THE OVERVIEW OF NUCLEOTIDES BIOSYNTHESIS .pptx

Biochemistry

1. GENERAL OVERVIEW OF NUCLEOTIDES BIOSYNTHESIS BY: GROUP 8

2. CONTENT: Overview of Nucleotide Chemistry and Introduction to Nucleotide Biosynthesis. Purine Biosynthesis. Pyrimidine Biosynthesis. Regulation of Nucleotide Biosynthesis. Defects, Disorders, and Implications of Nucleotide Biosynthesis.

3. Overview of Nucleic Acid Chemistry: A Brief History: In 1868, Swiss biologist, Friedrich Miescher isolated “nuclein” which was later identified as the DNA {Deoxyribonucleic acid}. In the early 20th century, Phoebus Levene, an American biochemist, identified the components of DNA as nucleotides consisting of a sugar, a phosphate group, and nitrogenous bases. In 1994, Oswald Avery, Colin MacLeod, and Maclyn McCarty conducted a ground-breaking experiment that proved DNA was the molecule responsible for carrying genetic information in bacteria.

4. In 1953, James Watson and Francis Crick, with the aid of Rosalind Franklin’s x-ray crystallography data, proposed the double helix structure of the DNA. RNA {Ribonucleic acid} was found to be inolved in protein synthesis and various cellular processes. DNA Sequencing techniques are later develoved, giving birth to Modern Genetics and the Human Genome Project.

5. What are Nucleic Acids? Nucleic acids are polymeric macromolecules made up of repeated units of nucleotides. Nucleotides are organic molecules that are the building blocks of DNA and RNA. They are composed of three main components: a sugar molecule, a phosphate group, and a nitrogenous base. The sugar molecule present in nucleotides can either be ribose (in RNA) or deoxyribose (in DNA). It provides the structural backbone of the nucleotide. The phosphate group is responsible for linking nucleotides together to form DNA or RNA chains. It also acts as a source of energy for various cellular processes. The chemistry of nucleotides involves various reactions, such as phosphorylation, which adds phosphate groups to the structure, and condensation reactions, which join nucleotides together via a phosphodiester bond. Additionally, nucleotides can undergo hydrolysis reactions, breaking the phosphodiester bond and releasing energy.

6. Functions of Nucleotides & Nucleic Acids Functions of Nucleotides : Energy for metabolism. Lipid, protein, and carbohydrate synthesis. Signal transduction. Building blocks of nucleic acids Function of RNA : Transfer of genetic information from the nucleus to the cytoplasm for proteins synthesis. Eg; mRNA, rRNA, tRNA. Function of DNA : Stores genetic material and are the molecular repositories of genetic information.

7. Introduction to Nucleotide Biosynthesis Nucleotide biosynthesis refers to the biochemical processes by which cells synthesize nucleotides from simpler precursors. Nucleotides can be synthesized de novo, starting from simple molecules such as amino acids, sugars, and carbon dioxide. The pathway differs for purine and pyrimidine biosynthesis. The purine nucleotides are synthesized by most of the tissues. However the major site is the liver. This pathway operates in the cytoplasm. Since the human being can synthesize the purine and pyrimidine bases de novo, they are said to be prototroph. So purines and pyrimidines are dietarily non-essential.

8. PURINE RIBONUCLEOTIDE BIOSYNTHESIS

9. DEFINITION Purine is a heterocyclic aromatic organic compound that consists of two rings (pyrimidine and imidazole) fused. Examples include adenine and guanine. They are important in DNA and RNA synthesis, energy metabolism, signal transduction coenzymes, cyclic nucleotides and other metabolic pathways. Purine Nucleotide comprises of a purine base (adenine or guanine) bounded to a sugar (ribose in RNA or deoxyribose in DNA) and one or more phosphate group.

10. PURINE AND PURINE NUCLEOTIDE

11. Sources of Individual Atom Many compounds contribute to the purine ring of nucleotide. The discovery of the source of individual atoms in purine is a fascinating story that involves a combination of chemical experiments and isotope labeling techniques.

12. SYNTHESIS Purine biosynthesis occurs in the cytosol of cells. The purine ring is built up in a series of 11 enzyme-catalyzed steps. Each enzyme is oligomeric , intermediate products that are produced during the reaction are not released. Instead, they are shuttled to the subsequent enzyme along the pathway .

13. METABOLIC PATHWAY FOR SYNTHESIS OF IMP

14. SYNTHESIS OF AMP AND GMP FROM IMP

15. It is worthy of note that this pathway is common to both plants and animals. However, there are some notable differences such as: Source of Purine precursors Regulation of de novo synthesis Nitrogen assimilation Pathway in specific enzymatic steps These differences reflect evolutionary adaptations and the specific needs of each organism.

