Amino Acids Intermediates of the Central Metabolic Pathway

OUTLINE: Protein Degradation (Catabolism) Fermentations Pyruvate Krebs’ Cycle Oxidative Phosphorylation Amino-Acid Degradation Dealing with the nitrogen Digestion Inside of cells Protein turnover Ubiquitin Proteosome Introduction and review Transport Glycogenolysis Glycolysis Other sugars Pasteur: Anaerobic vs Aerobic Electron transport Chemiosmotic theory: Phosphorylation Fat Catabolism diet storage Fatty acid Catabolism FOUR stages in the catabolism of lipids: Mobilization from tissues (mostly adipose) hormone regulated specific lipases glycerol Ammonia free transamination ß know mechanism Carbamoyl-phosphate synthetase Urea Cycle 4 Steps Ornithine transcarbamylase Arginino-succinate synthetase Arginino-succinase Arginase Energetics Urea Bi-cycle Dealing with the carbon Seven Families 1. ADENQ (Transaminase/deaminase Family) 2. RPH (Glu Family) Oxidase One-carbon (1-C) metabolism THF SAM 3. GSC (Pyruvate Family) PLP uses 4. MT – 1-C metabolism (a-Ketobutyrate Family) 5. FY – oxidases (Aromatic Family) 6. KW (a-Ketoadipate Family) 7. VIL (Branched-chain AA Family (BCAA)) Activation of fatty acids Fatty-acyl CoA Synthetase Transport carnitine Oxidation Rationale Saturated FA b-oxidation 4 steps: dehydrogenation hydration oxidation thiolase energetics Unsaturated FA energetics Odd-chain FA Ketone Bodies Other organelles Nucleic-Acid Degradation nucleotide to bases salvage vs oxidation purine pyrimidine Amino Acid Degradation: the carbon “skeletons” A. Concepts 1. Convergent 2. ketogenic/glucogenic The SEVEN 3. Reactions seen before B. Transaminase (A,D,E) / Deaminase (N,Q) Family (5) C. Related to biosynthesis (8) 1. Glu Family (R,P,H) a. b. (7) Families Introduce oxidases/oxygenases Introduce one-carbon metabolism (1C) 2. Pyruvate Family (G,S,C) a. PLP reactions a. 1-C metabolism In total there are 29 Nitrogen atoms in the 20 amino acids: 9 are given off as ammonia 18 are taken off in transaminase reactions 2 leave as urea There are ~75 reactions in total 3. a-Ketobutyric Family (M,T) D. Dedicated (7) 1. Aromatic Family (F,Y) a. oxidases/oxygenases 2. a-Ketoadipic Family (K,W) 3. Branched-chain Family (V,I,L) E. Convergence with Fatty Acids: propionyl-CoA 1 Amino Acid Degradation • • • Intermediates of the central metabolic pathway Some amino acids result in more than one intermediate. Ketogenic amino acids can be converted to ketone bodies. Seven to Acetyl-CoA • Leu,7 Ile,7 Thr, Lys,6 Trp,6 Phe,5 Tyr5 Glucogenic amino acids can be converted to glucose. Six to pyruvate3,1 NOTES: blue bkgd=ketogenic salmon bkgd=glucogenic Red=both keto- and gluco-genic Italics=different non-human pathways Bold=pathway discussed in class Ala, Cys, Gly, Ser, Thr, Trp Five to a-ketoglutarate Arg, Glu, Gln, His, Pro Four to succinyl-CoA7,4 Ile, Met, Thr, Val Two to fumarate5 Phe, Tyr 2,1 Two to oxaloacetate 1 Asp, Asn 1 Trans-/de-aminase family 2Glu family 3 Pyruvate family 4Alpha-keto butyric family 5 Aromatic family 6Alpha-keto adipic family 7 Branched-chain family Amino Acid Degradation This is what you need to Know from Lecture 22 oxidase dioxygenase 2 Amino Acid Degradation A,D,E Simple Transamination PLP PLP + + PLP Amino Acid Degradation N,Q Simple Deamination PLP + + PLP 3 A,D,E,N,Q Amino Acid Degradation • • • Intermediates of the central metabolic pathway Some amino acids result in more than one intermediate. Ketogenic amino acids can