1. Nucleic Acids Metabolism And Disorders
Know the:
Purine and Pyrimidine Pathway.
Pyrimidine Synthetic Reactions and Nitrogen Metabolism.
Regulation of these pathways.
Co-factors Required.
Sites of Defect and Related Diagnosis such as Gout or ,,,,,Severe Combined Immunodeficiency (SCID).
Role of PRPP and Ribonucleotide Reductase.

2. Digestion of Dietary Nucleic Acids
Nucleosidases are class of enzymes that catalyze the hydrolysis of nucleosides.
Endonuclease: any of a group of enzymes that degrade DNA or RNA molecules by breaking linkages within the polynucleotide chains.
Exonuclease: Any of a group of enzymes that catalyze the hydrolysis of single nucleotides from the end of a DNA or RNA chain.

3. Structures of Purines and PyrimidinesH
The Nucleic Acids:
Precursory monomers:
Uracil
(U)
RNA
only
The Nucleic Acids
Pyrimidine Base Purine Base C
Structures of Purines and Pyrimidines

4. Pentoses Found in Nucleic Acids
Numbering System of Purine & Pyrimidine Nucleosides

5. De novo Synthesis Precursors
Ribonucleotides!

6. Ribonucleotide Phosphates
Sources of the Individual Atoms in Purine Ring

7. Synthesis of 5-Phosphoribosyl-1-Phosphate, Showing
the Activator & Inhibitors of the Reaction
PRPP Synthetase: is the enzyme that catalyzes the reaction of alpha-d-riboe-5-phosphate and ATP to produce PRPP and AMP; a regulatory enzyme in purine & pyrimidine biosynthesis; enhanced activity of this enzyme results in an increase in purine biosynthesis leading to “Gout”.

8. Synthesis of Purine Nucleotides, Showing the
Inhibitory Effect of Some Structural Analogs
PRPP is an allosteric
Positive modulator in
the step 1.
AMP, CMP & IMP are
Inhibitors in step 1.

9. Conversion of IMP to AMP & GMP Showing
Feedback Inhibition

10. Salvage Pathways of Purine Nucleotide Synthesis
Lesch-Nyhan Syndrome is characterized by the deficiency of “hypoxanthine-guanine phosphoribosyl transferase (HGPRT)”, leads to accumulation of PRPP and uric acid, the condition is know as “Hyperuricemia”.
Hyperuricemia is the presence of high levels of uric acid / sodium urate crystals in the blood.
The upper end of the normal range of uric acid is 360 µmol/L (6 mg/dL) for women and 400 µmol/L (6.8 mg/dL) for men.
PRPP=Phosphoribosyl pyrophospate.

11. Lesch-Nyhan Syndrome (LNS)
LNS, which is also known as HGPRT deficiency or Kelley-Seegmiller syndrome.
Hypoxanthine Guanine Phosphoribosyltransferase (HGPRT) deficiency.
X-linked genetic rare genetic disorder that affects males.
Severe neurologic disease, characterized by self-mutilating behaviors such as lip and finger biting and/or head banging.
Up to 20 times the uric acid in the urine than in normal individuals. Uric acid crystals form in the urine.
Untreated condition results in death within the first year due to kidney failure.
Treated with allopurinol, a competitive inhibitor of xanthine oxidase.

12. Lesions of the Lips of Lesch-Nyhan Patient Caused by Self-mutilation

13. Conversion of Ribonucleotides to Deoxyribonucleotides
Ribonucleotide Reductase (RNR) that catalyzes the conversion of ribonucleoside diphosphate into deoxyribonucleoside diphosphate. RNR assembles deoxyribonucleotides for the synthesis of DNA.

14. Degradation of Purine Nucleotides to Uric Acid

15. Monosodium Urate Crystals
Tophaeceous Gout
Monosodium Urate Crystals
Gout: Recurrent acute arthritis of peripheral joints caused by the accumulation of monosodium urate crystals. Often presents as pain and swelling confined to one joint. The big toe joint is commonly affected. The problems partly arise because neutrophils release lysosomal enzymes as a result of damage to the phagosome membrane by ingested crystals: Colchicine acts to reduce the attack by inhibiting lysosome phagosome fusion.

16. Sources of the Individual Atoms in Pyrimidine Ring

17. Summary of the Difference between CPS-I & CPS-II

18. De novo Pyrimidine Synthesis

19. Synthesis of dTMP from dUMP, Ilustrating
Sites of Action of Antineoplastic Drugs
5-Fluorouracil: An antineoplastic agent, used especially in the treatment of cancers of the skin, breast, and digestive system.
Methotrexate: An anticancer drug that acts as a folic acid antagonist to interfere with cellular reproduction and is used in the treatment of psoriasis, certain cancers, and certain inflammatory diseases, such as rheumatoid arthritis.

