Metabolism of Lipids, Nucleotides, Amino acids, and Hydrocarbons LIPIDS | HSCI 4607, Study notes of Health sciences

Download Metabolism of Lipids, Nucleotides, Amino acids, and Hydrocarbons LIPIDS | HSCI 4607 and more Study notes Health sciences in PDF only on Docsity! Bacterial Physiology:HSCI 4607/5607 CH: 9 :Metabolism of Lipids, Nucleotides, Aminoacids, and Hydrocarbons LIPIDS: Introduction: Structurally lipids are heterogeneous group of substances. Their distinguished properties include: - They are made up of fatty acids - Highly soluble in nonpolar solvents such as ethanol, methanol, acetone, chloroform and so on. - Relatively insoluble in water. Lipids are important components of bacterial and eukaryotic cell membranes. The major lipid present in these membrane is phospholipid which is also called phophoglycerides. Phosphoglycerides are made up of fatty acids esterified to glycerol phosphates. Archaea also have phospholipids but they have different chemical structure and mode of synthesis. Fatty Acid Degradation: -Oxidation:Many bacteria when they grow on long chain fatty acids, they oxidize fatty acids to acetyl-CoA via pathway called -Oxidation. Reaction 1: In the first step the fatty acid is converted to Acyl-CoA derrivative in a reaction catalyzed by Acyl-CoA synthetase. This takes place in two steps: First the ATP molecule loses PP and gets attached to the fatty acid at carboxyl end to form Acyl adenylate (Acyl-AMP). In a second step the AMP molecule is replaced by CoASH to form Fatty Acyl-CoA. Reaction 2: In this step Acyl-CoA dehydrogenase oxidizes and forms double bond between the C2 and C3. Reaction 3: The double bond is hydrated by 3-hydroxyacyl- CoA hydrolase during this step. Reaction 4: The hydroxyl group is oxidized in this step to form keto group by L-3-hydroxyacyl-CoA dehydrogenase. Reaction 5: In the final step the carbonyl group of -keto acyl CoA is attacked by CoASH, displacing Acetyl-CoA as a product. This reaction is catalyzed by - ketothiolase. Fate of Acetyl-CoA: Acetyl-CoA thus released is metabolyzed to CO2 in aerobic bacteria via citric acid cycle or it can be utilized via glyoxylate cycle. The other product Fatty acyl CoA enters into another cycle of -oxidation to generate another molecule of Acetyl-CoA. Thus if the fatty acid is made up of even number of carbons, it is completely metabolized to Acetyl-CoA while if it is odd number chain then the last fragment of propionyl-CoA is metabolized by variety of oxidative path ways. One example is: Propionyl-CoA >> Acrylyl-CoA >> Lactyl-CoA >> Pyruvate Reaction 5: -ketoacyl-ACP is then reduced to the hydroxy derivative by an NADPH-dependent -ketoacyl-ACP reductase to 3- hydroxyl acyl-ACP, which is in reaction 6, dehydrated by dehydrase to yield unsaturated acyl-ACP derivative. Reaction 7: The unsaturated acyl-ACP is then reduced by enoyl-ACP reductase to saturated Acyl-ACP. The ACP chain is elongated by repetition of series of identical reactions initiated by attack of Malonyl-ACP on acyl-ACP chain to remove ACP. The biosynthetic pathway is possibly regulated through feed back inhibition. When acyl-ACP chain is completed, the acyl portion is immediately transferred to membrane phospholipids by the enzyme ‘Glycerol phosphate acyltransferase reactions’. For the synthesis of unsaturated fatty acids the Acyl-ACP or Acyl-CoA is dehydrated or desaturated by specific enzymes depending upon the type of bacteria and aerobic or anaerobic conditions. fi ap yee f CH;—Cl~SCoA + HCO; =f HO,C—CH, —C!~SCoA WA acetyl~SCoA /# - malonyl~SCoA AcPSH ACPSH 3 2 ‘CoASH CoASH i t CHE I~SACP HO,C |+CH,—C~SAcP ‘ ' t 9 Il CH;—C—CH,—C~SACP H i 1 CH, —¢—CH,—C~SACP a It CH;—CH=CH—C~SACP a CH;—CH,—CH, —C~SACP H oO fi i] CH; —(CH)5—CH CCH) —C~SACP | . 0 CH; —(CH)s—CH=CH—CH, —C~SACP OH 3-OH-decanoyl~SACP enoyl~SACP (f-y unsaturated) Fig. 9.4 Biosynthesis of fatty acids. Enyzmes: 1, acetyl-CoA carboxylase; 2, malonyl transacetylase; 3, acetyl transacetylase; 4, 3-ketoacyl-ACP synthase; 5, 3-ketoacyl-ACP reductase; 6, B-hydroxyacyl— 4 Nico, tassel crs Oo i 3-ketoacyl~SACP ‘NADPH + Ht NADP* 3-OH-acyl~SACP Ne H,0 Oo enoyl~SACP (c-B unsaturated) NADPH + H* NADP* acyl~SACP chain elongation, —_palmitoleic (cis-A? - hexadecenoic acid) cis-vacoenic (cis-A" - octadecenoic acid) ACP dehydrase; 7, enoyl-ACP reductase; 8, 3-hydroxydecenoyl-ACP dehydrase.  