Nitrogen Flashcards
What are the different N-containig compounds?
- Metabolites
- Purines
- Heme = Succinyl-CoA + Glycine
- Hormones
What is the role of Nitrogenase?
Expressed by Diazotroph bacteria → fixes atmospheric nitrogen
Turns stable N2 gas into NH3
N2 + 8H+ + 8e- + 16 ATP + 16 H2O → 2 NH3 + H2 + 16 ADP + 16 Pi
*requires ATP to reduce these stable bonds (triple bond)
*FIXATION
What is the Haber-Bosch reaction?
N2 + 3H2 → 2 NH3
*In bacteria in the ground
What is assimilation of Nitrogen?
2 NH3 → {Glutamine synthetase} → Glutamine
There is a symbiotic association between bacteria and yeast in the soil (associated with the roots) → Bacterias fix Nitrogen (Nitrogenase catalyses N2 → 2 NH3, ATP-dependent)
NH3 is taken up by plants which assimilate it in their cells (Many different nitrogen assimilation reactions for ex: Glutamine synthetase catalyses NH3 → Glutamine)
What are the 4 most important nitrogen assimilation reactions?
a-ketoglutarate (0N) → {Glutamate dehydrogenase} → Glutamate (1N) (→ other AA)
Glutamate (1N) → {Glutamine synthetase} → Glutamine (2N) (→ Purine nucleotides, AA, tryptophan, histidine)
Aspartate (1N)} → {Asparagine synthetase} → Asparagine (2N)
CO2, ATP → {Carbamoyl phosphate synthetase} → Carbamoyl phosphate (→ Arginine, pyrimidine, urea)
What is the role of pepsin?
- Secreted in the stomach
- 1st protein digestion enzyme → polypeptides
- Activated at pH ~2
- Cleaves after Phe, Leu, Trp, Tyr
What is the role of trypsin?
- 2nd protein digestion enzyme of GI tract (polypeptides → peptides)
- Secreted by the pancreas into the duodenum
- Cleaves after Arg, Lys
What is the role of chymotrypsin?
- 3rd protein digestion enzyme (polypeptides → peptides)
- Secreted by the pancrease into the duodenum
- Activated by trypsin
- Cleaves after Phe, Trp Tyr
What is the role of Aminopeptidase and Carboxypeptidase A?
- 4th protein of digestion enzyme (peptides → amino acids)
- Secreted by the pancrease into the small intestine (taken up by the brush border)
- Non-specific cleavage → Aminopeptidase cleaves of the N-terminus / Carboxypeptidase cleaves of the C-terminus
How does uptake of AA into enterocytes work? What is the exception?
20 AA with different combinations of dipeptides and tripeptides uptaken → many many specific transporters at the brush border of enterocytes
General rule → imported via Na+ and H+ symporters
Exception in neonatal mammals:
Whole milk proteins are endocytosed and degraded in lysosome (AA go into circulation) or pass unscathed through the enterocyte to circulation
What are essential, non-essential and conditionnally essential amino acids?
Essential → AA you can’t synthesize, you need to ingest in diet
Non-essential → AA you can synthesize (ex: Alanine, Asparagine, Aspartate, Glutamate, Serine)
Conditionnally essential → requires essential AA as a strating material to synthesize them (ex: Cysteine requires methionine and Tyrosine requires Phenylalanine)
What are the different cellular uses of the amino acid pool?
- Energy production
- Synthesis of gluocse or fatty acids
- Synthesis of nonprotein molecules that contain nitrogen
*in cells, only have the L enantiomer (side-chain on the left, COO- down and NH2 up)
What are the different principles of the amino acid pool?
- Homogenous → no matter the source (diet or endogenous/ vegetable or animal), alanine is alanine for ex
- Dynamic (constant breakdown and synthesis)
- Constant size → Body protein (~10kg of dry mass) + free AA pool (~0.1kg) in a 70 kg adult)
- All AA must be aailable in the pool at the same time for protein synthesis
*The body can’t store N-containing molecules as it does for carbohydrates and lipids → animals must replenish nitrogen supplies through the diet to replace nitrogen lost through catabolism
What is the effect positive and negative AA balance?
Equilibrium: Intake = Outflow
Positive balance: Intake > Outflow → growth, pregnancy, weight lifting, etc.
