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Harper’s Illustrated Biochemistry (31st ed)BIOSYNTHESIS OF THE NUTRITIONALLY NONESSENTIAL AMINO ACID All vertebrates can form certain amino acids from amphibolic intermediates or from other dietary amino acids. The intermediates and the amino acids to which they give rise are α-ketoglutarate (Glu, ...

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Harper’s Illustrated Biochemistry (31st ed)

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BIOSYNTHESIS OF THE NUTRITIONALLY NONESSENTIAL AMINO ACID

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All vertebrates can form certain amino acids from amphibolic intermediates or from other dietary amino acids. The intermediates and the amino acids to which they give rise are α-ketoglutarate (Glu, Gln, Pro, Hyp), oxaloacetate (Asp, Asn), and 3-phosphoglycerate (Ser, Gly). Cysteine, tyrosine, and hydroxylysine are formed from nutritionally essential amino acids. Serine provides the carbon skeleton and homocysteine the sulfur for cysteine biosynthesis. In Scurvy, a nutritional disease that results from a deficiency of vitamin C, impaired hydroxylation of peptidyl proline and peptidyl lysine results in a failure to provide the substrates for cross-linking of maturing collagens. Phenylalanine hydroxylase converts phenylalanine to tyrosine. Since the reaction catalyzed by this mixed function oxidase is irreversible, tyrosine cannot give rise to phenylalanine. Neither dietary hydroxyproline nor hydroxylysine is incorporated into proteins because no codon or tRNA dictates their insertion into peptides. Peptidyl hydroxyproline and hydroxylysine are formed by hydroxylation of peptidyl proline or lysine in reactions catalysed by mixed-function oxidases that require vitamin C as cofactor. Selenocysteine, an essential active site residue in several mammalian enzymes, arises by cotranslational insertion from a previously modified tRNA.

CATABOLISM OF PROTEINS & AMINO ACID NITROGEN (chap28,harper) 

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Human subjects degrade 1% to 2% of their body protein daily at rates that vary widely between proteins and with physiologic state. Key regulatory enzymes often have short half-lives. Proteins are degraded by both ATP-dependent and ATPindependent pathways. Ubiquitin targets many intracellular proteins for degradation. Liver cell surface receptors bind and internalize circulating asialoglycoproteins destined for lysosomal degradation. Polyubiquitinated proteins are degraded by proteases on the inner surface of a cylindrical macromolecule, the proteasome. Entry into the proteasome is gated by a donut-shaped protein pore that rejects entry to all but polyubiquitinated proteins.

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Fish excrete highly toxic NH3 directly. Birds convert NH3 to uric acid. Higher vertebrates convert NH3 to urea. Transamination channels amino acid nitrogen into glutamate. GDH occupies a central position in nitrogen metabolism. Glutamine synthase converts NH3 to nontoxic glutamine. Glutaminase releases NH3 for use in urea synthesis. NH3 , CO2 , and the amide nitrogen of aspartate provide the atoms of urea. Hepatic urea synthesis takes place in part in the mitochondrial matrix and in part in the cytosol. Changes in enzyme levels and allosteric regulation of carbamoyl phosphate synthase I by N-acetylglutamate regulate urea biosynthesis. Metabolic diseases are associated with defects in each enzyme of the urea cycle, of the membrane-associated ornithine permease, and of NAGS. The metabolic disorders of urea biosynthesis illustrate six general principles of all metabolic disorders. Tandem mass spectrometry is the technique of choice for screening neonates for inherited metabolic diseases. In normal adults, nitrogen intake matches nitrogen excreted. Positive nitrogen balance, an excess of ingested over excreted nitrogen -- accompanies growth and pregnancy. Negative nitrogen balance, where output exceeds intake -- surgery, advanced cancer, and the nutritional disorders kwashiorkor and marasmus Ammonia, which is highly toxic, arises in humans primarily from the α-amino nitrogen of amino acids. Tissues therefore convert ammonia to the amide nitrogen of the nontoxic amino acid glutamine Subsequent deamination of glutamine in the liver releases ammonia, which is efficiently converted to urea, which is not toxic However, if liver function is compromised, as in cirrhosis or hepatitis, elevated blood ammonia levels generate the urea cycle provides a useful molecular model for the study of other human metabolic defects Normally, 1-2% muscle protein turnover or degredation. Increases when undergoing structural rearrangement, for example, uterine tissue during pregnancy, skeletal muscle in starvation 75% of the amino acids liberated by protein are reutilized Excess are not stored for future use Amino acids not immediately incorporated into new protein are rapidly degraded . The major portion of the carbon skeletons of the amino acids is converted to amphibolic intermediates, while in

