Nitrogen Anabolism, Nucleotides & Disease

Which organisms can synthesize all 20 common amino acids, and how many can mammals synthesize?

Plants and bacteria synthesize all 20 common amino acids; mammals can synthesize about half of them (nonessential), while the rest must be acquired in the diet (essential or conditionally essential).

List the 5 major nonessential amino acids reviewed in lecture.

Alanine (Ala), Asparagine (Asn), Aspartate (Asp), Glutamate (Glu), and Serine (Ser).

How is Alanine synthesized, and what enzyme catalyzes this reaction?

Synthesized from pyruvate via transamination from glutamate, catalyzed by Alanine Aminotransferase (ALT).

Note Takeaway: Are all transamination reactions degradative?

No; not all transaminations are degradative—they are reversible and also function as biosynthetic reactions to make nonessential amino acids.

Describe the glucose-alanine cycle between skeletal muscle and the liver.

In skeletal muscle, glycolysis produces pyruvate, which is transaminated with glutamate to form alanine; alanine travels in the blood to the liver, where it is transaminated back to pyruvate for gluconeogenesis to produce blood glucose.

How is Aspartate synthesized via transamination, and what enzyme catalyzes it?

Synthesized from oxaloacetate (OAA) by transamination from glutamate, catalyzed by Aspartate Aminotransferase (AST).

How can Aspartate be formed directly from Asparagine?

By hydrolysis (deamidation) of asparagine, catalyzed by the enzyme Asparaginase.

How is Asparagine synthesized, and what are the cofactors/donors required in mammals?

Synthesized by the amidation of aspartate, catalyzed by Asparagine Synthetase; requires ATP (hydrolyzed to AMP + PPi) and uses Glutamine as the nitrogen donor (forming glutamate).

How does Asparagine Synthetase prevent free ammonia from escaping into the cell during catalysis?

Asparagine synthetase has an intramolecular ammonia tunnel: the amide group from glutamine is cleaved at the catalytic site and channeled directly through the tunnel to the active site where amidation of aspartate takes place.

Application Question: Bacteria have an asparagine synthetase that uses ammonium (NH4+) as the nitrogen donor, whereas mammals use glutamine. Why do mammals use glutamine instead of free ammonium?

Free ammonia/ammonium is toxic to mammalian cells (especially the brain), so mammals safely shuttle nitrogen inside glutamine and use an ammonia tunnel within asparagine synthetase so free NH3 is never released into the cell.

What are the three major reactions that synthesize or interconvert Glutamate?

1. Transamination: alpha-KG + Amino Acid <-> Glutamate + alpha-Keto Acid (via Transaminase); 2. Reductive Amination: alpha-KG + NH3 + NADPH <-> Glutamate + NADP+ (via Glutamate Dehydrogenase / GDH); 3. Hydrolysis: Glutamine + H2O <-> Glutamate + NH3 (via Glutaminase).

What glycolytic intermediate provides the carbon chain for Serine, and what is Serine's role in one-carbon metabolism?

Serine's carbon chain is derived from 3-phosphoglycerate; serine is a precursor of glycine, and its beta-carbon is transferred to tetrahydrofolate (THF) via serine hydroxymethyltransferase.

Glutamate serves as the direct metabolic precursor to which three other amino acids?

Glutamine, Proline, and Arginine.

List the 6 conditionally essential amino acids reviewed in lecture.

Arginine (Arg), Cysteine (Cys), Glutamine (Gln), Glycine (Gly), Proline (Pro), and Tyrosine (Tyr).

Why are certain amino acids classified as "conditionally essential"?

They can be synthesized by the body under normal conditions, but rely on essential amino acid precursors (e.g., Tyr requires Phe; Cys requires Met) or are needed in higher amounts than the body can produce during growth, stress, or illness.

Which metabolic cycle synthesizes Arginine?

The Urea Cycle (from ornithine -> citrulline -> argininosuccinate -> arginine).

