Nucleic Acids - Structure and Function

Nucleic Acids - Chemistry, Function, & Metabolism

• Learning Objectives: Discuss the structure of nitrogenous bases, the biological roles of DNA and RNA, and associated disorders.
• Topic Outcomes:
  • Describe the structure, function, and biological role of nucleosides, nucleotides, and their analogues.
  • Describe the structure, function, and types of nucleic acids (DNA and RNA).
  • Explain purine and pyrimidine biosynthetic pathways and their regulation.
  • Explain the role of ribonucleotide reductase.
  • Describe disorders associated with purine and pyrimidine metabolism.

Nitrogenous Bases

• Planar, aromatic, and heterocyclic structures
• Derived from purine or pyrimidine
• Base numbering is "unprimed"
• Includes: Adenine (A), Guanine (G), Cytosine (C), Thymine (T), and Uracil (U).

Sugars

• Pentoses (5-carbon sugars)
• Numbering of sugars is "primed"
• Includes D-Ribose and 2'-Deoxyribose
• 2'-Deoxyribose lacks a 2' hydroxyl group.

Nucleosides

• Result from linking a sugar (ribose or deoxyribose) with a purine or pyrimidine base through an N-glycosidic linkage.
• Purines bond to the 1' carbon at the N9 position.
• Pyrimidines bond to the 1' carbon at the N1 position.

Nucleotides

• Result from linking one or more phosphates to a nucleoside through esterification at the 5' end of the sugar.
• Phosphates can be bonded to either C3 or C5 atoms.
• Forms mono-, di-, or triphosphates.
• Examples: Adenosine Monophosphate (AMP), 2'-Deoxythymidine Monophosphate.

Nucleotides (continued)

• Monomers for nucleic acid polymers
• Important energy carriers (ATP, GTP)
• Components of coenzymes (FAD, NAD+, Coenzyme A)
• RNA is a polymer of ribonucleotides.
• DNA is a polymer of deoxyribonucleotides.
• Both DNA and RNA contain Adenine, Guanine, and Cytosine.
• Ribonucleotides contain Uracil.
• Deoxyribonucleotides contain Thymine.

Naming Conventions

• Nucleosides: Purine nucleosides end in "-sine" (e.g., adenosine, guanosine); Pyrimidine nucleosides end in "-dine" (e.g., thymidine, cytidine, uridine).
• Nucleotides: Add "mono-," "di-," or "triphosphate" to the nucleoside name (e.g., adenosine monophosphate, cytidine triphosphate).

Nucleotide Metabolism

• Purine Ribonucleotides: Formed de novo; first purine derivative is Inosine Monophosphate (IMP).
• Purine ring components are derived from aspartate, glutamine, glycine, and formate.
• AMP and GMP are formed from IMP.

Purine Nucleotides

• Purine ring components are derived from aspartate, formate, glutamine, and glycine.
• Uric acid is a final breakdown product.

Purine Nucleotide Synthesis

• ATP plays a key role
• PRPP is a precursor to pyrimidine, histidine, and tryptophan synthesis
• Channeling reactions help increase overall rate.

IMP Conversion to AMP and GMP

• Different pathways for AMP and GMP synthesis from IMP.
• Requires different enzymes and energy sources

Regulatory Control of Purine Nucleotide Biosynthesis

• GTP plays a role in AMP synthesis, and ATP plays a role in GMP synthesis (reciprocal control).
• PRPP is a central molecule in the pathway, and its levels affect the entire process.
• Feedback inhibition by nucleotides (ADP, GDP, AMP, GMP, and others)
• Some enzymes have allosteric sites on multiple nucleotides, for regulation

Purine Catabolism and Salvage

• Ingested nucleic acids are degraded to nucleotides by pancreatic enzymes and intestinal enzymes in the intestine.
• Nucleosides are then absorbed and further degraded.
• Uric acid is the primary end product in humans.
• Salvage pathways allow the organism to reuse bases and nucleotides.

Intracellular Purine Catabolism

• Nucleotides are broken down to nucleosides by 5'-nucleotidase.
• Purine nucleoside phosphorylase (PNP) and other enzymes convert nucleosides into bases like hypoxanthine, xanthine, and guanine.
• Xanthine is oxidized to uric acid by xanthine oxidase.