16. PURINE SALVAGE PATHWAY The Purine Salvage Pathway is a biochemical pathway in which certain cells like erythrocytes and brain cells that cannot carry out de novo synthesis of purine nucleotide use free purines (adenine, guanine, and hypoxanthine) gotten from nucleic acid turnover (particularly RNA) and diet and directly convert them to their corresponding nucleotides It accounts for 90% of daily purine synthesis because most purine bases are recycled rather than degraded and it requires less energy than the de novo pathway for purine synthesis. Defect in the enzyme HGPRT causes Lesch Nyhan Syndrome

17. DEGRADATION OF NUCLEOTIDE While the majority of purines are salvaged through the purine salvage pathway, few others from sources such as dietary intake of purine rich food, excess endogenous purines that are not utilised for nucleotide biosynthesis and those gotten from endogenous turnover of DNA and RNA provide purine for degradation. The end product is uric acid (2, 6, 8-trioxypurine) in humans. Most animals (other than primates) however oxidize uric acid by the enzyme uricase to allantoin , where the purine ring is cleaved. Allantoin is then converted to allantoic acid and excreted in some fishes. Further degradation of allantoic acid may occur to produce urea in amphibians, most fishes and molluscs and later to ammonia (in marine invertebrates).

18. PYRIMIDINE BIOSYNTHESIS

19. DE NOVO SYNTHESIS Unlike in purine synthesis, in pyrimidine synthesis, the pyrimidine ring is first made, then it is attached to ribose phosphate. (PRPP) Precursors: N3 : Glutamine C4,C5, C6&N1 : Aspartic acid C2: Carbondioxide.

20. Steps: C a r b a m o y l p h o s p h a t e s y n t h e s i s O c c u r s i n c y t o p l a s m E n z y m e i s c a r b a m o y l phosphate s y nthetase I I T h e r e a c t i o n i s A T P dependent . 2. Rate Limiting step Formation of carbamoyl aspartate Enzyme: aspartate transcarbamoylase (ATC)

21. 3. Formation of Pyrimidine ring Cyclization of Pyrimidine ring by removal of water. Formation of dihydro orotic acid Enzyme; dihydro orotase 4. Oxidation Removal of H from C5 & C6 Production of Orotic Acid Enzyme: dihydro orotate dehydrogenase Catalized by mitochrondrial NAD+

22. 5. Formation of OMP Addition of ribose-5-phosphate ( from PRPP) to orotic acid Formation of Orotidine monophosphate or orotidylic acid. Catalyzed by orotate phosphoribosyl transferase 6. Decarboxylation Formation of UMP by removal of CO2 from C7 of OMP Catalyzed by OMP decarboxylase

23. 7. Synthesis of triphosphates UMP is phosphorylated to UDP through ATP and nucleoside monophosphate kinase UDP is phosphorylated to UTP through another ATP and nucleoside diphosphate kinase 8. Formation of CTP CTP is synthesised from UTP by animation Glutamine provides the nitrogen CTP synthetase catalyses the reaction.

24. Alternatively; from UDP Ribonucleotide reductase converts UDP to dUDP by a thioredoxin-dependent reaction Thymidylate synthase catalyses the transfer of methyl group from, N5, N10- methylene tetrahydrofolate to produce dTMP

25. Salvage Pathway Like purines, pyrimidines can serve as precursors in the salvage pathway to be converted to the respective nucleotides by Pyrimidines phosphoribosyltransferase. Utilizes PRPP as source of R5P Regulation of Pyrimidine Synthesis In prokaryotes, ATC is allosterically inhibited by CTP and activated by ATP In mammals; CPS II is inhibited by UTP and UDP and activated by PRPP OMP decarboxylase is inhibited by CMP & UMP

26. Degradation of Pyrimidine nucleotides They undergo similar reactions with purine; dephosphorylation, deamination and cleavage of glycosidic bonds. End product of pyrimidine catabolism; CO2, NH3, b-alanine, b-aminoisobutyrate.

27. REGULATION OF NUCLEOTIDE BIOSYNTHESIS

28. Regulation of purines nucleotides biosynthesis - phosphoribosylpyrophosphate(PRPP) availability. This inturn depends on the availability of: 1. PRPP synthetase 2. Ribose 5-phosphate PRPP glutamyl amidotransferase is inhibited by purines nucleotides e.g AMP, GMP. Adenylsuccinate synthetase Is inhibited by AMP. IMP dehydrogenase Is inhibited by GMP.

