urea cycle Flashcards
what are amino acids?
building blocks of proteins and share a general structure consisting of :
Central carbon ( alpha-carbon ) : the central atom to which all other group attaches
Amino group NH2 - basic functional group that can accept a proton and become NH3
Carboxyl group COOH - an acidic functional group that can donate a proton
Hydrogen atom - single hydrogen atom bonded to the central carbon
Side chain ( R group ) - variable group that determines the unique properties of each amino acid ( non polar, polar, acidic , basic )
what is the fate of amino group NH2?
waste or reuse
what is the fate of carboyxlic acid group? COOH?
oxidation of alpha ketoacid
when we can utilize an amino acid?
when we remove the amino group
as long as the amino group is present we cant use the AA
after removing the amino group the AA becomes alpha ketoacid and can be used for other stuff
what is the alpha ketoacid of alanine ?
alanine without nh3 = pyruvate
end product of glycolysis and an intermediate of the glucose pathway
what is the alpha keto acid of glutamate ?
glutamate without nh3 = Alpha ketoglutarate
intermediate of TCA cycle
what is alpha ketoacid of aspartate ?
aspartate without NH3 = Oxaloacetate
intermediate of TCA cycle
whats the fate of nitrogen removed?
recycled or excreted
how do we remove amino group?
we dont have enzymes that can deaminate all AA
we can doeaminate glutamate because we have the enzyme glutamate dehydrogenase
glutamate dehydrogenase will remove the amino group as free ammonia converting the glutamate into alpha ketoglutarate ( it can also do the opposite )
since other AA cannot do this so we have special group of ENZYMES called —> TRANSAMINASES
What is the function of transaminases ?
transfer an amino group from an AA to an alpha ketoacid
converting the AA to alpha ketoacid and the alpha ketoacid to AA
EXAMPLE :
Alanine has amino group which can be transferred to oxaloacetate
this will convert alanine to pyruvate and oxaloacetate to aspartate
this is not useful because we are not deaminating we are just converting
So what do we do?
We try to move the amino group to glutamate then glutamate dehydrogenase can remove the amino group from glutamate completely
what are enzymes that can move amino group to glutamate ?
Alanine transaminase ( ALT )
alanine + alpha ketoglutarate = pyruvate + glutamate ( the amino has been move from alanine to alpha ketoglutarate )—-> THEN GLUTAMATE DEHY WILL REMOVE THE AMINO GROUP
Aspartate transaminases :
Aspartate + alpha ketoglutarate = oxaloacetate + glutamate
and glutamate dehy will remove the amino acid
this occur at liver usually so ALT and AST are liver function test
what is the co-enzyme required for transaminases ?
PLP
how do we transport ammonia to liver?
the deamination and transamination process usually occur at the liver so if we have free ammonia anywhere in the body how ccan we transport this to ammonia to the liver?
ammonia is very toxic so we cannot let move freely in the blood
Best carrier for ammonia are AA
1st mechanism : Through alanine
- In muscles ammonia from animo acid breakdown is transferred to pyruvate via ALT to form alanine
alanine travel to the liver where ALT will remove the ammonia from alanine n give it to glutamate
glutamate dehydrogenase will remove the ammonia and release it to UREA CYCLE for excretion
Then pyruvate is used for gluconeogensis , producing glucose ,which returns to muscle for energy
isnt it better to use AA which can 2 amino group per AA?
yes
glutamine and asparagine can hold 2 amino groups
the extra one is found in the R group
Glutamine is the main amino group CARRIER for this purpose
describe the mechanisms of using glutamine as a transporter ?
Glutamine synthetase will :
Convert glutamate + free ammonia = glutamine
non toxic transport form
glutamine is transported to the liver where glutaminase release ammonia for urea synthesis ( by glutaminase )
So now glutamine is converted back to glutamate
So we have this mechanism and alanine but GLUTAMINE IS THE MAIN ONE
why dont we use asparagine for ammonia transport?
asparagine synthetase uses amino group from glutamines R group
so it doesnt directly take a free ammonia
it steals from glutamine
what are the characteristics of urea cycle and ammonia?
ammonia is converted to urea for excretion
urea is less toxic than ammonia
Urea cycle occur mainly in liver
Urea = 2 ammonia ( 2 nitrogen )
2 nitrogen atoms of urea enter the urea cycle as:
NH3 ( produced mainly via glutamate
dehydrogenase )
and
amino N of aspartate
The Nh3 and HCO3 will be part of urea are incorporated first into CARBAMOYL PHOSPHATE
where is the location of urea cycle?
mitochondria and cytoplasm
what is the first reaction ?
this reaction is not consider this part of the urea cycle by many text books !!
Synthesis of carbamoyl phoshpate
Straight forward reaction:
HCO3 + ammonia = carbamoyl phoshpate
by : Carbamoyl phosphate synthetase 1 ( CPS1 )
Requires 2 ATP ( ENERGY DEMANDING )
Irreversible and it is in the MITOCHONDRIA
Committed step of urea cycle and is subject to regulations
what does formation of carbamoyl phosphate require?
N- acetyl glutamate as an activator
2 ATP
Carbamoyl phosphate has amino group and phosphate and carbonyl group
so we only need to 1 more amino group and we have urea
what are the steps of urea cycle after forming carbamoyl phosphate ?