20. The Concept Map
for Nucleotide Metabolism

21. Reduction of Ribose- to Deoxyribose
di- or tri- phosphate
di- or tri- phosphate
Ribonucleotide
Reductase H
R12 R22 enzyme of Salmonella typhimurium

22. Purine Biosynthesis
PRPP=Phosphoribosyl Pyrophosphate

23. Purine Biosynthesis
Purine synthesis is critical to fetal development, therefore defects in enzymes will result in a nonviable fetus.
PRPP synthetase defects are known and have severe consequences (next slide).
PRPP synthetase superactivity has been documented, resulting in increased PRPP, elevated levels of nucleotides, and increased excretion of uric acid.

24. Phosphoribosyl Pyrophosphate (PRPP) Synthetase Defects
PRPP deficiency results in convulsions, autistic behavior, anemia, and severe mental retardation.
Excessive PRPP activity causes gout (deposition of uric acid crystals), along with various neurological symptoms, such as deafness.

25. Pyrimidine Synthesis Orotic aciduria UMP Synthase
Production of Uridine 5’-monophosphate (UMP) from orotate is catalyzed by the enzyme “UMP synthase”.
UMPS = Uridine monophosphate synthetase.

26. Pyrimidine Synthesis
Orotic aciduria refers to an excessive excretion of Orotic acid in urine.
Its hereditary form, an autosomal recessive disorder, can be caused by a deficiency in the enzyme Uridine monophosphate synthetase (UMPS), a bifunctional protein that includes the enzyme activities of Oroate phosphoribosyltransferase and Orotidine 5’-phosphate decarboylase.

27. Pyrimidine Synthesis
Deficiency in UMP synthetase activity.
Pyrimidine Synthesis is critical to fetal development just as purine metabolism is critical. Therefore an absolute deficiency of an enzyme of pyrimidine synthesis would be fatal.
A very low level of the enzyme UMP synthase has been documented, resulting in the condition orotic aciduria.
Due to the demand for nucleotides in the process of red blood cell synthesis, patients develop the condition of megaloblastic anemia, a deficiency of red blood cells.
Pyrimidine synthesis is decreased and excess orotic acid is excreted in the urine (hence the name orotic aciduria).

28. Purine Degradation
The enzyme “nucleotidase” is also known as purine nucleotide phosphorylase (PNP).
Purine Nucleotides from ingested nucleic acids or turnover of cellular nucleic acids is excreted by humans as uric acid.
Humans excrete about 0.6 g uric acid every 24 hours.

29. Young Child Born With Immune Deficiency Syndrome Plays In The Enclosed, Germ-free, Plastic Environment In Which He Must Live To Survive
Severe Combined Immunodeficiency (SCID)
is a severe form of heritable Immunodeficiency, autosomal recessive disorder due to deficiency of Adenosine Deaminase (ADA), its victims are extremely vulnerable to infectious diseases.
It accounts for about 15% of all cases of SCID. ADA deficiency may present in infancy, childhood and adolescence. Age of onset and severity is related to some
29 known genotypes associated with the disorder.

30. Adenosine Deaminase (ADA) and Purine Nucleoside Phosphorylase (PNP) Deficiency.
A deficiency of either ADA or PNP causes a moderate to complete lack of immune function.
Affected children cannot survive outside a sterile environment.
They may also have moderate neurological problems, including partial paralysis of the limbs.
When a compatible donor can be found, bone marrow transplant is an effective treatment.

31. Adenine Deaminase (ADA) Deficiency
The importance of adenosine deaminase (ADA) for the catabolism of dA, but not A, and the resultant accumulation of dATP when ADA is defective. A is normally salvaged by adenosine kinase (see Km values of A for ADA and the kinase, AK) and deficiency of ADA is not significant in this situation

32. Pyrimidine Degradation
Pyrimidines are generally degraded to intermediates of carbon metabolism (for example, succinyl-CoA) and ammonia (NH4+).
NH4+ is packaged as urea through the urea cycle and excreted by humans.
Defects in enzymes of pyrimidine degradation have been documented, resulting in increased levels of pyrimidines and neurological disorders.
No treatments are available and mechanisms are unknown.