What is the physiological role of Creatine and Phosphocreatine?

They act as a critical energy buffer and energy storage molecule in tissues with fluctuating energy demands, particularly skeletal muscle; when ATP falls short, phosphocreatine donates its phosphoryl group to ADP to rapidly regenerate ATP.

Which three amino acids are required to synthesize Creatine, and what does each contribute?

Arginine and Glycine provide the carbon and nitrogen framework; Methionine (via S-adenosylmethionine / SAM / AdoMet) donates a methyl (-CH3) group.

What enzyme phosphorylates Creatine in muscle tissue, and what is the product?

Creatine kinase phosphorylates creatine (using ATP) to form Phosphocreatine (creatine phosphate).

What is Creatinine, how is it formed, and what is its clinical significance?

A small amount of creatine and phosphocreatine spontaneously cyclizes into creatinine, a waste product excreted in urine that serves as a key clinical indicator of renal (kidney) function.

What signaling molecule is synthesized directly from Arginine?

Nitric oxide (NO), an important biological messenger.

What important tetrapyrrole ring system uses Glycine as a primary precursor?

Porphyrins (which form heme).

How is Tyrosine synthesized in the body, and why is it conditionally essential?

Synthesized by the hydroxylation of the essential amino acid Phenylalanine at C-4 of the phenyl ring; if dietary phenylalanine is insufficient, tyrosine becomes insufficient.

What percentage of ingested Phenylalanine is typically converted to Tyrosine?

Approximately 75% (3/4) of ingested phenylalanine is hydroxylated to form tyrosine.

What enzyme catalyzes the conversion of Phenylalanine to Tyrosine, and what cofactor does it require?

Phenylalanine hydroxylase; it is strictly dependent on the cofactor Tetrahydrobiopterin (BH4).

What are the biological characteristics of Tetrahydrobiopterin (BH4)?

It is a cofactor structurally similar to folic acid, but it is NOT a vitamin because humans synthesize it in the body starting from GTP.

Besides phenylalanine hydroxylase, which three neurotransmitter biosynthetic pathways require BH4 as an essential cofactor?

The biosynthesis of Dopamine, Noradrenaline (Norepinephrine), and Serotonin.

What are the three major physiological fates of Tyrosine in the cell?

1. Incorporated into protein structure; 2. Acts as an important phosphorylation acceptor in regulatory enzymes (e.g., receptor tyrosine kinases); 3. Serves as the precursor to catecholamine neurotransmitters.

Application Problem: A 1-year-old child with mental retardation has a deficiency of dihydrobiopterin reductase, an enzyme involved in the regeneration/synthesis of BH4. This deficiency leads to an increased blood level of which molecule?

Phenylalanine (because without BH4, phenylalanine hydroxylase cannot convert phenylalanine into tyrosine).

What is S-adenosylmethionine (SAM / AdoMet), and what is its primary biochemical role?

The most abundant methionine-containing metabolite; it serves as a universal methylating agent (one-carbon methyl donor) for around 300 metabolic and biosynthetic reactions, including the control of gene expression via DNA and histone methylation.

How is SAM synthesized from Methionine?

Methionine reacts with ATP in a reaction catalyzed by Methionine adenosyltransferase to form SAM (AdoMet).

Trace the steps of the Methionine Cycle from SAM to Homocysteine.

1. Methyl transferase transfers the methyl (-CH3) group from SAM to an acceptor (such as in creatine or epinephrine synthesis), converting SAM into S-adenosylhomocysteine (SAH / AdoHcy); 2. Adenosylhomocysteinase cleaves adenosine from SAH to yield Homocysteine.

How is Methionine regenerated from Homocysteine in the Methionine Cycle?

Methionine synthase (a Vitamin B12-dependent enzyme) transfers a methyl group from 5-methyl-THF (forming THF) onto homocysteine to regenerate methionine.

Why doesn't the Methionine Cycle eliminate the dietary requirement for Methionine?

