Unformatted text preview: Concepts in Biochemistry 3rd Edition R Boyer Chapter 19 Metabolism of Amino Acids and other Nitrogenous Compounds Dr. J. Davis 19.1 The NITROGEN CYCLE The released nitrogen can be taken up for use other biosynthetic processes or eliminated as urea, uric acid, or ammonia. Nitrogen atoms exist as either inorganic or organic compounds in either our atmosphere or in the earth [biosphere]. The most common Inorganic forms of Nitrogen are listed in Table 19.1 with their oxidation numbers/states. Note: the large range in the possible oxidation states from the most oxidized, NO3- ion to NH3 the most reduced. Molecular N2 [gas] is the most abundant form of Nitrogen which makes up ~ 80% of the atmosphere: N2 gas serves as a reservoir for all the nitrogen used in life forms [biosphere]. Only some soil bacteria/Cyanobacteria can tap directly into this reservoir to use N2 gas directly, however. 2 3 19.1 The NITROGEN CYCLE The Nitrogen Cycle, defines the flow of nitrogen atoms between the atmosphere and organisms, and is shown in Figure 19.1. Summary: 1) N2 gas is reduced to ammonia [NH3] by nitrogen-fixing bacteria; 2) NH3 plus water is converted to the ammonium ion. 3 Most ammonium ion, however, is rapidly converted to Nitrites via soil bacteria.
2 NH3 + 3 O2 2 NO2- + 2 H2O + 2 H+ 4 Fig 19.1 The Nitrogen cycle: the flow of N atoms between atmosphere and organisms 5 19.1 The NITROGEN CYCLE Nitrites are then converted to Nitrates by another species of bacteria: 2 NO2- + O2 2 NO3These processes, aka Nitrification, provides most of the nitrates needed for growth by plants. Note: some N can also enter the soil during lightning storms: 6 19.1 The NITROGEN CYCLE Soil bacteria and plants can reverse the nitrification process by the action of certain nitrate and nitrite reductases: NO3- + NADPH/H+ [nitrate reductase] NO2- + NADP+ + H2O
4 NO2- + 3 NADPH + 4H+ [nitrite reductase] NH + + 3 NADP+ + H2O + OH Plants use this Ammonium ion (formed in the soil) to synthesize amino acids. Animals acquire ALL their nitrogen thru the food chain by ingesting proteins from plants and animals that eats the plants.7 19.1 The NITROGEN CYCLE Nitrogen from plants/animals is recycled back to the soil by two processes: 1. Excretion of Nitrogen in the form of Urea or uric acid, which is converted to the ammonium ion by microbes. 2. Hydrolysis of proteins and other nitrogen compounds from dead/decaying plants & animals producing amino acids and other compounds, and releasing ammonia after microbial action. 8 19.1 The NITROGEN CYCLE
Biological Nitrogen Fixation - The Nitrogenase Complex For most animals, the only usable form of inorganic N comes from Ammonia. Ammonia is produced for the Nitrogen Cycle by reduction of N2 gas (performed by a few species of nitrogen-fixing bacteria). Nitrogen fixation (bacteria) occurs with specialized enzymes in the Nitrogenase complex under very mild conditions (~ 25 C; 1 Atm plus a source of electrons). Overall net reaction is: 9 19.2 Biosynthesis of Amino Acids ALL animals use the product of nitrogen fixation, the ammonium ion (NH4+), to incorporate nitrogen into organic molecules. The NH4+ ion, however, is very toxic to cells in high concentrations, so it must be detoxified before use inside cells by incorporating it into other organic molecules. The NH4+ ion is assimilated into 3 compounds: 1) Glutamic acid, 2) Glutamine, and 3) the compound Carbamoyl phosphate (CP). Amino acids Glutamic acid and glutamine are used to make other aa. Carbamoyl Phosphate is used in the synthesis of urea, pyrimidines, etc.
10 19.2 Biosynthesis of Amino Acids 11 19.2 Biosynthesis of Amino Acids Plants and bacteria incorporate ammonia into glutamic acid (Enz = Glutamate synthase). -Ketoglutarate + Glutamine + NADPH/H+ 2 Glutamic acids (Glutamate) 12 19.2 Biosynthesis of Amino Acids In plants/bacteria, the 2 reactions are coupled, giving a net reaction of: 13 19.2 Biosynthesis of Amino Acids
Essential and Nonessential Amino Acids (aa) All life forms can synthesize at least some of the 20 aa found in proteins. Plants & bacteria can synthesize all 20 amino acids. Humans can only make ~10 of 20; the rest must come from the diet (plants/other animals). Table 19.2 lists the 10 Essential (obtained from the diet) and 10 nonessential AA (synthesized by humans) in humans. Each of the 20 AA have a unique pathway of biosynthesis. Note: Fortunately, there are several common biosynthesis pathways.