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humans the amino nitrogen is converted to urea and excreted in the urine PROTEASES & PEPTIDASES DEGRADE PROTEINS TO AMINO ACID The relative susceptibility of a protein to degradation is expressed as its half-life (t 1/2) Half-lives of liver proteins range from under 30 minutes to over 150 hours Typical “housekeeping” enzymes such as those of glycolysis, have t 1/2 values of over 100 hours PEST sequences, regions rich in proline (P), glutamate (E), serine (S), and threonine (T), target some proteins for rapid degradation Intracellular proteases hydrolyze internal peptide bonds. The resulting peptides are then degraded to amino acids by endopeptidases that hydrolyze internal peptide bonds, and by aminopeptidases and carboxypeptidases that remove amino acids sequentially from the amino- and carboxyl-termini, respectively Degradation of blood glycoproteins follows loss of a sialic acid from the nonreducing ends of their oligosaccharide chains Extracellular (membrane-associated) and intracellular proteins are also degraded in lysosomes by ATPindependent processes Degradation of regulatory proteins with short half-lives and of abnormal or misfolded proteins occurs in the cytosol, and requires ATP and ubiquitin (stop codon) ubiquitin is a small polypeptide that targets many intracellular proteins for degradation Ubiquitin molecules are attached by non- `-peptide bonds formed between the carboxyl terminal of ubiquitin and the ε-amino groups of lysyl residues in the target protein (Figure 28–2) The residue present at its amino terminus affects whether a protein is ubiquitinated Amino terminal Met or Ser residues retard, whereas Asp or Arg accelerate ubiquitination Attachment of a single ubiquitin alters their subcellular localization and targets them for degradation Soluble proteins undergo polyubiquitination (4 or more) Subsequent degradation of ubiquitin-tagged proteins takes place in the proteasome The proteasome consists of a macromolecular, cylindrical complex of proteins, whose stacked rings form a central pore that harbors the active sites of proteolytic enzymes For degradation, a protein enters the central pore

INTERORGAN EXCHANGE MAINTAINS CIRCULATING LEVELS OF AMINO ACIDS

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maintenance of steady-state concentrations of amino acids depends on the net balance between release from endogenous protein stores and utilization by various tissues Muscle generates half of free amino acids while liver is the site of the urea cycle enzymes necessary for disposal of excess nitrogen Muscle and liver thus play major roles in maintaining circulating amino acid levels Figure 28–5 summarizes the postabsorptive state. Free amino acids (alanine and glutamine) are released from muscle into the circulation. Alanine is extracted primarily by the liver, and glutamine is extracted by the gut and the kidney gut and the kidney, both of which convert a significant portion to alanine Glutamine also serves as a source of ammonia for excretion by the kidney The kidney provides a major source of serine for uptake of liver and muscle, peripheral tissues Valine are released by muscle and taken up predominantly by the brain. Alanine is a key gluconeogenic amino acid (figure 28.6) The rate of hepatic gluconeogenesis from alanine is far higher than from all other amino acids Following a protein-rich meal, the splanchnic tissues release amino acids (Figure 28–7) while the peripheral muscles extract amino acids, in both instances predominantly branched-chain amino acids. Branchedchain amino acids thus serve a special role in nitrogen metabolism. In the fasting state they provide the brain with an energy source, and postprandially they are extracted predominantly by muscle, having been spared by the liver.

ANIMALS CONVERT alpha-AMINO NITROGEN TO VARIED END PRODUCTS

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ammonotelic (excrete ammonia) uricotelic (excreting nitrogen-rich uric acid) ureotelic and excrete nontoxic, highly water-soluble urea. Since urea is nontoxic to humans, high blood levels of it in renal disease are a consequence of impaired renal function BIOSYNTHESIS OF UREA Urea biosynthesis occurs in four stages: (1) transamination, (2) oxidative deamination of glutamate, (3) ammonia transport, and (4) reactions of the urea cycle (Figure 28–8)

