Biosynthetic Pathways FFP1 2022-2023 PDF

Royal College of Surgeons in Ireland – Medical University of Bahrain Biosynthetic Pathways Module : Foundations For Practice 1 FFP1 Class: MedYear1 semester 1 Lecturer : Paul O’Farrell Date : 3 October 2022 Learning Outcomes Describe the general features of anabolic pathways (thei...

Royal College of Surgeons in Ireland – Medical University of Bahrain Biosynthetic Pathways Module : Foundations For Practice 1 FFP1 Class: MedYear1 semester 1 Lecturer : Paul O’Farrell Date : 3 October 2022 Learning Outcomes Describe the general features of anabolic pathways (their requirement for energy and their use of electron donors in reduction reactions) Explain gluconeogenesis and its regulation Relate gluconeogenesis to the overall map of metabolism and discuss its relevance Relate the pentose phosphate pathway to the overall map of metabolism and discuss its relevance Outline the biosynthesis and degradation of nucleotides Outline the biosynthesis of amino acids and their use as precursors for other biomolecules Overview of catabolism NADPH NADH Lippencott’s 8.2 Catabolic and Anabolic Pathways 3 Steps in anabolism Form precursors Form complex molecules from simple precursors Link these complex molecules together Proteins, RNA/DNA, Lipids, carbohydrates All processes require energy Energy sources for anabolism ATP – high energy phosphate bonds NADH – high energy electrons – reducing power – Oxidative Phosphorylation to make ATP NADPH - high energy electrons – reducing power Gluconeogenesis Some tissues need glucose specifically as their preferred energy source – RBC, brain, testes, lens of eye Glycogen (a storage form of glucose) stores will only last 10-18 hrs When glycogen is depleted, glucose must be formed from other precursors Mainly : lactate, glycerol, (glucogenic) amino acids Problem: some steps of glycolysis are irreversible, so cannot simply reverse it (pyruvate dehydrogenase which converts pyruvate to acetyl CoA is also irreversible) Need special routes to go around irreversible steps Gluconeogenesis: Substrates: Glycerol (eg. from triglyceride backbone) Glycerol kinase  glycerol phosphate Dihydroxy acetone phosphate Glyceraldehyde-3-phosphate (glycolytic intermediate) Lactate (eg. from anaerobic glycolysis) To pyruvate by lactate dehydrogenase Amino acids To TCA intermediates and to oxaloacetate via TCA cycle reactions To glycolytic intermediates Carboxylation of pyruvate Glycolytic step: Pyruvate kinase Phosphoenolpyruvate  pyruvate; irreversible Gluconeogenic step(s): pyruvate carboxylase: pyruvate oxaloacetate ; occurs in mitochondrion, requires ATP PEP carboxykinase: oxaloacetate  PEP ; occurs in mitochondrion and in cytosol, requires GTP – (mitochondrial oxaloacetate cannot cross mitochondrial membrane in this form: converted to malate or aspartate which can cross and are reconverted in cytosol ) Dephosphorylation of fructose-1,6-bisphosphate Glycolytic step: Phosphofructokinase: fructose-6- phosphate  fructose-1,6-bisphosphate; irreversible Gluconeogenic step: Fructose 1,6 bisphosphatase reverses Control : Inhibited by AMP Inhibited by fructose 2,6, bisphosphate ( F-2,6-BP levels decreased bythe hormone, glucagon. Thus, glucagon increases rate of gluconeogenesis) Dephosphorylation of glucose-6- phosphate Glycolytic step: Hexokinase : glucose  glucose-6-phosphate; irreversible Gluconeogenic step(s) Glucose-6-phosphatase releases phosphate; occurs in Endoplasmic Reticulum Also requires glucose-6-phosphate translocase – transports G6P into ER Glucose-6-phosphatase only available in liver and kidney: these are the only gluconeogenic tissues; ie these are the only tissues that can release glucose to the bloodstream Gluconeogenesis and glycolysis 1 – pyruvate carboxylase 2 – PEP-carboxy kinase } Pyruvate kinase 3 – fructose-1,6-bisphosphatase }phosphofructokinase 4 – glucose-6-phosphatase (G-6-P translocase) } Hexokinase, glucokinase 2 ADP 2 ATP Note energy requirements Pentose Phosphate Pathway hexose monophosphate shunt/pathway phosphogluconate pathway A pathway that generates NADPH and 5-carbon sugars for biosynthetic processes More anabolic than catabolic Occurs in the cytoplasm Produces major proportion of body’s NADPH from its oxidative reactions Has two phases: – Oxidative phase where NADPH is produced – Cyclical phase where the 5-carbon sugars are made Pentose phosphate pathway and glycolysis G6P dehydrogenase 3 G6P PPP 2 F6P 3x CO2 ATP 6x NADPH 1 G3P Pentose Phosphate Pathway Oxidative phase (2 irreversible reactions) Overall: 1 molecule of Glucose-6-P  ribulose-5-P, CO2 & 2 NADPH NADP+ Catalysed by Glucose 6-phosphate NADPH +H+ dehydrogenase (G6PD) NADPH NADPH +H+ +H + NADP + and NADP + 6-phosphogluconolactone hydrolase Followed by a series of reversible reactions Pentose Phosphate Pathway. (NADP: nicotinamide adenine dinucleotide phosphate) Cyclical Phase (Reversible non-oxidative reactions) Catalyse the interconversion of 3,4,5,6,7-carbon sugars Products or intermediates can feed into Glycolytic pathway Ribose 5-P for DNA, RNA synthesis Regulation of the PPP Rate and direction of reversible reactions depend on supply of Glucose-6-P and demand for