Nucleic Acid Metabolism Quiz

Nucleic Acids Metabolism

• Nucleic acid metabolism encompasses two key aspects: biosynthesis (anabolism) and degradation (catabolism).
• The focus of metabolism includes purine and pyrimidine metabolism, as well as associated abnormalities.
• This metabolism is paramount to cellular functions, such as replication, transcription, and translation, which are vital to gene expression and cellular function.

Modern Relevance to Medicine

• Cancer therapy relies on targeting nucleic acid metabolism pathways to develop chemotherapeutic agents inhibiting DNA synthesis/repair.
• Understanding nucleic acid metabolism aids in diagnosing and treating numerous genetic conditions, facilitating gene therapy.
• Nucleoside analogs are used in antiviral treatments to combat viral infections by interfering with viral nucleic acid synthesis.
• Personalized medicine benefits from advances in genomics and RNA sequencing for tailoring treatments based on individual genetic profiles.

What Nucleic Acids Do

• Dictate the amino acid sequence in proteins.
• Carry genetic information passed from parent to offspring via chromosomes.
• Act as the fourth type of macromolecules.
• Link generations chemically.
• Are the source of genetic information within chromosomes.

Central Dogma of Molecular Biology

• DNA replication leads to identical copies of DNA.
• Transcription converts DNA's instructions to RNA.
• RNA translation interprets RNA's instructions to create proteins.
• This series of processes plays a crucial role in molecular biology.
• The processes involved in HIV replication that targets specific actions within the body.

Inhibitors of Nucleic Acid Synthesis

• 6-Mercaptopurine inhibits IMP conversion to AMP and GMP.
• Sulfonamides are analogs of PABA inhibiting folic acid synthesis.
• Acyclovir is converted to triphosphate, inhibiting viral DNA polymerase.
• Methotrexate inhibits dihydrofolate reductase & thymidylate synthase, crucial for DNA/RNA synthesis.
• Azaserine is a glutamine antagonist inhibiting purine and pyrimidine synthesis.
• Mycophenolic acid is a reversible, uncompetitive inhibitor of IMP dehydrogenase.
• 6-Thioguanine & 8-aza-guanine are anticancer agents inhibiting glutamine PRPP amidotransferase and the conversion of IMP to GMP.
• Fluorouracil is an anticancer drug converted to FdUMP, inhibiting thymidylate synthase.
• Zidovudine is an HIV/AIDS drug that terminates nucleotide formation.

Synthesis of Purine Ribonucleotides

• IMP is synthesized through the assembly of a purine base on ribose-5-phosphate.
• Kinases convert IMP-derived AMP and GMP to ATP and GTP.
• Purine nucleotide synthesis is regulated by feedback inhibition and feedforward activation.
• Salvage reactions convert purines to their nucleotide forms.

De Novo Biosynthesis of IMP

• The process starts with the synthesis of ribose-phosphate.
• A critical regulatory step is converting PRPP to 5-Phosphoribosyl-1-amine.
• Amidophosphoribosyl transferase is a key regulatory enzyme.
• Various amino acids play crucial roles.
• Several steps are involved in the process, utilizing molecules such as glycine, 5,10-methenyl-THF, glutamine, and aspartate.

Conversion of IMP to AMP & GMP:

• Shows feedback inhibition.
• Myofenolic acid is a reversible & uncompetitive inhibitor of IMP dehydrogenase.
• The drug prevents the rapid proliferation of T/B cells, critical for nucleic acid synthesis preventing graft rejection.

Conversion of Hypoxanthine to Adenine/Guanine

• Adenine/Guanine conversion involves changing a carbonyl oxygen to an amino group.
• The mechanism is common to both A and G conversions.

Formation of Di & Tri-phosphates

• Nucleoside monophosphates are converted to their di & triphosphate counterparts.
• Phosphate transfer from ATP (phosphorylation) catalyzed by specific nucleoside monophosphate kinases.
• Nucleoside diphosphate kinases are less specific for the process.

