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Biochemistry III > Final: AA Metabolism (Ben) > Flashcards

Final: AA Metabolism (Ben) Flashcards

1
Q

What is transamination?

Which AAs can be transaminated?

A
  • Reversible interconversion of amino acids and keto acids
  • Uses PLP bound to Lys (via Schiff base) of aminotransferase enyzme to exchange -oxo and -amino groups
  • All AAs except Lys, Thr, Pro and HydroxyPro
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2
Q

What are the rxns catalyzed by the enyzmes Alanine Aminotransferase and Aspartate Aminotransferase?

And what can their plasma elevation indicate?

A
  • Glutamate + Pyruvate α-Ketoglutarate + Alanine
    • ​indicates liver damage (enyzme AKA ALAT/GPT)
  • Glutamate + Oxaloacetate α-KG + Aspartate
    • ​indicates MCI (enzyme AKA ASAT/GOT)
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3
Q

What is oxidative deamination in terms of AA metabolism?

Which AA is deaminated most and by what enyzme?

What inhibits/activates this (in the forward direction)?

A
  • removal of nitrogen from an AA in the form of ammonia
  • most often Glu** is deaminated by **Glu Dehydrogenase
    • Glu + H2O + NAD+ α-KG + NH4+ + NADH + H+
  • ATP/GTP or NADH inhibit
  • ADP/GDP activate
    • b/c ADP means low E + thus need for Krebs intermediates
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4
Q

What are the first two steps of the urea cycle and where do they take place?

A
  1. Carbamoyl Phosphate Synthase I (RATE-LIMITING)
    • CO2 + NH3 —> Carbamoyl Phosphate
    • uses 2 ATP –> 2 ADP + 1 Pi
    • N-acetyl glutamate enhances ATP affinity
    • deficiency = hyperammonemia type I
  2. Ornithine Transcarbamoylase
    • Ornithine + Carbam. Phosph. —> L-citrulline + Pi
    • deficiency = hyperammonemia type II
  • both are in mitochondria of liver cells
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5
Q

After movement of L-citrulline into the cytosol…

what are the cytosolic reactions of the urea cycle?

A
  1. Arginosuccinate Synthase
    • Citrulline + Aspartate + ATP —> Arginosuccinate + AMP + PPi
    • (b/c 2 macroergic bonds broken, 2 “ATP equivalants” used)
  2. Arginosuccinate Lyase
    • ​​Arginosuccinate —> Fumarate + Arginine​
    • (fumarate goes to Krebs, makes more Asp via oxaloacetate + ASAT to refuel cycle)
  3. Arginase
    • ​​Arginine + H2O —> Urea + Ornithine
    • (urea transported to kidney, ornithine re-enters cycle at OTC step)
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6
Q

Urea Cycle Overview…

How much ATP is used?

What are the enyzmes?

Where do the products go?

A
  • 3 ATP used, 4 ATP “equivalents”
    • 2 by CPT-I and 1 by ASS (but 2 bonds broken, so 2 equivalents)
  • Urea Nitrogens:
    • 1st from ammonia and 2nd from Aspartate
  • Enzymes:
    • ​Carbamoyl Phosphate Synthase I –> Ornithine Transcarbamoylase –> Arginosuccinate Synthase –> Arginosuccinate Lyase –> Arginase
  • Products:
    • ​Urea goes to kidneys for excretion
    • Fumarate goes to TCA for Asp regeneration
    • Ornithine re-enters cycle
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7
Q

What are the 3 main routes for regulation of the urea cycle?

A
  1. Enzyme Induction - via high protein diet/starvation
  2. Allosteric Activation - of CPT-I via N-acetyl-Glu
  3. Intermediate Concentration - Arg from diet, Orn from synth
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8
Q

Other than transamination and oxidative deamination…

what 3 types of deamination can occur?

(via what enyzmes, etc.)

A
  1. Catabolic α-Amino Removal
    • via Serine/Threonine Dehydratases forming pyruvate/α-KG respectively and using PLP as a cofactor ( to remove H2O and add =O )
  2. Flavoprotein α-Amino Removal
    • ​​via L-amino oxidases** with an **FMN prosthetic group
  3. β/γ-Amino Removal
    • ​via glutaminase** or **asparaginase hydrolyzation of -R group amines
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9
Q

What are 3 routes for incorporation of free ammonia into larger molecules?

A
  1. Glutamate Dehydrogenase - alpha-KG + amm. = Glu
  2. CPT-I - incorporates NH3 into urea cycle
  3. Gln Synthetase
    • Glu + NH3 + ATP —> Gln + ADP + Pi
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10
Q

How can Asn be synthesized from other AAs?

A

Asparagine Synthetase

Gln + Asp + ATP —> Glu + Asn + AMP + PPi

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11
Q

How can glutamine also contribute to urinary nitrogen excretion?

A

Gln acts as a sort of transport form of NH3 in the blood (b/c of its two amine grps).

Once in the kidney, glutaminase** can remove the -R group amide (making Glu) and **transaminases can remove the alpha-amino group (making alpha-KG), both of which nitrogens can be excreted as ammonia.

