L21 - Amino Acid Metabolism

what are amino acids used for

when glucose and fats are low, they can be catabolized as energy and carbon skeleton (can be made into an energy source) - most available AAs are used to make proteins, signaling molecules, and other products like hemes, purines, pyrimidines, coenzymes, and biogenic amines

when does amino acid catabolism occur

during starvation - too much nitrogen is toxic, so the amino group has to be removed and N excreted through uric acid (noraml) or urea (when in excess)

what are carbon chains of amino acids converted into

things we can work with such as pyruvate, OAA, acetyl CoA, or alpha-ketoglutarate

how does nitrogen get excreted in the muscles

aminotransferase moves amino group to pyruvate from glutamate to produce alanine

how does nitrogen get excreted in the liver

alanine is a source for pyruvate and aspartate/urea cycle - moving amino acids to the liver allows for gluconeogenesis to happen

what does it mean if nutritional stress in a negative energy balance mean

in a caloric deficit - amino acids can be sources of carbon for gluconeogenesis

what happens in the liver when there is excess nitrogen, and the carbon is harvested during gluconeogenesis

the amino groups are funneled into alpha-ketoglutarate to form glutamate which is oxidatively deaminated by glutamate dehydrogenase to give ammonia to alpha-ketoglutarate - the ammonia is made into urea for excretion and the carbon atoms are metabolized to major metabolic intermediates

what are transaminases in amino group catabolism

can move the amino group around to make glutamate to be able to enter urea cycle - the alpha-amino groups are transferred onto alpha-keto acids to make the corresponding alpha-keto acids and alpha-amino acids - glutamine + alpha-ketoglutarate get converted to alpha-keto acid + glutamate

what enzymes perform deamidation in amino group catabolism

asparaginase and glutaminase

what does glutamate dehydrogenase do in amino group catabolism

glutamate will be metabolized to generate ammonia

what is the urea cycle in amino group catabolism

the cycle that is required to eliminate excess ammonium in the form of urea - a special cycle utilized to rid the body of nitrogen during times of nutrient deprivation when you are degrading muscle proteins to use the carbon for gluconeogenesis

what is the purpose of the tranamination reactions

to transfer amino group from amino acid to alpha-keto acid which uses vitamin B₆ derivate pyridoxal phosphate (PLP) - set the stage for ammonia excretion

what is the purpose of oxidative deamination

removes ammonia to produce urea which uses glutamate dehydrogenase

what is pyridoxal-5’-phosphate (PLP) and

a derivate of pyridoxine, which requires flavin mononucleotide (FMN) as a cofactor for this reaction

how does transaminase bind to Pyridoxal-5’-phosphate (PLP)

must form an enzyme-PLP schiff base which stabilizes the intermediate allowing for transfer of the amino group from the first to the second molecules

how are amino groups moved

(enzyme with amino linked to carbon from PLP) pyridoxal phosphate is the coenzyme for amino transaminase that is required for the reaction that stabilizes the intermediate - aldehyde group of PLP forms a Schiff-base linkage (internal aldimine) with the E-amino group of a specific lysine group of the aminotransferase enzyme

after PLP stabilizes the intermediate, how does the amino group get transferred from the first molecule to the second

the enzyme-bound pyridoxal phosphate reacts with the amino acid, which forms a schiff base of C=N and after the shift to the double bond, alpha-keto acid is released through hydrolysis of the schiff base and PLP is produced - pyridoxamine phosphate then forms a schiff base with alpha-keto this time, and after the second double bond shift, amino acid is released through hydrolysis of the Schiff base and enzyme-bound pyridoxal phosphate is regenerated

what donates and accepts the amino group when it is being transferred from molecules 1 (enzyme pyridoxal enzyme complex - E form) to molecule 2 (enzyme pyridoxyamine coenzyme complex - E’ form)

amino acid donates and keto acid accepts - results in turning glutamate into alpha-ketoglutarate, and aspartate into OAA

how is the nitrogen moved around between the amino acids

through three transamination reactions - to do this, transamination of alpha-ketoglutarate can be paired with the transfer of the amino group from alanine or aspartate and generates TCA intermediates that can enter the cycle