Phospholipid Synthesis: Phospholipids are the fatty acids covalently attached to glycerol phosphates. They are important constituents of cell membranes. Bacterial phospholipids also contain other molecules like amino acids, an amine or sugar covalently attached to them, e.g. Phosphatidyl serine contains amino acid serine. Synthesis: Their synthesis starts with glycolysis intermediate, Dihydroxy acetone phosphate (DHAP), which is reduced to Glycerol-3-Phosphate by enzyme glycerol phosphate dehydrogenase. In step 2, the fatty acids from newly synthesized Acyl-ACP are transferred to the C1 and C2 of the glycerol phosphate to yield the first Phospholipid called ‘Phosphatidic acid’. The enzyme catalyzing this reaction is G3P acyl transferase. Other phospholipids are synthesized from Phophatidic acid. NUCLEOTIDES: There are three components of nucletides: 1. Nitrogeneous base: Purine (Adenine or Guanine) or Pyrimidine (Thymine, Cytosine or Uracil). 2. Pentose Sugar:Ribose (RNA) or Deoxyribose (DNA) 3. Phosphate group. The nucleotide without phosphate is called nucleosides, that is nucleotides are nucleoside phosphates. The pyrimidine nucleosides are called as Cytidine, thymidine, uridine while purine nucleoside are called adenosine and guanosine. The corresponding nucleotides are referred as e.g. adenosine mono,or di, or tri phosphates (AMP, ADP, or ATP). Sometimes nucleoside monophosphates are also referred to as adenylic acid, guanylic acid, cytidylic acid, thymidylic acid or uridylic acid. In DNA the nucleoside phosphates contain deoxyribose where on C2 the hydroxyl group is replaced by hydrogen. STRUCTURES OF NUCLEOTIDES: Nay, wifi HO— ~0.HO HO— 0. HO la, 4 R zl No OH OH OH purine pyrimidine ribose deoxyribose wee men er OH OH OH OH OH nucleoside deoxynucleoside nucleoside monophosphate [NMP], i.e. a nucleotide Te wcbday x Oo, vant guanine idea weisatiie seul  The Synthesis of Pyrimidine Nucleotides: The pyrimidine ring of nucleotide is made from, Aspartate, Ammonia, and Carbon dioxide. The phosphoribosyl pyrophosphate donates the ribose phosphate moiety to the nucleotides. This pathway leads to the synthesis of Uridine triphosphate which serves as a precursor for the formation of cytidine triphosphate through ammonification. Methylation of UTP at 5th C forms thymidine triphosphate. Thus UTP serves as precursor for the synthesis of the other pyrimidines. Purine synthesis….. The imidazole ring serves as precursor and additional carbon atoms are contributed by CO2, aspartate and formyl-THF to ultimately form ‘Inosinic acid’. Inosinic acid is the precursor to all the purine nucleotides. Adenine nucleotide: Adenine nucleotide is formed by substitution of the carbonyl oxygen at C6 of IMP with an amino group from aspartate.This reaction requires GTP. Guanidine nucleotide:This is formed by oxidation of IMP at C2 followed by an amination of C2. Glutamine is the donor of amino group. The THF:The tetra hydrofolic acid (THF) derivatives which are synthesized from vitamin B folic acid, are important single carbon donor during purine biosynthesis. The deoxyribonucleotides: They are synthesized by reductive dehydration of ribonucleoside diphosphates, catalyzed by ‘Ribonucleoside diphosphate reductase’ which uses protein ‘thioredoxin’ as electron donor coupled with NADPH. Purine Biosynthetic Pathway Fig. 9.11 Metabolic origins of atoms in purines. 5-phosphoribosy!-1- eae pytophosphate ; ATe ADP +P, ribose —P S-phosphorlbosyl-5- aminolmidazole ay & > XN HAT 4 ribose—P S-phosphoribos: S-aminolmidazole- 4-carboxylc acid ATP + asp \ ADP +P, one) - glycine + ATP \ on OH S-phosphoribosyl- ADP +P, s.phosphoribosyl- amine slycinesmide formyl-THE 3 THE oN NK Gh, ‘cHo Fi ha Xe cto) m 1 ATP Ue (w) NH gue ape®™* of yn Hose —P +B, Hose —1 5-phosphoribosyl-N- S-phosphoribosy1-N- formylelyeineamidine Tormylglycineamide Gh \9 HONE “TS boon LD = ) awed a ni SZ tioteF HN S-phosphoribosyl-4- Goon i ‘ ribose —P carboxamide S.phosphoriboeyl-4- aminolml (N-succinocarboxyamide)- S-aminolmidazole formyl-THF 3 ‘THF HN’ N, HN oe @ N —— Inosiate acd EMT S-phospho Fig. 9.12 Biosynthesis of purine nucleotides. Enzymes: 1, PRPP amidotransferase; 2, phosphori- bosylglycineamide synthetase; 3, phosphoribosylglycineamide formyltransferase; 4, phosphoribosyl- formylglycineamidine synthetase; 5, phosphoribosy!