Amino Acids and Nucleotides

What are the 5 non-essential amino acids highlighted in lecture?

Alanine, Asparagine, Aspartate, Glutamate, and Serine.

What are the 6 conditionally essential amino acids highlighted in lecture?

Arginine, Cysteine, Glutamine, Glycine, Proline, and Tyrosine.
(Anally Crushed Guys Get Pretty Tense)

How is Alanine synthesized?

From pyruvate via transamination from glutamate (by ALT).

What is the Glucose-Alanine cycle?

Muscle converts pyruvate to alanine, which travels in blood to the liver to be converted back to pyruvate for gluconeogenesis.

How does Transaminase synthesize Glutamate?

Alpha-ketoglutarate + Amino Acid < - > Glutamate + Alpha-keto acid.

How does Glutamate Dehydrogenase (GDH) synthesize Glutamate?

Alpha-ketoglutarate + NH3 + NADPH < - > Glutamate + NADP+ (reductive amination).

How does Glutaminase synthesize Glutamate?

Glutamine + H2O < - > Glutamate + NH3 (hydrolysis).

Which three amino acids use Glutamate as a direct biosynthetic precursor?

Glutamine, Proline, and Arginine.

What are the two ways Aspartate is synthesized?

1. Transamination of oxaloacetate from glutamate (by AST); 2. Hydrolysis of asparagine by asparaginase.

How is Asparagine synthesized?

Amidation of aspartate by asparagine synthetase using glutamine (N donor) and ATP -> AMP + PPi.

Why does mammalian asparagine synthetase use glutamine instead of free ammonia?

Free ammonia is toxic; glutamine safely shuttles nitrogen into an intramolecular tunnel inside the enzyme.

What is the glycolytic precursor of Serine, and how is Serine converted to Glycine?

Serine comes from 3-phosphoglycerate. Serine hydroxymethyltransferase (PLP-dependent) transfers serine's beta-carbon to THF to form Glycine.

How is Tyrosine synthesized, and why is it conditionally essential?

Phenylalanine hydroxylase hydroxylates C-4 of phenylalanine. It becomes essential if phenylalanine is deficient or the enzyme is defective.

What cofactor is required by Phenylalanine hydroxylase, and what else uses it?

Tetrahydrobiopterin (BH4, made from GTP). Also required to synthesize dopamine, norepinephrine, and serotonin.

Application: A child has a deficiency of dihydrobiopterin reductase (needed to make BH4). What accumulates in the blood?

Phenylalanine (because phenylalanine hydroxylase cannot convert it to tyrosine without BH4).

Which 3 amino acids are needed to synthesize Creatine, and what does each provide?

Arginine and Glycine provide the carbon-nitrogen backbone; Methionine (via SAM) provides a methyl group.

How is Phosphocreatine formed, and what is its role in muscle?

Formed by creatine kinase using ATP. It acts as an energy buffer that donates a phosphate to ADP to regenerate ATP during high demand.

What is Creatinine, and what is its clinical use?

A waste product formed by spontaneous cyclization of creatine/phosphocreatine; used as an indicator of renal function.

What is S-adenosylmethionine (SAM / AdoMet), and how is it synthesized?

The main methylating agent for ~300 metabolites (DNA, histones, creatine, epinephrine). Made from Methionine + ATP by methionine adenosyltransferase.

How is SAM converted to Homocysteine in the Methionine Cycle?

1. Methyltransferase removes the methyl group from SAM -> S-adenosylhomocysteine (SAH); 2. Adenosylhomocysteinase removes adenosine -> Homocysteine.

How is Homocysteine recycled back into Methionine?

Methionine synthase (Vitamin B12-dependent) transfers a methyl group from 5-methyl-THF to homocysteine.

How is Cysteine formed from the Methionine Cycle?

Cystathionine beta-synthase (B6-dependent) converts homocysteine -> cystathionine -> cysteine (homocysteine supplies the sulfur).