Negative balance: Intake < Outflow → Illness, surgery trauma, cancer cachexia
Where is the carbon skeleton of AA recycled?
- To glucose
- TCA intermediates
*Must be deaminated: AA → carbon backbone + NH3 (toxic)
What is considered to be a high [amminium]? What is the effect of high [NH3]?
normal blood [ammonium] < 50mM
high concentration → Disturbance of consciousness, coma, convulsion, death
Found in the blood as ammonium (NH4+): NH3 + H+ + OH- ←→ NH4+ + OH-
*Still must be detoxified → Urea cycle (in the liver) → Urea is excreted in urine which is then degrade by bacteria and they regenerate N2
Which are the 2 most abundant AA?
- Alanine
- Glutamine → key AA for protein synthesis, N-compounds, non-toxic storage vehicle for NH4+ (Glutamate + NH3 → Glutamine)
What is the importance/role of Glutamine synthtase and Glutaminase?
They regulate the pool of glutamine (both in the peripheral tissues and in the liver)
*Glutamine is the circulating form in the blood as it carries a NH3
Glutamine → {glutaminase releases NH3} → Glutamate → {glutamate dehydrogenase release NH3} → aKG
Where in the body are the following enzymes found?
- Transaminases
- Glutamine synthtases
- Glutaminase
- Glutamine dehydrogenase
Transaminase and Glutamine synthetase → peripheral tissues (including muscles for example)
Glutaminase and Glutamine dehydrogenase → release NH3 → in the liver only (→ urea cycle)
Which is the 1st enzyme responsible for detoxifying NH3 during exercise?
Exercise → AA breakdown for energy production (fill CAC) → release of NH3
In the peripheral tissues, GLUTAMINE SYNTHETASE puts the free NH3 onto Glutamate → to make Glutamine which will act as a carrier for the NH3 through circulation to the liver → urea cycle
What reaction is catalysed by Glutamine synthetase
Glutamate (OH-C(R)=O) → y-Glutamyl phosphate (consumes 1 ATP) → Glutamine (H2N-C(R)=O)
*NH3 comes from AA breakdown
*Phosphate acts as a high-energy intermediate to help generating the C-N bond
*In peripheral tissues
What reaction is catalysed by Glutaminase?
*In the liver only
Glutamine → {uses H2O, releases NH4+} → Glutamate
*Opposit reaction as Glutamin Synthetase
*NH4+ goes to the urea cycle
What is the difference between a synthase and a synthetase?
Synthetase → uses ATP
Synthase → does not use ATP
What is a deamination reaction?
Give 2 examples of enzymes.
It removes the nitrogen group from a molecule and releases it as NH4+
Enzyme IN THE LIVER:
- Glutaminase
- Glutamate dehydrogenase
*NH4 is released to the urea cycle so has to be in the liver
What drives the Glutaminase reaction forward?
Consumption of NH4 by the urea cycle → net concentration gradient between products and substrates
*Almost only in the liver (minor in the kidney)
What are key features of the Glutamate dehydrogenase deamination?
Glutamate → a-ketoglutarate + NH4+
- In the mitochondrial matrix of the kidney, liver and nevous tissues
- Uses NAD+ or NADP+ as an electron acceptor/co-enzyme
∆G˚’ = 30kJ/mol → endergonic
*Consumption of NH4 by the urea cycle + consumption of aKG by the CAC drives the reaction forward in vivo (would not occur in a petri dish)
What regulates glutamate dehydrogenase?
Regulated by the energy state:
- Low ADP (and NAD(P)) = allosteric activator
- High GTP (and NAD(P)H) = allosteric inhibitor
What is the reverse reaction to Glutamate dehydrogenase?
*Same enzyme
Glutamate synthesis:
a-Ketoglutarate + NH4+ + NAD(P)H → Glutamate + H2O + NAD(P)+
What is different in the nitrogen metabolism of cancer cells?
Glutamate, Glutamine and NH3 in circulation sent for disposal are taken up as a source of energy by cancer cells
What are transamination pairs?
Give examples.
Amino acid (-NH3) and its keto acid (=O)
Glutamate - a-Ketoglutarate
Aspartate - Oxaloacetate
Alanine - Pyruvate
*Both can be ana/cataplerotic transamination reactions
What if the required co-factor for transamination reactions?