Formation of Deoxyribonucleotides from Ribonucleotides

• Deoxyribonucleotides are derived form corresponding nucleotides by reducing the 2'-C of ribose.
• This enzymatic conversion is catalyzed by ribonucleotide reductase.
• NADPH donates a pair of H-atoms.
• Ribonucleoside diphosphate/triphosphates work as substrates.

Regulatory Control of Purine Nucleotide Biosynthesis

• Purine biosynthesis is precisely regulated by feedback inhibition.
• Four key enzymes are involved in feedback regulation: PRPP synthetase, glutamine phosphoribosyl amidotransferase, adenylosuccinate synthetase, and IMP dehydrogenase.
• The step where PRPP synthetase converts ribose-5-phosphate to Phosphoribosyl pyrophosphate is regulated.
• Glutamine phosphoribosyl amidotransferase is activated by PRPP and competitively inhibited by AMP, GMP, and IMP.
• Adenylosuccinate synthetase is competitively inhibited by AMP without affecting GMP synthesis.
• IMP dehydrogenase is competitively inhibited by GMP without affecting AMP synthesis.

Purine Salvage Pathways

• Free purines released during nucleic acid degradation are converted into nucleotides through salvage pathways.
• Adenine phosphoribosyltransferase and hypoxanthine/guanine phosphoribosyltransferase are crucial enzymes in these pathways.

Digestion & Degradation of Nucleic Acids/Purine Nucleotides in the Gastrointestinal Tract (GI tract)

• Ingested nucleic acids are degraded into nucleotides by pancreatic nucleases and intestinal phosphodiesterases.
• Nucleotides are converted to nucleosides, and nucleosides are further degraded or absorbed.
• Bases are reused in salvage pathways.
• Most bases are degraded into uric acid and excreted in urine.

Degradation of Purines in Humans

• Purines in humans are degraded to urate.
• Many enzymes are involved in the process, including nucleotidases, nucleoside phosphorylases, deaminases, and xanthine oxidases.
• Urate is the final product and excreted.

AMP Degradation/Catabolism

• AMP is degraded to IMP by AMP deaminase.
• Nucleotidase hydrolyzes AMP to adenosine and IMP to inosine.
• Adenosine is deaminated to inosine and inosine is converted to hypoxanthine.
• Xanthine oxidase oxidizes hypoxanthine to xanthine, and then xanthine to uric acid.
• Uric acid is the end product and excreted in urine.

GMP Degradation/Catabolism

• GMP is degraded to GMP by nucleotidase.
• GMP is converted to guanosine.
• Guanosine is converted to guanine, and guanine is deaminated to xanthine.
• Xanthine oxidase converts xanthine to uric acid.

The Fate of Uric Acid

• In primates, uric acid is the final product and excreted.
• In other mammals, uric acid is oxidized to allantoin, which is then hydrolyzed to allantoic acid.
• Some organisms convert uric acid to glyoxylic acid.

Degradation of Uric Acid

• Excretion or degradation, depending on species
• Breakdown by marine invertebrates down to ammonia.

Pyrimidine Metabolism

• Pyrimidine biosynthesis involves de novo pathways and salvage pathways.
• Pyrimidine catabolism focuses on the breakdown of pyrimidine nucleotide bases.

De Novo Synthesis of Pyrimidine Nucleotides

• Pyrimidine ring synthesis occurs before the ribose-5-phosphate attachment.
• Specific atoms of the pyrimidine ring are derived from bicarbonate, ammonia, and aspartate.

De Novo Biosynthesis of Pyrimidines: Step-by-Step

• Step 1: Synthesis of carbamoyl phosphate from bicarbonate, ammonia, and ATP.
• Step 2: Carbamoyl phosphate reacts with aspartate to form N-carbamoyl aspartate, a committed step.
• Step 3: Dihydroorotase acts on N-carbamoyl aspartate to form dihydroorotate. This step removes water.
• Step 4: Dihydroorotate is oxidized to orotate via dihydroorotate dehydrogenase.
• Step 5: Orotate reacts with PRPP to create orotidine 5'-monophosphate (OMP).
• Step 6: OMP is decarboxylated to form UMP by orotidylate decarboxylase.

