Protein Biochemistry Flashcards
Urea Cycle comprises the following:
Ornithine is the backbone that is recycled in this process
- Ornithine—> Citrulline
i. catalyzed by Ornithine transcarbamylase - Citrulline + Aspartate—> Argininosuccinate
i. (catalyzed by Arginonosuccinate synthase) - Argininosuccinate–> Arginine
i. (catalyzed by Argininosuccinate lyase) - Arginine–> Ornithine + Urea
i. (catalyzed by Arginase)
Carbamoyl phosphate synthetase I (initial step in Urea Cycle entry)
a. Important urea cycle enzyme found in mitochondria.
i. Carbamoyl phosphate synthetase I: Ornithine—> Citrulline
b. Reaction: bicarbonate + ammonia–> carbamoyl phosphate uses 2 of the 3 ATPs in urea cycle.
c. N-acetylglutamate is an allosteric activator of Carbamoyl phosphate synthetase I.
d. Arginine is an activator of N-acetylglutamate synthase, which catalyzes the following reaction: acetyl CoA + glutamate to N-acetylglutamate
Transport of ammonia
a. Ammonia cannot be transported through blood, so alternative mechanisms are needed such as those that rely on urea.
b. Glutamine serves as a means of transport, since it can “hold” two ammonia groups.
c. Glu dehydrogenase serves as a control pt for protein metabolism specifically by controlling the direction of either nitrogen removal or incorperation into amino acids
d. Most tissues use glutamine synthetase to convert glutamate to glutamine for transport to the liver (to enter the urea cycle).
How muscle is unique in ammonia transport
a. Muscle is different where alanine is used instead of glutamine for transport in the Alanine-Glucose Cycle.
b. This is because in muscle there is a build-up of pyruvate from glycolysis and pyruvate can be converted to alanine for transport to liver (transamination).
c. The liver, in turn, can use the alanine to convert back to pyruvate (transamination) and glucose remade (gluconeogenesis) can then be delivered back to the muscle.
Arginine in nerve and muscle function (X-talk and alternative reactions related to urea cycle).
a. NO synthase converts arginine–> citrulline to produce NO, an important molecule used as a neurotransmitter.
b. In the urea cycle, arginine–> ornithine can either be catalyzed by arginase or alternatively can be catalyzed by several enzymes to produce creatine phosphate for energy (muscle).
Ketogenic versus glucogenic (categorizing the breakdown of amino acids) describes the outcome of the keto acid
a. Glucogenic: produces pyruvate or Kreb Cycle intermediates.
b. Ketogenic: produces no net production of glucose.
c. Examples:
i. Glucogenic: Oxaloacetate in Kreb Cycle comes from aspartate transamination
ii. Ketogenic: Lysine and leucine are the ketogenic amino acids since breadown gives Acetyl-CoA (i.e. only 2 carbons)
Decarboxylation of branched-chain amino acids
a. Branched Chain Amino Acids include leucine, valine, and isoleucine.
b. First, these three amino acids are deaminated by branched-chain aminotransferase to produce a-keto acids.
c. Second, they are decarboxylated by branched-chain a-ketoacid dehydrogenase complex.
i. Maple Syrup Urine Disease (MSUD) occurs when this dehydrogenase complex is deficient and there is consequently a build up of the a-keto acids in urine (“sweet smelling”).
Maple Syrup Urine Disease (MSUD)
a. Maple Syrup Urine Disease (MSUD) occurs when this branched-chain a-ketoacid dehydrogenase complex is deficient and there is consequently a build up of the a-keto acids in urine (“sweet smelling”).
b. Normally, these three amino acids are deaminated by branched-chain aminotransferase to produce a-keto acids.
i. Second, they are decarboxylated by branched-chain a-ketoacid dehydrogenase complex.
c. Without the Decarboxylation step, there will be a build up of alpha-keto acids
Thyroid Chemistry (product derived from Tyr)
a. Tyrosine is used to make T4 (prohormone) that is converted to T3 (hormone).
b. Thyroid stimulating hormone (TSH): Stimulates iodide (I-) uptake and stimulates release of T4,T3.
c. Thyroid peroxidase: Oxidizes iodide (I-) to (I2).
i. Thyroglobulin (Tg): Contains Tyr residues iodinated to form T4,T3.
ii. Thyroxin binding globulin (TBG): Transports T4,T3.
Porphyrin (Heme) Summary
specialized products derived from Gly and TCA intermediate
a. Porphyrins such as Heme are cyclic molecules made of 4x pyroles primarily produced in liver.
i. Porphyrins bind Fe2+ (iron).
b. To produce a porphyrin the following reactions take place:
1. Gly + succinyl CoA—> δ -Aminolevulinic acid (ALA) (catalyzed by δ-Aminolevulinate synthase)
- 2xALA—> Porphobilinogen (catalyzed by by δ-Aminolevulinate dehydratase)
- Porphobilinogen—-> Protoporphyrin IV (catalyzed by 4 enzymes)
- Protoporphyrin IX—> Heme (catalyzed by Ferrochelatase)
c. Porphyrias are the general term for diseases in porphyrin synthesis.
d. Lead inhibits two enzymes in porphyrin synthesis (δ-Aminolevulinate dehydratase, ferrochelatase)”lead poisining”.
