Biosynthesis Amino Acids & Nucleotides

OUTLINE: Introduction and review Transport Glycogenolysis Glycolysis Other sugars Pasteur: Anaerobic vs Aerobic ANABOLISM II OUTLINE: Exam-1 material Fermentations Pyruvate Krebs’ Cycle Oxidative Phosphorylation Biosynthesis of Fatty Acids and Lipids Fatty Acids contrasts Control of fatty acid metabolism Diversification of fatty acids Exam-2 material Electron transport Chemiosmotic theory: Phosphorylation Fat Catabolism Fatty acid Catabolism elongation desaturation Eicosanoids Prostaglandins and Thromboxane Exam-3 material Triacyl glycerides Membrane lipids Mobilization from tissues (mostly adipose) Activation of fatty acids Transport; carnitine Oxidation: b-oxidation, 4 steps: Glycerophospholipids Sphingolipids Isoprene lipids: Cholesterol Protein Catabolism Amino-Acid Degradation Dealing with the nitrogen; Urea Cycle Dealing with the carbon; Seven Families Ketone body synthesis Mevalonate Cholesterol bile acids steroids metabolism control of cholesterol biosynthesis Nucleic Acid & Nucleotide Degradation PHOTOSYNTHESIS: Overview and Key experiments: Light Reactions Exam-4 material energy in a photon/pigments Reaction center &Photosystems (PSII & PSI) Proton Motive Force – ATP Carbon Assimilation – Calvin Cycle Rubisco/Oxygenase (Glycolate cycle) ANABOLISM III OUTLINE: Biosynthesis of Amino Acids and Nucleotides remaking Ru 1,5P 2 Overview and regulation C4 versus C3 plants Kornberg cycle - glyoxylate Nitrogen cycle Nitrogen fixation nitrogenase complex Carbohydrate Biosynthesis in Animals precursors/Cori cycle Gluconeogenesis reversible steps irreversible steps – four Glycogen Synthesis Nitrogen assimilation Plants Nitrate/nitrite reductases Animals UDP-Glc/Glycogen synthase/branching Glutamine synthetase Glutamate synthase (GOGAT) Pentose-Phosphate Pathway oxidative-NADPH non-oxidative-Ribose 5-P Amino-acid Biosynthesis Regulation of Carbohydrate Metabolism Anaplerotic reactions Biosynthesis of Fatty Acids location & transport Synthesis; acetyl-CoA carboxylase + FAS non-essential essential Nucleotide Biosynthesis Secondary products of amino acids (ACP priming & 4 steps) Biosynthesis Amino Acids & Nucleotides Non-essential Amino acids: These are very few steps and often the same Arg-Val-His-Ile-Leu-Lys-Met-Phe Thr-Trp enzyme(s) used for degradation. Professor A.V.HILL M.P. was a Tea Totaller same as AA #steps degradation From? Asp Glu Ala Asn Gln Pro [Arg Ser Gly Cys Tyr 1 1 1 1 1 3(1) 3(1) 3 1 2 1 ✓ ✓ ✓ – – (✓) (✓) – ✓ ✓ ✓ Red=biosynthesis specific OAA a-KG Pyr Asp Glu Glu/Arg Pro] 3PGA Ser Ser/Met Phe Transaminase route Amidation route Glu Family 3-PGA Family From Essential Family Green=essential 1 Biosynthesis Amino Acids & Nucleotides Ala, Asp, Glu, Gln, Asn Transaminase route Amidation route GPTA AMP + PPi Gln + ATP Asparagine Synthetase GOTA ADP + + NH4+ + ATP Glutam ine Synthetase GOTA Biosynthesis Amino Acids & Nucleotides Glu Family: Pro (Arg) NADP+ + H+ D1 -pyrroline-5-carboxylate reductase NADPH In mammals, Glu is only reduced in intestines. Then the semialdehyde goes to Orn and through Urea Cycle to Arg. In most tissues, it is converted to Arg using the degradation pathway for Pro. oxaloacetate GOTA aspartate In bacteria, Glu is acetylated. This limits the un-catalyzed cyclization of the Glu-semialdehyde before its converted to Orn. 2 Biosynthesis Amino Acids & Nucleotides 3-PGA Family: Ser Serine Derives from 3-Phosphoglycerate of Glycolysis NAD+ phosphoglycerate dehydrogenase Pi phosphoserine phosphatase NADH H2O phosphoserine aminotransferase PLP à • Oxidation transamination à to yield serine dephosphorylation Biosynthesis Amino Acids & Nucleotides 3-PGA Family + From Essential Family: Gly, Cys Serine contributes to Glycine and Cysteine Glycine is reverse of degradation Cysteine carbons are from Ser Bacterial/plants Sulfation through APS Serine “S” Glycine Methionine Cysteine In bacteria and plants, sulfates are the source of S through APS. In mammals, the Cys-sulfur is recycled from methionine degradation…... 