Topic 2 Anabolism of Biomolecules (Part I) PDF

Topic 2 Anabolism of Biomolecules (Part I) BIOL 2036SEF / S236F Cellular and Molecular Biology 2 Topic Covered ▪ ▪ Metabolism of Carbohydrates Metabolism of Fatty Acids ▪ ▪ ▪ Readings: Chapter 15, Biology Metabolism of Amino Acids Metabolism of Nucleotides Tool and Techniques for Metabolomic Studies...

Topic 2 Anabolism of Biomolecules (Part I) BIOL 2036SEF / S236F Cellular and Molecular Biology 2 Topic Covered ▪ ▪ Metabolism of Carbohydrates Metabolism of Fatty Acids ▪ ▪ ▪ Readings: Chapter 15, Biology Metabolism of Amino Acids Metabolism of Nucleotides Tool and Techniques for Metabolomic Studies 1 What is Metabolism? 4 Metabolism is a network of metabolic /biochemical reactions. ▪ Carried out in living cells. ▪ In a well organized, integrated and regulated manner. ▪ Related to various biomolecules viz ▫ Carbohydrates ▫ Lipids ▫ Proteins ▫ Nucleoproteins ▪ 5 ▪ Metabolism involves interconversions of chemical compounds in the body. ▪ Metabolite precursors are transformed to end products via many specific intermediates. 6 ▪ Metabolism is the sum of the chemical changes that convert: ▫ Nutrients into energy. ▫ Chemically complex substances of cells into simpler forms. ▫ Chemically simple substances into functional complex biomolecules. CATABOLISM : ​The process that is breaking down of things : A series of degradative chemical reactions that break down complex molecules into smaller units, and does not require energy because it is releasing energy. ANABOLISM : ​The process to building up of things : Chemical reaction that synthesizes molecules from the smaller components and usually require energy in process 7 8 The Sun is Energy for Life  Phototrophs (Plants) use light to drive synthesis of organic molecules.  Heterotrophs (Animals) use these as building blocks.  CO2,O2 and H2O are recycled. 10 Importance Of Metabolism ▪ Normal Metabolism is vital for health, growth, reproduction and good survival of human beings. 11 https://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/21-molecules-to-metabolism/anabolism-and-catabolism.html 2 Glucose Metabolism 13 What is Glucose Metabolism ? ▪ There are 4 main processes that involved in glucose metabolism : i) Gluconeogenesis ii) Glycogenolysis iii) Glycolysis iv) Glycogenesis 14 ▪ What is Glucose Metabolism ? i) Gluconeogenesis - Process to produce/provide from pyruvate into glucose. ▪ ii) Glycogenolysis - Process to stimulate the conversion of glycogen into glucose. - Catabolism process 15 ▪ What is Glucose Metabolism ? iii) Glycolysis - The process to break down the glucose (sugar) to form energy. - Catabolism process. - The end product are pyruvic acid and ATP. iv) Glycogenesis - The process to store the break down of glucose (sugar) when changed into glycogen. - Anabolism process. The pathway in the carbohydrate metabolism : ▪ Carbohydrate metabolism involved the small intestine where the monosaccharides are observed into the capillary blood. Concentration of glucose in blood are controlled by insulin, glucagon and epinephrine. ▪ - When the concentration of glucose in blood is increase, insulin is secreted by the pancreas. ▪ - When the concentration of glucose in blood is decrease, glucagon and epinephrine are secreted to stimulate the conversion of glucagon into the glucose through glycogenolysis. 16 17 ▪ - Because of little ATP that produced by glycolysis process, the reaction are then continue to pyruvic acids into acetyl-CoA, then to citric acid in the citric acid cycle. ▪ - Pyruvic also can be converted into lactic acid compared to acetyl CoA because of the strenuous muscle activities. When the muscle in the resting time, the lactic acids then will convert into pyruvic acid which then undergo the gluconeogenesis process. ▪ - The conversion of glucose into glycogen by glycogenolysis also could occur and because glucose is not needed on that time. 18 19 Glycolysis and Gluconeogenesis Glycolysis and Gluconeogenesis - As we know, the gluconeogenesis occur when the glucose level in blood are low. Then, these substrate are needed to genesis new glucose: ▪ 1) Amino acids 2) Lactate 3) Glycerol 4) Pyruvate. ▪ - Gluconeogenesis require anabolic pathway to synthesize the formation of glucose from amino acids, lactate and glycerol which then it also need energy to break down pyruvate. 