What is Glutathione (GSH), and what is its cellular role?

A tripeptide of Glutamate, Cysteine, and Glycine. It is a major antioxidant/reducing agent that neutralizes peroxides and reactive oxygen species.

What enzyme uses Glutathione to reduce peroxides, and what unique cofactor does it have?

Glutathione peroxidase (a selenoprotein containing selenocysteine); converts 2 GSH + R-OOH -> GSSG (oxidized dimer) + H2O + R-OH.

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

Glutamate & Aspartate: excitatory neurotransmitters; D-Serine: NMDA receptor co-agonist; Glycine: inhibitory neurotransmitter in spinal cord/brainstem/retina.

What are the first two steps of Catecholamine synthesis from Tyrosine?

1. Tyrosine -> DOPA (via Tyrosine hydroxylase); 2. DOPA -> Dopamine (via DOPA decarboxylase, releases CO2).

How is Dopamine converted into Norepinephrine and Epinephrine?

3. Dopamine -> Norepinephrine (via Dopamine-beta-hydroxylase); 4. Norepinephrine -> Epinephrine (via Phenylethanolamine N-methyltransferase, uses a methyl group from SAM).

Application: How is GABA synthesized from Glutamate, and what is its function?

Synthesized via Vitamin B6 (PLP)-dependent decarboxylation by glutamic acid decarboxylase. It is the major inhibitory neurotransmitter.

How is Serotonin (5-hydroxytryptamine) synthesized, and what does it regulate?

Tryptophan -> 5-hydroxytryptophan (via tryptophan-5-hydroxylase) -> Serotonin (via aromatic L-AA decarboxylase). Regulates mood, sleep, digestion, clotting, and libido.

What is the difference between a nucleotide and a nucleoside?

A nucleotide has a nitrogenous base, a pentose sugar, and 1+ phosphates; a nucleoside lacks the phosphate group.

Which nitrogenous bases are Purines and which are Pyrimidines?

Purines (2 rings): Adenine (A) and Guanine (G). Pyrimidines (1 ring): Cytosine (C), Thymine (T, DNA only), and Uracil (U, RNA only).

How does de novo ring construction differ between Purines and Pyrimidines?

Purine rings are built atom-by-atom directly onto ribose (PRPP); the pyrimidine ring is built first as Orotate before PRPP is attached.

How is PRPP (5-phosphoribosyl-1-pyrophosphate) synthesized?

Ribose 5-phosphate + ATP -> PRPP + AMP, catalyzed by PRPP synthetase (ribose phosphate pyrophosphokinase).

Which two precursors supply the atoms of the pyrimidine ring?

Aspartate and Carbamoyl phosphate.

Contrast mammalian CPS-I and CPS-II.

CPS-I is mitochondrial, uses free NH3 + CO2, and functions in the Urea Cycle. CPS-II is cytosolic, uses Glutamine + CO2 + 2 ATP (via an ammonia tunnel), and starts Pyrimidine synthesis.

What is the eukaryotic CAD complex?

A multifunctional cytosolic enzyme containing the first 3 enzymes of pyrimidine synthesis: CPS-II, Aspartate transcarbamoylase (ATCase), and Dihydroorotase.

Trace the steps from Carbamoyl phosphate + Aspartate to Orotate.

1. ATCase forms N-carbamoylaspartate; 2. Dihydroorotase cyclizes it to L-dihydroorotate (-H2O); 3. Dihydroorotate dehydrogenase oxidizes it to Orotate (using NAD+).

How is Orotate converted to UMP (Uridylate)?

1. Orotate phosphoribosyltransferase adds PRPP to form OMP (Orotidylate); 2. Orotidylate decarboxylase removes CO2 to form UMP (both steps are on bifunctional UMP Synthase).

How is UMP converted into UTP and CTP?