33. Dihydropyrimidine dehydrogenase (DHPD) is responsible for the catabolism of the end-products of pyrimidine metabolism (uracil and thymine) to dihydrouracil and dihydrothymine. A deficiency of DHPD leads to accumulation of uracil and thymine. Dihydropyrimidine amidohydrolase (DHPA) catalyses the next step in the further catabolism of dihydrouracil and dihydrothymine to amino acids. A deficiency of DHPA results in the accumulation of small amounts of uracil and thymine together with larger amounts of the dihydroderivatives.

34. The role of Uridine Monophosphate Hydrolases (UMPH) 1 and 2 in the catabolism of UMP, CMP, and dCMP (UMPH 1), and dUMP and dTMP (UMPH 2).

35. CDP-choline phosphotransferase (CDP-CP) Deficiency causes Haemolytic Anaemia.
CDP-Choline Phosphotransferase Deficiency
CDP-choline phosphotransferase (CDP-CP) catalyses the last step in the synthesis of phosphatidyl choline. A deficiency of this enzyme CDP-CP is proposed as the metabolic basis for the selective accumulation of CDO- choline in the erythrocytes of rare patients with an unusual form of “haemolytic anaemia”.

36. Pyrimidine and Purine Salvage
Free Purine and Pyrimidine bases are constantly released in cells during the metabolic degradation of nucleotides.
Free Purine and Pyrimidine bases are in large part salvaged and reused to make nucleotides.
Salvage of free nucleotides consumes much less energy than de novo nucleotide synthesis and is the energetically preferred source of nucleotides for nucleic acid synthesis.
Salvage pathway: A recycling metabolic pathway in which biomolecules such as nucleotides are synthesized from intermediates in the degradative pathway for those biomolecules. The intermediate materials would otherwise be waste products.

37. Purine Salvage
Salvage of the free purine bases guanine and hypoxanthine (the deamination product of adenine)
often involves the enzyme hypoxanthine-guanine phosphoribosyltransferase (HGPRT).
Salvage of free adenine is accomplished by the enzyme adenine phosphoribosyltransferase (APRT), converting free adenine and PRPP to adenosine monophosphate (AMP).

38. Purine Salvage
HGPRT = Hypoxanthine-Guanine Phosphoribosyltransferase.

39. Salvage Pathways of Nucleic Acids Metabolism

40. Allopurinol and Hypoxanthine

41. Gout Elevated uric acid levels in the blood.
Uric acid crystals will form in the extremities with a surrounding area of inflammation. This is called a tophus and is often described as an arthritic “great toe”.
Can be caused by a defect in an enzyme of purine metabolism or by reduced secretion of uric acid into the urinary tract.
Gout
tophus

42. Pyrimidine Salvage
Pyrimidine salvage defects have not been clinically documented.

43. Intracellular uric acid crystal under polarised light (left) and under non-polarised light (right)
With time, elevated levels of uric acid in the blood may lead to deposits around joints. Eventually, the uric acid may form needle-like crystals in joints, leading to acute gout attacks. Uric acid may also collect under the skin as tophi or in the urinary tract as kidney stones.

44. Additional Gout Foot Sites: Inflamation In Joints Of Big Toe, Small Toe And Ankle.
Gout-Early Stage: No Joint Damage.
Gout-Late Stage: Arthritic Joint.
Tophi: A deposit of urates in the skin and tissue around a joint or
in the external ear, occurring in gout.

45. For which of the following reactions S-adenosyl methionine
(SAM), serve as a methylating agent?.
A. Conversion of dopamine to norepinephrine.
B. Synthesis of creatine from creatine phosphate.
C. Synthesis of phosphatidylcholine from phosphatidylethanolamine.√
D. Conversion of dUMP to dTMP.
E. Formation of methionine from homosycteine.
Answer: C. The The conversion of dopamine to norepinephrine
Involved in the hydroxylation reaction. (SAM methylates
norepinephrine to form epinephrine). The synthesis of creatine
requires SAM, not the conversion conversion of creatine
phosphate to creatine.

46. Pregnant women frequently suffer from folate deficiencies.
A deficiency of folate would decrease the production of:
A. creatine phosphate from creatine.
B. all of the pyrimidines required for RNA synthesis.
C. the thymine nucleotide required for DNA synthesis.√
D. phosphatidylcholimne from diacylglycerol and CDP-choline.
Answer: C. The only pyrimidine that requires folate for its
synthesis is thymine (dUMP → dTMP). Folate is required for
incorporation of carbons 2 and 8 into all purine molecules. The
synthesis of creatine phosphate and of phosphatidylcholine do not
require folate. Folate deficiencies during pregnancy can lead to
neural tube defects (e.g., spina bifida) in the fetus.