Xanthine Oxidase

• A homodimeric protein that contains electron transfer proteins, FAD, and a Mo-pterin complex.

• Catalyzes the conversion of xanthine to uric acid.

• Transfers electrons to oxygen; generates hydrogen peroxide (H₂O₂), which is toxic.

• H₂O₂ is further converted to oxygen and water by catalase.

• The Purine Nucleotide Cycle*

• A cycle involves the conversion of AMP to IMP and back.

• Aspartate is deaminated to fumarate during the cycle.

Uric Acid Excretion

• Humans excrete uric acid crystals in urine.
• Birds, reptiles, and some insects excrete uric acid as insoluble crystals (paste form).
• High concentrations of uric acid in humans or animals may cause kidney stones

Purine Salvage

• Adenine phosphoribosyl transferase (APRT) and hypoxanthine-guanine phosphoribosyl transferase (HGPRT) catalyze the addition of a ribose-phosphate to free bases..
• This allows the reuse of purine bases.

Gout

• Gout arises from impaired excretion or overproduction of uric acid.
• Uric acid crystals can accumulate in joints, causing inflammation.

Allopurinol

• Allopurinol is a xanthine oxidase inhibitor that is used to treat gout.
• It inhibits uric acid formation.

Lesch-Nyhan Syndrome

• A genetic disorder caused by deficient HGPRT.
• Leads to increased levels of uric acid and neurological symptoms such as spasticity, aggression, and self-harm.

Purine Autism

• High levels of purine production may be present in 25% of the autistic population.

Pyrimidine Ribonucleotide Synthesis

• Uridine monophosphate (UMP) is synthesized first.
• CTP is synthesized from UMP.
• Pyrimidine ring is first synthesized; then attached to ribose-5-phosphate.

Pyrimidine Synthesis

• 2 ATP and bicarbonate needed in first step.
• Condensation Reactions between Carbamoyl Phosphate and Aspartate; forming Dihydroorotate;
• Final Reaction is catalyzed by OMP Decarboxylase; releasing CO2

UMP Synthesis Overview

• 2 ATPs are required, one is used in the initial step.
• Two reactions form carbamoyl aspartate and dihydroorotate.
• Dehydrogenase converts the reaction to orotate to orotate monophosphate.
• Ribose attaches to the orotate by Phosphoribosyl transferase forming orotidylate
• This molecule is then converted to UMP.

OMP Decarboxylase

• This enzyme is extremely efficient, with high catalytic proficiency.

UTP and CTP Synthesis

• Nucleoside monophosphate kinases convert UMP to UDP and then UTP.
• CTP is generated from UTP.
• Glutamine contributes to the amide nitrogen for the process.

Regulatory Control of Pyrimidine Synthesis

• Bacteria and animals differ in their regulatory mechanisms.
• UDP and UTP inhibit carbamoyl phosphate synthetase II, one of the rate-limiting enzymes.
• ATP and PRPP can activate the enzyme, promoting pyrimidine synthesis.

Degradation of Pyrimidines

• Pyrimidines are degraded similarly to purines.
• Steps are: dephosphorylation, deamination, and glycosidic bond cleavage.
• Uracil is converted to ẞ-alanine, which can be further metabolized
• All these steps result in the excretion of the final products into the urine, in the form of soluble crystals.

Deoxyribonucleotide Formation

• Deoxyribonucleotides are synthesized from corresponding ribonucleotides.
• Biosynthetic pathways are only for ribonucleotide production.

Adenosine Deaminase Deficiency

• Adenosine deaminase (ADA) is essential in purine degradation.
• ADA deficiency (or mutations), results in severe combined immunodeficiency (SCID), a severe immunodeficiency.
• ADA deficiency leads to the build-up of toxic compounds, and the buildup of compounds blocks the normal function of the immune system, preventing lymphocytes (white blood cells that are essential for the immune response) to function at an optimal level.
• All known ADA mutations affect the active site of this enzyme.

Adenosine Deaminase

• The α/β barrel domain structure determines the enzyme's function.
• The "TIM barrel" is a central barrel structure with 8 twisted parallel beta-strands connected by beta-turns and alpha-helices.
• The active site in the bottom of the funnel-shaped pocket is formed by loops in the protein.
• Adenosine deaminase is found in glycolytic enzymes; present in proteins that bind and transport metabolites.