Kinases use 2 ATP to phosphorylate UMP -> UDP -> UTP. Cytidylate (CTP) synthetase then converts UTP -> CTP using Glutamine and ATP.

How is dUMP converted to dTMP?

Thymidylate synthase transfers and reduces a 1-carbon group from N5,N10-methylene-THF to dUMP, producing dTMP and 7,8-dihydrofolate (DHF).

How is Tetrahydrofolate (THF) regenerated after the Thymidylate synthase reaction?

Dihydrofolate reductase (DHFR) reduces DHF -> THF using NADPH; serine hydroxymethyltransferase then transfers a carbon from serine to form N5,N10-methylene-THF.

How is pyrimidine synthesis regulated in mammals vs. bacteria?

Mammals: CPS-II is inhibited by UTP and activated by PRPP/ATP; CTP synthetase is activated by GTP. Bacteria: ATCase is inhibited by CTP and activated by ATP.

What are the catabolic end-products of pyrimidine degradation?

Nitrogen becomes NH4+ -> Urea. Cytosine and Uracil carbons -> Acetyl-CoA; Thymine carbons -> Succinyl-CoA.

Which precursors donate the atoms of the purine ring?

Glutamine (2 amide N), Glycine (2 C, 1 N), Aspartate (1 N), Formate/THF (2 C), and CO2 (1 C).

What is Step 1 (first committed step) of de novo purine synthesis?

Glutamine-PRPP amidotransferase transfers an amino group from glutamine to C-1 of PRPP to form 5-phosphoribosylamine.

What is Step 2 of de novo purine synthesis, and which amino acid donates the first core ring atoms?

GAR synthetase uses ATP to add all 3 atoms of Glycine to 5-phosphoribosylamine to form GAR (glycine provides the first multi-atom backbone of the ring).

What is Step 11 of de novo purine synthesis, and why is IMP important?

IMP synthase closes the ring to form Inosinate (IMP), the first completed purine nucleotide and the branch point for AMP and GMP synthesis.

How is IMP converted to AMP?

1. Adenylosuccinate synthetase adds Aspartate to IMP using GTP -> Adenylosuccinate; 2. Adenylosuccinate lyase cleaves off Fumarate -> AMP.

How is IMP converted to GMP?

1. IMP dehydrogenase oxidizes IMP -> XMP (using NAD+); 2. GMP synthetase converts XMP -> GMP using Glutamine and ATP.

Why does AMP synthesis use GTP while GMP synthesis uses ATP?

Reciprocal energy need ensures balanced pools of adenine and guanine nucleotides.

What do Nucleoside monophosphate and diphosphate kinases do?

Monophosphate kinases: ATP + NMP < - > ADP + NDP. Diphosphate kinases: NTP(donor) + NDP(acceptor) < - > NDP(donor) + NTP(acceptor).

What are the feedback inhibition checkpoints in de novo purine synthesis?

ADP inhibits PRPP synthetase; IMP, AMP, and GMP inhibit Glutamine-PRPP amidotransferase; AMP inhibits adenylosuccinate synthetase; GMP inhibits IMP dehydrogenase.

What are the two enzymes of the Purine Salvage Pathway?

1. HGPRT: combines PRPP with free Guanine -> GMP or with Hypoxanthine -> IMP; 2. APRT: combines PRPP with free Adenine -> AMP.

What enzyme converts ribonucleotides to deoxyribonucleotides, and what reduces it?

Ribonucleotide reductase (converts NDPs to dNDPs). It is regenerated by Thioredoxin (via thioredoxin reductase/NADPH) or Glutaredoxin (via glutathione).

Trace the degradation of GMP and AMP to Uric Acid.

GMP -> Guanosine -> Guanine -> Xanthine. AMP -> Adenosine (via 5'-nucleotidase) -> Inosine (via adenosine deaminase) -> Hypoxanthine -> Xanthine -> Uric Acid (last two steps via Xanthine oxidase).