1. Transamination reactions interconvert pairs of αamino acids and α-keto acids (Figure 28–9). Transamination reactions, which are freely reversible, also function in amino acid biosynthesis. All of the common amino acids except lysine, threonine, proline, and hydroxyproline participate in transamination. Alanine aminotransferase and glutamate aminotransferase catalyze the transfer of amino groups to pyruvate (forming alanine) or to αketoglutarate (forming glutamate). Since alanine is also a substrate for glutamate aminotransferase, the α-amino nitrogen from all amino acids that undergo transamination can be concentrated in glutamate. This is important because l-glutamate is the only amino acid that undergoes oxidative deamination at an appreciable rate in mammalian tissues. The formation of ammonia mainly via the alpha-amino nitrogen of L-gluamate. Transamination occurs via a “ping-pong” mechanism characterized by the alternate addition of a substrate and release of a product. Pyridoxal phosphate (PLP), a derivative of vitamin B6 , is present at the catalytic site of all aminotransferases, and plays a key role in catalysis. During transamination, PLP serves as a “carrier” of amino groups. Schiff base can rearrange in various ways L-GLUTAMATE DEHYDROGENASE OCCUPIES A CENTRAL POSITION IN NITROGEN METABOLISM

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Liver GDH activity is allosterically inhibited by ATP, GTP, and NADH, and is activated by ADP Transfer of amino nitrogen to α-ketoglutarate forms lglutamate. Hepatic l-glutamate dehydrogenase (GDH), which can use either NAD+ or NADP+ , releases this nitrogen as ammonia (Figure 28–12).

Amino Acid Oxidases Remove Nitrogen as Ammonia 

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l-Amino acid oxidase of liver and kidney convert an amino acid to an α-imino acid that decomposes to an α-keto acid with release of ammonium ion (Figure 28–13). The reduced flavin is reoxidized by molecular oxygen, forming hydrogen peroxide (H2 O2 ), which then is split to O2 and H2 O by catalase The ammonia produced by enteric bacteria and absorbed into portal venous blood and the ammonia produced by tissues are rapidly removed from circulation by the liver and converted to urea. ammonia is toxic to the central nervous system, it reacts with α-ketoglutarate to form glutamate

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if portal blood bypass the liver, systemic blood ammonia may attain toxic levels. Can occur if you have cirrhosis Symptoms of ammonia intoxication include tremor, slurred speech, blurred vision, coma, and ultimately death Formation of glutamine is catalyzed by mitochondrial glutamine synthase. Glutamine to serve as a carrier of nitrogen, carbon and energy between organs glutamine synthase plays a major role in ammonia detoxification and acid-base homeostasis because it can cause severe brain damage, multiorgan failure and death of neonate Hepatic glutaminase levels rise in response to high protein intake while renal kidney-type glutaminase increases in metabolic acidosis Ammonia production from intracellular renal amino acids, especially glutamine, increases in metabolic acidosis and decreases in metabolic alkalosis Formation & Secretion of Ammonia Maintains Acid-Base Balance Urea is the Major End Product of Nitrogen Catabolism in Humans The major metabolic role of ornithine, citrulline and argininosuccinate in mammals is urea synthesis. urea synthesis occur in the matrix of the mitochondrion, and other reactions in the cytosol metabolism of citrulline take place in the cytosol Cleavage of arginine by arginase releases urea Ornithine and lysine are potent inhibitors of arginase Arginine also serves as the precursor of the potent muscle relaxant nitric oxide (NO) in a Ca2+ -dependent reaction catalyzed by NO synthase. Major changes in diet can increase the concentrations of individual urea cycle enzymes 10- to 20-fold. For example, starvation elevates enzyme levels, presumably to cope with the increased production of ammonia that accompanies enhanced starvation-induced degradation of protein. GENERAL FEATURES OF METABOLIC DISORDERS

1. Similar or identical clinical signs and symptoms can accompany various genetic mutations in a gene that encodes a given enzyme or in enzymes that catalyze successive reactions in a metabolic pathway. 2. Rational therapy is based on an understanding of the relevant biochemical enzyme-catalyzed reactions in both normal and impaired individuals. 3. The identification of intermediates and of ancillary products that accumulate prior to a metabolic block provides

the basis for metabolic screening tests that can implicate the reaction that is impaired. 4. Definitive diagnosis involves quantitative assay of the activity of the enzyme suspected to be defective.

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Metabolic diseases associated with glycine catabolism include glycinuria and primary hyperoxaluria.

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Two distinct pathways convert cysteine to pyruvate. Metabolic disorders of cysteine catabolism include cystine-lysinuria, cystine storage disease, and the homocystinurias.

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Threonine catabolism merges with that of glycine after threonine aldolase cleaves threonine to glycine and acetaldehyde.

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Following transamination, the carbon skeleton of tyrosine is degraded to fumarate and acetoacetate. Metabolic diseases of tyrosine catabolism include tyrosinosis, Richner–Hanhart syndrome, neonatal tyrosinemia, and alkaptonuria.