20 21 ▪ Important events in Glycolysis - There are 4 important events that happen in glycolysis: ▪ i) Substrate level phosphorylation which is the phosphate group from ATP are transferred to glucose. ▪ ii) 6C molecules of glucose is broken down with two 3C molecules. ▪ iii)2 electrons are transferred to the coenzyme NAD ▪ iv)The energy is in ATP form. 22 3 Protein Metabolism 24 ▪ Protein Protein are the important tissue builders in body which it can help in the cell structure, functions, haemoglobin formation to carry oxygen, enzyme for metabolic reaction and other functions in the body. Also in supply the nitrogen for the DNA and RNA genetic materials and the energy production. This is because, protein contain long chain of amino acids. 25 ▪ Protein Metabolism Protein metabolism is the process to breakdown foods are used by the body to gain energy. During protein metabolism, some of the protein will converted into glucose through gluconeogenesis process. (Formation of glucose from non-carbohydrate sources). 26 Amino Acid Metabolism 27 28 Krebs cycle Amino acids degradation ▪ The general ways of amino acids degradation ▪ 1. Deamination - Elimination of amino group from amino acid with ammonia formation. - Types of deamination : i) Oxidative ii) Reductive iii)Hydrolytic iv)Intramolecular 2. Transamination 3. Decarboxylation 29 30 Deamination ▪ - Elimination of amino group from amino acid with ammonia formation. ▪ - Types of deamination : i) Oxidative ii) Reductive iii) Hydrolytic iv) Intramolecular 31 ▪ Oxidative Deamination L-Glutamate dehydrogenase present in both cytosol and mitochondria to the liver. ​L-Glutamate takes part in amino acids deamination. ▪ Removes the amino groups as an ammonium ion from glutamate ▪ Provides alpha-ketoglutarate for transamination. 32 ▪ transfers an amino group to a ketoacid to form new33 amino acids. ▪ responsible for the deamination of most amino acids ▪ This is one of the major degradation pathways which convert essential amino acids to nonessential amino acids ▪ The enzyme that involved is aminotransferase (transaminase) ▪ There are different reaction of transaminases between alanine aminotransferase and aspartate aminotransferase. Transamination 34 Glutamate's amino group, in turn, is transferred to oxaloacetate in a second transamination reaction yielding aspartate. Glutamate + oxaloacetate ↔ α-ketoglutarate + aspartate 35 36 Transamination pathway 37 38 Decarboxylation ▪ The process to remove of carbon dioxide from the amino acid with formation of amines. ▪ The enzyme that involved is decarboxylases. The coenzyme is pyrpdoxalphosphate 39 ▪ Synthesis and/or collection of amino acids is critical for cell survival. They not only serve as the building blocks for proteins but also as starting points for the synthesis of many important cellular molecules including vitamins and nucleotides. ▪ 12 out of 22 amino acids are readily synthesized by the body. Because these 12 amino acids are not required in our diet, they are called nonessential amino acids. The other 10 are considered essential amino acids because they must be acquired through the diet. Anabolism of Amino Acids 40 41 Essential amino acids Number Amino acid’s Name 1 (essential in preterm infants) Arginine 2 Non-essential amino acids Number Name of Amino acid 1 Alanine 2 Aspargine Histidine 3 Aspartic Acid 