Pyridoxal phosphate
What are important features of Pyridoxal-5’-Phosphate (PLP)
- Derived from Vitamin B6 (found in food)
- Involved in many different reactions → transaminations, decraboxylations, racemizations, eliminations, aldolizations
C 4’ aldehyde group → will bind covalently to a-amino groupe of enzyme residue/substrate
Phosphate group → called the “handle” → for binding to the PLP coenzyme
3-OH group improves catalytic efficiency
Pyrimidine ring → electron sink involved in resonance for stabilization of carbanion intermediates
Explain the “ping-pong” mechanism of transamination catalysed by transaminases.
Resting state → PLP for an internal schiff base with the enzyme
- a-AA #1 forms an external Schiff base with PLP, the enzyme is detached
- Hydrolysis and release of a-keto acid #1 → transient transfer of NH2 to PLP/PMP
- a-keto acid #2 forms a schif base using PMP (with the NH2 left from AA #1)
- Regeneration of PLP-enzyme and release of a-AA #2
*Most transaminases prefer a-Ketoglutarate as Keto acid #2
What is the definition of a ping-pong mechanism?
It is an enzymatic reaction in which no ternary complex is formed (double-displacement)
Substrate → Intermediate + released Product → Intermediate + 2nd substrate → Final product
What are 3 common PLP-dependent transamination reactions?
Pyruvate → Alanine
Oxaloacetate → Aspartate
a-Ketoglutarate → Glutamate
What is Type II Tyrosinemia?
It is an inherited recessive defect in Tyrosine catabolism
→ Caused by a deficiency in Tyrosine Aminotransferase in the liver (transamination) due to a non-sense mutation
Leads to:
- Photophobia/ Cornea keratitis
- Sensitive skin / blistering lesions on palms and soles
- Mental retardation / microencephaly
- Behavioral problems
*Transamination = Tyrosine → 4-hydroxyphenylpyruvate
What is the Cahill cycle?
Glucose-Alanine Cycle → betwee liver and muscles
It recycles alanine in the muscles to regenerate glucose in the liver
Muscles: (Glucose →) Pyruvate → Alanine
Liver: Alanine → Pyruvate (→ Glucose)
*2 transmination reactions
Which 2 transminases are involved in the Cahill Cycle?
ALT-2:
- Skeletal muscle
- Uses pyruvate as keto-acid (adds NH3 to it to form alanine)
ALT-1:
- Liver
- Uses a-Ketoglutarate as keto-acid (release NH3 from alanine) → releases pyruvate → glucose (gluconeogenesis)
What prosthetic groups serve as co-factors for transaminases?
PLP? PMP? PPP? Vit B6? Vit B12?
PLP and PMP
Which of the following prefer(s) a-KG as a substrate?
- Glutaminase
- Glutamate dehydrogenase
- ALT2
- Aspartate transaminase
- Tyrosine aminotransferase
- Proline transaminase
- Glutaminase → YES
- Glutamate dehydrogenase → YES
- ALT2 → it generates a-KG, ALT-1 does
- Aspartate transaminase → YES
- Tyrosine aminotransferase → YES
- Proline transaminase → doesn’t exist
Which amino acids to not have specific transaminases ?
Lysine
Proline
Threonine
What are the different Transamination reactions? (Transaminases)
Aspartate transaminase
Alanine transaminase
Tyrosine aminotransferase
Branched-chain AA aminotransferase
Who was the urea cycle discrovered by?
Krebs and Hanseleit in 1932
*First metabolic pathway defined
What is the source of NH4 of the Urea cycle?
*Not transamination
Glutamine is transported to the mitochondria
1. Release from Glutamine (Glutaminase)
2. Deamination of Glutamate (Glutamate Dehydrogenase)
→ released in the mitochondria
*Urea cycle is compartmentalized
What is the 1st reaction of the urea cycle?
NH4+ + HCO3- + 2 ATP → Carbamoyl phosphate
- Catalysed by CPS1 (Carbamoyl phosphate synthetase 1)
- Inside the mitochondrial matrix
- CO2 (HCO3-) comes form the CAC
- Rate-limiting step
What are the similarities/differences between the PDC and CPS1?
