Amino Acid Catabolism Intermediates of the Central Metabolic Pathway

OUTLINE: Protein Degradation (Catabolism) Introduction and review Transport Glycogenolysis Glycolysis Other sugars Pasteur: Anaerobic vs Aerobic Digestion Inside of cells Protein turnover Ubiquitin Proteosome Exam-1 material Fermentations Pyruvate Krebs’ Cycle Oxidative Phosphorylation Exam-2 material Electron transport Chemiosmotic theory: Phosphorylation Amino-Acid Degradation Dealing with the nitrogen Fat Catabolism Exam-3 material diet storage Fatty acid Catabolism FOUR stages in the catabolism of lipids: Ammonia free transamination ß know mechanism Carbamoyl-phosphate synthetase Urea Cycle 4 Steps Ornithine transcarbamylase Arginino-succinate synthetase Arginino-succinase Arginase Mobilization from tissues (mostly adipose) hormone regulated specific lipases glycerol Activation of fatty acids Fatty-acyl CoA Synthetase Transport carnitine Oxidation Energetics Urea Bi-cycle Dealing with the carbon Rationale Saturated FA b-oxidation 4 steps: dehydrogenation hydration oxidation thiolase energetics Unsaturated FA energetics Odd-chain FA Ketone Bodies Other organelles 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)) 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) In total there are 29 Nitrogen atoms in the 20 amino acids: 9 are given off as ammonia 3. a-Ketobutyric Family (M,T) 18 are taken off in transaminase reactions a. 1-C metabolism 2 leave as urea D. Dedicated (7) There are ~75 reactions in total a. PLP reactions 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-ketoglutarate2,1 Arg, Glu, Gln, His, Pro Four to succinyl-CoA7,4 Ile, Met, Thr, Val Two to fumarate Phe, Tyr 5 Two to oxaloacetate1 Asp, Asn 1 Trans-/de-aminase family family 3 Pyruvate family 4Alpha-keto butyric family 5 Aromatic family 6Alpha-keto adipic family 7 Branched-chain family 2Glu Amino Acid Degradation A,D,E Simple Transamination PLP PLP + + PLP 2 Amino Acid Degradation N,Q Simple Deamination PLP + + PLP Amino Acid Degradation • • • A,D,E,N,Q 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-ketoglutarate2,1 Arg, Glu, Gln, His, Pro Four to succinyl-CoA7,4 Ile, Met, Thr, Val Two to fumarate Phe, Tyr 5 Two to oxaloacetate1 Asp, Asn ✓ Trans-/de-aminase family 1 2Glu family Pyruvate family 4Alpha-keto butyric family 5 Aromatic family 6Alpha-keto adipic family 7 Branched-chain family 3 3 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 29 N 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 4 Amino Acid Degradation: One Carbon H • Tetrahydrofolate is formed from folate. H H H dihydro Folic Acid – 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 5 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-ketoglutarate2,1 Arg, Glu, Gln, His, Pro Four to succinyl-CoA7,4 Ile, Met, Thr, Val Two to fumarate Phe, Tyr Two to oxaloacetate1 Asp, Asn 5 ✓ Trans-/de-aminase family ✓2Glu family 1 3 Pyruvate family butyric family 5 Aromatic family 6Alpha-keto adipic family 7 Branched-chain family 4Alpha-keto 6 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 G,S,C Amino Acid Degradation Pyruvate Family Glycine • Pathway #1: glycine cleavage enzyme PLP 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 PLP All these uses of PLP; let’s have a closer look • Pathway #3: D-amino oxidase – relatively minor pathway – ultimately oxidized to oxalate – major component of kidney stones oxalate O2 cysteine dioxygenase NAD+ O2– – Reverse reaction major feeder of onecarbon to THF serine/threonine PLP, lipoate, THF, FAD transaminase PLP spontaneous O2– NADH 3-sulfinoalanine || O – apparently major pathway in mammals – separation of three central atoms – releases CO2 and NH3 – methylene group is transferred to THF – mechanism like PDH complex SO3– H2O 3-sulfinyl-pyruvate a-ketoglutarate glutamate Bile Acids 7 Amino Acid Degradation 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 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 8 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 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 H2O Schiff-base hydrolysis O Schiff-base hydrolysis imine/Schiff base eneamine 9 Amino Acid Degradation PLP Catalyzes Many Types of Reactions ③ ① Acid donates proton to leaving group (water when Y=OH) ④ O–H | Base abstracts proton from b-carbon ① ① ③ Base abstracts proton from a-carbon ② Protonation of PLP aldehyde carbon ② H Ca-bond: 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? 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 ② ① ① ③ Base abstracts proton from a-carbon 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 10