47. Excessive degradation of AMP and GMP would result in
increase during excretion of:
A. creatine
B. urea
C. uric Acid.√
D. thiamine
E. thymine
Answer: C. The purine bases, adenine (A) and guaninie (G), are
oxidized to uric acid, which is excreted in the urine. Excessive
production of uric acid can result in the condition known as gout.

48. Which of the following statement about heme and iron
metabolism is correct?
A. Iron is stored in the liver as transferrin.
B. Iron (as Fe2+) is inserted into protoporpyrin IX in the last step.
of heme synthesis
C. δ-ALA synthase catalyzes the regulated and rate-limiting step in heme biosynthesis.√
D. The major route for bilirubin excretion is via the urine.
E. The iron produced by heme degradation is excreted in the feces.
Answer: C. The first rate-limiting step in heme biosynthesis
involves the condensation of glycine and succinyl CoA to form
Delta-ALA. Iron is stored as ferritin and transported in the blood
in transferrin. As Fe2+, it is inserted into protoporpyrin IX to form
heme. When heme is degraded to form bilirubin (which is excreted
mainly via the intestine), iron is returned to the body’s iron stores
and is not excreted. Bleeding is the only significant means by which iron is lost from the body.

49. The component that would be elevated to the greatest extent
in the blood of a person suffering from Gout is:
A. bilirubin.
B. uric acid.√
C. creatine kinase.
D. blood urea nitrogen.
E. creatinine.
Answer: B.

50. The genetic defect in the hypoxanthine guanine
phosphoribosyl transferse (HGPRT) will leads to:
parkinson’s disease.
cystinuria.
pellagra.
lesch-Nyhan syndrome.√
hartnup’s disease.
Answer: D. The defect in the purine salvage enzyme HGPRT
causes Lesch-Nyhan syndrome.

51. De novo pyrimidine synthesis requires:
A. phosphorobosyl pyrophosphate (PRPP) for the initial step.
B. tetrahydrofolate for the incorporation of carbon 2 and 8.
C. both carbon and nitrogen of aspartate to form the ring.√
D. NH4+ as a substrate for carbamoyl phosphate synthetase II.
E. glycine as the source of two nitrogens in the ring. Rue for purine
Answer: C. Options A and B are true for purine synthesis. During
pyrimidine synthesis, the entire aspartate molecule is incorporated
Into the ring. Glutamine is the substrate for carbamoyl phosphate
synthase II, the enzyme involved in pyrimidine biosynthesis. (NH4+
Ions is the substrate for the synthase I in the ureea synthesis).
Glycine supplies one nitrogen for purine synthesis.

52. 5-Fluorouracil (5-FU) is an effective chemotherapeutic agent
because interferes with DNA synthesis by directly inhibiting
the reaction in which:
A. FH2 → FH4.
B. dUMP → TMP.√
C. glutamine+ PRPP → Phosphoribosylamine.
D. methyl B12 → B12.
E. methionine → S-Adenosyl methionine.
Answer: B. Methotrexate inhibits reaction A. 5-FU inhibits
reaction B. The remaining reactions are not directly affected by
5-FU. Reaction C is the first step in purine biosynthesis, and
reaction D provides the methyl group for the biosynthesis of
methionine from homocysteine.

53. This enzyme recognizes allopurinol as a substrate and is then
inhibited by the product of enzyme catalysis.
A. PRPP synthetase.
B. Hypoxanthine-guanine phosphoribosyl transferase.
C. Adenosine deaminase.
D. PRPP amidotransferase.
E. Xanthine oxidase.√
Answer: E.

54. A 12-week-old infant with a history of persisent diarrhea and
candidiasis is seen for a respiratory tract infection with
Pneumocystis carinii. A chest x-ray confirms pneumonia and
Reveals absence of a thymic shadow. Trace IgG is present in his
serum, but IgA and IgM are absent. His red blood cells completely
lack an essential enzyme in purine degradation. The product
normally formed by this enzyme is:
A. Guanine monophosphate.
hypoxanthine.
inosine.√
xanthine.
xanthine monophosphate.
Answer: C. The child most likely has severe combined
immunodefciency caused by adenosine deaminase (ADA)
deficiency. This enzyme deaminates adenosine (a nucleotide) to
form inosine (another nucleoside). Hypoxanthine and xanthine are
both purine bases, and the monophosphates are nucleotides.