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12
Q

Which AAs are ketogenic, glycogenic and both?

A
  • Both Glyco- and Ketogenic:
    • Ile, Thr, Phe, Tyr, Trp
    • I’ll Throw (a) Phew Tyres (and you’ll) Trip
  • Ketogenic only:
    • ​Leu, Lys
    • (AAs starting with L make products usually made from Lipids)
  • Glycogenic only:
    • ​Gly, Cys, Glu, Gln, Asp, Asn, Ser, Pro, Val, Met, His, Ala
    • (all others…)
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13
Q

What B-vitamin, along with single-carbon units donated by amino acids, contributes to the formation of various nucleotides?

What is the 1st step in the utilization of this vitamin?

A

Folic Acid / Folate (B9)

  • Dihydrofolate Reductase
    • ​uses 2 NADPH to reduce folate in two steps
    • 1st to H2F, then to H4F
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14
Q

After formation of H4F…

What two amino acids can contribute single-carbon units directly to H4F?

What results from this?

A
  1. Tryptophan
    • makes N10-Formyl-H4F which can go into purine synthesis (or lose H2O to become methenyl-H4F)
  2. Histidine
    • ​​makes N5-formimino-H4F which continues to form other precursors
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15
Q

After addition of a carbon via His…

what happens to N5-formimino-H4F next?

A
  • It can lose NH4 to become N5,N10-methenyl-H4F
  • Then Glycine or Serine can contribute to the molecule to form N5,N10-methylene-H4F w/ use od NADPH
  • methylene**-H4F can go on to **TMP synthesis (from dUMP)
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16
Q

What is the last step in the modification of folic acid to form biosynthetic intermediates?

A
  • N5,N10-Methylene-H4F is reduced via Methylene-H4F Reductase (MTHFR)to form N5-Methyl-H4F (using NADH)
  • Methyl-H4F can enter the SAM cycle
  • remember motherfucker for MTHFR enzyme!
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17
Q

Describe the SAM cycle and its 4 enyzmes.

A
  1. Homocysteine Methyltransferase (w/ methyl-B12)
    • HCys + Methyl-H4F –> Methionine + H4F
  2. Met Adenosyl Transferase
    • Met + ATP –> S-Adenosyl-Met + PPi + Pi
  3. SAM-dependent Methylases
    • SAMe –> S-Adenosyl-Hcy + -CH3
  4. S-A-Hcy Hydrolase
    • S-A-Hcy + H2O –> Adenosine + Hcy
18
Q

How can Cysteine be synthesized?

Where do the precursors come from + whats the prosthetic grp?

A

Cystathionine Synthase

plus PLP

  • Homocysteine + Serine —> Cystathionine + H20
  • Cystathionine + H2O –> Cysteine + α-ketobutyrate + NH4+
  • the HCys comes from the SAM cycle
19
Q

Which AAs can form succinyl-CoA?

What must they first become to enter the succinyl-CoA forming pathway?

(And how do they get there?)

A

Met, Thr, Val, Ile

(Met Three Valiant Islanders)

  • all first become α-ketoacids
  • Met –(SAM cycle)–> HCys –(Cysta. Synthase)–> α-ketobutyrate
  • Thr –(Thr Dehydratase)–> α-ketobutyrate
  • Val, Ile –> α-ketoacids
20
Q

Once Met/Thr/Val/Ile have been converted to α-ketoacids…

how are they converted to succinyl-CoA?

4 steps

A
  1. Branched-Chain α-Ketoacid DH** (TPP, lipoic acid, FAD, NAD+, CoA)**​​
    • α-ketoacid –> propionyl-CoA + CO2 + NADH + H+
  2. Propionyl-CoA Carboxylase (+ biotin)
    • propionyl-CoA + ATP –> D-methylmalonyl-CoA + ADP + Pi
  3. Methylmalonyl-CoA Racemase (switches D -> L)
  4. Methylmalonyl-CoA Mutase (+ 5-adenosyl cobalamine B12)
    • L-methylmalonyl-CoA –> succinyl-CoA
21
Q

If Ile and Val both can eventually form succinyl-CoA…

why is one only glycogenic while the other is both glyco- and ketogenic?

A
  • Isoleucine has more carbons in its R group and thus must give off an acetyl-CoA on the way to becoming succinyl-CoA
  • acetyl-CoA can go on to form ketone bodies
22
Q

What kind of products can Leu form (glyco-/keto-) ?

How?

A

Leu is Ketogenic

  • like other BCAAs it forms an α-ketoacid via BCAA Transaminase
  • then BC-αKA-DH turns it into isobutyryl-CoA which undergoes beta oxidation-like rxns to form HMG-CoA and then Acetyl-CoA and Acetoacetate
    • produces NADH and FADH2 (like B-oxidation)
23
Q

Which AAs form oxaloacetate?

How?

A

Asp and Asn

  • Asn + H2O –(asparaginase)–> Asp + NH4+
  • —(ASAT)—> Oxaloacetate
  • remember ASAT uses PLP
24
Q

Which AAs form pyruvate?

Two of them do so in one reaction… which?