Because Methionine is an essential amino acid; the cycle only recycles homocysteine that originally came from methionine after SAM-dependent methylation, and some homocysteine is diverted away to synthesize cysteine.

How is Cysteine connected to the Methionine Cycle?

Methionine provides the sulfur atom for cysteine synthesis via homocysteine (homocysteine is converted to cystathionine by B6-dependent cystathionine beta-synthase, and then to cysteine); therefore, insufficient methionine leads to insufficient cysteine.

How are the Methionine Cycle and the Folate Cycle linked?

Regenerating methionine from homocysteine requires a methyl group supplied by 5-methyltetrahydrofolate (5-methyl-THF), catalyzed by B12-dependent Methionine Synthase.

What is Glutathione (GSH), and which three amino acids compose it?

Glutathione is a tripeptide cellular reducing agent and major antioxidant derived from Glutamate, Cysteine, and Glycine (present in plants, animals, and some bacteria).

What is the structural difference between reduced glutathione (GSH) and oxidized glutathione (GSSG)?

Reduced glutathione (GSH) exists as a monomer with a free thiol (-SH) group on its cysteine residue; oxidized glutathione (GSSG) is a dimer of two GSH molecules linked by a covalent disulfide (S-S) bond.

Write the chemical reaction showing how Glutathione neutralizes toxic peroxides.

2 GSH + R-O-O-H -> GSSG + H2O + R-OH (reduces harmful peroxides into harmless water and alcohol).

What enzyme catalyzes the reduction of peroxides using glutathione, and what unique trace element/amino acid does it require?

Glutathione Peroxidase; it is a selenoprotein containing Selenocysteine—without selenium, oxidative damage runs rampant.

What are the direct neurotransmitter roles of unmodified Glutamate, Aspartate, D-Serine, and Glycine?

1. Glutamate: main excitatory neurotransmitter (acts via NMDA receptors); 2. Aspartate: excitatory neurotransmitter; 3. D-Serine: co-agonist of NMDA-type glutamate receptors that modulates receptor activity; 4. Glycine: inhibitory neurotransmitter in the spinal cord, brainstem, and retina.

What are the three Catecholamines, where are they synthesized, and what is their physiological function?

Dopamine, Norepinephrine, and Epinephrine; synthesized in the brain, nerve tissues, or adrenal glands; released in response to physical or emotional stress (fight-or-flight response) and associated with reward, attention, and arousal.

Trace the 4-step enzymatic pathway that synthesizes Catecholamines from Tyrosine.

1. Tyrosine -> Dihydroxyphenylalanine (DOPA) via Tyrosine hydroxylase (uses O2); 2. DOPA -> Dopamine via DOPA decarboxylase (releases CO2); 3. Dopamine -> Norepinephrine via Dopamine-beta-hydroxylase (uses O2); 4. Norepinephrine -> Epinephrine via Phenylethanolamine N-methyltransferase (uses SAM/AdoMet as methyl donor).

Which step in Catecholamine synthesis specifically requires SAM (AdoMet)?

The final step: methylation of Norepinephrine to form Epinephrine, catalyzed by Phenylethanolamine N-methyltransferase.

How is GABA (gamma-aminobutyrate) synthesized, and what cofactor is required?

Synthesized in a single step by the decarboxylation of Glutamate, catalyzed by Glutamic acid decarboxylase, which requires Pyridoxal Phosphate (PLP / Vitamin B6).

What is the physiological function of GABA?

It is the major inhibitory neurotransmitter in the brain; it reduces neuronal excitability and prevents excessive nervous signaling.

Application Problem: A 12-year-old boy with epilepsy is started on a benzodiazepine, which promotes the activity of GABA. GABA is derived from glutamate by which type of reaction?

Decarboxylation (specifically PLP/Vitamin B6-dependent decarboxylation).

What amino acid is the precursor to Serotonin, and what are Serotonin's physiological functions?

Derived from Tryptophan; plays a key role in mood, sleep, digestion, blood clotting, and sexual desire.