intermediates NADPH NADP+ NADPH +H+ Glucose-6-P Regulated mainly at glucose-6- dehydrogenase P dehydrogenase reaction- NADPH acts as a competitive 6-Phospho- inhibitor gluconolactone Insulin increases G6PD gene expression so pathway activity increases in well fed state NADPH vs NADH NADPH: Nicotinamide Adenine Dinucleotide Phosphate Used mainly in biosynthetic reactions NADH Nicotinamide Adenine Dinucleotide Used mainly in energy yielding reactions (oxidative phosphorylation) The presence or absence of the phosphate means that these two reducing agents are generally not acted on/used by the same enzymes. They are not metabolically interchangeable Uses of NADPH Biosynthetic – lipid synthesis Cholesterol synthesis Steroid hormone synthesis Sphingomyelin synthesis Fatty acid synthesis Certain phospholipids Protective - helps combat oxidative stress, regenerates reduced glutathione (GSH) Nucleotide biosynthesis and degradation Purine biosynthesis (A,G) Pentose phosphate pathway Source of atoms in Purine Activator: Inorganic Phosphate (Pi) ring structure PRPP synthetase ATP Inhibitor: Purine nucleotides AMP (PRPP) Precursor activation Feed back inhibition Activator:PRPP Folic Acid / Vitamin B9 PRPP amidotransferase Inhibitor: AMP, GMP, IMP 5’-Phosphoribosylamine dADP Sugar moiety of PRPP(phosphoribosyl-1- Ribonucleotide reductase pyrophosphate) is ribose GTP ATP producing ribonucleotides AMP ADP ATP IMP Reduced to deoxyribonucleotides GMP GDP GTP ATP GTP Ribonucleotide reductase Inosine 5’-monophosphate Common intermediate dGDP Pyrimidine biosynthesis (C,T,U) Glutamine + CO2 Source of atoms in Pyrimidine ring 2 ATP Activated by ATP & PRPP Carbamoyl phosphate synthetase II 2ADP Inhibited by UTP Carbamoyl phosphate Pyrimidine ring synthesized before being attached to ribose-5-P PRPP (donates ribose-5’-phosphate) OMP Orotidine 5’-monophosphate UMP Uridine monophosphate : Common intermediate dUDP UDP UTP CTP thymidylate synthase Cofactor: Tetrahydrofolate = Folic acid dTTp dDTP dTMP Nucleotide degradation 1. Pyrimidines Bases are broken down to simple carbon skeletons [β-Alanine or β -Aminoisobutyrate] and degraded 2. Purines Bases are either reused (‘Salvaged’) or degraded: Pu bases Xanthine Uric acid Excretion Clinical aspects 1. Many anti-cancer (chemotherapy) drugs act by inhibiting dTMP synthesis; this prevents cell- division by preventing DNA replication - eg methotrexate, 5-FU 2. Excessive breakdown of purine bases can lead to a condition called ‘Gout’; this is due to an excess of uric acid which can precipitate as crystals. The crystals cause inflammation of the joints & kidneys with severe pain 3 Adenosine deaminase: enzyme in degradation pathway for AMP. Genetic deficiency leads to severe immunodeficiency. Key Points amino acids as source of atoms for purine and pyrimidine rings , ribose from pentose phosphate pathway, common intermediates in purine and pyrimidine biosynthesis IMP – (G,C) OMP – (C,T,U) general regulatory mechanisms – feedback inhibition and precursor activation clinical relevance of the pathways gout (purines) chemotherapy (thymidylate synthase and dihydrofolate reductase) Biosynthesis of amino acids Essential and non-essential Essential Non-essential Arginine Alanine Histidine Asparagine Isoleucine Aspartate Leucine Cysteine* Lysine Glutamate Methionine Glutamine Phenylalanine Glycine Threonine Proline Tyrptophan Serine Valine Tyrosine* Amino acid structure Carbon skeleton O R CH C O- NH3+ Amino group Transamination Aminotransferases move amide groups between different carbon backbones Aminotransferases are reversible non-essential amino acids can be Lippencott’s 19.7 generated by transamination of ketoacids Transamination Aminotransferases move amide groups between different carbon backbones Aminotransferases are reversible non-essential amino acids can be generated by transamination of ketoacids Amidation Glutamate + ATP + NH3 Glutamine Glutamine + ADP + phosphate synthetase Aspartate + ATP + Glutamine Asparagine Asparagine +AMP + PPi + Glutamate synthetase Glutamine synthetase reaction also important mechanism to transport ammonia in non-toxic form Synthesis of non-essential aa from metabolic intermediates glucose glycine 3-PG serine Asparagine glutamine proline α-ketoglutarate NH3 (glutamate dehydrogenase) Synthesis of non-essential aa Amino acid Source Reaction alanine pyruvate transaminase aspartate oxaloacetate transaminase glutamate α-ketoglutarate transaminase, GDH asparagine aspartate Asparagine synthase glutamine glutamate Glutamine synthase proline glutamate cyclisation serine 3-phosphoglycerate (series of reactions) glycine serine Serine hydroxymethyl transferase Biosynthesis of physiologically active amines GABA, histamine, serotonin, epinephrine, norepinephrine & dopamine are all amino acid derivatives. – Serotonin synthesized from tryptophan – epinephrine, norepinephrine & dopamine synthesized from tyrosine – Histamine synthesized from histidine – GABA synthesized from glutamate Biosynthesis involves decarboxylation of a precursor amino acid. Biosynthesis of physiologically active amines Additional resources Reading: Lippincotts Biochemistry Ch 12, 13 Meisenberg and Simmons Ch 20