I am a Master's student in Biochemistry at the Karolinska Institutet in Stockholm, Sweden. I have a range of notes from courses that I undertook as part of my Bachelor's studies. These notes are detailed and in depth that focus on many aspects of how the urea cycle works. These notes contain refere...
Test Bank - Lehninger Principles of Biochemistry, 8th Edition (Nelson, 2022), Chapter 1-28 | All Chapters
TEST BANK FOR LEHNINGER PRINCIPLES OF BIOCHEMISTRY NELSON 6TH EDITION
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The Urea Cycle:
If not reused for the synthesis of new amino acids or other nitrogenous products, amino groups are channelled into a
single excretory end product (Fig. 18–10). Most aquatic species, such as the bony fishes, are ammonotelic, excreting
amino nitrogen as ammonia. The toxic ammonia is simply diluted in the surrounding water. Terrestrial animals require
pathways for nitrogen excretion that minimize toxicity and water loss. Most terrestrial animals are ureotelic, excreting
amino nitrogen in the form of urea; birds and reptiles are uricotelic, excreting amino nitrogen as uric acid.
In ureotelic organisms, the ammonia deposited in the mitochondria of hepatocytes is converted to urea in the urea
cycle. This pathway was discovered in 1932 by Hans Krebs (who later also discovered the citric acid cycle) and a
medical student associate, Kurt Henseleit.
Urea production occurs almost exclusively in the liver and is the fate of most of the ammonia channeled there.
The urea passes into the bloodstream and thus to the kidneys and is excreted into the urine.
Urea is the major disposal form of amino groups derived from amino acids, and accounts for about 90% of the
nitrogen-containing components of urine. One nitrogen of the urea molecule is supplied by free ammonia, and the
other nitrogen by aspartate. [Note: Glutamate is the immediate precursor of both ammonia (through oxidative
deamination by glutamate dehydrogenase) and aspartate nitrogen (through transamination of oxaloacetate by AST).]
The carbon and oxygen of urea are derived from CO2. Urea is produced by the liver, and then is transported in the
blood to the kidneys for excretion in the urine.
Glutamate is the immediate precursor of both ammonia (through oxidative deamination by glutamate dehydrogenase)
and aspartate nitrogen (through transamination of oxaloacetate by AST). In effect, both nitrogen atoms of urea arise
from glutamate, which, in turn, gathers nitrogen from other amino acids.
Ammonia produced in the liver is USED for synthesis of amino acids, nucleotides, and other amines…
BUT if it’s not used, it is converted to UREA.
Step 1: Formation of carbamoyl phosphate:
Formation of carbamoyl phosphate is not technically part of the urea cycle, but it is essential for urea
synthesis
The urea cycle begins inside liver mitochondria, but three of the subsequent steps take place in the cytosol; the cycle
thus spans two cellular compartments.
The first amino group to enter the urea cycle is derived from ammonia in the mitochondrial matrix—NH4 _ arising by
the pathways described for transamination previously. The liver also receives some ammonia from the portal vein
from the intestine from bacterial ox. Of AA’s. Ultimately, the nitrogen atom derived from this ammonia becomes one
of the nitrogens of urea.
Whatever its source, the NH4 _ generated in liver mitochondria is immediately used, together with CO2 (as HCO3)
produced by mitochondrial respiration, to form carbamoyl phosphate in the matrix. The enzyme catalysing this rxn
(carbamoyl phosphate synthase 1) is a regulatory enzyme which is distinct from its’ cytosolic form (carbamoyl
phosphate synthase 2) which plays a separate role in pyrimidine synthesis, this is an ATP dependent RXN.
Ammonia reacts with CO2 (as HCO3-) in an ATP-dependent reaction.
Glutamine is utilized as the endogenous source of ammonia by all types of CPS31,46,47,48 except CPS12. The
inability of human CPS1 to use glutamine is explained by the replacement by serine (Ser294) in this enzyme of the
, key catalytic cysteine of the catalytic triad of histidine, glutamate and cysteine34,49 used for glutamine hydrolysis
by other CPSs (Cima et al. 2015 Scientific Reports, Nature).
Step 2: Formation of Citrulline:
The carbamoyl phosphate, which functions as an activated carbamoyl group donor, now enters the urea cycle.
The cycle has four enzymatic steps. First, carbamoyl phosphate donates its carbamoyl group to ornithine to form
citrulline, with the release of Pi.
The reaction is catalyzed by ornithine transcarbamoylase, and the citrulline passes from the mitochondrion to the
cytosol.
Ornithine and citrulline are basic amino acids that participate in the urea cycle, moving across the inner mitochondrial
membrane via a cotransporter. They are not incorporated into cellular proteins because there are no codons for these
amino acids.
Ornithine, arising in the cytosol, is transported to the mitochondrial matrix via the action of ornithine translocase
encoded by the ORNT1 gene. The ORNT1 transporter is a member of the solute carrier family of transporters and as
such is also identified as SLC25A15.
Step 3: Formation of arginosuccinate:
The second amino group now enters from aspartate (generated in mitochondria by transamination and transported into
the cytosol) by a condensation reaction between the amino group of aspartate and the ureido (carbonyl) group of
citrulline, forming argininosuccinate.
The RXN requires ATP and proceeds via a citrullyl-AMP intermediate. see Lehn diagram of urea cycle (it’s printed
).
The a-amino group of aspartate provides the second nitrogen that is ultimately incorporated into urea. The formation
of argininosuccinate is driven by the cleavage of ATP to adenosine monophosphate (AMP) and pyrophosphate. This is
the third and final molecule of ATP consumed in the formation of urea.
Argininosuccinate synthetase is encoded by the ASS1 gene located on chromosome 9q34.1 which is composed of 18
exons that generate two alternatively spliced mRNAs that generate the same 412 amino acid protein. The human
genome contains at least 14 copies of the ASS1 gene all of which are pseudogenes except the one on chromosome 9
which encodes the functional enzyme.
Step 4: Formation of Arginine & fumerate:
Argininosuccinate is cleaved by argininosuccinate lyase to yield arginine and fumarate. The arginine formed by this
reaction serves as the immediate precursor of urea.
Fumarate produced in the urea cycle is hydrated to malate, providing a link with several metabolic pathways. For
example,
1. The malate can be transported into the mitochondria via the malate shuttle, reenter the tricarboxylic acid
cycle, and get oxidized to oxaloacetate (OAA), which can be used for gluconeogenesis (see p. 120).
2. Alternatively, the OAA can be converted to aspartate via transamination (see Figure 19.8), and can enter the
urea cycle.
This is the only reversible step of the urea cycle!!
Argininosuccinate lyase is functional as a homotetrameric complex. The argininosuccinate lyase protein is encoded by
the ASL gene located on chromosome 7q11.21 and is composed of 17 exons that generate several alternatively spliced
mRNAs.
Step 5: Formation of Ornithine & urea!
The cytosolic enzyme arginase cleaves arginine to yield urea and ornithine. Ornithine is transported into the
mitochondrion to initiate another round of the urea cycle.
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