be converted to ketone bodies. Seven to Acetyl-CoA • Leu,7 Ile,7 Thr, Lys,6 Trp,6 Phe,5 Tyr5 Glucogenic amino acids can be converted to glucose. Six to pyruvate3,1 Ala, Cys, Gly, Ser, Thr, Trp Five to a-ketoglutarate Arg, Glu, Gln, His, Pro Four to succinyl-CoA7,4 Ile, Met, Thr, Val Two to fumarate5 Phe, Tyr 2,1 Two to oxaloacetate 1 Asp, Asn ✓ Trans-/de-aminase family 2Glu family 3 Pyruvate family 4Alpha-keto butyric family 5 Aromatic family 6Alpha-keto adipic family 7 Branched-chain family 1 Amino Acid Degradation: the carbon “skeletons” A. Concepts 1. Convergent 2. ketogenic/glucogenic The SEVEN 3. Reactions seen before B. Transaminase (A,D,E) / Deaminase (N,Q) Family (5) C. Related to biosynthesis (8) 1. Glu Family (R,P,H) a. b. (7) Families Introduce oxidases/oxygenases Introduce one-carbon metabolism (1C) 2. Pyruvate Family (G,S,C) a. PLP reactions a. 1-C metabolism 3. a-Ketobutyric Family (M,T) D. Dedicated (7) 1. Aromatic Family (F,Y) a. oxidases/oxygenases 2. a-Ketoadipic Family (K,W) 3. Branched-chain Family (V,I,L) E. Convergence with Fatty Acids: propionyl-CoA Before Glu 29 N 4 Amino Acid Degradation Amino Acid Degradation R,P,H Glu Family Arginine degradation is part of the urea cycle. PLP Proline, arginine, and histidine are all converted to glutamate. Histidine-ammonia lyase uricanase Histidine Urocanate Imidazolonepropionase Imidazolonepropionate Three new metabolic concepts used: 1) Other uses of PLP 2) Oxidases & oxygenases 3) One-carbon metabolism Glu-formimino transferase Formimino glutamate N 5N 10- M ethenyl N 5- Form im ino TH F TH F 5 Amino Acid Degradation: One Carbon H • Tetrahydrofolate is formed from folate. H H H dihydro Folic Acid (B9) – an essential vitamin – Folate is reduced to dihydrofolate, then to tetrahydrofolate (THF) • It is used in a wide variety of metabolic reactions. • THF can transfer 1-carbon in different oxidation states. – CH3, CH2OH, and CHO • Carbon generally comes from serine. • Forms are interconverted on THF before use. The other half of one-carbon metabolism is SAM, which is connected to N5-methyl-THF Amino Acid Degradation: One Carbon S-Adenosyl-Methionine (SAM or adoMet) SAM is Better at Transferring CH3 Transferable methyl • S-adenosylmethionine is the preferred cofactor for methyl transfer in biological reactions. – Methyl in SAM is 1000 times more reactive than THF-methyl group. • It is synthesized from ATP and methionine in the ”SAM Cycle” (part of a-ketobutyrate family (M,T)) • Regeneration of SAM uses N5-methyl THF. – The only known use of N5-methyl THF in mammals 6 Amino Acid Degradation: One Carbon ➔ SAM • Tetrahydrofolate is formed from folate. – an essential vitamin – Folate is reduced to dihydrofolate, then to tetrahydrofolate (THF) • It is used in a wide variety of metabolic reactions. • THF can transfer 1-carbon in different oxidation states. – CH3, CH2OH, and CHO • Carbon generally comes from serine. • Forms are interconverted on THF before use. We’ll come back to 1-C metabolism when we see what happens to Met Amino Acid Degradation • • • R,P,H Intermediates of the central metabolic pathway Some amino acids result in more than one intermediate. Ketogenic amino acids can be converted to ketone bodies. Seven to Acetyl-CoA • Leu,7 Ile,7 Thr, Lys,6 Trp,6 Phe,5 Tyr5 Glucogenic amino acids can be converted to glucose. Six to pyruvate3,1 Ala, Cys, Gly, Ser, Thr, Trp Five to a-ketoglutarate Arg, Glu, Gln, His, Pro Four to