In both cases, the substrate enters the cycle → tightly regulated
Differences
- CPS1 requires ATP
- PDC runs when we need to generate ATP (inhibited by high ATP)
What chemical reactions does CPS1 catalyse? (Chemical relevance of the intermediates)
Carbamoyl Phosphate Synthetase 1
1. HCO3- + ATP → activates the Carbon (carboxyphosphate high-energy intermediate)
2. Addition of NH3, release of Pi → Carbamate
3. Consume an ATP for high-energy Carbamoyl phosphate
How is CPS1 regulated?
*Carbamoyl Phosphate Synthetase 1
Allosteric activation by NAG (N-acetylglutamate = Acetyl-CoA + Glutamate)
Arginine stimulates NAGS (NAG synthase) to produce NAG
- NAG production is proportional to [AA] → to keep the pool of AA constant size
- Lots of Arginine and Glutamate are an indication of large AA pool → stimulate NAG production
*Abundance of AA activates CPS1
What are the difference between CPS-1 and CPS-2?
*Carbamoyl Phosphate Synthetase
CPS-1:
- UREA synthesis
- Mitchondrial protein
- Absolutely needs NAG
- Uses NH4+
CPS-2:
- Pyrimidine synthesis
- Cytoplasmic protein
- No need for NAG
- Uses Glutamine as NH3 donor
*Compartmentalization ensures that both en product (Pyrimidine and Urea) are made and are regulated independently
Which enzyme mutations can lead to hyperammonia in humans?
CPS-1 deficiency (missense mutation) → Hyperammonemia, liver failure and death at very young age
NAGS deficiency (nonsense mutation) → very similar to CPS-1 deficiency
GDH (Glutamate Dehydrogenase) gain-of-function mutation → in the GTP allosteric binding site → can’t be shut down → hyperammonia/hyperinsulinisum
(Generate more NH4 than the body can process)
What reaction is catalysed by Ornithine Transcarbamoylase (OTC)?
Carbomoyl phosphate + Ornithine → Citrulline
- Transfers carbamoyl group onto Ornithine
- Ornithine in imported into the mitochondria by membrane transporter
*After this step, Citrulline is transported back to the cytoplasm for the rest of the urea cycle
What is the effect of a mutation in OTC and in the Ornithine/Citrulline transporter?
HyperAmmonemia
*OTC = Ornithine Transcarbamoylase
What is ORC1?
the transporter responsible for antiport of Ornithine and Citrulline in/out of the mitochondria?
What is the role of Arginosuccinate Synthtase (ASS)?
It catalyses the 2nd step (a/b) of the urea cycle (in the cytoplasm) → Addition of the 2nd amino group in the Urea
*ENERGY DEMANDING
A) Formation of Citrulyl-AMP
Citrulline + ATP → Ccitrullyl-AMP (high-energy)
- Release PPi which is hydrolysed (drives the reaction)
B) Nucleophilic attack by a-amino group of Aspartate; release of AMP
Citrullyl-AMP + Aspartate → Argininosuccinate + AMP
*Urea has 2 Amino groups total
What happens in step 4 & 5 of the urea cycle?
(Starting with Arininosuccinate)
Step 4: Arginosuccinase
Argininosuccinate → Arginine (release Fumarate)
Step 5: Arginase hydrolyses Arginine
Arginine + H2O → Urea + Ornithine (goes back in cycle)
Where does urea go when released from the urea cycle?
What is the structure of Urea?
Urea → Kidney through the blood since it is non-toxic → Urine
*Structure of Urea:
H2N-C(=O)-NH2
Where does the aspartate come from in the urea cycle?
*Source of the 2nd nitrogen
Comes from Glutamate (→ a-KG) in the mitochondria through action of the aspartate aminotransferase (Oxaloacetate → Aspartate)
Then Aspartate is transported to the cytoplasm through the malate/aspartate shuttle (the same that allows transport of NADH into the mitochondria for CAC)
*2nd Nitrogen comes from aspartate in the cytosol, but ultimitealy comes from glutamate in the mitochondria
*Glutamate can either release NH4 or give its N to oxaloacetate
What is the energy balance of the Urea cycle?