What are the 3 main one-carbon transfer cofactors and what does each carry?

Biotin carries CO2 (most oxidized); Tetrahydrofolate (THF) carries intermediate 1-C states; SAM carries methyl (-CH3) groups (most reduced).

Contrast Kwashiorkor and Marasmus.

Kwashiorkor: acute protein deficiency causing fatty liver and belly/ankle edema from osmotic imbalance. Marasmus: severe deficiency of all macronutrients causing tissue wasting without edema.

What is the defect and presentation of Maple Syrup Urine Disease (MSUD)?

Deficiency of Branched-Chain Keto Acid Dehydrogenase (BCKDH) causes buildup of Val, Leu, Ile and their alpha-ketoacids, leading to sweet-smelling urine and neurological damage.

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

Phenylalanine hydroxylase deficiency causes buildup of phenylalanine and phenylpyruvate (neurological impairment); treated with a low-Phe diet supplemented with Tyrosine.

What enzyme deficiency causes Homocystinuria, and what vitamin is its cofactor?

Cystathionine beta-synthase deficiency (requires Vitamin B6), causing buildup of homocysteine in blood and urine.

How is Heme degraded during the erythrocyte life cycle?

Old RBCs (after 120 days) are broken down in the spleen/liver; heme is degraded to bilirubin -> converted to bile pigments in the liver -> excreted in feces and urine.

How does Folic Acid deficiency damage DNA?

Low dTMP synthesis causes Uracil (U) to be incorporated into DNA instead of Thymine (T); DNA repair creates strand breaks when removing the uracil.

How do 5-Fluorouracil (5-FU) and Methotrexate block nucleotide synthesis?

5-FU converts to 5-Fluoro-dUMP, which covalently inhibits Thymidylate synthase (depleting dTMP/dTTP). Methotrexate inhibits Dihydrofolate reductase (DHFR).

What causes Orotic Aciduria, how does it present, and how is it treated?

Deficiency of UMP Synthase (orotate phosphoribosyltransferase & OMP decarboxylase). Causes high urinary orotic acid and megaloblastic anemia unresponsive to B12/folate; treated with Uridine.

How does Adenosine Deaminase (ADA) deficiency cause SCID?

dATP accumulates and inhibits Ribonucleotide reductase, blocking DNA synthesis in immune cells.

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

Genetic deficiency of HGPRT (purine salvage), causing excess uric acid, neurological dysfunction, and compulsive self-destructive behavior.

What causes Gout, how does Allopurinol treat it, and what pathway increases with treatment?

Caused by excess uric acid crystals in joints from purine catabolism. Allopurinol inhibits Xanthine oxidase (via oxypurinol), which increases purine salvage of hypoxanthine and guanine.

What is the defect in Methylene-THF Reductase (MTHFR) deficiency?

Decreased conversion of 5,10-methylene-THF to 5-methyl-THF impairs homocysteine remethylation to methionine, causing homocysteine buildup and vascular damage.

What is the "Folate Trap" in Vitamin B12 deficiency, and why does it cause Megaloblastic Anemia?

Without B12, Methionine synthase cannot convert 5-methyl-THF back to THF; this depletes 5,10-methylene-THF needed for dTMP/DNA synthesis, producing large, immature RBCs (megaloblasts/macrocytes).

What are the metabolic roles of Vitamins B1, B2, B3, and B5?

B1 (Thiamine): glucose/AA/nucleotide metabolism; B2 (Riboflavin): FMN/FAD precursor; B3 (Nicotinamide): NAD precursor; B5 (Pantothenic acid): Coenzyme A precursor.

What are the metabolic roles of Vitamins B6, B7, B9, and B12?

B6 (Pyridoxine): AA synthesis/degradation cofactor; B7 (Biotin): carboxylation reactions; B9 (Folate): 1-carbon transfers/nucleotide synthesis; B12 (Cobalamin): 1-carbon metabolism & propionate catabolism.