5. The DNA sequence of the gene that encodes a given mutant enzyme is compared to that of the wild-type gene to identify the specific mutation(s) that cause the disease. 6. The exponential increase in DNA sequencing of human genes has identified dozens of mutations of an affected gene that are benign or are associated with symptoms of varying severity of a given metabolic disorder. METABOLIC DISORDERS ARE ASSOCIATED WITH EACH REACTION OF THE UREA CYCLE Five well-documented diseases represent defects in the biosynthesis of enzymes of the urea cycle. Clinical symptoms common to all urea cycle disorders include vomiting, avoidance of high-protein foods, intermittent ataxia, irritability, lethargy, and severe mental retardation. The most dramatic clinical presentation occurs in full-term infants who initially appear normal, then exhibit progressive lethargy, hypothermia, and apnea due to high plasma ammonia levels.

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Metabolic disorders of phenylalanine catabolism include PKU and several hyperphenylalaninemias.

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Neither nitrogen of lysine participates in transamination. The same net effect is, however, achieved by the intermediate formation of saccharopine. Metabolic diseases of lysine catabolism include periodic and persistent forms of hyperlysinemia-ammonemia.

The goal of dietary therapy is to provide sufficient protein, arginine, and energy to promote growth and development while simultaneously minimizing the metabolic perturbations.

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The catabolism of leucine, valine, and isoleucine presents many analogies to fatty acid catabolism. Metabolic disorders of branched-chain amino acid catabolism include hypervalinemia, maple syrup urine disease, intermittent branched-chain ketonuria, isovaleric acidemia, and methylmalonic aciduria.

Analysis of Neonate Blood by Tandem Mass Spectrometry Can Detect Metabolic Diseases 

The powerful and sensitive technique of tandem mass spectrometry (see Chapter 4) can in a few minutes detect over 40 analytes of significance in the detection of metabolic disorders such as acidemias, aminoacidemias, disorders of fatty acid oxidation, and defects in the enzymes of the urea cycle

Catabolism of the Carbon Skeletons of Amino Acids 

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Excess amino acids are catabolized to amphibolic intermediates that serve as sources of energy or for the biosynthesis of carbohydrates and lipids. Transamination is the most common initial reaction of amino acid catabolism. Subsequent reactions remove any additional nitrogen and restructure hydrocarbon skeletons for conversion to oxaloacetate, α-ketoglutarate, pyruvate, and acetyl-CoA.

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LIPID METABOLISM lipids are a heterogeneous group of compounds, including fats, oils, steroids, waxes, and related more of physical properties. property of being (1) relatively insoluble in water and (2) soluble in nonpolar solvents such as ether and chloroform. They are important dietary constituents not only because of the high energy value of fats, but also because essential fatty acids and fat-soluble vitamins and other lipophilic micronutrients are contained in the fat of natural foods Dietary supplementation with long chain omega3 fatty acids is believed to have beneficial effects such as cardiovascular disease, rheumatoid arthritis, dementia

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fat stored in adipose tissue serve as thermal insulator nonpolar lipid act as electrical insulator allowing rapid propagation depolarization waves along myelinated nerves Lipids are transported in the blood combined with proteins in lipoprotein particles Biomedical conditions such as obesity, diabetes mellitus, and atherosclerosis CLASSIFICATION OF LIPID 1. Simple lipid - fats and waxes which are esters of fatty acids with various alcohols Fat- Esters of fatty acids with glycerol. Oils are fats in the liquid state Waxes - Esters of fatty acids with higher molecular weight monohydric alcohols 2. Complex lipids - are esters of fatty acids containing groups in addition to an alcohol and one or more fatty acids. Phospholipids – aside from fatty acids and an alcohol, lipid contains a phosphoric acid residue. They frequently have nitrogen-containing bases (eg, choline) and other substituents. In many phospholipids the alcohol is glycerol (glycerophospholipids), but in sphingophospholipids it is sphingosine, which contains an amino group Glycolipids (glycosphingolipids) - Lipids containing a fatty acid, sphingosine, and carbohydrate Other complex lipids - Lipids such as sulfolipids and amino lipids. Lipoproteins may also be placed in this category 3. Precursor and derived lipids - fatty acids, glycerol, steroids, other alcohols, fatty aldehydes, ketone bodies, hydrocarbons, lipid-soluble vitamins and micronutrients, and hormones Neutral lipids – uncharged, acylglycerols (glycerides), cholesterol, and cholesteryl esters.

Fatty acids are aliphatic carboxylic acids 

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Fatty acids occur in the body mainly as esters in natural fats and oils, but are found in the unesterified form as free fatty acids, a transport form in the plasma Natural fats contain an even number of ca...