3 Isoleucine 4 Cysteine 4 Leucine 5 Cystine 5 Lysine 6 Glutamic acid 7 Glutamine 6 Methionine 8 Glycine 7 Phenyalanine 9 Hydroxyproline 8 Threonine 10 Proline 9 Tryptophan 11 Serine 10 Valine 12 Tyrosine 13 (Non-essential in adults) Arginine 42 43 4 Lipids Metabolism 45 Oxidation of Fatty acid ▪ Activation of fatty acids take place at outer mitochondrial membrane ▪ Transport fatty acyl CoA into mitochondria ▪ Degradation of acetyl CoA in the mitochondrial matrix through boxidation 46 ▪ Fatty acids are converted to CoA thioesters by acytl-CoA synthetase ▪ The PPi released is hydrolysed by a pyrophosphatase to 2 Pi ▪ Two phosphoanhydride bonds are consumed to activate one of the fatty acid to thioester Activation of fatty acids 47 Transport fatty acyl CoA into mitochondria ▪ The carnitine shuttle system ▪ Fatty acyl CoA is converted to acylcarnitine by carnitine acyltransferase 1 (CPT1) ▪ Acylcarnitine enters into mitochondrial by translocase ▪ The acyl group then transferred back to CoA by carnitine acyltransferase 2 (CPT2) 48 49 Degradation of acetyl CoA ▪ B-oxidation is the catabolic process by which the fatty acids molecule are broke down in the mitochondria to produce actylCoA ▪ Enzyme that involved are acylCoA dehydrogenase, enoyl-CoA hydratase, hydroxyacyl-CoA dehydrogenase and ketoacylCoA thiolase. 50 Degradation of acetyl CoA ▪ During B-oxidation NADH are produced during catalysed by hydroxyaryl-CoA dehydrogenase are FADH2 are produced during the catalysed by acyl-CoA dehydrogenase. ▪ NADH and FADH2 are used by the electron transport chin to form ATP. 51 52 Lipid anabolism ▪ Lipid anabolism is also called lipogenesis. When glycerol binds with fatty acids, mono-/di-/triglycerides are formed. Almost any organic substrate can be used to to synthesize lipids because because lipids, amino acids, and carbohydrates can be converted to acetyl-CoA. 53 Fatty acid synthesis 54 Comparison of b-oxidation and fatty acid synthesis 5 Nucleotide Metabolism 56 Introduction ▪ Purines and pyrimidines are nitrogencontaining heterocycles, cyclic compounds whose rings contain both carbon and other elements. Nucleosides are derivatives of purines and pyrimidines that have a sugar linked to a ring nitrogen. ▪ ▶ ▪ ▶ Nucleotides are nucleosides with a phosphoryl group esterified to a hydroxyl group of the sugar. 57 Bases, Nucleosides and Nucleotides ▪ 58 Ingested nucleic acids and nucleotides, which are dietarily nonessential, are degraded in the intestinal tract to mononucleotides, which may be absorbed or converted to purine and pyrimidine bases. 59 Process involved in nucleotides biosynthesis ▪ Synthesis from amphibolic intermediates (synthesis de novo). ▪ Phosphoribosylation of purines ▪ Phosphorylation of purine nucleosides. ▪ Conversion of purines, their ribonucleosides, Biosynthesis of purine nucleotides and their deoxyribonucleosides to mononucleotides involves so called “salvage reaction. ▶ Liver is the major site for purine nucleotide synthesis. ▶ Erythrocytes, polymorphonuclear leukocytes and brain cannot produce purines. ▶ Folic acid is essential for the synthesis of purine nucleotides. Folic (methotrexate) are employed to control cancer. 60 Biosynthesis Of Pyrimidine Nucleotides ▪ ▶ ▪ ▶ ▪ ▶ The catalyst for the initial reaction is cytosolic carbamoyl phosphate synthase II, a different enzyme from the mitochondrial carbamoyl phosphate synthase I of urea synthesis. Compartmentation thus provides two independent pools of carbamoyl phosphate. PRPP, an early participant in purine nucleotide synthesis, is a much later participant in pyrimidine biosynthesis. Mammalian cells reutilize few free pyrimidines, “salvage reactions” convert the ribonucleosides uridine and cytidine and the deoxyribonucleosides thymidine and deoxycytidine to their respective nucleotides. 