succinyl-CoA7,4 Ile, Met, Thr, Val Two to fumarate5 Phe, Tyr 2,1 Two to oxaloacetate 1 Asp, Asn ✓ Trans-/de-aminase family ✓2Glu family 3 Pyruvate family 4Alpha-keto butyric family 5 Aromatic family 6Alpha-keto adipic family 7 Branched-chain family 1 7 Amino Acid Degradation: the carbon “skeletons” A. Concepts 1. Convergent 2. ketogenic/glucogenic The SEVEN 3. Reactions seen before B. Transaminase (A,D,E) / Deaminase (Q,N) Family (5) C. Related to biosynthesis (8) 1. Glu Family (R,P,H) a. b. (7) Families Introduce oxidases/oxygenases Introduce one-carbon metabolism (1C) 2. Pyruvate Family (G,S,C) a. PLP reactions a. 1-C metabolism 3. a-Ketobutyric Family (M,T) D. Dedicated (7) 1. Aromatic Family (F,Y) a. oxidases/oxygenases 2. a-Ketoadipic Family (K,W) 3. Branched-chain Family (V,I,L) E. Convergence with Fatty Acids: propionyl-CoA 29 N Amino Acid Degradation 8 G,S,C Amino Acid Degradation Pyruvate Family Glycine • Pathway #1: glycine cleavage enzyme – apparently major pathway in mammals – separation of three central atoms – releases CO2 and NH3 – methylene group is transferred to THF – mechanism like PDH complex PLP decarboxylation M icrobes hydrolyze H 2S & am m onia with desulfhydrase or TA then SHà SCN • Pathway #2: hydroxylation to serine à pyruvate via SerOHMe transferase & Set/Thr dehydratase O2 cysteine dioxygenase NAD+ O2– – Reverse reaction major feeder of onecarbon to THF serine/threonine PLP, lipoate, THF, FAD a-elimination NADH b-elimination All these uses of PLP; let’s have a closer look PLP • Pathway #3: D-amino oxidase 3-sulfinoalanine transaminase PLP spontaneous O2– SO3– H2O 3-sulfinyl-pyruvate oxalate a-ketoglutarate glutamate || O – relatively minor pathway – ultimately oxidized to oxalate – major component of kidney stones Amino Acid Degradation Bile Acids G,S,C Glycine Pyruvate Family: Glycine Cleavage Enzyme See Sapling animated Figures Decarboxylation – N 5-N 10-methylene-THF This is similar to how THF was used to pick off the formimino group in His catabolism http://media.saplinglearning.com/priv/he/lehninger/aem/1820c_glycine_cleavage.html 9 Mechanism of Glycine Decarboxylase • In plants, this same ortholog of Gly-clevage enzyme is called Gly decarboxylase • Flux through rubisco reaction and glycolate pathway can be high in bright sun, so plants need a lot of glycine decarboxylase. – makes up 50% of protein in some plant leaves – but non-photosynthetic parts of plants (tubers, etc.) have little glycine decarboxylase Glycine Decarboxylase Is Abundant in Photosynthetic Parts of Plants Amino Acid Degradation Pyruvate Family: Serine hydroxymethyl transferase PLP Serine a-elimination H2O G,S,C Serine/Glycine See Sapling animated Figure (shows GlyàSer) THF Glycine E-aldimine (external) N 5-N 10-methylene THF 10 Amino Acid Degradation Pyruvate Family: Ser/Thr dehydratase G,S,C Serine See Sapling animated Figures (shows a concerted mech) b-elimination b a H2O b-elimination deprotonation 2 H2O 2 H2O Schiff-base hydrolysis O O O Schiff-base hydrolysis eneamine imine/Schiff base Amino Acid Degradation PLP Catalyzes Many Types of Reactions ③ ① Base abstracts proton from b-carbon ① ① ③ ② Acid donates proton to leaving group (water when Y=OH) ④ O–H | Base abstracts proton from a-carbon Ca-bond: Protonation of PLP aldehyde carbon ② H ④ ③ ① Transamination of Amino Acids ② Decarboxylation of Amino Acids ③ a-elimination of Amino Acids After Ca-H abstracted ① : ② Racemization of Amino Acids ③ b-elimination of Amino Acids ④ g-elimination of Amino Acids How do the enzymes control which bond to destabilize? 