Trace the 2-step enzymatic synthesis of Serotonin from Tryptophan.

1. Tryptophan -> 5-hydroxytryptophan via Tryptophan-5-hydroxylase (uses O2 and BH4); 2. 5-hydroxytryptophan -> Serotonin (5-hydroxytryptamine) via Aromatic L-amino acid decarboxylase (releases CO2, uses PLP).

What cofactor is universally required for the amino acid decarboxylation reactions that yield biological amines and neurotransmitters?

Pyridoxal phosphate (PLP, derived from Vitamin B6).

What are the three structural components of a nucleotide, and how does a nucleoside differ?

A nucleotide consists of: 1. A nitrogenous base (purine or pyrimidine); 2. A pentose sugar (ribose or deoxyribose); and 3. One or more phosphate groups. A nucleoside is the molecule WITHOUT a phosphate group (base + pentose only).

List the major Purine and Pyrimidine bases and specify whether they appear in DNA, RNA, or both.

Purines (2-ring system): Adenine (A) and Guanine (G) are in both DNA and RNA. Pyrimidines (1-ring system): Cytosine (C) is in both DNA and RNA; Thymine (T) is only in DNA; Uracil (U) is only in RNA.

Beyond building DNA and RNA, what are three major cellular functions of Adenine nucleotides?

1. Carry chemical energy in the cell (ATP); 2. Serve as components of many enzyme cofactors (NAD+, FAD, CoA); 3. Serve as intracellular signaling molecules (cAMP).

Contrast de novo nucleotide synthesis with salvage pathways.

De novo pathways build nucleotides from simple metabolic precursors (amino acids, ribose 5-phosphate, CO2, NH3) and are energy-expensive; Salvage pathways recycle free bases and nucleosides released from nucleic acid breakdown.

What happens to dietary DNA and RNA that we ingest?

Ingested nucleic acids are degraded in the digestive tract through the sequential action of nucleases.

In de novo nucleotide synthesis, what is the key difference in how the ring is built between Purines and Pyrimidines?

In Purine synthesis, the base ring is synthesized step-by-step while ALREADY attached to ribose 5-phosphate (starting from PRPP). In Pyrimidine synthesis, the pyrimidine ring is built first (as orotate), and ribose 5-phosphate is attached AFTER ring formation.

Which amino acids serve as the main nitrogen and carbon precursors in de novo Purine vs. Pyrimidine synthesis?

Glutamine provides most amino groups in both pathways; Glycine is the main precursor for Purines; Aspartate is the main precursor for Pyrimidines.

What is PRPP (5-phosphoribosyl-1-pyrophosphate), and how is it synthesized?

PRPP is an activated pentose intermediate synthesized from Ribose 5-phosphate (from the pentose phosphate pathway) and ATP, catalyzed by Ribose phosphate pyrophosphokinase (also called PRPP synthetase): Ribose 5-phosphate + ATP -> PRPP + AMP.

What two molecules provide all the atoms for the de novo synthesis of the Pyrimidine ring (orotate)?

Aspartate and Carbamoyl phosphate.

List the 6 sequential milestones of the Pyrimidine biosynthesis pathway.

1. Formation of Carbamoyl-aspartate; 2. Formation of Orotate (orotic acid); 3. Formation of OMP (orotidylate); 4. Formation of UDP/UTP (via UMP); 5. Formation of CTP; 6. Formation of dTMP.

Compare Carbamoyl Phosphate Synthetase II (CPS-II) and Carbamoyl Phosphate Synthetase I (CPS-I).

CPS-II is located in the cytosol, uses Glutamine as its nitrogen donor, and makes carbamoyl phosphate for Pyrimidine synthesis. CPS-I is located in the mitochondria, uses free Ammonia (NH3), and makes carbamoyl phosphate for the Urea Cycle. (Bacteria have only a single enzyme).

Why do eukaryotic cells maintain separate mitochondrial and cytosolic carbamoyl phosphate pools?