29. Regulation of pyrimidine nucleotides biosynthesis Carbomylphosphate synthetase Is the regulatory enzyme, and it is activated by PRPP & ATP Is inhibited by UDP & UTP. OMP decarboxylase Is inhibited by UMP & CMP.

30. Some Associated Disorders Adenylsuccinase deficiency; This leads to low level of adenine nucleotide. To replenish the adenine nucleotide, a patient can be treated with: -Oral supplement of adenine for several months (10mg/kg per day) -Allopurinol (5-10mg/kg per day) Phosphoribosyl pyrophosphate synthetase superactivity; PRPP amidotransferase is physiologically not saturated with PRPP. This leads to an increase in the synthesis of purines nucleotides, and this will eventually lead to an increase in production of uric acid. It can be corrected by the administration of allopurinol, which inhibits xanthine oxidase. As a result, more hypoxanthine accumulates, which is about 10 fold more soluble than uric acid.

31. Hereditary orotic aciduria; Occurs due to the deficiency of orotate phosphoribosyl transferase & OMP decarboxylase. It can be corrected by taking diet rich in uridine and cytidine. These compounds provide through phosphorylation, pyrimidine nucleotides required for DNA and RNA synthesis. Also UTP inhibits carbomylphosphate synthetase II and blocks the synthesis of orotic acid.

32. DEFECTS, DISORDERS, AND IMPLICATIONS OF NUCLEOTIDE BIOSYNTHESIS

33. There are several implications of defect on various biological processes and systems. Here are some of the implications; 1. Impaired DNA replication and repair : Nucleotides are the building blocks of DNA, and defect in nucleotide biosynthesis can lead to an insufficient supply of nucleotide for DNA replication and repair. This can result in errors in the DNA sequence, leading to mutations and genomic instability. 2. Reduced cell proliferation : Nucleotides are also essential for cell proliferation and growth. Defect in nucleotide biosynthesis can hinder the production of nucleotides required for cell division, resulting in slower or impaired cell proliferations.

34. 3. Impaired RNA synthesis and protein production: Nucleotides are also crucial for synthesizing RNA molecule, which are involved in various cellular processes, including protein production. A defect in nucleotide biosynthesis can lead to disruption of RNA synthesis and reduce protein production.

35. DISORDERS OF PURINE METABOLISM Uric Acid is the end product of purine metabolism in humans. The normal concentration of uric acid in the serum of adults is in the range of 3-7 mg/dl. In women, it is slightly lower (by about 1 mg) than in men. The daily excretion of uric acid is about 500-700 mg. Hyperuricemia : refers to an elevation in the serum uric acid concentration. This is sometimes associated with increased uric acid excretion ( uricosuria ).

36. Gout: is a metabolic disease associated with overproduction of uric acid. The prevalence of gout is about 3 per 1,000 persons, mostly affecting males. At the physiological pH, uric acid is found in a more soluble form as sodium urate . In severe hyperuricemia , crystals of sodium urate get disposited particularly in the joint, this causes inflammation in the joints resulting in a painful gouty arthritis .

37. TYPES OF GOUTY ARTHRITIS Gouty Arthritis are of Two types: Primary and Secondary Primary: it is an inborn error of metabolism due to overproduction of uric acid. These are the important metabolic defects (enzymes) associated with primary gout: PRPP synthetase PRPP glutamylamidotransferase HGPRT deficiency Glucose 6-phosphatase deficiency Elevation of glutathione reductase Secondary: is due to various disease causing increased synthesis or decreased excretion of uric acid.

38. LESCH-NYHAN SYNDROME Lesch-Nyhan Syndrome is a rare genetic condition that affects many males. The syndrome is caused by mutation of HPRT 1-gene that is encoding the enzymes hypoxanthine-guanine phosphoribosyltransferase (HGPRT) which leads to increased amounts of uric acid in the body. Symptoms 1. Motor and neurological problem 2. Aggressive behavior and learning disability 3. Irresistible urge to bite their fingers and lips

39. DISORDERS OF PYRIMIDINE METABOLISM Orotic Aciduria : This is a rare metabolic disorder characterized by the excretion of orotic acid in urine, severe anemia and retarded growth. It is due to the deficiency of the enzymes orotate phosphoribosyl transferase and OMP decarboxylase of pyrimidine synthesis. But also, certain drugs may lead to orotic aciduria e.g. allopurinol. Treatment : Feeding diet rich in uridine or cytidine Reye’s Syndrome : This is considered as a secondary orotic acidura . It is believed that a defect in ornithine transcarbamoylase (of urea cycle) causes the accumulation of carbamoyl phosphate this is then diverted for the increased synthesis and excretion of orotic acid.

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