14 15 19.2 Biosynthesis of Amino Acids
Common features in biosynthesis of AA: (1) There are six (6) biosynthetic families of amino acids, based on common precursors (See Figure 19.5); (2) All amino acids obtain their carbon skeletons from either a glycolysis, a CAC or a PP pathway intermediate; and (3) The amino group usually always comes from the amino acid, glutamic acid. The 6 biosynthetic families of AA include precursors include: 1) Pyruvate, 2) Oxaloacetate (OAA), 3) -ketoglutarate, 4) ribose-5-PO4, 5) 3-phosphoglycerate, and 6) the Phosphoenolpyruvate + Erythrose-4-PO4 family. 16 Fig 19.5 The Six Biosynthetic Families of Amino Acids 17 Catabolism of Amino Acids Chapter Seven 19.3 Catabolism of Amino Acids Amino acids Are Not important sources of fuel for most tissues. Amino acids can be used for energy under certain conditions: 1) when dietary AA are great excess (over/above needs for biosynthesis); 2) when normal process of protein recycling releases excess AA for catabolism; 3) During starvation or untreated diabetes, structural and catalytic proteins can be degraded to AA used for energy metabolism. In general: each AA has it own unique pathway for catabolism. Note: However, the degradative pathways for ALL amino acids are the same in all organisms. Catabolism of aa (as compared to carbohydrates/fats) requires the initial removal of the amino groups.
19 19.3 Catabolism of Amino Acids Note: A general metabolic principle that is applicable to all catabolic/anabolic pathways: Biomolecules are converted using as few steps as possible to a main stream metabolite. The process of digesting proteins to generate dietary amino acids is shown in the next slide. Figure 19.11 then shows the general scheme for amino acid metabolism. The usual 1st step is : the removal of the amino group [Deamination]. a) The amino group then proceeds in one direction, while b) the carbon skeleton is converted to a CAC intermediate. c) The ultimate fate of the NH4+ ion depends on the organism species and the cellular conditions.
20 Fig 19.11 General Pathway for Amino Acid Catabolism 21 Digestion of Proteins The end result of protein digestion is the hydrolysis of all peptide bonds to produce free amino acids. 22 19.3 Catabolism of Amino Acids
Fate of Dietary amino acids Mixtures of released aa are distributed to peripheral tissue for biosynthetic use or to the liver for catabolism. Recall: Amino acids in the diet come from ingested proteins [meat, etc]. Degradation begins in the stomach with proteolytic enzymatic hydrolysis by peptidase enzymes (Table 19.5). The primary proteolytic enzyme in the stomach is Pepsin. Pepsin cleaves peptide bonds on amino side of Phe, Tyr, Trp. The partially degraded peptides then proceed to the intestine, where several peptidases (including trypsin, chymotrypsin, aminopeptidase, and carboxypeptidase) are active. Note: many of these enzymes exist as inactive forms, aka Zymogens that require cleavage for full activation.
23 24 19.3 Catabolism of Amino Acids
AA Deamination via Transamination Initial phase of aa catabolism (Figure 19.11) is the removal of amino group by a common process: transamination. The Transamination process transfers the amino group to an -keto acid (usually -ketoglutaric acid). -ketoglutaric acid + AA Glutamate + -keto acid Example: -ketoglutarate + Ala Glutamate + Pyruvate [Enz = Alanine Aminotransferase]. Note: The acceptor (a-KG) becomes a new amino acid; the donor becomes an -keto acid (See next slide). 25 Enzyme: Aminotransferase is used to remove amino groups from -amino acid and to pass it off to a keto acid (-ketoglutaric acid). 26 19.3 Catabolism of Amino Acids
AA Deamination via Transamination The general strategy for transamination is to remove the amino group, and to collect it in one specific type of molecule, Glutamic acid (Glutamate). Glutamate is the single source of amino groups for continued nitrogen metabolism (biosynthesis and excretion). Several different Aminotransferase enzymes are present in the cytoplasm; most all use the same type of prosthetic group: PYRIDOXAL PHOSPHATE [PLP] to transport the Amino group (See Figure 19.12). PLP is a vitamin B6 derivative; it acts as an intermediate carrier of the amino group before donating it to the -keto 27 acid. Fig 19.12 Structures of Two Forms of Pyridoxal Phosphate 28 19.3 Catabolism of Amino Acids
Catabolism of Carbon Skeletons The fate of the residual carbon skeleton is: degradation to one or two of the possible 7 intermediates that can then be shunted into the CAC [Figure 19.13]. Amino acids can be divided into two basic groups based on their mode of degradation: as 1) Ketogenic amino acids, or as 2) Glucogenic amino acids. Ketogenic AA are degraded to Acetyl-CoA or Acetoacetate which form ketone bodies. Ketogenic AA include: Leu, Lys, Phe, Trp, Tyr; plus Iso. 29 19.3 Catabolism of Amino Acids
Catabolism of Carbon Skeletons 2) Glucogenic AA are degraded to Pyruvate, Ketoglutarate, Succinyl CoA, Fumarate, Oxaloacetate, all of which can also be used to synthesize glucose. Glucogenic amino acids include: most all other AA: Ala, Cys, Gly, Ser, Trp, etc. 30 Fig 19.13 Fates of carbon skeletons from amino acid catabolism 31 32 Elimination of NH4+ Ion Chapter Seven Fig 19.11 General Pathway for Amino Acid Catabolism 34 19.4 ELIMINATION OF NH4+
ELIMINATION OF NH4+ ion Amino groups removed during catabolism of AA are collected into one molecule, Glutamic acid (Glutamate) via the transamination process. Utilization of a single biomolecule to collect nitrogen is an efficient/economical process which allows the use of 1 set of reactions for the recovery of nitrogen. The combination of transamination with glutamate deamination provides a coupled process for the removal of amino groups (See Figure below).