It represents a cellular division of labor (compartmentalization), keeping metabolite pools localized in the specific compartment where they are needed (mitochondria for urea disposal vs. cytosol for pyrimidine synthesis).

Write the reaction catalyzed by cytosolic Carbamoyl Phosphate Synthetase II (CPS-II) and describe its special structural feature.

Glutamine + CO2 + 2 ATP -> Carbamoyl phosphate + 2 ADP + Pi + Glutamate. CPS-II uses an internal transfer tunnel to move unprotonated ammonia from the glutamine hydrolysis site to the biosynthetic site, preventing protonation of NH3 to NH4+.

Trace the reactions from Carbamoyl phosphate and Aspartate to Orotate.

1. Aspartate + Carbamoyl phosphate -> N-Carbamoylaspartate + Pi (via Aspartate transcarbamoylase / ATCase); 2. N-Carbamoylaspartate -> L-Dihydroorotate + H2O (condensation/cyclization via Dihydroorotase); 3. L-Dihydroorotate + NAD+ -> Orotate + NADH + H+ (via Dihydroorotate dehydrogenase).

What is the CAD complex in eukaryotic pyrimidine biosynthesis?

A single multifunctional cytosolic protein complex containing the first 3 enzymes of pyrimidine synthesis: 1. CPS-II (Carbamoyl phosphate synthetase II); 2. ATCase (Aspartate transcarbamoylase); 3. Dihydroorotase.

How is Orotate converted into UMP (Uridylate / Uridine 5'-monophosphate)?

1. Orotate reacts with PRPP (N-1 of the ring attacks PRPP, releasing PPi) to form Orotidylate (OMP), catalyzed by Orotate phosphoribosyltransferase; 2. OMP is decarboxylated (releasing CO2) to form UMP, catalyzed by Orotidylate (OMP) decarboxylase. (In humans, both activities are on a single bifunctional enzyme called UMP Synthase).

What is remarkable about the catalytic rate enhancement of OMP Decarboxylase?

It enhances the reaction rate by a factor of 1.1 x 10^17; the half-life of the uncatalyzed reaction would be 3 billion years!

How is UMP converted into UTP and then CTP?

1. UMP is phosphorylated twice by nucleoside kinases (using 2 ATP -> 2 ADP) to form UDP and then UTP; 2. Cytidylate synthetase (CTP synthase) converts UTP into CTP using an amino group from Glutamine (forming glutamate) and requiring 1 ATP (via an acyl phosphate intermediate).

What is the role of CTP Synthetase (specifically isoform CS-II), and how is it regulated?

CS-II is a rate-limiting enzyme in the biosynthesis of pyrimidine precursors for DNA and RNA; it is allosterically activated by GTP (a purine), which helps balance the cellular pools of C and G nucleotides.

How is dUMP converted into dTMP, and what two enzymes are required in this cycle?

1. Thymidylate synthase transfers a one-carbon unit from N5,N10-methylenetetrahydrofolate to dUMP and reduces it to a methyl group, forming dTMP and oxidizing the cofactor to 7,8-dihydrofolate (DHF); 2. Dihydrofolate reductase (DHFR) reduces DHF back to tetrahydrofolate (THF) using NADPH.

How is THF converted back into N5,N10-methylenetetrahydrofolate after the DHFR reaction?

Serine hydroxymethyltransferase (a PLP-dependent enzyme) transfers a one-carbon group from Serine to THF, regenerating N5,N10-methylene-THF and releasing Glycine.

How is Pyrimidine biosynthesis regulated via feedback inhibition in mammals vs. bacteria?

In mammals, CPS-II (the first committed step) is inhibited by UTP and activated by PRPP and ATP. In bacteria, Aspartate transcarbamoylase (ATCase) catalyzes the regulated step: it is allosterically inhibited by the end-product CTP (increases K0.5) and accelerated/activated by ATP.

