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50 Cards in this Set
- Front
- Back
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How is Ser made?
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3 Phosphosglycerate
Add NAD+ Get 3-Phophohydroxy-pyruvate transaminated to 3-phosphoserine H20 boots the Pi Ser |
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What does Ser transhydroxymethylase do?
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transfers the methylene group to THF to form Gly
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How does Ser get turned into Cys?
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requires Met to substitute a sulfur for side chain oxygen
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What is tetrahydrofolate?
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carrier of activated one-carbon units.
Has 3 units: --pteridine ring --p-aminobenzoate --(Glu)n Carbon is bound to N-5 or N-10 or both |
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What are the groups carried by tetrahydrofolate?
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methyl -CH3(most reduced)
methylene -CH2- (intermediate) formyl -CHO formimino -CHNH Methenyl -CH= |
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What is the reaction of Gly synthase?
What's sort of the general idea from the reactant and products? |
CO2 + NH4+ + N5,N10-methyleneTHF + NADH --> Gly + THF + NAD+
See how THF derivatives serve as one carbon donors in a variety of biosyntheses. |
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What's the major source of 1-carbon units?
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3-PG --> Ser --> Gly + N5,N10-methyleneTHF
So thus 1 carbon units can be derived from carbohydrates |
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What is SAM?
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S-adenosylmethionine
a methyl donor THF can carry a methyl but doesn't have a high transfer potential. Enter SAM. Met + adenosyl group from ATP |
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What makes SAM activated?
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positive charge on adjacent S when adensoyl group is added
Wants to get rid of that methyl group |
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What does SAM get broken down to when it transfers its methyl group?
What can that product then be converted back to? |
S-adenosylhomocysteine and then gets hydrolyzed to adenosine and homocysteine
homocysteine usees Met synthase to transfer a methyl group from N5-methylTHF to regenerate Met |
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What is the activated methyl cycle?
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methyl groups enter when homocysteine is converted to Met and then the addition of the AMP activates the S to make SAM
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What is nitrogen fixation?
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reduction of N2 to NH3 by nitrogenase complex.
Nitrogenase complex has 2 proteins. A reductase and a nitrogenase Reductase provides e's via ATP hydrolysis Nitrogenase uses e's to reduce N2 to NH3 2 ATP per e |
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Why are glutamate and glutamine valuable in amino acid biosynthesis?
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They add the NH4+ into the equation
Glu adds a-amino group Gln adds side chain N |
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What is the reaction that Glu dehydrogenase catalyzes?
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NH4+ + a-ketoglutarate (a-KG) + NADPH + H+ --> Glu + NADP+ + H2O
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What is the reductant in biosynthesis of Glu?
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NADPH
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What does a-KG and NH4+ form?
why is this significant? |
Schiff base that is easily protonated.
The schiff base is protonated in such a way that only the L-Glu is formed (NADPH plays a role) |
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What reaction does Gln synthetase catalyze?
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addition of second ammonium ion to Glu to make Gln.
synthetase so its a hydrolysis of ATP rxn Glu + ATP--> Glu side chain acyl-Pi (high energy/excludes water) + NH3+ -->Gln + Pi |
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Name the essential amino acids?
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His
Ile Leu Lys Met Phe Thr Trp Val Usually the more steps / complex a.a.'s are the ones we've lost the ability to make |
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What are 3 a-ketoacids that can be converted to amino acids in one step through addition of amino group?
What cofactor do they require? |
a-KG, OAA, pyruvate
PLP which determines that they only form L configuration NH4+ + a-KG-->Glu (reduction with NADPH) OAA+Glu--> Asp + a-KG pyruvate + Glu --> Ala + a-KG |
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What residue provides the N for the PMP transamination reaction for the synthesis of Asp Ala and Glu?
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Lysine residue of transaminase.
Glu comes in and makes it PMP |
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HWhat is the key thing to remember about the conversion of Asp to Asn?
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Asp activated by adenylation, not phosphorylation.
It's the same reaction essentially as Glu to Gln, but instead of getting phos'd, Asp gets adenylated from ATP. |
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what's the difference between mammals and prokaryotes about where the N comes from for making Asn?
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In bacteria comes from ammonia
in mammals N comes from Gln (no exposure to toxic NH4+ in cell) |
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How is Pro made from Glu?
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Glu + ATP-->high energy acyl Pi intermediate-->glutamic y-semialdehyde-->cyclization to ^1-pyrroline-5-carboxylate
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How is Arg made from Glu?
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Glu + ATP-->high energy acyl-Pi intermediate-->glutamic y-semialdehyde + Glu -->ornithine + a-KG and from the ornithine you get Arg
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What is the precursor to Ser?
What is the intermediate? |
3-phosphoglycerate
3-phosphohydroxypyruvate |
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Explain how Ser is made?