55. The anticancer drug 6-mercaptopurine is activated by the enzyme
xanthine oxidase. A cancer patient being treated with
6-mercaptopurine develops hyperurecemia, and the physician
decides to give the patient allopurinol.
What effect will allopurinol have on the activity of
6-mercaptopurine?
Enhanced deactivation of 6-marcaptopurine.
Enhanced elimination of 6-mercaptopurine as uric acid.
Enhanced retention and potentiation of activity.√
Deceased inhibition of PRPP glutamylamidoransferase.
Inosine.
Xanthine.
Answer: C. Because allopurinol inhibits xanthine oxidase, the
6-mercatopurine will not be deactivated as rapidly.

56. The anticancer drug 6-mercaptopurine is activated by the enzyme
xanthine oxidase. A cancer patient being treated with
6-mercaptopurine develops hyperurecemia, and the physician
decides to give the patient allopurinol.
Resistance of neoplastic cells to the chemotherapeutic effect of
6-mercaptopurine would most likely involve loss or inactivation of
a gene encoding,
Thymidilate synthase.
Hypoxanthine phosphoribosyltransferase.√
Purine nucleoside phosphorylase.
Orotic acid phosphoribosyltransferase.
Adenosine deaminase.
Answer: B. HPRT is required for activation of 6-mercaptopurine
to its ribonucleotide and inhibition of purine synthesis. The other
enzymes listed are not targets for this drug..

57. The Severe combined immunodeficiency (SCID) arises from
inhibition of lymphocyte proliferation because B and T cells are
particularly sensitive to allosteric inhibition of which of the following
Enzymes of purine nucleotide metabolism?
Xanthine oxidase.
Dihydrofolate reductase reductase.
Adenosine deaminase.
Ribonucleotide reductase.√
Hypoxanthine-guanine phosphoribosyltransferase.
Answer: D. Impaired immune function in severe combined immunodeficiency
(SCID) is the direct result of blocked DNA synthesis due to inadequate
supplies of deoxyribonucleotides in B and T cells. This effect arises by dATP-
induced allosteric inhibition of ribonucleotide reductase, which catalyzes
reduction of the 2’-hydroxyl groups on ADP and GDP to form dADP and dGDP.
The ultimate cause of many cases of SCID is adenosine deaminase deficiency,
which leads to accumulation of dATP and consequent inhibition of ribonucleotide
reductase. Although the other enzymes mentioned are also involved in
purine nucleotide metabolism, their deficiencies do not lead to SCID.

58. A 68-year-old woman complains of fatigue that has worsened over
the past month. She has experienced recent bouts of nausea and
diarrhea. History indicates that, she changed her diet in order to
lose some weight 3 months before she started experiencing these
Symptoms,. Blood work reveals a macrocytic anemia. Neurological
examination is within normal limits.
These findings suggest a deficiency of which of the following
vitamins?
Niacin (B3).
Riboflavin (B2).
Vitamin B12.
Folic acid.√
Vitamin C.
Answer: D.

59. Methotrexate is a potent anticancer agent that serves dividing cells
of deoxyribonucleotides through direct inhibition of the following
enzymes?
Ribnucleotide reductase.
Xanthine oxidase.
Carbamoyl phosphate synthase II.
Anemia.
Thymidilate synthetase.√
Answer: E.

60. A 2-year-old boys mother is concerned about his tendency to bite
himself to the point of bleeding. The boy’s fingers show scarring
and several scabs, and his lips are swollen and bruised. He exhibits
poor coordination, poor muscle tone, and frequent jerking
movements of his arms and legs. He is significantly delayed in
speech. His urine is orange in color and “gritty”.
Which of the following is the most likely diagnosis?
Tay-Sachs disease.
Gout.
Lesch-Nyhan syndrome.√
Severe combined immunodeficiency.
Cerebral palsy.
Answer: C.

61. A 47-year-old man complains of pain in the joints of his big toe,
which are obviously swollen and tender. The pain has been chronic
but became intolerable the day after thanksgiving when he had a
large meal and several glasses of red wine. He is obese, and his
past medical history is significant for removal of kidney stones.
Which of the following involved in the pathophysiology of this patient’s condition?.
Elevated orotic acid.
Elevated uric acid.
Deficiency of folic acid.
Anemia.
Hypoglycemia.
Answer: B.
Whether his gout arises from impaired excretion of uric acid or is due to a mutation of PRPP synthase cannot be determined from the data. Analysis of his blood may confirm the gout if high concentrations of uric acid (hyperurecemia) are present.