11 Amino Acid Degradation PLP Catalyzes Many Types of Reactions③ Acid donates proton to leaving group (water when Y=OH) ④ Base abstracts proton from b-carbon ① ① ① ③ Base abstracts proton from a-carbon ② ② Protonation of carbanion at a-carbon H Ca-bond: ① Transamination of Amino Acids ② Decarboxylation of Amino Acids ③ a-elimination of Amino Acids After Ca-H abstracted ① : The enzyme orients the Ca–H, –Y, or – R so that the orbitals are parallel to the p-cloud, thus driving it from sp3 to sp2 and breaking the bond. ② Racemization of Amino Acids ③ b-elimination of Amino Acids ④ g-elimination of Amino Acids Amino Acid Degradation • • • G,S,C Intermediates of the central metabolic pathway Some amino acids result in more than one intermediate. Ketogenic amino acids can be converted to ketone bodies. Seven to Acetyl-CoA • Leu,7 Ile,7 Thr, Lys,6 Trp,6 Phe,5 Tyr5 Glucogenic amino acids can be converted to glucose. Six to pyruvate3,1 Ala, Cys, Gly, Ser, Thr, Trp Five to a-ketoglutarate Arg, Glu, Gln, His, Pro Four to succinyl-CoA7,4 Ile, Met, Thr, Val Two to fumarate5 Phe, Tyr 2,1 Two to oxaloacetate 1 Asp, Asn ✓ Trans-/de-aminase family ✓2Glu family ✓3Pyruvate family 4Alpha-keto butyric family 5 Aromatic family 6Alpha-keto adipic family 7 Branched-chain family 1 12 Amino Acid Degradation: the carbon “skeletons” A. Concepts 1. Convergent 2. ketogenic/glucogenic The SEVEN 3. Reactions seen before B. Transaminase (A,D,E) / Deaminase (Q,N) Family C. Related to biosynthesis (8) 1.Glu Family (R,P,H) a. b. (7) Families 5 enzymes 7 enzymes Introduce oxidases/oxygenases Introduce one-carbon metabolism (1C) 5 enzymes 2. Pyruvate Family (G,S,C) a. PLP reactions a. 1-C metabolism 3. a-Ketobutyric Family (M,T) 5 (+BCDHC) enzymes = D. Dedicated (7) 1. Aromatic Family (F,Y) a. 7 enzymes 8+4 (BCDHC +5) enzyme oxidases/oxygenases 2. a-Ketoadipic Family (K,W) 3. Branched-chain Family (V,I,L) E. Convergence with Fatty Acids: propionyl-CoA Before MT BCTA + BCDHC +5/4/3 e 29 N Amino Acid Degradation 13 Amino Acid Degradation • Methionine degradation involves transfer of sulfur to serine, generating cysteine. a-Ketobutyrate Family Methionine Adenosyltransferase M,T DNA methylTransferase SAM THF B12 Vitamin B12 Methionine synthase SAM Cycle N5-methylTHF ba a PLP b S-adenosylhomocysteine (SAH) Adenosylhomocysteinase ③ b-elimination • The main pathway for threonine degradation involves the same enzyme used for Ser. Adenosine PLP g ③ b-elimination cystathionine serine/ b a PLP ④ g-elimination Amino Acid Degradation: One Carbon Summary of One-Carbon Metabolism pyruvate SAM Cycle Homocystinuria X a-ketobutyric DMG=dimethyl-Gly 14 Amino Acid Degradation • • • M,T Intermediates of the central metabolic pathway Some amino acids result in more than one intermediate. Ketogenic amino acids can be converted to ketone bodies. Seven to Acetyl-CoA • Leu,7 Ile,7 Thr, Lys,6 Trp,6 Phe,5 Tyr5 Glucogenic amino acids can be converted to glucose. Six to pyruvate3,1 Ala, Cys, Gly, Ser, Thr, Trp Five to a-ketoglutarate Arg, Glu, Gln, His, Pro Four to succinyl-CoA7,4 Ile, Met, Thr, Val Two to fumarate5 Phe, Tyr 2,1 Two to oxaloacetate 1 a-ketobutyric Asp, Asn ✓1Trans-/de-aminase family ✓2Glu family ✓3Pyruvate family ✓4Alpha-keto butyric family 5 Aromatic family adipic family 7 Branched-chain family 6Alpha-keto 15