Synthesis of 1 Urea molecules requires hydrolysis of 4 high-energy phosphate groups:
2 NH4+ + HCO3- + 3 ATP + H2O → Urea + 2 ADP + 4 Pi + AMP + 2H+
Energy gain:
GDH generates a-KG = 10 ATPs
Fumarate → Malate → Oxaloacetate = 1 NADH
-4 ATPs + 12.5 ATPs = + 8.5 ATPs
True or False? All the CO2 generated during metabolism is excreted from the body by exhalation.
False
Some of it goes to Urine by Urea cycle
How does the body avoid NH3 toxicity?
- Glutamine synthetase incorporates NH3 to glutamine
- Muscle pyruvate is converted to alanine
- Carboyl-Phosphate Synthetase assimilate NH4
- 2x NH3 moieties are incorporated in urea, which is excreted by the kidney
How is urea production regulated?
- High [arginine] stimulates urea production
- CPS-1 is activated by substrate availability → further activated by NAG
What are the metabolic fates of the product of urea cycle?
A) Deamination of aspartate generates a-ketoglutarate which serves in the Citric Acid Cycle
B) Arginosuccinate generates Succinate which serves in the Citric Acid Cycle
C) Urea is exported to the kidney
D) The recycling of fumarate to the CAC permits production of NADH
C) Urea is exported to the kidney
D) The recycling of fumarate to the CAC permits production of NADH
What is the main general pathway of AA breakdown
Amino Acid → NH3 + Carbon Skeleton
NH3 → Urea Cycle
Carbon Skeleton → CO2 + H2O + Glucose + Acetyl-CoA + Ketone Bodies → CAC or PDC
*Carbon Skeletons of AA vary greatly → 7 amphibolic intermediates
What are the 3 catabolic outcomes for AA backbones ?
Glucogenic:
- 100% anaplerotic
- Pyruvate or CAC → Gluconeogenesis → Glucose exported to other tissues
Ketogenic
Leucine, Lysine → Ketone bodies → Exported to blood to serve as energy source in heart & brain → produce NADH
- No net production of glucose from Leu and Lys
Glucogenic/Ketogenic:
Threonine, Isoleucine, Phenylalanine, Tryptophan, Tyrosine → Both types of intermediates
How are branched-chain amino acid broken down?
What are the branched-chain AA?
Valine, Isoleucine, Leucine
*Not degraded in the liver
- Branched-chain aminotransferase
- in muscle, adipose, kidney and brain tissue
- AA → its corresponding a-keto acid
- Aminotransferase reaction - Branched-chain a-keto acid dehydrogenase
a-Keto acid → Acyl-CoA derivatives
- Consumes CoA-SH and releases CO2
What happens when there is a deficiency in branched-chain a-keto acid dehydrogenase?
Maple syrup urine disease
What is the branched chain ketoacid dehydrogenase complex like?
How is it regulated?
Very similar to PDC → E1, E2, E3 (E2, E3 are identical)
*But for branched AA breakdown
Regulated by BCKDH-complex phosphorylation
Active form = E1 non-phosphorylated
Inactive form = E1 phosphorylated
*a-ketoisocaproate (leucine’s ketoacid) inhibits BCKDH kinase (so activates the reaction)
What are the non-essential AA?
How are they synthesized?
Pyruvate → {aminotransferase} → Alanine
Oxaloacetate → {aminotransferase} → Aspartate → {asparagine synthetase, Glutamine → Glutamate} → Asparagine
a-Ketoglutarate → {aminotransferase} → Glutamate → {Glutamine synthetase} → Glutamine
What is methionine used for in the cell?
Methyl donor (-S-CH3)
- Protein synthesis start codon
- Synthesis of Cysteine
- One-carbon metabolism (PE → PC)
- Methylation of histones in chromatin
What are the different intermediates of the methionine cycle?
Which vitamin is involved?
Methionine → S-Adenosylhomocysteine → Homocysteine → Methionine → …
- Methionine + ATP → S-Adenosyl-methionine → Sulfonium (easily attacked by nucleophiles to give methyl, ex: 1-carbon pathway)
- Homocysteine → Cystein synthesis
Homocysteine → {Methionine Synthase, B12} → Methionine
What reactions are involved in homocysteine metabolism?
