Biochemistry-Amino Acid Synthesis & Degradation Flashcards
A mother gives birth to a healthy baby. A few hours after birth the baby becomes lethargic. She brings the child into the hospital the next day and the baby is vomiting, has hypothermia, respiratory alkalosis, encephalopathy and cerebral edema. What congenital defect is causing this child’s condition?
The child has orotic acidemia. This happens when the enzyme that converts carbamoyl phosphate to citrate in the mitochondria is defective. Carbamoyl phosphate builds up and is transported into the cytosol where it reacts with aspartate and CPSII takes it to carboy-aspartate, then it goes on to form orotic acid which goes out into the urine.
What lab results are common to all of the disorders in the urea cycle?
High NH4+, low urea and high glutamine (because Glu is the main carrier of free ammonia in the blood)
A mother brings in her newborn boy complaining of lethargy, irritability and hyperventilation 36 hours after birth. Over the next 24 hours, the lethargy increased and progressed to coma requiring mechanical ventilation. Hemodialysis was started at 5 days and the child died after one week. Two of the mother’s four brothers died shortly after birth from encephalitis. Labs at 36 hours reveal high blood pH, low blood CO2 and low BUN. On day 5 high plasma ammonium, high glutamine, Arg/Citrulline undetectable and high orotic acid in the urine. What is the pathogenesis of this disease?
The child has ornithine transcarbamoylase deficiency. Loss of the enzyme causes build up of carbamoyl phosphate in the mitochondria and prevents formation of citrulline, arginine and urea. Upstream, carbamoyl phosphate leaves the mitochondria and is converted to orotic acid, hence the orotic acid in the urine. Also upstream, CPSI isn’t as active from excessive amounts of carbamoyl phosphate and NH4+ builds up. This pushes the equilibrium of glutamine synthetase from glutamate to glutamine and Gln builds up.
What lab values would you expect to see in a patient with carbamoyl phosphate synthetase (CPS I) deficiency?
Ammonia increase, glutamine increased, carbamoyl phosphate decreased, orotic acid decreased, citrulline decreased, arginine down and urea down.
What molecules are commonly attached to drugs so that they can be excreted in the urine? How is this used to treat defects in the urea cycle?
Glycine and glutamine. When people have urea cycle malfunction, you can give benzoate and phylacetate. The body tags these with glycine and glutamine, which are nitrogen carries, and they are excreted, taking the excess nitrogen with it.
What are the three key enzymes in amino acid and nitrogen metabolism?
PLP (pyridoxal phosphate does everything), BH4 (tetrahydrobiopterin catalyzes ring hydroxylations) and FH4 (tetrahydrofolate transfers single carbons)
What enzyme is the quintessential cofactor?
The C=O forms a bond with the nitrogen of the amino acid and can go on to form many different things.
Why are essential amino acids essential?
We cannot synthesize the carbon skeleton.
What is a semi-essential amino acid?
Carbon skeleton can be synthesized from glucose but not in sufficient quantity
Glucogenic amino acids
Carbon skeleton can be converted to glucose: NONESSENTIALS: Ala, Asp, Asn, Cys, Glu, Gln, Gly, Pro, Ser and Tyr (both gluco and ketogenic). ESSENTIALS: Arg, His, Met, The, Val and Iso, Phe, Trp (last 3 are both gluco and ketogenic)
Ketogenic amino acids
Carbon skeleton can be converted to acetyl CoA. ESSENTIALS: tyrosine is both gluco and ketogenic. NONESSENTIALS: Leucine and Lysine. Iso, Phe and Trp are both gluco and ketogenic.
What else do you need essential amino acids for besides protein synthesis?
Neurotransmitters
What are the essential amino acids?
*
What are the nonessential amino acids?
*
How do we synthesize Ala?
Transamination of pyruvate
How do we synthesize Glu? Why is it important that we can do this?
TCA cycle alpha-ketoglutarate transamination to glutamate. You need to get to glutamate so you can get to Gln, Pro and Arg
How do we synthesize Asp? Why is it important that we can do this?
TCA cycle OAA transamination to aspartate. You need to get to aspartate so you can get Asn.
How do we synthesize Ser? Why is it important that we can do this?
Phosphoglycerate goes to Ser. This is important because you need to be able to do this so you can form Gly and Cys. This is also important because Ser -> Gly is important in developing the one carbon pool for THF (shown below).
How does synthesis of Arg take place?
You can’t just take Arg out of the urea cycle, otherwise you bleed the cycle. A new glutamate enters the cycle -> ornithine -> citrulline -> argininosuccinate -> arginine and that arginine is now taken out of the cycle
Why are the TCA intermediates called the amphibolic intermediates?
They can be used to break down amino acids to CO2 and H2O or can be used to synthesize other molecules from amino acids
What enzymes are responsible for phenylketonuria?