-aminoimidazole synthetase; 6, phosphoribosy- laminoimidazole carboxylase; 7, phosphoribosylaminoimidazole succinocarboxamide synthetase; 8, adenylosuccinate lyase; 9, phosphoribosylaminoimidazolecarboxamide formyltransferase; 10, IMP cyclohydrolase. Abbreviations: gin, glutamine; glu, glutamate; asp, aspartate; fum, fumarate; THE, tetrahydrofolate. up Sb0—P artate, Se > * ? LO : bute P 3 ATP, sin, H,0 ‘AMP, glu, PP, ° N HN oe H N ¥ ribose—P Fig. 9.13 Synthesis of AMP and GMP from IMP. Enzymes: 1, adenylosuccinate synthetase and adenylosuccinate lyase; 2, IMP dehydrogenase; 3, GMP synthetase. Abbreviations: IMP, inosinic acid; AMP, adenylic acid; XMP, xanthylic acid; GMP, guanylic acid.  Glutamate/Glutamine synthesis: There are two different ways in which glutamate is synthesized in cell. 1. This is catalyzed by enzyme ‘Glutamate dehydrogenase’ which carries out reductive amination of -ketoglutarate. The KM of this enzyme for ammonia is high (>1mM), therefore this pathway is operative only under high concentration of ammonia. 2. Under low concentration bacteria use combination of two enzymes for the incorporation of ammonia. One is L-glutamine synthetase which incorporates ammonia into glutamate to form glutamine using ATP as a energy source. The other enzyme is glutamate synthase which transfers newly incorporated ammonia into glutamine to -ketoglutarate to form glutamate. This enzyme is also known as ‘Glutamine -oxoglutarate aminotransferase’ (GOGAT) enzyme. NADPH is the electron donor in this reaction. Glutamate synthesis pathways: COOH COOH ¢=0 H,N—C—H CH, + NADPH + H* + NH; —=——— CH, + NADP* + H,0 ia ie COOH COOH K-kets guaterale Chanter ab®. Fig. 9.16 The glutamate dehydrogenase reaction. Glutamate/Glutamine Synthesis COOH COOH HaN-C—H app app+pi [NH] 9 2N-F7# CH, CH 'H, 1 'H, (on e-Lii] o 0 L-glutamate L-glutamine } F b. + NADP* NADPH + H E BE FE ; | T meet H,.N|-C—H ¢=0 ; H; ; ti H, s COOH yo bak L-glutamate a-ketoglutarate 9.17 The GS and GOGAT reactions. Enzymes: 1, L-glutamine synthetase; 2, glutamine: a- _ oxoglutarate aminotransferase, also called the GOGAT enzyme, or glutamate synthase. COOH = apt NYPH +H" COOH giuramate %f*tOBlutarate COOH | \ J | B= 6-08 1 c=0 2 H.N-C—H CH,0-(P) CH,0-(P) CH,O-(P) 3-phosphoglycerate phosphohydroxy- phosphoserine pyruvate H,0 3 Pi tl ‘nan CoasH CH3-C~SCoA | H,N-C-H ; H.N—C—H CH,O—C—CH, CH,OH O-acetylserine L-serine H,S THF 6 4 methylene- a CH;COOH THF + H,0 I HN~C-H CH,NH, CH,—SH glycine cysteine Fig. 9.19 The synthesis of serine, glycine, and cysteine from 3-PGA. Enzymes: 1, phosphoglycerate dehydrogenase; 2, phosphoserine aminotransferase; 3, phosphoserine phosphatase; 4, serine hydroxymethyltransferase; 5, serine transacetylase; 6, O-acetylserine sulfhydrylase.  Catabolism of amino acids: The catabolism of amino acid always starts with removal of amino group to generate the -keto acid which eventually enters into citric acid cycle. All of the 20 amino acids are degraded to seven intermediates that enter citric acid cycle. These intermediates are: Pyruvate, acetyl-CoA, acetoacetyl- CoA, -ketoglutarate, succinyl CoA, fumerate and oxaloacetate. asparagine acetoacetyl~ CoA | <t— phenylalanine Ne tyrosine oxaloacetate Seyproptin. | ete cid cycle 1 i fumarate a-ketoglutarate | <<—— glutamate eS, ms tyrosine succinyl~CoA aspartate phenylalanine f oe ee ri valine Fig. 9.20 Fates of the carbon skeletons of amino acids. Amino acid carbon can be used to synthesize all the cell components or be oxidized to CO}. In the absence of the glyoxylate cycle, carbon entering at acetyl-CoA cannot be used for net glucogenesis except in some strict anaerobic bacteria that can carboxylate acetyl-CoA to pyruvate (Chapter 13),