To produce a porphyrin the following reactions take place:
- Gly + succinyl CoA—> δ -Aminolevulinic acid (ALA) (catalyzed by δ-Aminolevulinate synthase)
- 2xALA—> Porphobilinogen (catalyzed by by δ-Aminolevulinate dehydratase)
- Porphobilinogen—-> Protoporphyrin IV (catalyzed by 4 enzymes)
- Protoporphyrin IX—> Heme (catalyzed by Ferrochelatase)
Porphyrin (Heme) degradation:
a. Reactions Heme—> biliverdin (green)—> bilirubin (red-orange)—> bilirubin diglucuronide—> urobilinogen–> stercobilin (brown)
b. Bilirubin is transported in blood via albumin.
c. In liver, bilirubin is conjucated with glucuronic acidbilirubin diglucuronide (or otherwise known as conjugated bilirubin).
d. In intestine, bilirubin diglucuronide is oxidizedstercobilin.
e. Jaundice occurs when bilirubin cannot be processed properly (i.e. hemolytic jaundice occurs when too many RBCs lyse, neonatal jaundice when bilirubin diglucuronide is not produced fast enough by low levels of bilirubin glycuronyltransferase).
alanine aminotransferase (ALT)
Review
ALT catalyzes the transfer of an amino group from L-alanine to α-ketoglutarate, the products of this reversible transamination reaction being pyruvate and L-glutamate.
L-glutamate + pyruvate ⇌ α-ketoglutarate + L-alanine
*NH3 moves from the Glutumate to the Alanine
Aspartate aminotransferase
(AST)
Review
Aspartate transaminase catalyzes the interconversion of aspartate and α-ketoglutarate to oxaloacetate and glutamate.
Aspartate (Asp) + α-ketoglutarate ↔ oxaloacetate + glutamate (Glu)
*NH3 moves form Asp to the Glu
Urea Cycle Introduction
a. The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions occurring in many animals that produces urea ((NH2)2CO) from ammonia (NH3).
i. In mammals, the urea cycle takes place primarily in the liver, and to a lesser extent in the kidney.
b. Organisms that cannot easily and quickly remove ammonia usually have to convert it to some other substance, like urea or uric acid, which are much less toxic.
i. Insufficiency of the urea cycle occurs in some genetic disorders (inborn errors of metabolism), and in liver failure. The result of liver failure is accumulation of nitrogenous waste, mainly ammonia, which leads to hepatic encephalopathy.
Urea Cycle
*Critical Slide
a. The urea cycle consists of five reactions: two mitochondrial and three cytosolic.
b. The cycle converts two amino groups, one from NH4+ and one from Asp, and a carbon atom from HCO3−, to the relatively nontoxic excretion product urea at the cost of four “high-energy” phosphate bonds (3 ATP hydrolyzed to 2 ADP and one AMP).
c. Ornithine is the carrier of these carbon and nitrogen atoms.
The Urea Cycle
Overview
Net Reaction:
3ATP + HCO3- + NH4(N)+ + Aspartate(N) ——-> 2ADP + AMP + 2Pi + PPi + fumarate + urea
What is the Control point for Protein Catabolism (Urea Cycle)
Carbamoyl phosphate synthetase I:
a. Important urea cycle enzyme found in mitochondria.
b. Reaction:
2ATP + HCO3− + NH4+ –> 2ADP + Carbamoyl phosphate + Pi
c. N-acetylglutamate is an allosteric activator of Carbamoyl phosphate synthetase I.
i. Arginine is an activator of N-acetylglutamate synthase, which catalyzes the following reaction: acetyl CoA + glutamate to N-acetylglutamate
Carbamoyl phosphate synthetase I
is a control point for protein catabolism
a. The reaction catalyzed by Carbamoyl phosphate synthetase I is one of the most complicated known.
b. Uses two ATPs to add one phosphate and ammonia.
i. ~10 mutations found in this enzyme lead to early onset of associated
ii. “urea cycle disorder” (with subsequent increased ammonia in blood).
Transport of ammonia
a. Because ammonia is toxic, glutamine is used to transfer it from peripheral tissues to the
• Kidneys where it is removed in the form of ammonia (through urine).
• Liver where it is removed in the form of urea (through blood to kidney).
Muscle versus other tissues transport Nitrogen a different way to the tissues
*Critical Slide
a. Most tissues use glutamine synthetase to convert glutamate to glutamine for transport to the liver (to enter the urea cycle).
b. Muscle is different where alanine is used instead of glutamine for transport in the Alanine-Glucose Cycle.
i. This is because in muscle there is a build-up of pyruvate from glycolysis and pyruvate can be converted to alanine for transport to liver (transamination).
ii. The liver, in turn, can use the alanine to convert back to pyruvate (transamination) and glucose remade (gluconeogenesis) can then be delivered back to the muscle.
Transport of ammonia
Different Tissues
a. Liver: Urea Cycle produces urea for transport through blood to kidney.
b. Peripheral Tissue: Glutamine produced for transport to Liver.
c. Muscle: Alanine produced for transport to Liver.
d. Kidney: Removes urea and remove ammonia (from Gln).