amino acid metabolism

amino acid catabolism accounts for

10-15% of human energy production

nitrogen cannot be stored in a usable form because

NH₄⁺ is toxic

nitrogen that is lost as a result of protein and nucleic acid degradation must be

replenished through diet

three reasons why proteins are constantly degraded

• to store nutrients in the form of proteins and break them down in times of metabolic need (significant in muscles)

• to eliminate the accumulation of abnormal proteins

• short half-lives of all enzymes (seconds, to days, to weeks, to months)

nitrogen balance

the daily intake of nitrogen (from proteins) equals the amount of nitrogen excreted (in waste)

ATP-independent process of amino acid degradation

• degrades proteins in lysosomes

• lysosomes contain acidic proteases that non-selectively digest protein particles

ATP-dependent process of amino acid degradation

• ubiquitin-proteasome pathway

• degrades proteins containing ubiquitin polymers in the proteasome

• uses three different protease activities located in the central core of proteasome

ubiquitin

• regulatory protein with seven lysine residues which serve as linking sites between ubiquitin monomers

• the C-terminal glycine of ubiquitin serves as the attachment site to targeted proteins or to other ubiquitin monomers

• at least four ubiquitin subunits linked between glycine and lysine tags a protein for proteasomal degradation

enzymes involved in ubiquitination

• E1- attach ubiquitin to E2 enzymes

• E2- attach ubiquitin to target proteins

• E3- facilitate ubiquitination of target proteins by forming a complex with E2 enzymes and target proteins (ubiquitin ligases)

attachment of ubiquitin to a target protein

• ubiquitin is activated through an ATP dependent reaction which links ubiquitin to E1

• ubiquitin is then transferred to E2 which releases E1 and leads to the formation of an E2-E3 complex

• ubiquitination of target protein initiates the polyubiquitination process which links at least four ubiquitin subunits together through a series of gly76-lys48 linkages

gastrin

a small peptide hormone that gets released when food enters the stomach; it triggers the release of gastric juices containing HCl and the secretion of pepsinogen (zymogen of pepsin)

the increasing acidity in the stomach

denatures dietary proteins, allowing for greater chances of peptide bond hydrolysis, and activates pepsin by autocatalytic cleavage of pepsinogen (maximally active at a pH value of around 2)

proteases

• pepsin— cleaves long polypeptide chains into a mixture of smaller peptides in the stomach (low pH)

• enteropeptidase— a protease that specifically activates several proteolytic zymogens released from the pancreas

• trypsin and chymotrypsin— cut proteins and larger peptides into smaller peptides in the small intestine

• aminopeptidase and carboxypeptidases A and B— degrade peptides into amino acids in the small intestine

secretin

a hormone secreted into the blood in response to low pH in the small intestine; stimulates the pancreas to secrete bicarb into the small intestine to bring pH back to neutral conditions (which allows for enteropeptidase activity)

cholecystokinin

a hormone secreted into the blood in response to the arrival of peptides in the duodenum; stimulates the secretion of pancreatic proteases trypsinogen, chymotrypsinogen, and procarboxypeptidases A and B

proteolytic cascade

• enteropeptidase cleaves trypsinogen resulting in the active trypsin

• trypsin cleaves and activates more trypsinogen as well as other zymogens

pancreatic trypsin inhibitor protects the pancreas against

self digestion (pancreatitis)

free amino acids are transported into

epithelial cells lining the small intestine, get exported to the blood, and travel to the liver

amino acids which play a key role in the transport and distribution of other amino acids

alanine, glutamate, glutamine, and aspartate

glutamate provides nitrogen for amino acid biosynthesis through the action of

aminotransferase enzymes, which transfer the alpha amino group from an amino acid to alpha-ketoglutarate which yields glutamate and an alpha-keto acid analog of the amino acid (reversible reactions)

pyridoxal phosphate (PLP)

a coenzyme used as a prosthetic group by all aminotransferases; first accepts amino group of amino acid and releases corresponding alpha-keto acid, then transfers amino group to alpha-ketoglutarate or oxaloacetate

urea is derived from

• nitrogen

  • the ammonium released when glutamate or glutamine is deaminated

  • aspartate which is formed when oxaloacetate is transaminated by aspartate aminotransferase

• carbon

  • bicarb from citrate cycle

• oxygen

  • from water produced by citrate cycle

why are certain aminotransferases used as an indicator of liver health

buildup of aspartate aminotransferases and alanine aminotransferases mean that the liver is not functioning properly

nitrogen assimilation

the processes used by plants and prokaryotes to incorporate nitrogen (usually as ammonium) into organic compounds

the primary nitrogen carriers in the cell are the amino acids

glutamate and glutamine

when animals eat plants, the glutamate and glutamine they ingest provide

the nitrogen needed to synthesize a variety of biomolecules

glutamine is the primary source of amino groups for the biosynthesis of

nucleotide bases, carbamoyl phosphate, and the side chains of tryptophan and histidine

ammonia assimilation

the incorporation of ammonium into glutamate and glutamine

• glutamine synthetase (found in all organisms)

• glutamate synthase (found in plants, bacteria, and some insects)

