotides. The intestinal epithelial cells contain alkaline phosphatase activity, which will convert nucleotides to nucleosides. Other enzymes within the epithelial cells tend to metabolize the nucleosides to uric acid, or to salvage them for their own needs. Approximately 5% of ingested nucleotides will make it into the circulation, either as the free base or as a nucleoside. Because of the minimal dietary uptake of these important molecules, de novo synthesis of purines and pyrimidines is required.
  • #76: 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)
  • #77: About 80% of uric acid formed in the body is excreted in urine. The remaining is probably excreted in the bile. The amount of uric acid excreted in the urine varies between 0.5 - 0.6 gm/day. It is mainly in the form of uric acid . The uric acid excretion is approximately halved on a purine-free diet, . Thus, controlling the dietary supply of purines helps preventing hyperuricemia.
  • #78: In lower primates and other mammals, the copper-dependent uricase enzyme converts uric acid to allantoin by oxidative decarboxylation. In birds and reptiles, uric acid is the chief end product of not only purines but also protein nitrogen.
  • #81: CLASSIFICATION — Persistent hyperuricemia is a common biochemical abnormality that results from excessive urate production and/or diminished renal uric acid excretion. (See "Uric acid balance".) Persistent hyperuricemia can be divided into two categories: Primary hyperuricemia, which usually lasts indefinitely, describes urate saturation arising in the absence of coexisting diseases or drugs that alter uric acid production or excretion. Secondary hyperuricemia refers to excessive urate production (table 1) or diminished renal clearance (table 2) that is the result of another disease, drug, dietary product, or toxin. CLINICAL SYNDROMES — The three classic stages in the natural history of progressive urate crystal deposition disease (gout) are: Acute gouty arthritis Intercritical (or interval) gout Chronic recurrent and tophaceous gout
  • #82: Urolithiasis - stones in urinary tract: the formation or presence of stony masses in the urinary tract, or the medical condition resulting from thisMicrosoft® Encarta® 2009. © 1993-2008 Microsoft Corporation. All rights reserved.
  • #84: fluid lubricating joints: a clear viscous fluid that lubricates the linings of joints and the sheaths of tendonsMicrosoft® Encarta® 2009. © 1993-2008 Microsoft Corporation. All rights reserved.
  • #86: Colchicine - poisonous plant extract: a poisonous extract of autumn crocus plants. Use: to inhibit cell division and cause chromosome doubling in plants, to treat gout.Microsoft® Encarta® 2009. © 1993-2008 Microsoft Corporation. All rights reserved.
  • #87: INTRODUCTION — Pharmacologic modalities employed in the treatment of gout can be classified as antiinflammatory, prophylactic, and antihyperuricemic. These designations reflect the three distinctive aims of treatment: Antiinflammatory therapy for prompt and safe termination of the acute arthritic attack Antiinflammatory prophylaxis for prevention of recurrences of acute gouty arthritis Antihyperuricemic (urate-lowering) therapy for prevention and reversal of the consequences of urate crystal deposition in joints (gouty arthropathy), urinary tract (nephrolithiasis), renal interstitium (rarely producing renal failure due to urate nephropathy), and tissues and parenchymal organs (tophi) Dietary control by avoidance of nucleic acid-rich diets, e.g., liver and meat particularly of old animals and birds is recommended. Dairy products, eggs and meat of young animals are more suitable.
  • #88: PATHOGENESIS — SCID is a syndrome caused by mutations in different genes whose products are crucial for the development and function of both T and B cells [2]. In some cases, the molecular defect prevents only T cell function, while B cells are normal. However, since B cells require signals from T cells to produce antibody, serious T cell dysfunction precludes effective humoral immunity. Natural killer (NK) cells, a non-T, non-B lymphocyte subset exhibiting cytotoxic activities, develop via a pathway distinct from B and T cells. NK cells are present in approximately 50 percent of patients with SCID and may provide a degree of protection against bacterial and viral infections in these patients. Determining the presence or absence of NK cells is also helpful in classifying patients with SCID.
  • #89: IN-CLASS QUESTION: EXPLAIN THE BIOCHEMISTRY THAT RESULTS WHEN A PERSON HAS ADA DEFICIENCY (HINT: LYMPHOID TISSUE IS VERY ACTIVE IN DEOXYADENOSINE PHOSPHORYLATION)
  • #95: Orotic acidosis and orotic aciduria types I and II are very rare genetic condition accompanied with poor growth and hypochromic megaloplastic anemia with defective maturation of red cells and leukopenia. They are treatable by supplementing cytidine or uridine that replenishes the deficiency by being converted into UMP. This also feedback inhibits carbamoyl phosphate synthetase II and oroticacid synthesis to ease the acidosis. Allopurinol and azauridine cause orotic aciduria because their catabolites inhibit OMP decarboxylase.