What are the end products of Pyrimidine catabolism (degradation)?

Degradation releases NH3/NH4+, which enters the urea cycle to form Urea, plus CO2; the carbon skeletons of Cytosine and Uracil are degraded to Acetyl-CoA, while the carbons of Thymine are degraded to Succinyl-CoA.

List the exact metabolic origins of all 9 ring atoms in a Purine ring.

Glycine contributes 2 carbons and 1 nitrogen (C4, C5, N7); Aspartate contributes 1 nitrogen (N1); Glutamine amide nitrogen contributes 2 nitrogens (N3, N9); Formate (via N10-formyl-THF) contributes 2 carbons (C2, C8); CO2 contributes 1 carbon (C6).

Clicker Question: Which amino acid contributes the first atoms (and nitrogen) in step 1 vs. the first full carbon/nitrogen backbone atoms in step 2 of purine biosynthesis?

In Step 1, Glutamine donates the first nitrogen (amino group) to PRPP; in Step 2, Glycine contributes the first carbon/nitrogen core atoms (3 atoms total) to the developing purine ring.

Describe Step 1 (the first committed step) and Step 2 of de novo Purine synthesis (MUST KNOW).

Step 1: Glutamine-PRPP amidotransferase transfers an amino group from glutamine to C-1 of PRPP (releasing PPi and glutamate) to form 5-phosphoribosylamine. Step 2: GAR synthetase adds 3 atoms from Glycine onto 5-phosphoribosylamine (requiring ATP -> ADP + Pi) to form Glycinamide ribonucleotide (GAR).

Summarize the general chemical events of Steps 3-10 of IMP biosynthesis.

Step 3: Formyl transfer from N10-formyl-THF (GAR transformylase); Step 4: NH3 transfer from Gln, uses ATP (FGAR amidotransferase); Step 5: First ring closure, uses ATP (FGAM cyclase / AIR synthetase); Step 6/7: Carboxylation using HCO3-/CO2; Step 8: Condensation with Aspartate, uses ATP (SAICAR synthetase); Step 9: Elimination of Fumarate leaving Asp's nitrogen (SAICAR lyase); Step 10: Second formyl transfer from N10-formyl-THF to form FAICAR (AICAR transformylase).

Describe Step 11 of Purine biosynthesis (MUST KNOW).

IMP Synthase catalyzes the dehydration and cyclization (second ring closure) of FAICAR to form Inosinate (IMP), the first completed purine nucleotide and the branch point for AMP and GMP synthesis.

Trace the 2-step conversion of IMP into AMP (Adenylate) (MUST KNOW).

1. Adenylosuccinate synthetase attaches Aspartate to IMP, driven by the hydrolysis of GTP (-> GDP + Pi), forming adenylosuccinate; 2. Adenylosuccinate lyase cleaves off Fumarate to yield AMP.

Trace the 2-step conversion of IMP into GMP (Guanylate) (MUST KNOW).

1. IMP dehydrogenase oxidizes IMP using NAD+ (-> NADH) to form Xanthylate (XMP); 2. GMP synthetase transfers an amino group from Glutamine (forming glutamate) onto XMP, driven by ATP (-> AMP + PPi), to yield GMP.

Note Takeaway: How is energy cross-regulated at the IMP branch point to balance purine pools?

To make AMP, you need GTP; to make GMP, you need ATP. This reciprocal energy requirement ensures balanced synthesis of adenine and guanine nucleotides.

How are Nucleoside Monophosphates (NMPs) converted into Diphosphates (NDPs) and Triphosphates (NTPs)?

1. Nucleoside monophosphate kinases use ATP to form NDPs: ATP + NMP <-> ADP + NDP; 2. Nucleoside diphosphate kinases convert NDPs to NTPs: NTP(donor) + NDP(acceptor) <-> NDP(donor) + NTP(acceptor).

Describe the 4 feedback inhibition mechanisms regulating de novo Purine biosynthesis.

