urea cycle Flashcards by mohamed nascer

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 )

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what is the fate of amino group NH2?

waste or reuse

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what is the fate of carboyxlic acid group? COOH?

oxidation of alpha ketoacid

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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

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what is the alpha ketoacid of alanine ?

alanine without nh3 = pyruvate

end product of glycolysis and an intermediate of the glucose pathway

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what is the alpha keto acid of glutamate ?

glutamate without nh3 = Alpha ketoglutarate

intermediate of TCA cycle

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what is alpha ketoacid of aspartate ?

aspartate without NH3 = Oxaloacetate

intermediate of TCA cycle

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whats the fate of nitrogen removed?

recycled or excreted

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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

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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

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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

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what is the co-enzyme required for transaminases ?

PLP

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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

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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

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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

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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