Nucleotide Metabolism: Synthesis and Degradation

• Nucleotide metabolism involves the synthesis and degradation of nucleotides.
• Nucleotides and nucleosides play crucial roles in various biological processes.

Learning Objectives

• Understanding the structure of nucleotides and nucleosides is a key objective.
• Focus on synthesizing purines and pyrimidines.
• Learn the degradation pathways of purine and pyrimidine nucleotides.
• Grasp the association between diseases and the synthesis and degradation of purines and pyrimidines.

Overview of Nucleotide Functions

• Nucleotides provide energy for metabolism in the form of ATP.
• They are structural components of enzyme cofactors like NAD+ and FAD.
• Nucleotides act as second messengers in signal transduction, such as cAMP.
• They carry activated intermediates in synthesizing carbohydrates, lipids, and conjugated proteins, like UDP-glucose.

Nucleic Acid functions

• Nucleic acids are responsible for storing genetic information (DNA).
• They transmit genetic information (mRNA).
• Nucleic acids enable the processing of genetic information (ribozymes).
• They allow for protein synthesis via tRNA and rRNA

Nucleotide Structure

• Nucleotides consist of a nitrogenous base, a pentose monosaccharide, and one to three phosphate groups.
• Nitrogen-containing bases in nucleotides include purines and pyrimidines.

Nucleotides and Nucleosides

• A nucleotide is composed of a nitrogenous base, a pentose sugar, and a phosphate group.
• A nucleoside is composed of a nitrogenous base and a pentose sugar.
• A nucleobase is just a nitrogenous base.

Nucleosides

• Nucleosides are formed by adding a pentose sugar to a base through a glycosidic bond.
• If the sugar is ribose, the resulting nucleoside is a ribonucleoside.
• If the sugar is deoxyribose, the resulting nucleoside is a deoxyribonucleoside.
• Examples of ribonucleosides include adenosine, guanosine, cytidine, and uridine.
• Deoxyribonucleosides are named with a 'deoxy' prefix.
• The base and sugar in nucleosides are numbered independently.

Nucleotides

• Nucleotides are formed when one or more phosphate groups are added to a nucleoside.
• The 1st phosphate is attached via an ester linkage to the 5'-OH of the pentose.
• Nucleotides can be mono-, di-, or triphosphates.
• Phosphate groups in nucleotides are negatively charged at neutral pH.
• Nucleic acids contain one phosphate moiety per nucleotide.
• Examples include AMP, ADP, and ATP.

Purines and Pyrimidines

• Both DNA and RNA possess the same purine bases: Adenine (A) and guanine (G).
• Cytosine (C) is a pyrimidine base present in both DNA and RNA.
• DNA contains thymine (T), whereas RNA contains uracil (U) in their second pyrimidine base.

Unusual Bases

• Species of DNA and RNA include unusual bases.
• Methylation, acetylation, and glycosylation are common nucleotide modifications.

Synthesis of Purine Nucleotides

• Purine rings are assembled on ribose-5-phosphate in the liver.

• Ribose-5-phosphate, generated in the hexose monophosphate shunt, serves as the starting compound.

• 5-Phosphoribosyl-1-pyrophosphate (PRPP) acts as an activated pentose participating in purine synthesis.

• Since the sugar moiety is ribose, the end products yield ribonucleotides.

• Ribose undergoes reduction when deoxyribonucleotide is required.

• Glutamine transfers its amide nitrogen to PRPP, forming 5-phosphoribosylamine (committed step).

• PRPP glutamyl amidotransferase, activated by PRPP, undergoes feedback inhibition by nucleotides like AMP, GMP, and IMP.

• 4 steps require ATP

• 2 steps require N-formyl tetrahydrofolate as a carbon donor.

• Synthetic inhibitors block the growth of rapidly dividing cells.

Inhibitors of Purine Synthesis

• Sulfonamides resemble para-aminobenzoic acid (PABA).
• Sulfa drugs hinder bacterial folic acid synthesis, inhibiting microbial proliferation.
• Sulfonamides are harmless to humans because humans acquire folic acid through diet.
• Folic acid analogs such as methotrexate inhibit the synthesis of purine nucleotides, controlling cancer.
• Proliferation of normal cells is affected by these inhibitors because they cause ailments like anemia, baldness and scaly skin etc.

Synthesis of Adenosine and Guanosine Monophosphate

• GTP is required for AMP synthesis, while ATP is required for GMP synthesis.
• These reactions are inhibited by their products.
• Mycophenolic acid reversibly inhibits inosine monophosphate dehydrogenase, depriving rapidly proliferating T and B cells of nucleic acids & prevents rejection of graft organ.

Conversion of Nucleoside Monophosphates to Nucleoside Diphosphates

• Kinases do not distinguish between ribose and deoxyribose.
• ATP acts as a phosphate source due to its high concentration.