A

Ala, Ser, Gly, Cys

Al + Sarah Glide (into the) Cysteine (chapel)

  • Alanine becomes pyruvate directly via ALAT
    • remember ALAT uses PLP
  • Serine Dehydratase
    • Serine —> Pyruvate + NH4+
    • also uses PLP, water is removed but then re-used
25
Q

maybe make a card on Serine catabolism/synthesis…

its a pain in the ass

A

yup

26
Q

How does Gly eventually form pyruvate?

A

Via conversion to serine

  • Serine Hydroxymethyltransferase (+ PLP)
    • Serine + H4F –> Glycine + N5,N10-Methylene-H4F
27
Q

Since Gly and Ser and interconvertible…

what can be used to catabolize either of them?

A

Glycine Cleavage Complex

  • uses NAD+ and H4F to break Gly down into HCO3- and NH4+
  • deficiency = nonketotic hyperglycinemia
    • mental retardation + death (b/c Gly = inhibitory NT)
28
Q

What is the biogenic amine of serine?

How is it made and what can be made from it?

A

Ethanolamine

  • decarboxylation of serine
  • contributes directly to phospholipids or is methylated via SAM to form choline
29
Q

How can Cys form pyruvate?

A
  • Transamination to mercaptopyruvate then loss of sulfate to form pyruvate
30
Q

What important functional group donor molecule can a byproduct of pyruvate formation from Cys contribute to?

A

Sulfate from mercaptopyruvate can for PAPS

  • 3-phosphoadenosine-5-phosphosulfate
  • donates sulfur to various molecules
31
Q

What is the biogenic amine of cysteine?

What is it used for?

A

Taurine

  • oxidization of cysteine forms cystine (sulfate in place of sulfhydryl) and then decarboxylation and oxidation forms taurine
  • contributes to bile acid conjugation + brain development
32
Q

Which AAs form alpha-ketoglutarate?

Generally, how?

A

Glu/Gln, Pro, Arg, His

(Gluttonous Professionals Are History)

  • all are first converted to glutamate which can be transaminated to alpha-KG
  • ( structure-wise … notice that it is Glu with a =O replacing the amine )
33
Q

How is proline converted to another AA which can be transaminated into a Krebs cycle intermediate?

A
  1. Proline Oxidase
    • proline + H2O –> pyrroline-carboxylate + ROS
  2. Spontaneous Conversion
    • pyrroline-carboxlate –> Glu-γ-semialdehyde
  3. NADP+ Dehydrogenation
    • ​​forms Glu
34
Q

How is histidine converted to another AA which can from a Krebs cycle intermediat?

A
  1. Histidase
    • ​​Histidine –> NH4+ + urocanic acid
    • Urocanic Acid –> Formimino-Glutamate
    • H4F + formimino-glutamate –> Glu + Formimino-H4F
35
Q

How do glutamine and arginine form glutamate as an intermediate in alpha-KG synthesis?

A
  • Arginine
    • becomes ornithine in the urea cycle which is transaminated to Glu-γ-semialdehyde and then NADP dehydrogenated to Glu
  • Glutamine
    • Glutaminase: Gln + H2O –> Glu + NH<span>3</span>
36
Q

How can glutamate form an important neurotransmitter?

And then how is that NT broken down?

A
  1. Glu decarboxylase (+ PLP)
    • removes CO2 to form GABA
  2. GABA transaminase
    • GABA + alpha-KG –> Glu + succinate semialdehyde
  3. SSA Dehydrogenase
    • SSA + NAD+ –> succinate + NADH + H+
37
Q

What two important molecules are formed from Arginine?

(one signaling molecule + one P donor)

How?

A
  1. Creatine
    • Arg + glycine –> intermediate –> SAM methylation –> creatine –> creatine kinase –> creatine-P
  2. NO
    • Arg + 2O2 + 3/2 NADPH –> NO + citrulline + 3/2 NADP+
38
Q

What is the biogenic amine of histidine?

How is it formed?

A
  • Histamine
    • Histidine Decarboxlase ( + PLP )
      • His –> histamine + CO2
  • important in vasodilation, allergy, HCl secretion etc.
39
Q

Of Phe and Tyr… one is essential…

which one and why is the other non-essential?

A

Phenylalanine is essential.

  • Tyrosine can be made from it via Phenyalanine Hydroxylase
  • Phe + H4F-Biopterine + O2 –> Tyr + H2F-Biopterine + H2O
  • deficiency = phenylketonuria
40
Q

What kind of products (glyco/keto) does Tyr break down into?

Which specific products?

Via what intermediate?

A

Both glycogenic and ketogenic products

Via several (hopefully) unimportant steps starting with a transamination and formation of homogentisate as an intermediate…

Fumarate** (glycogenic) and **Acetoacetate (ketogenic) are formed

41
Q

What kind of products (keto/glyco) does tryptophan degrade into?

4 things

A
  1. Alanine - glycogenic
  2. Formate - contributes to formyl-H4F (+ thus purines)
  3. NAD+ precursors
  4. Acetoacetyl-CoA - ketogenic

(not sure via what steps…)

42
Q
A

Biochemistry III (35 decks)

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