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3-Phosphoglycerate gets oxidized to 3-Phosphohydroxypyruvate. This a-Kacid is transaminated with Glu to produce 3-phosphoserine which gets hydrolyzed to Ser
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What is Ser a precursor to?
What is the enzymes that catalyze the rxns? |
Cys
Met sulfur substition for side chain oxygen Gly Ser transhydroxymethylase takes the side chain methylene group and transfers it to THF |
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What are the 3 oxidation states of THF?
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most reduced
Methyl N-5 intermediate methylene -CH2- most oxidized formyl -CHO, formimino -CHNH, methenyl -CH= CO2=biotin |
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What is the role of THF?
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versatile carrier of activated one carbon units
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What are the 2 ways Gly can be synthesized?
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Ser hydroxymethylaseferase or Gly synthase (CO2 + N5-N10 THF)
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What is the major source of one carbon units?
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carbohydrates
3PG-->Ser-->Gly + N5, N10-methylene THF |
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What is usually the activated methyl donor?
How is it made? Why is it a better methyl transferer? |
S-adenosylmethionine (SAM)
Met + ATP --> SAM + Pi + PPI Has an activated S+ adjacent to methyl group |
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What does Met synthase do?
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regenerates Met from getting a methyl from N5 THF to add to the homocysteine.
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What is homocysteine a precursor to?
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Met (add N5 THF and Met synthase)
Cys (condense with Ser and cystathionine B-synthase & cystathioniase) |
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When making Cys from homocysteine where does the S and where does the carbon skeleton come from?
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S is from homocysteine
Carbon skeleton is from Ser |
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What are the key elements that we need to know for E coli's biosynthesis of Phe, Tyr and Trp?
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PEP, Erythrose 4-Phosphate
stuff stuff stuff Chorismate-->Phe, Tyr, Trp |
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Describe the prephenate branch for the formation of Phe.
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chorismate
mutase prephenate (dehydration / decarboxylation) phenylpyruvate + Glu = Phe |
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Describe the prephenate branch for formation of Tyr.
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chorismate
mutase prephenate (oxidative decarboxylation) p-hydroxyphenylpyruvate + Glu = Tyr |
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Describe the anthranilate branch to form Trp
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Chorismate
Gln amidation loss of pyruvate= anthranilate 5-phosphoribisoyl-1-PPi (PRPP) stuff stuff stuff indole Ser = Trp |
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Describe Trp synthase
What about this enzyme enables it to work with that tricky hydrophobic indole? |
2 subunits
a-subunit gets indole from indole-3-glycerol Pi B-subunit has PLP and aids in the condensation rxn between Ser and indole. Substrate channeling keeps the indole from diffusing out. The a-subunit waits to make the indole until the aminoacrylate Schiff base is formed in the B subunit |
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Describe regulation of 3 phosphoglycerate dehydrogenase.
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feedback of product inhibits the 1st irreversible step
3-phosphoglycerate dehydrogenase oxidizes 3-PG to 3-phosphohydroxypyruvate which eventually ends up as Ser This enzyme has 4 monomers and each monomer has Ser binding domain in addition to catalytic site reduced Vmax of enzyme when 4 Ser are bound for complete inhibition |
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describe how branched pathways require more sophisticated regulation
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Val, Ile and Leu all start from the same committed step.
But to make Val or Leu you need hydroxyethyl-Tpp + pyruvate And to make Ile you need hydroxyethyl-TPP + aKB. So the levels of pyruvate and aKB are going to determine which branch makes more and |
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What is reversible covalent modification?
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attachment of AMP to hydroxyl group of Tyr residue in subunit of Gln synthetase
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How is Gln Synthetase regulated?
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Cumulative feedback
Trp, His, carbamoyl-Pi, CTP, AMP all inhibit reversible covalent modificaiton adenylated = less active and more susceptible to cumulative feedback inhibition |
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what is adenylyl transferase?
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the enzyme that either adenylates Gln synthetase or deadenylates it.
has 2 forms Pa=adenylates Pd=deadenylates |
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What is uridylyl transferase?
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covalently converts Pa to Pd in adenylyl transferase
ATP and a-KG stimulate UT Gln inhibits UT |
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Why do high levels of a-KG and ATP signal the uridylation of Pa form of Adenylyl Transferase?
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high levels of ATP and a-KG signal we have high energy charge and we have the carbon skeletons so let's make some stuff. Tells Gln synthetase to go.
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What is the amino acid precursor to NO?
What's the catalytic enzyme? |
Arg
nitric oxide synthase |
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What are the cofactors that you need to make NO from Arg?
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NADPH and O2
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How do you make porphyrins in mammals?
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Succinyl CoA + Gly
d-aminolevulinate synthase |
