Nitrogen Stuff Flashcards
What are the 3 ways the body can remove toxic NH4+?
1) NH4+ + NADPH+ alpha-ketoglutarate–>glutamate + NADP+ via glutamate dehydrogenase
2) glutamate–>glutamine via glutamine synthase
3) NH4+ + CO2 + 2 ATP–>carbamoyl phosphate via carbamoyl phosphate synthase
What’s the cofactor needed for transamination rxns?
pyridoxal phosphate, vitamin B6
Pyroxidal phosphate (B6) is a cofactor for which other rxns?
decarboxylations, dehydration of beta-hydroxyamino acids, racemizations of alpha-amino acids, removal of H2S from cysteine
What rxns do ALT and AST catalyze?
1) alanine + alpha-ketoglut–>pyruvate + glutamate
2) aspartate + alpha-ketoglut–>glutamate + OAA
What are the normal NAD ratios in the liver?
NADPH/NADP+ is high, NADH/NAD+ low—if the liver needs energy, NADH will be generated for e- transport chain, and if energy rich, NADPH generated for biosynthestic rxns
Dehydratase rxns (uses B6 as cofactor)
serine and threonine follow this pathway
1) serine–> -H2O –> -NH3 –> pyruvate
Desulfhydrases (uses B6 as cofactor)
homocysteine –> -H2S –> -NH3 –> alpha-ketobutyrate –> succinyl CoA
Regulation of urea cycle (keeping nitrogen balance)
1) in a protein free diet, less urea excreted in urine, fewer urea cycle enzymes
2) in a high protein diet, high gluconeogenesis from amino acids, levels of urea cycle enzymes greatly increase
3) urea used because you get rid of 2 ammonia groups and it’s H2O soluble, has low reactivity
What’s the problem with ketogenic amino acids, and which ones are they?
the carbons in ketones and acetyl-CoA can’t be changed into glucose, only into fatty acids (they become ketone bodies); they are lysine and leucine
What happens to the glucogenic amino acids? (body prefers this path)
degraded into pyruvate or TCA cycle intermediates, will form phosphoenolpyruvate, then glucose (gluconeogenesis from these bad boys)–they’re a great source of glucose once glycogen stores are gone!
What are the ketogenic/glucogenic amino acids?
isoleucine, phenylalanine, tyrosine, tryptophan, threonine; intermediates can be ketogenic and glucogenic
Catecholamine synthesis
1) tyrosine hydroxylase 1st step (rate-limiting), requires tetrahydrobiopterin as cofactor (forms DOPA from tyrosine)
2) aromatic amino acid decarboxylase needs B6 (forms dopamine)
3) dopamine beta-hydroxylase (requires ascorbic acid and oxygen (forms norepi)
4) SAM as methyl donor (forms epi)
What degrades catecholamines?
monoamine oxidase, MOA inhibitors are anti-depressants
What’s the deal with melanins?
they’re formed from tyrosine; if you’re an albino, you can’t convert tyrosine to melanins
What is tryptophan the precursor of?
serotonin, melatonin, NAD+; deficiency can cause niacin deficiency (pellagra)
How is GABA formed?
glutamate–>GABA (via glutamate decarboxylase)
How is histamine formed?
histamine–>histidine (via histidine decarboxylase, uses B6 as cofactor, decarboxylation rxn)
Which rxns does the body need 1-carbon groups for?
1) formation of methionine from homocysteine
2) biosynthesis of purines and pyrimidines
3) biosynthesis of glycine from CO2 and NH4+ by glycine synthase
What are some carriers of one-carbon groups?
1) biotin (vitamin B7), remember from glycolysis?