Carbamoyl phosphate + Ornithine = Citrulline
by : Ornithine transcarbamoylase ( IN MITOCHONDRIA )
Then
Citrulline leave mitochondria and go to the cytoplasm using antiport mechanism ( Citrulline pumped out and ornithine into the mitochondria )
3 Reactions in cytoplasm :
1- Citrulline + aspartate = argininosuccinate
by Argininosuccinate synthase
aspartate is the second source of ammonia in urea
( So one free amino group from glutamate and the 2nd from aspartate )
2- Argininoosuccinate = Fumerate + arginine
by- Argninoosuccinate lyase
3- Arginine = urea + Ornithine
by arginase
Ornithine will moved back to mitochondria to repeat the cycle
what happens to the fumerate generated by the 2nd step in cytoplasm?
Used to recycle asparate
Fumerate —> malate —> oxaloacetate
oxaloacetate + glutamate —-> Alpha ketoglutarate + aspartate
by AST
but this is in the mitochondria how is it done in the cytoplasm?
we use CYTOSOLIC ISOZYMES
energy consuming but its worth it
what is CPS2? carbamoyl phosphate synthase 2?
in cases of CPS1 deficiency CPS2 will take over
CPS2 is a cytosolic enzyme ( CPS1 IS MITOCHONDRIA )
involved in pyrimidine biosynthesis , distinct from CPS1 which functions in the urea cycle
CPS2 catalyzes the first committed step in pyrimidine synthesis using glutamine instead of the free ammonia as the nitrogen donor
In cases of CPS1 deficiency we cant form Carbamoyl phosphate from free ammonia and HCO3 so we will have hyperammonia
ammonia builds up because it cannot be converted to carbamoyl phosphate for urea production
Glutamine synthtase uses the free ammonia to form glutamine trying to buffer ammonia since CPS2 uses glutamine as nitrogen donor , higher glutamine levels will enhance CPS2 activity leading to increased pyrimidine synthesis
Orotic acid ( by product of pyrimidine biosyntehsis ) will be excreted in urine in cases of CPS1
CPS2 doesnt compensate for CPS1 deficiency
what are the enzymes of urea cycle found in mitochondria?
CPS1
Ornithine transcarbamylase
what are the enzymes of urea cycle found in cytoplasm?
Arginino succinate synthase ( citurillin + aspartate )
Argininnosuccinate lyase ( Arginninisuccinate = fumerate + arginine )
Arginase ( arginine = urea + orthinine )
what is the transporter that help in urea cycle ?
Ornithine / citrulline transporter
the end product is ornithine need to go back to mitochondria to form more citrulline
and
Citrulline formed in the mitochondria needs to go cytoplasm for the rest of the cycle
how do we regenerate asparate using fumerate in the cytoplasm even though TCA cycle happen in mitochondria?
Cytosolic isozymes
Fumarate —> malate —> oxaloacetate
by fumerase and malate dehydrogenase
Oxaloacetate + glutamate = Aspartate + alpha ketoglutarate
by AST
where does the complete urea cycle happen?
the complete set of enzymes is in the liver
to complete it
however some enzymes of the pathway are found in other cells and tissue where they generate arginine and ornithine which are precusors for other molecules
for example Arginiosuccinate synthase ( ciillutrine + asparate ) which is found in most tissues
kidney has all enzymes except arginase (cant complete the cycle )
brain doesnt have orthinine transcarbomylase so it cant form citrulline from ornithine
describe hyperammonemia ?
Occurs when blood NH3 levels are above normal
occurs due to genetic or the liver is compromised
NH3 is neurotoxic to CNS
symptoms :
Tremors
slurring of speech
vomitting
cerebral edema
bluring of vision
coma and death
what are 2 types of hyperammonemia ?
Acquired due to :
Viral hepatitis
Heptatoxins - aflatoxins
liver cirrhosis
hepatic or biliary obstruction collaterals portal blood shunted into systemic circulation
Heridetary due to :
Genetic deficiency of 5 enzymes of the urea cycle
1- Hpyerammonaemia Typ1 —> DEFICIENCY IN CPS1 ( most common )
2- Ornithine transcarbomylase is most common - sex linked -males ( ornithinemia
Females are carriers
if ornothine transcarbomylase is deficient what accumulates ? Ornithine
other 4 enzymes are autosomal reccesive
what happens if we have hyperammonemia in liver failure?
our body will do everything to get rid of it
Starts converting glutamate to glutamine but by doing this we are depleting glutamate which is big problem cuz :
1- Glutamate is neurotransmitter
2- depleting glutamate we dont have AA for protein synthesis
we can overcome this by :
Convert alpha ketoglutarate to glutamate using glutamate dehydrogensase
but also big problem cuz we will deplete alpha ketolgutarate and will stop TCA cycle and no energy for brain
what is the treatment of hyperammonemia ?
Limit protein intake
phenyl butyrate ( given orally )—>
converted to phenylacetate = condense with glutamine forming phenylacetly glutamine which is water soluble product and excreted
Gets rid of glutamine not free ammonia
consequences of ammonia toxicity?
1- High NH3 would drive glutamine synthase =
Glutamate + ATP + NH3 = glutamine + ADP
This depletes glutamate - neurotransmitter and precursor for synthesis of neurotransmitter GABA
2- depletion of glutamate and high ammonia level would drive glutamate dehydrogenase reaction to reverse :
Alpha ketoglutarate + NH4 + NADHP = Glutamate + NADP
This results in depletion of alpha ketoglutarate an essential TCA cycle could impair energy metabolism in the brain
3- high glutamine in the brain will enhance the outflow of glutamine from the brain cells which is carried by the same transporter which allow the entry of tryptophan and this will increase the production of serotonis in the brain cell ( which is a neurtotransmitter )
more glutamine pumped out = more tryptophan in ( neurotransmitter )
what is the clinical significance of urea?
Increase of levels uremia
may occur in number of disease can be classified as :
Prerenal
Renal
postrenal