1. PRPP Synthetase is inhibited by ADP (and AMP/GMP); 2. Glutamine-PRPP amidotransferase is feedback-inhibited by IMP, AMP, and GMP; 3. Adenylosuccinate synthetase is feedback-inhibited by AMP; 4. IMP dehydrogenase is feedback-inhibited by GMP.

What are the two enzymes of the Purine Salvage Pathway, and what reactions do they catalyze?

1. Hypoxanthine-guanine phosphoribosyltransferase (HGPRT): salvages free Guanine + PRPP -> GMP + PPi, and free Hypoxanthine (the deamination product of adenine) + PRPP -> IMP + PPi; 2. Adenosine phosphoribosyltransferase (APRT): salvages free Adenine + PRPP -> AMP + PPi.

How are ribonucleotides converted into deoxyribonucleotides, and trace the two electron-transfer pathways that regenerate the enzyme.

Ribonucleotide reductase converts ribonucleotides (NDPs) to deoxyribonucleotides (dNDPs) by oxidizing its active-site dithiols (-SH HS-) to a disulfide (S-S). It is reduced back to -SH HS- via two routes: 1. NADPH -> FADH2/FAD (via Thioredoxin reductase) -> Thioredoxin -> Ribonucleotide reductase; 2. NADPH -> Glutathione (GSH) -> Glutaredoxin (via Glutaredoxin reductase) -> Ribonucleotide reductase.

Trace the Purine Degradation Pathway from GMP and AMP down to Uric Acid.

For GMP: GMP -> Guanosine (via 5'-nucleotidase) -> Guanine + Ribose (via nucleosidase) -> Xanthine + NH3 (via Guanine deaminase). For AMP: AMP -> Adenosine (via 5'-nucleotidase) -> Inosine + NH3 (via Adenosine deaminase) -> Hypoxanthine + Ribose (via nucleosidase) -> Xanthine (via Xanthine oxidase, producing H2O2). Finally: Xanthine -> Uric acid (via Xanthine oxidase).

What happens if Adenosine Deaminase (ADA) is deficient or inhibited?

Deoxyadenosine builds up and is converted to dATP; high dATP allosterically inhibits Ribonucleotide Reductase, which blocks the synthesis of all other dNTPs, impairing DNA synthesis in lymphocytes and causing Severe Combined Immunodeficiency (SCID).

How does the end product of Purine catabolism vary across different organisms?

Primates, birds, and some reptiles excrete Uric acid; most other mammals and vertebrates oxidize uric acid further to excrete Allantoin; other organisms (fish, amphibians, invertebrates) excrete allantoate, urea, or NH4+.

Compare the three major cofactors involved in biological one-carbon transfer reactions.

1. Biotin: transfers carbon in its most oxidized state (CO2); 2. Tetrahydrofolate (H4 folate): transfers one-carbon units in intermediate oxidation states (methylene, formyl, methyl); 3. S-Adenosylmethionine (SAM / AdoMet): transfers carbon in its most reduced state (methyl groups, -CH3).

Contrast Kwashiorkor and Marasmus in terms of nutritional deficiency and clinical presentation.

Kwashiorkor: acute protein malnutrition (inadequate protein intake despite some calories); causes irritability, neurotransmitter deficits, enlarged fatty liver, and a "big belly" with ankle/foot edema due to osmotic imbalance in the blood. Marasmus: severe deficiency in ALL macronutrients (proteins, carbs, and lipids); causes extreme tissue and muscle wasting ("skin and bones") with NO edema.

What is Maple Syrup Urine Disease (MSUD), what enzyme is defective, and what are the symptoms?

An autosomal recessive defect in Branched-Chain Alpha-Keto Acid Dehydrogenase (BCKDH) that blocks the breakdown of the 3 branched-chain amino acids (Valine, Leucine, and Isoleucine). BCAAs and their alpha-ketoacids accumulate in the blood and urine, causing sweet maple-syrup-smelling urine, poor feeding, vomiting, ketoacidosis, seizures, coma, and irreversible neurological damage if untreated.