It can be a deficiency in dihydropteridine reductase that prevents you from generating tetrahydrobiopterin (BH4). It can also be a deficiency in phenylalanine hydroxylase that prevents direct addition of OH to Phe to form Tyr.
How do we catabolize branched chain amino acids?
Isoleucine, leucine and valine 1st undergo transamination to their beta-keto derivative. Then they undergo oxidative decarboxylation by a keto acid dehydrogenase. These then go on to degradation pathways similar to beta-oxidation.
How is the final breakdown product of many amino acids degraded?
Proprionyl CoA is a final breakdown product of many amino acids. Proprionyl CoA carboxylase breaks it down to methylmalonyl Coa, then methylmalonyl CoA mutase converts it to succinyl CoA. Remember that you need B12 for the final reaction!
Why is skeletal muscle the internal steak? How is it different from steak?
It can release all 20 amino acids for the body during the fasted state. It is different from steak because it releases 25% Ala, 25% Gln and 10% branched chain amino acids (fewer branched chain amino acids are released because they are being converted to Ala and Gln)
What are the two main amino acids release by muscle during the fasted state? Where do they go?
Ala goes to the liver for gluconeogenesis. Glutamine goes to the kidney to unload 2 nitrogens as ammonia and neutralize keto-acids; it also goes to the gut and bone marrow to participate in synthesis of purines and pyrimidines for these rapidly dividing tissues (enterocyte turnover and hematopoiesis).
What accounts for 20% of the ATP used by the kidney in the fasted state?
Gln goes to the kidney and releases 2 NH4+ to buffer blood keto-acids. It is now alpha-ketoglutarate, which is used for ATP in the kidney.
How does ammonia eliminate H+ from the blood?
NH3 freely diffuses across the renal tubule cell wall into the glomerular filtrate. There it picks up NH4+ and can no longer diffuse across the wall and is excreted in the urine. It helps PO4 do its job.
How is alpha-ketoglutarate oxidized for energy in the kidney?
The first oxidative decarboxylation yields energy as it is converted to succinate. However, succinate can’t produce energy if it just stays in the TCA cycle, so it has to convert to OAA -> PEP by PEPCK -> Pyruvate in the gluconeogenic pathway -> acetyl CoA -> Acetyl CoA enters TCA cycle and is used for energy.
How does the kidney help out the liver if it is damaged, especially during the fasted state?
Gln -> Glu -> Alpha-ketoglutarate -> OAA -> PEP -> Glucose via gluconeogenesis in renal cortex. This helps maintain blood glucose.
What amino acids does the muscle use for energy during the fasted state?
Branched chain AAs (Iso, Val, Leu). Lots of NADH and NADPH is produced in getting these amino acids down to Acetyl CoA and Succinyl CoA. Acetyl CoA goes around the TCA cycle and produces ATP. Succinyl CoA can go all the way back around to alpha-ketoglutarate and then go on to form glutamate by transamination and then form glutamine (to carry waste nitrogen).
What is the main source of Ala production in muscle during the fed and fasted state?
Glucose -> Pyruvate -> transamination to Ala from waste nitrogen due to branched chain amino acid break down. Ala goes into the blood and onto the liver. Ala -> Pyruvate, waste NH3 goes to urea and is excreted in the urea.
What is causing the seizures, somnolescence, apnea, coma and cerebral edema seen when people have ammonia toxicity?
Ammonia builds up and shifts Glu/Gln balance toward Gln. You lose Glu which is a key NT and intermediate of the TCA cycle. Gln enters mitochondria of astrocytes and hydrolyzes to Glu and NH3. Intramitochondrial NH3 induces formation of ROS and the mitochondrial transition permeability pore opens and the cell starts to apoptose. NH3 also increases cell permeability to Ca2+ which can induce apoptosis.
What does your pancreas do in response to the Atkin’s diet?
Both insulin and glucagon go up in response to a carbohydrate free diet. Insulin will stimulate the uptake of amino acids and protein synthesis in the muscle. The liver is more sensitive to glucagon, so all the amino acids that are gluconeogenic are converted to glucose.
What happens to fuel metabolism when you are stressed out?
Glucocorticoids shift fuels around to boost what is required by the immune system. Glucocorticoids cause muscle to degrade and release amino acids. The amino acids are picked up by the liver, undergo gluconeogenesis, blood glucose levels skyrocket and glycogen synthesis starts. AAs are also used to make acute phase proteins. Glucocorticoids also stimulate the release of fatty acids from adipose tissue and provide fuel for the liver.
Why are people in negative nitrogen balance after surgery?
Stress response induces release of glucocorticoids. Glucocorticoids cause amino acid degradation from muscle protein so that they can go through gluconeogenesis and provide sugar for the immune cells and protein for acute phase reactants that the liver is making.