2) tetrahydrofolate (THF, tetrahydrofolate acid)
Explain folic acid (vitamin B9)
1) folate is an essential vitamin (we can’t make the p-amino benzoic acid), rapidly dividing cells use a lot of folate
2) folic acid–>dihydrofolic acid–>tetrahydrofolic acid (biologically active form) via dihydrofolic acid reductase
What do methotrexate and aminopterin inhibit? (anti-folate drug)
dihydrofolic acid reductase, prevents dihydrofolate from being converted into active THF; means dividing cells stop being able to divide since dTMP synthesis inhibited
Describe the formation of N5-methyl-tetrahydrofolate
1) THF–>N5, N10-methylene TH4–>N5-methyl-tetrahydrofolate
2) this rxn is non-reversible! (except in conversion of homocysteine to methionine)
Describe the interconversion of serine and glycine
1) serine + THF –> glycine + N5, N10-methylene THF
2) glycine + NAD+ –> CO2 + NH4+ +NADH + H+ (via glycine cleavage enzyme)
3) glycine + 5,10-methylene-THF –> serine + THF (via serine hydroxymethyl transferase), serine further coverted to pyruvate
What do sulfa drugs (sulfonamides) do? (anti-folates)
inhibit bacterial synthesis of p-amino benzoic acid, stops folate synthesis; can be bad in people too though, since it can block nucleotide synthesis
What is the major carrier of methyl groups?
SAM, S-adenosylmethionine, formed from methionine (via methionine adenosyl-transferase); SAM then accepts methyl group via methyltransferase to form S-Adenosyl homocysteine
Describe the synthesis of cysteine from homocysteine
1) homocysteine + serine –>cystathionine, via cystathionine synthase (requires B6 as cofactor)
2) cystathionine–>cysteine and alpha-ketobutyrate (via cystathionase)
Which rxns require cobalamin (vit B12)?
1) homocysteine + N5-methylene-THF–>methionine + THF (B12 cofactor needed for homocysteine methyltransferase)
2) methylmalonyl CoA–> succinyl CoA (B12 cofactor)
What happens in the folate trap?
1) folate converted to THF, then N5 form
2) however, because B12 deficient, N5 can’t be converted to THF to form methionine from homocysteine since homocysteine methyltransferase needs B12 as cofactor
3) folate stuck in irreversible N5-methylene-THF form–causes megaloblastic anemia
What does azaserine (glutamine analog, chemo drug) do?
blocks amide transfer from glutamine; basically, it stops all amination rxns, so glutamine can’t form glutamate (including rate-limiting 1st step of purine synthesis); stops CTP synthase, PRPP aminotransferase, GMP synthase, asparagine synthase, CPSII, FGAR aminotransferase
What is PRPP, and what does it do?
formed from R5P (pentose-phosphate shunt) and ATP (catalyzed by PRPP synthase), needed for synthesis of purines and pyrimidines, NAD/FAD (nucleotide coenzymes)
What is the nucleotide ring of IMP (purine precursor) made of?
glutamine, glycine, CO2, aspartate, and two 1-carbon fragments from 1-carbon folate pool (THF)
How do you make AMP and GMP from IMP?
1) IMP–>adenylosuccinate–>AMP (add aspartate, like rxn in urea cycle, then remove fumarate)
2) IMP–>XMP–>GMP (glutamine nitrogen group transfered to XMP to form GMP)
How does feedback inhibition work?
PRPP synthetase and PRPP amidotransferase 9first 2 steps in rxn) are feedback-inhibited by IMP, GMP, AMP
What does HGPRT (hypoxanthine-guanine phosphoribosyl transferase) do?
creates IMP and GMP from hypoxanthine or guanine (catalyzes formation of nucleotides); defects in this enzyme cause gout
How are pyrimidines made?
NH3+CO2–>carbamoyl phosphate–>pyrimidine ring (made of carbamoyl phosphate and aspartate); this ring then goes on to react with PRPP (this carbamoyl phosphate made in cytosol, not like urea cycle in liver where it’s made in mitochondria)
What happens to patients with an OTC (ornithine transcarbaoylase) deficiency?
carbamoyl phosphate can’t react with ornithine to contine urea cycle; since carbamoyl phosphate a precursor to pyrimidines, lots of pyrimidines build up with this deficiency
Describe further pyrimidine synthesis
1) carbamoyl phosphate + aspartate conjugation–>dihydroorotate
2) dihydroorotate–>orotate–>orotidne phosphate–>UMP
3) UMP–>UDP–>UTP–>CTP
Describe feedback inhibition with pyrimidine synthesis
not very well understood (multifunctional enzymes coordinate multiple steps); pyrimidine nucleotides inhibit aspartate transcarbamoylase and dihydroorotase
What does ribonucleotide reductase do? What inhibits it? Where is ribonucleotide reducatse located?