*Cysteine metabolism
Serine → {PLP} → Cystathionine → {PLP} → Cysteine
*Transsulfation
*Homocysteine + Serine + {PLP} → a-Ketobutyrate + Cysteine + {PLP}
a-Ketobutyrate → Propinoyl-CoA → Methylmalonyl-CoA → {coenzyme B12} → Succinyl-CoA → CAC
What is Hyper-Homocysteinemia?
*Too much Homocysteine in the blood / imbalance between the rate of production and breakdown of Homocysteine
Caused by:
- B12, Folic acid deficiencies
- Mutations in the Cystathionine beta-Synthase enzme converting Homocysteine to Cystathionine
What different type of diseases is Hyper-Homocysteinemia associated with?
- Cardiovascular disease
- Homocysteine interferes with formation of CT → blood vessel defects (lesion → plaque clots) - Cognitive impairment / Dementia
- General reduction in the ability to reason, judge, concentrate, associated with some types of depressions - Developemtnal tube defects
a) Neural tube defects (ex: Spina Bifida)
- failure of the neural tube to form or close properly → severe paralysis
b) Anencephaly (failure of the brain to develop) → invariably fatal in infants
What type of amino acid is Cysteine?
(Essential, Non-essential, Conditional)
Conditional-essential
*Transulfuration using PLP
What are the different co-factors requires in methionine metabolism?
Vit B6 required as PLP is derived from it
Vit B8 / Biotin → binds to CO2 and acts as carbon donor
Vit B9 / Folic Acid → required for MTHFR reaction
Vit 12 → …
FINISH L30 S36
What are the effects of a Vitamin B12 deficiency?
Leads to elevated homocysteine levels and health problems (deficiency is rare as very low levels of V12 are needed)
Symptoms of mild Vit B12 deficiency → anemia, nausea, constipation, gas
Symptoms of severe Vitamin B12 deficiency → Numbness, Insomnia, Memory loss, Dizziness, lack of balance, depression Digestive problems, Liver enlargmenet, Eye problems, Hallucinations, Neurological damage, etc.
*B12 is also produced by bacteria
What is the MTHFR reaction?
MTHF reductase catalyzes:
5,10-Methylene-THF → {NADPH → NADP+} → 5-Methyl-THF
*MTHFR is the rate-limiting step for providing 5-Methyl-THF → homocysteine processing → methionine
Wich of the following is/are tue about methionine metabolism?
1) The tetrahydrofolate (THF) molecule contains glutamate units.
2) An impaired funciton of methyl-tetrahydrofolate reductase (MTHFR) enzyme can cause hyper-homocysteinemia
3) Low folate-containing diets activate folate synthesis in humans
4) N10-formyl-THF differs from N5,N10-methylene THF in that the 1st is a methyl donor in the thymidylate synthase reaction.
5) S-adenosylmethionine (SAM) and THF pathways are both part of the “one-carbon” metabolism
1) The tetrahydrofolate (THF) molecule contains glutamate units.
2) An impaired funciton of methyl-tetrahydrofolate reductase (MTHFR) enzyme can cause hyper-homocysteinemia
5) S-adenosylmethionine (SAM) and THF pathways are both part of the “one-carbon” metabolism
Which of the following is/are true about patients whose tumors have a reduced/lost expression of the urea cycle enzyme argininosuccinase synthase (ASS1)?
1) ASS1-deficient tumour cells are unable to synthesize arginine de novo
2) patients with ASS1-deficient tumors are likely to suffer from hyperammonemia
3) Patients with an ASS1-deficient tumor lack fumarate, which is necessary to run the TCA-cycle
4) Those tumor cells rely on the TCA cycle to synthesize aspartate
5) Those tumor cells gain the advantage of preserving cellular aspartate
*Cancer cells have upregulation of these enzymes, but don’t run the urea cycle (only in the liver)
1 → Correct
2 → Excess ammonia from cancer cells is brought to the liver for urea cycle
3 → Other pathways to synthesize fumarate
4 → Nope
5 → Correct
Why can’t the backbone of ketogenic AA be used to make glucose during gluconeogenesis?
A) They do not contribute any net gain of carbons to the CAC.
B) Because the backbone is used to make fumarate, feeding the CAC
C) Because no oxaloacetate is available during starvation
D) They are immediately oxidized as CO2 in the first turn of the CAC
A) They do not contribute any net gain of carbons to the CAC.
C) Because no oxaloacetate is available during starvation