why is it important that the transfer of nitrogens between amino acids is reversible

it allows the body to seamlessly switch between amino acid degradation and amino acid synthesis based on immediate metabolic needs - vital for N homeostasis

what does asparagine require in amino acid catabolism

requires deamidation because it has two amino acids to get to OAA - asparagine to (asparaginase) aspartate to (transaminase) OAA - produces ammonia from water and glutamate from alpha-ketoglutarate

how is glutamine deamidated

turns glutamine into glutamate using water and glutaminase, and releases ammonium

how is the amino group removed from glutamate

glutamate dehydrogenase reaction which removes the alpha amino group from glutamate to produce free ammonia and alpha-ketoglutarate

what does glutamate dehydrogenase reaction require

cofactor NAD⁺/NADP⁺ or NADH/NADPH depending on what direction it is running in - produces ammonia which moves on to get used in the carbamoyl synthase reaction, and alpha-ketoglutarate is recycled back to the transamination reaction or TCA cycle

why does the body need to generate new carbon molecules through amino acid catabolism

for the TCA cycle and ketogenesis - because of this, amino acids can alter flux of gluconeogenesis, although it doesn’t alter it directly, but instead through enzymatic reactions, regulation, and hormone signaling

what are the glucogenic fates of the catabolism of amino acids

alanine, arginine, asparagine, and glutamate

what are the glucogenic and ketogenic-catabolic fates of amino acids

threonine

how does serine get converted to pyruvate

through transamination where the amino group is not transferred to another compound

what happens in valine degradation

three step process where the alpha-amino group is removed via transamination using alpha-ketoglutarate and releases glutamate, and then the branched-chain alpha-keto acid dehydrogenase complex catalyzes an oxidative decarboxylation reaction where the carbon skeleton of valine becomes attached to CoA (releases NADH and CO₂), and finally, the third step is catalyzed by acyl-CoA dehydrogenase which is the same enzyme that participates in fatty acid oxidation

what are the enzymes and cofactors used in the three steps of valine degradation

transaminase with alpha-ketoglutarate, branched-chain alpha-keto-acid dehydrogenase complex with NAD⁺ and CoA, and acyl-CoA dehydrogenase with Q

why is threonine both glucogenic and ketogenic

its metabolism breaks down into acetyl-CoA (ketones) and glycine (glucose) which can enter both glucose production pathways and fat/ketone body production pathways - glycine is first converted to serine which can be further converted into pyruvate which can enter gluconeogenesis to make glucose

how does the body get rid of excess ammonia that amino acid catabolism just produced

the urea cycle which runs during starvation when amino acid catabolism is high, so there are high levels of ammonia production

what does the urea cycle require

CO₂, ammonium ion, and arginine as substrates, but then also needs 3 ATP total

how is urea the is produced in urea cycle excreted

into the blood stream, then cleared by the kidney and dumped into the urine - 2 reactions occur in the mitochondria with the remaining 3 in the cytosol

urea - has 2 nitrogen atoms

where is the first nitrogen in urea derived from

from glutamate that generates ammonia to enter the carbamoyl phosphate reaction, where ammonia, ATP, and bicarbonate are synthesized to carbamoyl phosphate, which combines with ornithine to make citrulline

where is the second nitrogen in urea derived from

from aspartate after a transamination reaction from OAA - aspartate combines with citrulline to form argininosuccinate (both nitrogen atoms are on this molecule)

what happens to argininosuccinate after it is generated containing the 2 nitrogens of urea

argininosuccinate is cleaved into arginine and fumarate, and then arginine is cleaved by arginase to form urea with the 2 Ns

what activates carbamoyl phosphate synthetase

N-acetylglutamate, which is derived from glutamate combining with acetyl-CoA - allosterically activates

what is the first mitochondria reaction in ammonia detoxification

bicarbonate, ammonia, and 2 ATPs are required for carbamoyl phosphate synthetase I to make carbamoyl phosphate - this is the rate-limiting step