1) ADP–>dADP
2) GDP–>dGDP
3) CDP–>dCDP
4) UDP–>dUDP
5) inhibited by hydroxyurea (chemo drug)
6) it’s only in dividing cells–vast minority of cells in body
What does thymidylate synthase do? What inhibits it?
1) converts dUMP–>dTMP (precursor to dTTP), uses N5, N10-THF to transfer methylene and generate dihydrofolate
2) inhibited by 5-fluorouracil (chemo drug, blocks thymine synthesis)
Where does the methyl group in the dUMP–>dTMP rxn come from?
serine–>glycine conversion, also generates N5, N10-methylene-THF; serine comes from glycolysis intermediates, then carbon group transferred to this rxn
How does 5-fluorouracil work?
it’s a suicide inhibitor of thymidylate synthase; F-dUMP interacts with thymidylate synthase and N5, N10-methylene-THF; when 5-fluorouracil present, it traps thymidylate synthase in a complex with F-dUMP so no dTMP can be made
What do nucleoside phosphorylases do?
convert nucleosides to free bases and ribose-1-phosphate or deoxyribose-1-phosphate; they also catalyze the reverse rxns
How are purines degraded?
AMP/IMP–>hypoxanthine/guanine–>xanthine–>uric acid (via xanthine oxidase, requires molybdenum)
1) dephosphorylation
2) deamination
3) separation of base from ribose
4) oxidation to uric acid
How are pyrimidines degraded?
1) uracil–> beta-alanine–>malonyl CoA
2) thymine–>beta-aminoisobutyric acid–>methyl-malonyl CoA
3) undergo phosphorylation, separation of base and ribose, deamination, degredation of base
What does allopurinol do?
suicide inhibits xanthine oxidase, blocks production of uric acid (also used as a chemo precursor)
What’s the mechanism of ADA (adenosine deaminase) deficiency?
too much adenosine/deoxyadenosine since ADA can’t convert them to inosine; this feedback inhibits ribonucleotide reductase, which stops DNA synthesis, WBCs can’t proliferate (disease combined with SCID)
What’s the degradation of 3-C amino acids?
alanine/serine/threonine/cysteine/glycine–>pyruvate
What’s the degradation of 4-C amino acids?
aspartate/asparagine (converted to aspartate first)–>OAA
What’s the degradation of 5-C amino acids?
glutamine/histidine (needs THF in last step)/arginine/proline (arginine/proline steps reversible)–>glutamate–>alpha-keto acid
What’s the degradation of branched-chain amino acids?
valine/leucine/isoleucine–>alpha-keto acids
1) valine–>propionyl CoA–>methylmalonyl CoA–>succinyl CoA
2) leucine–>acetyl CoA/acetoacetate (ketogenic)
3) isoleucine–>acetyl CoA (ketogenic) or propionyl CoA–>methylmalonyl CoA–>succinyl CoA
What happens to methionine, isoleucine, valine?
methylmalonyl CoA–>succinyl CoA
What happens to phenylalanine/tyrosine?
needs phenylalanine hydroxylase (BH4 as cofactor), ultimately become fumarate
What happens to lysine?
acetyl CoA, ketogenic (like leucine and sometimes isoleucine)
What are the 3 common ways to add NH3 to molecules?
1) transamination
2) Asp–>fumarate
3) Glutamine–>glutamate
What’s another way to make serine?
the 3-phosphoglycerate mechanism; important because this is a direct 1-carbon contribution from glycolysis cycle