• glutamate dehydrogenase (found in all organisms)

glutamine synthetase

• converts glutamate to glutamine using ammonium (requires ATP)

• primary entry point for ammonium into biomolecules

• allows ammonium transport from peripheral tissues to liver to be excreted as urea

glutamate synthase

• transfers the amide nitrogen from glutamine to alpha-ketoglutarate to form two molecules of glutamate

• NAD(P)H is oxidized

• animals depend on plants for this

glutamate dehydrogenase

• interconverts alpha-ketoglutarate and glutamate in the presence of high ammonium

• most often generates ammonium for carbamoyl phosphate synthesis by doing the more favorable reverse reaction

cells cannot store

amino acids that accumulate as a result of protein degradation

• must be recycled for protein synthesis or deaminated in order to reuse their carbon skeleton for other metabolic pathways (glycolysis, the citrate cycle, gluconeogenesis, fatty acid synthesis, ketogenesis)

• deamination generates ammonium which is used to synthesize other nitrogen containing biomolecules or excreted as urea

amino acids transported to the liver have three sources

• digestion of dietary proteins

• glutamine, which comes from glutamate and ammonium through glutamine synthase (in peripheral tissues)

• alanine which is formed by alanine aminotransferase (removes excess nitrogen from skeletal muscle)

how ammonium enters the urea cycle in the liver

• carbamoyl phosphate, the ammonium can come from either glutamine or glutamate

• aspartate which is converted from glutamate through aspartate aminotransferase

alanine-glucose cycle

• removes excess nitrogen from amino acid catabolism during exercise

• links nitrogen metabolizing reactions in muscle and liver cells with alanine as the nitrogen carrier

• pyruvate is converted to alanine with alanine aminotransferase (uses glutamate)

• alanine is exported to the blood and taken in by the liver to regenerate glutamate and pyruvate by the reverse reaction (deaminated)

• glutamate is metabolized by glutamate dehydrogenase to release ammonium for urea synthesis

• pyruvate is used to synthesize glucose via gluconeogenesis and exported back to the muscles

net reaction of the urea cycle

in humans, urea is synthesized in the liver and transported

through the blood to the kidneys where it is concentrated and excreted in urine

reactions of the urea cycle that take place in the mitochondria

• mitochondria— carbamoyl phosphate synthetase I and ornithine transcarbamoylase

steps of the urea cycle

• carbamoyl phosphate (first nitrogen atom) is formed in the mitochondrial matrix by ATP-dependent carbamoyl phosphate synthetase I

• citrulline is formed from carbamoyl phosphate and ornithine by ornithine transcarbamoylase

• citrulline is exported to the cytosol to form argininosuccinate from aspartate (second nitrogen atom) which is catalyzed by argininosuccinate synthetase and pyrophosphatase

• argininosuccinate is cleaved by argininosuccinase to yield fumarate and arginine (arginine contains both nitrogen atoms)

• arginase converts arginine to urea and ornithine to complete the cycle

urea cycle regulation

• carbamoyl phosphate synthetase I is positively allosterically regulated by N-acetylglutamate which is formed from glutamate and acetyl-CoA

• formation of N-acetylglutamate is positively regulated by arginine

• glutamate and arginine stimulate flux through the urea cycle by increasing the rate of carbamoyl phosphate synthesis

the krebs bicycle/ the aspartate-argininosuccinate shunt

• fumarate is converted to malate in the cytosol by an isozyme of fumarase

• malate is transported into the mitochondrial matrix through the malate-aspartate shuttle and converted into oxaloacetate though malate dehydrogenase

• oxaloacetate is used as substrate with glutamate in the aspartate aminotransferase reaction to generate aspartate which is transported back to the cytosol

• aspartate is then used to form argininosuccinate

glucogenic amino acids (formed from amino acid catabolism)

amino acids whose carbon chains can be used to form glucose and glycogen via gluconeogenesis

• pyruvate— ala, cys, gly, ser, thr, trp (group 1 degradation pathway)

• alpha-ketoglutarate— arg, glu, gln, his, pro (group 2 degradation pathway)

• succinyl-CoA— ileu, met, thr, val

• fumarate— phe, tyr

• oxaloacetate— asp, asn

ketogenic amino acids (formed from amino acid catabolism)

amino acids whose carbon chains can be used to form ketone bodies

• leu, ileu, thr, lys, phe, tyr, trp

essential amino acids

arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine

amino acids are derived from metabolic intermediates in

glycolysis, PPP, and the citrate cycle

• tyrosine and phenylalanine come from phosphoenolpyruvate

oxaloacetate derived amino acids

aspartate, asparagine, lysine, threonine, and methionine

pyruvate derived amino acids

alanine, isoleucine, valine, and leucine

heme which is essential to cytochromes, hemoglobin, and myoglobin comes from

glycine

tyrosine is important in

metabolic signaling and neurotransmission, it is also the precursor to melanin pigments in hair and skin (mutations in tyrosinase cause albinism)

alkaptonuria and phenylketonuria

• AKU causes black urine and prevents complete breakdown of tyrosine and phenylalanine

• PKU causes elevated levels of phe in the body which can cause adverse neurological symptoms