3 Biosynthesis Amino Acids & Nucleotides 3-PGA Family + From Essential Family: Cys, Tyr Biosynthesis of Cys from Homocysteine and Ser in Mammals The sulfur for Cysteine and nearly all of Tyrosine come from Essential Amino Acids C C C via same enzymes used in degradation Biosynthesis Amino Acids & Nucleotides Essential Amino acids: These require many steps and unique to those used for degradation. Asp/Pyruvate Family Aromatic Family Histidine Met Thr Lys Ile Val Leu Phe Trp His 7 5 9 10 4 7 10 12 10 –Asp/Cys/THF/Glu –Asp/Glu –Asp/Pyr/Glu –Asp(Thr)/Pyr/Glu –Pyr/Glu –Pyr/AcCoA/Glu –E4P/PEP/Glu –E4P/PEP/Gln/R5P/Ser –R5P/ATP/Gln/Glu 4 Biosynthesis Amino Acids & Nucleotides Asp/Pyruvate Family: Lys, Met, Thr, Ile, Val, Leu Oxaloacetate Yields Asp, which Yields Met and Thr, which along with Pyruvate Yields Lys, Val, Ile and Leu, which needs Acetyl-CoA Acetyl-CoA NH 4+ | –OOC-C-C-COO– Asp/Pyruvate Family Asp H+ + 4Asp + 5Pyr + 1Acetyl-CoA + 6ATP + 6NADPH + 2NAD+ + 2 Me-THF à Lys + Met + Thr + Ile + Val + Leu + 5NADP+ + 5H+ + 6Pi + 4CO2 + 2NADH + 4H2O + THF ATP O || NH 4+ | NADPH P O || Asp-b-semialdehyde Specific for anabolism P –O-C-C-C-COO– HO-C-C-C-COO– SB/dehy O || –OOC-C-C Homoserine H2O NADPH Pyr Succ-CoA P C-C-C-COO– | NADPH NH 4+ | 2H2O 4+ O OH NH || | | –OOC-C-C-C-C-C-COO– NH4+ HC-C-C-COO– ATP NH 4+ | HO NH4+ | | Asp-b-phosphate P –C-C-C-COO– Same as in catabolism Pyr Thr C-C-COO– NH4+ CO2 C-C-C-COO– a-ketobutyrate Pyr NH 4+ NH 4+ | | –OOC-C-C-S-C-C-C-COO– || C-C| | | Succ–NH NH4+ | –OOC-C-C-C-C-C-COO– Succ | NH4+ N5-m ethyl-THF NH 4+ NH 4+ | | –OOC-C-C-C-C-C-COO– NH 4+ | H3C-S-C-C-C-COO– | | C-C–OH | C C-C-C–OH | C O=C-COO– | C-C-C | C Glu C-COO– | C-C-C | C Ile | C-COO– Val AcCoA O=C-COO– NH 4+ | | C-C | C Glu Lys CO2 NH4+ | –OOC-C-C-C-C-C-NH4+ O || C-C-CoA H2O NH 4+ | PLP Met HO–C-COO– HO–C-COO– Succ–NH NH4+ | –OOC-C-C-C-C-C-COO– | HS-C-C-C-COO– hom ocysteine C=O | C NADPH B12 Glu Pyr + NH4+ NH 4+ | C-C-COO– TPP | C=O | C Cystathionine C-C-COO– HO | O HO || –OOC-C-C-C-C-C-COO– | Cys Succ O || C-C-C-COO– O Succ-O-C-C-C-COO– || O || Succ-CoA NH 4+ | O – C-COO | HO–C-COO– | C-C C-C | | C C a -ketoisovalerate – HO–C-COO | C-COO– | C-C | C NAD+ O=C-COO– CO2 | C | C-C | C Glu NH4+ | C-C-C-C-COO– | C Leu 5 Biosynthesis Amino Acids & Nucleotides Essential Amino acids: These require many steps and unique to those used for degradation. Asp/Pyruvate Family Aromatic Family Histidine Met Thr Lys Ile Val Leu Phe Trp His 7 5 9 10 4 7 10 12 10 –Asp/Cys/THF/Glu –Asp/Glu –Asp/Pyr/Glu –Asp(Thr)/Pyr/Glu –Pyr/Glu –Pyr/AcCoA/Glu –E4P/PEP/Glu –E4P/PEP/Gln/R5P/Ser –R5P/ATP/Gln/Glu Biosynthesis Amino Acids & Nucleotides Aromatic Family: Phe, Trp Aromatic Amino Acids Derive from PEP and Erythrose 4Phosphate (and Rib5P and Ser) • Very complicated and amazing chemistry! • Rings must be synthesized and closed and then oxidized to create double bonds. • Chorismate is a common intermediate. Ribose 5-phosphate Serine 6 Biosynthesis of Chorismate, a Key Intermediate in Aromatic Amino Acid Biosynthesis Chroism ate Biosynthesis Amino Acids & Nucleotides Aromatic Family: Phe, Trp prephenate dehydratase TA CO2 + H2O