what is the second mitochondria reaction in ammonia detoxification

carbamoyl phosphate combines with ornithine to make citrulline, using ornithine transcarbamoylase - citruline then exits the mitochondria

what happens once citrulline exits the mitochondria into the cytosol

it combines with aspartate (generated by the transamination reaction) to form argininosuccinate, which is catalyzed by argininosuccinate synthetase and requires ATP

what happens to arginnosuccinate in ammonia detoxification in the cytosol

it gets cleaved by argininosuccinate lyase and makes arginine and fumarate - arginine is then cleaved by arginase and forms urea

where do the 2 nitrogens of urea come from

one comes from ammonia, while the other comes from aspartate

how does nitrogen get removed removed from the body during normal function/not when starvation is happening

normally during nutrient abundance or simply as a course of normal metabolism, we harvest carbon from dietary sources and get rid of nitrogen via uric acid synthesis and secretion - uric acid eventually moves to the urine for excretion

what is used to produce uric acid

purine metabolism (starting with the sugar backbone) which requires synthesis of purine ring, and glutamine is a key nitrogen donor

what is hypoxanthine

an intermediate product to uric acid

what does purine metabolism lead to

hypoxanthine production and the xanthine oxidase reaction - first is purine breakdown, then enzyme conversion, and then excretion

what are purines broken down into

xanthine and hypoxanthine

what does xanthine oxidase do

converts xanthine and hypoxanthine into uric acid

what are the intermediate that start synthesis

transamination reactions, arginine (urea cycle), asparagine/glutamine (synthetase reaction), and serine for one-carbon metabolism

what are the 5 starting molecules to build amino acids

alpha-ketoglutarate, OAA/aspartate, pyruvate, 3-phosphoglycerate, and phosphenolpyruvate/erythrose-4-phosphate

what are the amino acids in the alpha-ketoglutarate family

glutamate, glutamine, proline, arginine, and lysin

what are amino acids that are in the OAA/aspartate family

aspartate, asparagine, methionine, theronine, and lysine

what are the amino acids in the pyruvate family

alanine, valine, leucine

what are the amino acids in the 3-phosphoglycerate family

serine, glycine, cesteine

what are the amino acids in the phosphoenolpyruvate/erythrose-4-P family

phenylalanine, tyrosine, and tryptophan

how many amino acids does transamination directly synthesize

3 directly and another 2 amino acids require synthetase reactions - amino group provides the nitrogen

how is aspartate converted into asparagine

by using glutamine as an amino acid and ATP, asparagine synthetase can convert aspartate into asparagine - in the same vein, glutamine synthetase uses ammonia as a donor to synthesize glutamine from glutamate

what is the importance of glutamate

is a starting molecule for arginine and proline - has the same 5 carbon chain

how is serine derived from glutamate

3-phosphglycerate is the starting molecule in the glycolysis pathway, and there are 3 reactions that first oxidation the substrate, then transamination where the amino group is received from glutamate and then a dephosphorylation

what does serine use to generate glycine

uses one-carbon metabolism and the enzyme serine hydroxymethyltransferase, and the tetrahydrofolate functions as a carrier of one-carbon units in several reactions of amino acid and nucleotide metabolism - serine can give up 1 methyl group to tetrahydrofolate

how does serine generate cysteine

cysteine contains a sulfur group, so does a two step enzymatic pathways containing sulfur incorporation

what is the methionine synthase reaction

leads to methionine, and requires cysteine and uses one carbon metabolism - converts homocysteine to methionine using methionine synthase

why are amino acids with aromatic group more difficult to synthesize

phosphoenolpyruvate and erythrose-4-P are the starting molecules, and this requires many steps for full synthesis of these amino acids - very high metabolic cost, and the complexity of the rings requires specialized, multi-step enzymatic pathways

what is one-carbon metabolism

sometimes metabolism needs to move one carbon units around in order to carry out a synthetic or degrading process - this system uses several different one-carbon carriers

what are some of the sources of one-carbon units

serine, glycine, histidine, formaldehyde, and formate