Salvage Pathway for Purines

• Free purines are formed through normal nucleic acid turnover and dietary intake.
• Purines can convert into corresponding nucleotides through the salvage pathway.
• PRPP provides the ribose-5-phosphate source for this reaction.
• Reaction irreversibility results from PPi release and hydrolysis.

Synthesis of Deoxyribonucleotides

• 2'-deoxyribonucleotides, required for DNA synthesis, are synthesized from ribonucleoside diphosphatase.
• The synthesis occurs with C2 ribose moiety reduction.
• Thioredoxin has a coenzyme function in ribonucleotide reductase.
• Two cysteines separate the two amino acids that compose thioredoxin.

Regulation of Deoxyribonucleotide Synthesis

• Ribonucleotide reductase is regulated by both catalytic and allosteric sites.
• The enzyme dATP inhibition prevents all four nucleosides diphosphate synthesis and supplies enough deoxyribonucleotides for DNA synthesis.
• Activity increases via trisphosphate nucleotide binding as deoxythymidine enables GDP to be reduced to dGDP.

Degradation of Purine Nucleotides

• Purine nucleotide degradation takes place in the small intestine.
• Nucleic acids go through hydrolysis into nucleotides.
• Purine bases are not recycled for nucleic acid biosynthesis; they convert into uric acid.

Disease Association with Purine Degradation

• Gout arises from the end product of purine metabolism.

• GOUT, caused by uric acid overproduction or underexcretion, is a metabolic disease with high uric acid levels in the blood.

• Sodium urate crystals form in soft tissues, and particularly joints, during severe hyperuricemia.

• Formation of uric acid stones may occur.

• Attacks are treated with anti-inflammatory agents and long-term treatment involve lowering the uric acid levels.

• Drugs inhibiting uric acid synthesis or increasing renal excretion of uric acid is prescribed.

• Adenosine Deaminase (ADA) is necessary for adenosine breakdown.

• Results in accumulation of adenosine which is converted to its (deoxy)ribonucleotide form.

• Higher dATP levels and slower enzyme activity prevent nucleotide production.

• Severe immunodeficiency is caused since the Lymphocytes are highly active via the cytosolic enzyme.

• Cells lose the ability to synthesize DNA.

• Lesch-Nyhan syndrome: is caused by hypoxanthine-guanine phosphoribosyltransferase (HGPRT) deficiency, an enzyme needed for the pathway.

• HGPRT deficiency causes PRPP to accumulate, increasing GMP and IMP synthesis as degradation occurs.

• Excessive uric acid buildup characterizes this males only characterized syndrome.

• Neurological anomalies such as mental retardation, aggressive behavior, learning disability etc, lead to self-mutilation by biting fingers and lips.

Pyrimidine Synthesis and Degradation

• Unlike purine rings, pyrimidine rings are synthesized before being attached to ribose-5-phosphate.

Synthesis of Carbamoyl Phosphate

• Carbamoyl phosphate is synthesized using ATP, glutamine, and CO2.

• The reaction is catalyzed by CPS-II.

• Regulation of pyrimidine synthesis in mammalian cells sees the carbamoyl phosphate synthetase II domain of CAD inhibited by UTP, and activated by PRPP.

• Aspartate transcarbamoylase is the regulated step in prokaryotic cells and is inhibited by CTP.

• Orotic aciduria: mutations in orotate phosphoribosyltransferase and OMP decarboxylase affect UMP synthase, and lead to poor growth, megaloblastic anemia, and excess orotate in urine.

• Uridine administration can improve anemia and lower orotate excretion.

• Pyrimidine is converted to orotidine monophosphate (OMP).

• PRPP is the ribose-phosphate donor.

• The process becomes irreversible upon its release.

• Purine and pyrimidine synthesis requires glutamine, aspartic acid, and PRPP.

• CPS-II is inhibited by uridinetriphosphate and activated by PRPP.

• Pyrimidine synthesis increases when carbomyl phosphate is highly available due to defective urea cycle via CPS-I.

Synthesis of Cytidine Triphosphate

• CTP synthase catalyzes the amination of UTP by glutamine and ATP.

Synthesis of Deoxythymidine Monophosphate

• Conversion of dUMP to dTMP requires methylene tetrahydrofolate via the methyl group.
• Thymidylate synthase inhibitors include thymine analogs like 5-fluorouracil.
• Tetrahydrofolate is inhibited by Methotrexate because it is an anti-enzyme agent in cancer.

Degradation and Salvage of Pyrimidines

• Pyrimidine rings open and degrade into highly soluble products like beta-alanine and beta-aminoisobutyrate, producing NH3 and CO2.
• Pyrimidines convert to respective nucleotides via phosphorylation in the salvage pathway.

Practice Questions

• Which of the following is a precursor for purine synthesis? A) Glycine
• Which of the following is the enzyme responsible for the regulatory step of pyrimidine synthesis? B) Carbomylphosphate synthase II
• Which of the following is a precursor for purine and pyrimidine synthesis? A) Aspartic Acid