chorismate mutase NADPH + PEP CO2 NADP+ prephenate dehydrogenase TA anthranilate synthase E4P Tryptophan 7 Biosynthesis Amino Acids & Nucleotides Trp Synthase PEP E4P Tryptophan Histidine Derives from Ribose 5-Phosphate Ribose 5-Phosphate ATP Ribose Phosphate Pyrophosphokinase AMP PRPP •Synthesized from ribose 5phosphate via ribose phosphate pyrophosphokinase – a highly regulated allosteric enzyme 8 Biosynthesis Amino Acids & Nucleotides Essential vs. Nonessential and Conditionally Essential Amino Acids • Essential amino acids must be obtained as dietary protein. • Nonessential amino acids are easily made from central metabolites. TABLE 18-1 Nonessential and Essential Amino Acids for Humans and the Albino Rat Nonessential Alanine Asparagine Aspartate Conditionally essentiala Arginine Cysteine Glutamine Essential Histidine Isoleucine Leucine Glutamate Serine Glycine Proline Tyrosine Lysine Methionine Phenylalanine Threonine Tryptophan Valine aRequired to some degree in young, growing animals and/or sometimes during illness. • Consumption of a • Conditionally Essential amino acids variety of foods are made from essential, or become supplies all the essential in certain physiological essential amino acids. conditions. Biosynthesis Amino Acids & Nucleotides Non-essential Amino acids: These are very few steps and often the same Arg-Val-His-Ile-Leu-Lys-Met-Phe Thr-Trp enzyme(s) used for degradation. Professor A.V.HILL M.P. was a Tea Totaller same as AA #steps degradation From? Asp Glu Ala Asn Gln Pro [Arg Ser Gly Cys Tyr 1 1 1 1 1 3(1) 3(1) 3 1 2 1 ✓ ✓ ✓ – – (✓) (✓) – ✓ ✓ ✓ Red=biosynthesis specific OAA a-KG Pyr Asp Glu Glu/Arg Pro] 3PGA Ser Ser/Met Phe Transaminase route Amidation route Glu Family 3-PGA Family From Essential Family Green=essential 9 ANABOLISM III: Biosynthesis Amino Acids & Nucleotides 1) Nitrogen fixation: N2 à NH4 2) Nitrogen assimilation: incorporation of ammonia into biomolecules 3) Biosynthesis of amino acids a) non-essential b) essential 4) Biosynthesis of nucleotides a) sources b) de novo purines (R)(as nucleotides*); salvage; regulation c) de novo pyrimidines (Y)(as bases); making nucleotide; regulation d) deoxy-ribonucleotides, dTMP, and phosphorylation to NTP & dNTP e) regulating levels for DNA synthesis 5) Control of nitrogen metabolism 6) Biosynthesis and degradation of heme; other 2° products of amino acids *Bases synthesized while attached to ribose-5-P; products are RMP (R is one-letter code for purine, Y is one letter code for pyrimidine) [R,Q,N,R,W (in),H(Im)] [24 other Ns] 10 Clinical Correlations Murder or Misdiagnosis? • Poisoning with ethylene glycol: in 1937 a company Massingill made a elixir of sulfa-drug using ethylene glycol as an emulsifier • 107 people died • Prompted the Federal Government to for the Food and Drug Administration (FDA) Sweet, LD50 100 ml, t½ is 18 h Acute lactic acidosis • In 1979, Ryan Stallings was brought to ER with vomiting, lethargy, and hyperventilation. • Blood work revealed lactic acidosis and bicarb treatment saved him. • But, lab tests revealed unusual component, that was identified as ethylene glycol. Ryan was put in protective custody. • Foster parents brought Ryan back to ER 2 months • Lab tests revealed propionic later with same thing. Ryan died. acid, not ethylene glycol. • Mother, Patricia, was arrested for 1st degree • Eventually Patricia was murder. released at new trial. • While in custody, David and Patricia had another • Children had Methylmalonyl child, David Jr. Aciduria • David brought to another hospital with same symptoms. Kidney failure X 11