Amino Acid Metabolism Flashcards

Protein Degradation

• Nonselective degradation of proteins: Occurs in well-nourished cells via lysosomes.
• ATP-dependent degradation: Mediated by the 26S proteasome, which degrades ubiquitinated proteins.
• Ubiquitination steps (prior to ATP-dependent degradation):
  • Ubiquitin is attached via a thioester to a ubiquitin-activating enzyme.
  • Ubiquitin is transferred to cysteine on a ubiquitin-conjugating enzyme.
  • Activated ubiquitin is transferred to a lysine of the previously bound protein.
  • The protein is linked to at least four tandemly linked ubiquitin units.
• Protein Lifetime: The lifetime of a protein in cells actively involved in metabolism can change in response to changes in metabolic hormone levels.
• KFERQ proteins:
  • Contain the KFERQ pentapeptide sequence (or a similar sequence).
  • Are selectively degraded in tissues that atrophy after a prolonged fast (starvation).
• Proteins targeted for destruction via the ubiquitin pathway include:
  • Proteins with a destabilizing N-end rule component.
  • Proteins with a PEST sequence.
  • Proteins that contain the RING finger E3 component named E3a.
  • Proteins with polyubiquitin chains.
• Advantages of constant protein degradation and reformation:
  • Nutrients can be stored as proteins, which can be used during periods of metabolic need.
  • Damaged proteins are eliminated so they do not accumulate.
  • Metabolism can be efficiently regulated by the synthesis and degradation of enzymes.
• Enzyme A in a Linear Pathway: Likely has high rates of degradation and synthesis. This is for an enzyme involved in the metabolism of metabolite C to metabolite D, where enzyme A is part of a linear pathway involving ten enzymes ultimately converting B to F. High levels of F directly alter the activity of enzyme A and result in control over the overall pathway

Amino Acid Deamination

• Aminotransferases: Utilize a coenzyme synthesized from vitamin B6.
• Majority of amino acids are deaminated: By a transamination reaction.
• Aminotransferase reaction:
  • Involves an enzyme-PLP Schiff base.
  • Results in the formation of an a-ketoacid.
• Clinical significance: The presence of SGOT and SGPT in the serum indicates potential heart attack or liver damage.
• Glutamate Deamination: Oxidative deamination of glutamate generates NAD(P)H and a-ketoglutarate.
• GDH Mutation: A mutation in GDH of patients with HI/HA (hypoglycemia/hyperammonemia) results in a decrease in allosteric control of GDH via GTP. This will be observed in the patients as an increase in ammonia and an increase in NADH.

The Urea Cycle

• Channeling: A phenomenon in which intermediates are directly transferred from one active site to another.
• Glucose Synthesis: Fumarate to malate to oxaloacetate can result in glucose synthesis.
• Arginine to Urea + Ornithine: Takes place in the cytosol.
• Ornithine + Carbamoyl-phosphate to Citrulline: Takes place in the mitochondrial matrix.
• Carbamoyl phosphate is produced by combining NH3, PO4^{3-}, and HCO_3^{-}.
• Enzyme-bound adenylated intermediate: Argininosuccinate synthetase catalyses a reaction via an enzyme-bound adenylated intermediate.
• Urea Cycle Controls: Substrate concentration of the cycle enzymes, allosteric activation of carbamoyl phosphate synthetase I and concentration of glutamate control the urea cycle

Breakdown of Amino Acids

• C1 units transfer: The cofactor THF (tetrahydrofolate) is used to transfer C1 units such as methyl, formyl, and methenyl groups.
• Ketogenic amino acids: Can be converted to fatty acids and ketone bodies.
• Glucogenic amino acids: Ala, Cys, Gly, Ser, and Thr are all degraded to pyruvate and are considered glucogenic.
• Leucine catabolism: The pathway begins with a-ketoglutarate and generates HMG-CoA.
• Maple syrup urine disease: Is caused by a genetic deficiency in the enzyme BCKDH, the disease is fatal unless promptly treated, there is a buildup of the branched-chain a-keto acids and patients with the disease excrete urine that smells like maple syrup.
• Phenylalanine:
  • The enzymatic degradation of phenylalanine requires the biopterin cofactor.
  • Individuals with defects in phenylalanine catabolism require tyrosine in their diet.
  • An inability to hydroxylate phenylalanine results in increased blood levels of phenylalanine, causing mental retardation.
• MTHFR Mutation: Individuals with an alanine to valine mutation in N5, N10 – methylenetetrahydrofolate reductase (MTHFR) typically have higher levels of homocysteine, have increased risk for cardiovascular disease, typically have increased incidence of oxidative damage to the walls of blood vessels and are at increased risk, if female, of giving birth to a child with a neural tube defect.
• Aminotransferase Breakdown: Alanine to Pyruvate is catalyzed by aminotransferase

Amino Acid Biosynthesis

• Glutamine Synthetase: The enzyme glutamine synthetase is critical to regulating nitrogen metabolism.
• Serine, Cysteine, and Glycine Precursor: 3-phosphoglycerate is the common precursor to serine, cysteine, and glycine.
• Tryptophan Synthase:
  • Indole can pass between active sites via a channel in the enzyme.
  • Tryptophan synthase catalyzes two distinct reaction steps to form tryptophan.
  • The enzyme has two states, an "open" and "closed", to ensure that bound indole is not lost to solvent.
  • The indole group is produced following release of glyceraldehyde-3-phosphate from the indole-glycerol-3-phosphate.
• Bacterial glutamine synthetase activity:
  • Is inhibited allosterically by tryptophan.
  • Is inhibited allosterically by glucosamine-6-phosphate.
  • Is activated by nine allosteric feedback inhibitors.
  • Is altered by covalent modification.
• Glutamine:
  • It is formed from a-ketoglutarate
  • It donates an amino group to aspartate to form asparagine.
• cyclic carbohydrate precursor: Histidine and tyrosine require a cyclic carbohydrate precursor for synthesis.
• chorismate: chorismate is an important intermediate in the production of Trp, Tyr, and Phe and is a derivative of glucose.
• Essential Amino Acids: Met, Lys, His, Val are essential amino acids for adult humans
• Aminotransferase First Step: Glutamine synthesis uses an aminotransferase in the first step of the synthesis.

Other Products of Amino Acid Metabolism

• Bilirubin Degradation: Infants who cannot properly degrade bilirubin develop jaundice.
• Neurotransmitters: Dopamine, epinephrine, and norepinephrine are synthesized from the amino acid tyrosine.
• Decarboxylation cofactor: Pyridoxal-5'-phosphate is usually used as a cofactor by enzymes catalyzing decarboxylation steps that synthesize neurotransmitters from amino acids.
• Heme biosynthesis is inhibited in lead poisoning.
• Nitric Oxide (NO): NOS catalyzes the synthesis of nitric oxide (NO), a molecule that signals vasodilation, from the precursor arginine

Nitrogen Fixation

• Nitrogen Fixation: Organisms known as diazotrophs can fix nitrogen into metabolically useful molecules.
• Nitrogenase:
  • Contains unique redox centers that contain both Fe and Mo.
  • Changes in conformation as a result of ATP hydrolysis.
  • Carries out a reaction that reduces nitrogen to NO.
• Nitrogen Reduction Cost: The total cost of nitrogen reduction is 16 ATP and 8 transferred electrons. It can be written as 16
  ewline ATP + 8e^{-}.