4 35 Coupled Transamination/Deamination Reaction 36 19.4 ELIMINATION OF NH4+ The toxicity of the NH4+ ion is due to its negative effect on the Enzyme = Glutamate Dehydrogenase. -Ketoglutarate + NADH/H+ + NH4+ Glutamate + NAD+ + H2O At high concentrations, NH4+ ion shifts the equilibrium towards the right, lowering the concentration of ketoglutarate available for the CAC. For tissues that rely heavily on aerobic metabolism of glucose [like brain cells], this is especially bad. 37 19.4 ELIMINATION OF NH4+ The ammonium ion [NH4+] is excreted in various ways depending on the organism/species: 1. Terrestrial vertebrates, including mammals, excrete ammonium ion in the form of UREA. 2. Birds, insects, and reptiles convert excess ammonium ion to URIC ACID for disposal. 3. Marine invertebrates [fish, arthrodpods, etc] excrete NH4+ ion directly into the ocean [See Chemical structures]. The UREA cycle, the main pathway for elimination of NH4+ ion from animals, was discovered by Hans Krebs [Krebs (CAC) cycle]. The UREA cycle consists of 5 steps to convert NH4+ ions into UREA [Figure 19.16].
38 19.4 ELIMINATION OF NH4+
The UREA Cycle (Animals) (cont.) 39 40 Fig 19.17 Reactions of the UREA cycle 41 Pathway of Nitrogen from an Amino acid to Urea-- Another view 42 19.4 ELIMINATION OF NH4+
The UREA Cycle (Animals) (cont.) Note: Some of the enzymes are located in the cytoplasm and some inside mitochondria. Transport processes are required to get the products of the cycle where they can be used. The Arginine synthesis part of the pathway occurs in all animals, but the enzyme ARGINASE [last step of cycle], is only present in those organisms that excrete UREA as the waste product. The process of creating UREA (Urea cycle) occurs only in the Liver.
43 19.4 ELIMINATION OF NH4+
The Net reaction for the Urea cycle is: 44 The flow of nitrogens into Urea. 45 19.4 ELIMINATION OF NH4+
A brief word on Some Metabolic Disorders of the UREA Cycle Most diseases that cause a complete blockage of the Urea cycle are likely lethal There exist no known alternative to removal of NH4+ ion!! However genetic disorders causing partial blockage of the enzymes/reactions in the pathway are known. Clinical symptoms include: 1) Elevated levels of NH4+ ion in blood/urine or hyperammonemia; 2) Nausea/illness after ingestion of proteins; and 3) Gradual mental retardation (if not treated). 46 Overview: Protein and Amino Metabolism 47 19.4 ELIMINATION OF NH4+
A brief word on Some Metabolic Disorders of the UREA Cycle Therapeutic treatments include: 1) Dietary changes, low protein diets supplemented with mixtures of -keto acids. Purpose here is twofold: 1) The -keto acids pick up excess NH4+ ion via combined reactions of Glutamate DH and transamination; and 2) with the correct -keto acids, they are converted to essential amino acids (theoretically) missing from the low protein diet [Figure 19.18]. 48 Fig 19.18 Keto acids used in the treatment of Urea cycle Genetic defects 49 19.5 Amino Acids as Precursors of Other Biomolecules Amino acid catabolism involves many interesting reactions including participation in several specialized metabolic pathways leading to several important natural products. Table 19.7 gives a listing of some of these nitrogen containing products: Neurotransmitters, hormones, skin pigments (melanin), cell messenger biomolecules (nitric oxide), porphyrins (heme and chlorophyll), purines and pyrimidines [RNA/DNA], etc. 50 51 END of Chapter 19 Chapter Seven ...
View Full Document