61 62 63 1. FOLATE BIOCHEMISTRY ▪ ▪ ▪ Tetrahydrofolate is synthesized by two mechanisms: ▫ Conversion of folate to dihydrofolate and dihydrofolate to tetrahydrofolate is catalyzed by dihydrofolate reductase (DHFR). ▫ Methyltetrahydrofolate from liver stores is converted to tetrahydrofolate, a reaction that requires VITAMIN B12. Two steps in the conversion of 5phosphoribosylamine to IMP (purine synthesis) use tetrahydrofolate as a carbon donor. Tetrahydrofolate is also involved in the generation of dTMP from dUMP (pyrimidine synthesis) – this reaction is catalyzed by thymidylate synthase (see 2A below). PYRIMIDINE SYNTHESIS A. The rate limiting step in DNA synthesis is the conversion of UMP to B. Uridine monophosphate (UMP) Thymidine monophosphate (TMP) 5-fluorouracil (5FU) C. TMP, which is catalyzed by thymidylate synthase. Conversion of UMP to UDP is catalyzed by pyrimidine monophosphate kinase; this reaction is important in the development of resistance to 5-FU. One step in the degradation of thymidine nucleotides is catalyzed by dihydropyrimidine dehydrogenase; an inherited deficiency of this enzyme leads to greatly increased sensitivity to 5-FU. 64 PURINE SYNTHESIS A. De novo purine synthesis begins with the conversion of B. 6-mercaptopurine dose - 6-MP 6-thioguanine nucleotide - 6-TG C. D. ribose-5-phosphate to 5-phosphoribosyl-1-pyrophosphate (PRPP), a reaction catalyzed by PRPP synthetase (PRPS). The first committed step in purine synthesis is the formation of 5-phosphoribosylamine via the enzyme glutamyl amidotransferase (GPAT). IMP and GMP can also be created by via the “salvage pathway” whereby PRPP is combined with hypoxanthine or guanine bases (including 6-MP and 6-TG) by the actions of hypoxanthine-guanine phosphoribosyl transferase (HGPRT). 6-MP and 6-TG (and their naturally occurring analogues) inhibit guanylyl kinase, preventing the conversion of GMP to GDP and causing "pseudofeedback inhibition" of PRPS, GPAT, HGPRT and the 2 steps that lead to the formation of XMP and AMP from IMP. One route for the degradation of purine nucleotides (and 6-MP and 6-TG) occurs via conversion of IMP to uric acid. Two steps in that process, conversion of hypoxanthine to xanthine and xanthine to uric acid, are catalyzed by the enzyme xanthine oxidase. This enzyme is inhibited by ALLOPURINOL. 65 66 CONVERSION OF RIBONUCLEOTIDES TO DEOXYRIBONUCLEOTIDES ▪ This reaction is catalyzed by ribonucleotide reductase. 67 ▪ Humans convert adenosine and guanosine to uric acid. Catabolism of purines ▪ Adenosine is first converted to inosine by adenosine deaminase. ▪ In mammals other than higher primates, uricase converts uric acid to the water soluble product allantoin. ▪ Since humans lack uricase, the end product of purine catabolism in humans is uric acid. ▪ Uric acid is degraded into allantoic acid and finally to ammonia in animals other than human 68 69 Catabolism of pyrimidines ▪ Pyrimidine catabolism are highly water-soluble: CO2, NH3, β-alanine, and β-aminoisobutyrate. ▪ Excretion of β-aminoisobutyrate increases in leukemia and severe x-ray radiation exposure due to increased destruction of DNA. ▪ Humans probably transaminate βaminoisobutyrate to methylmalonate semialdehyde, which then forms succinyl-CoA. ▪ Since the end products of pyrimidine catabolism are highly water-soluble, pyrimidine overproduction results in few clinical signs or symptoms. 70 71 ▪ Coordinated regulation of purine and pyrimidine nucleotide biosynthesis ensures their presence in proportions appropriate for nucleic acid biosynthesis and other metabolic needs. ▪ ▶ Pyrimidine nucleotides are synthesized from the precursors aspartate, glutamine and CO2, besides ribose 5-phosphate. are degraded to amino acids, nomely βalanine and β ▪ aminoisobutyrote which are then metabolized ▪ ▶ Pyrimidines 72 Thanks! Any questions? You can find me at [email protected] & Tel: 27685938