What causes Phenylketonuria (PKU), what accumulates, and how is it treated?

Caused by a deficiency of Phenylalanine hydroxylase (or its BH4 cofactor), leading to high blood phenylalanine and high urinary phenylpyruvate (formed via transamination). It damages nerve formation, causing delayed mental/social skills, microcephaly (smaller head size), hyperactivity, and seizures; treated with a low-phenylalanine diet supplemented with Tyrosine (which becomes essential).

What causes Homocystinuria, what enzyme and vitamin are involved, and what are its biochemical effects?

Caused by a deficiency in Cystathionine beta-synthase (which requires Vitamin B6 / PLP as a cofactor), resulting in a toxic buildup of homocysteine in the blood and urine and impaired cysteine synthesis; high-dose Vitamin B6 can sometimes kickstart residual enzyme activity.

What happens during Heme degradation, and why is this pathway physiologically important?

Old erythrocytes (~120-day lifespan) are broken down by spleen and liver macrophages; iron-porphyrin (heme) is degraded to Bilirubin, which the liver processes into hydrophilic bile pigments excreted in feces and urine. This breakdown pathway protects cells from oxidative damage, while excess bilirubin accumulation causes jaundice (yellowing of eyes/skin).

How does Folic Acid deficiency impair DNA structure and function?

Folic acid deficiency (affecting ~10% of the population and up to 50% in impoverished communities) reduces Thymidylate Synthase activity (dUMP -> dTMP); high dUMP causes Uracil (U) to be misincorporated into DNA instead of Thymine (T). DNA repair mechanisms repeatedly excise the uracil, creating single- and double-strand breaks associated with cancer, heart disease, and neurological impairment.

How do the chemotherapeutic drugs 5-Fluorouracil (5-FU) and Methotrexate block DNA synthesis?

5-FU is a prodrug converted in cells to 5-Fluoro-dUMP (FdUMP), a suicide inhibitor that forms a permanent covalent adduct with Thymidylate Synthase and methylene-THF, halting dTMP synthesis. Methotrexate (along with aminopterin and trimethoprim) competitively inhibits Dihydrofolate Reductase (DHFR), preventing THF regeneration and starving the cell of dTMP.

Application Problem: A 53-year-old man with metastatic colon adenocarcinoma is treated with 5-fluorouracil (5-FU). The 5-FU kills cancer cells by decreasing the intracellular concentration of which molecule?

Deoxythymidine triphosphate (dTTP), because 5-FU inhibits thymidylate synthase, blocking dTMP (and thus dTTP) production.

What is Orotic Aciduria, what enzyme is deficient, and how is it diagnosed and treated?

The most common genetic error in de novo pyrimidine synthesis (autosomal recessive); caused by a deficiency of UMP Synthase (which carries both orotate phosphoribosyltransferase and OMP decarboxylase activities). Presents in the first year of life with growth failure, developmental retardation, high urinary orotic acid, and severe megaloblastic anemia that does NOT respond to Vitamin B12, folic acid, or iron. Treated with oral Uridine (which bypasses the block via salvage to make UMP/UTP, inhibiting CPS-II).

Application Problem: A 3-year-old boy has leukopenia, developmental retardation, high urinary orotic acid, and megaloblastic anemia unresponsive to iron, folic acid, or B12. What metabolic pathway is defective?

A defect in Pyrimidine metabolism (specifically UMP synthase deficiency / Orotic aciduria).

What causes Lesch-Nyhan Syndrome, and what are its clinical features?

Caused by a severe genetic deficiency of Hypoxanthine-Guanine Phosphoribosyltransferase (HGPRT), inactivating the purine salvage pathway. Leads to excess uric acid production (gout-like symptoms), defective dopaminergic neurons, basal ganglia dysfunction, poor coordination, intellectual deficits, hostility, and compulsive self-destructive behavior (biting lips and fingers).