Overview of De Novo Synthesis of Pyrimidines

• Shows the key steps and enzymes involved in the synthesis of pyrimidines from carbamoyl phosphate, aspartate.
• Diagram the process from bicarbonate, ammonia and glutamine to finally synthesizing UMP.

De Novo Biosynthesis of Pyrimidines: Step 7 (Continuation)

• Uridylate (UMP) is converted to UTP through steps using ATP and kinases.
• Specific UMP kinase & less specific UDP kinase play critical roles.

Synthesis of Cytidine Triphosphate (CTP) from UTP

• Forming CTP involves replacing a carbonyl with an amino group on UTP using ATP with the action of CTP synthetase.
• Glutamine acts as the nitrogen donor in animals, while ammonia serves the same role in bacteria.

Overview of Thymidylate Biosynthesis

• Thymidylate synthesis processes converting dUMP to dTMP.
• This conversion is crucial for DNA synthesis and involves specific enzymes.
• Glycine, serine, and 10-formyl-THF play key roles in the process.
• 5-Fluorouracil is a crucial inhibitor of this synthesis in cancer treatment.

Salvage Pathway Synthesis of Pyrimidines

• Free pyrimidines released during nucleotide breakdown are salvaged and recycled for pyrimidine nucleotide synthesis.
• Pyrimidine phosphoribosyltransferase enzyme is key in this process, using PRPP as the source of ribose-5-phosphate.

Feedback Regulatory Control of Pyrimidine Synthesis

• Regulation in bacteria occurs at aspartate transcarbamoylase (ATCase).
• In animals, regulation is at carbamoyl phosphate synthetase II (CPS II).
• UDP & UTP inhibits CPS II.
• ATP & PRPP activate CPS II.
• OMP decarboxylase is competitively inhibited by UMP & CMP.
• Inhibition of PRPP synthetase in purine synthesis also regulates pyrimidine synthesis.

Overview of Pyrimidine Biosynthesis Regulation

• Diagrams show the key regulatory steps and enzymes involved in the feedback regulation of pyrimidine biosynthesis.
• Highlights enzyme regulation by substrate and end product inhibition.

Catabolism/Degradation of Pyrimidine Nucleotides

• CMP and UMP are dephosphorylated by nucleotidase to form nucleosides.
• Nucleosides are cleaved to produce ribose-1-phosphate and free pyrimidine bases (cytosine, uracil, thymine) via nucleosidase or phosphorylase.
• Cytosine is converted to uracil, which is further degraded.
• Thymine is broken down to CO2, NH4, and β-aminoisobutyrate.
• Products are excreted in urine or converted to CO2, H20, and NH4+.

Abnormalities in Nucleic Acid Metabolism

• Gout is a painful arthritis associated with increased uric acid formation.
• Treatment involves inhibiting xanthine oxidase (e.g., allopurinol).
• Lesch-Nyhan syndrome results from HGPRT deficiency leading to excess purines.
• Treatment involves managing behavioral issues.
• Von Gierke's Disease (Type 1 glycogen storage disease) is caused by glucose-6-phosphatase deficiency, leading to hypoglycemia and purine overproduction.
• Xanthine oxidase deficiency causes hyperuricemia (high uric acid).
• Enzyme replacement therapy can prove beneficial.

Orotic Aciduria

• A genetic deficiency of either orotate phosphoribosyltransferase or orotidylate decarboxylase leads to orotic aciduria.
• This results in the excretion of orotic acid and leads to megaloblastic anemia.
• The treatment involves using uridine to bypass the missing enzymes.

Some Clinical Relevance of Nucleotide Synthesis

• Thymidylate synthesis is crucial for cell proliferation, making enzymes involved valuable drug targets.
• Chemotherapeutic agents like 5-fluorouracil, raltitrexed, methotrexate, and trimethoprim target involved enzymes in various cancers to inhibit.
• In 2002, research found that some organisms lack thymidine kinase yet survive on a thymidine deficient media.
• This observation led to the discovery of flavin-dependent thymidylate synthase.