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50 Cards in this Set

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How is Ser made?
3 Phosphosglycerate
Add NAD+
Get 3-Phophohydroxy-pyruvate
transaminated to 3-phosphoserine
H20 boots the Pi
Ser
What does Ser transhydroxymethylase do?
transfers the methylene group to THF to form Gly
How does Ser get turned into Cys?
requires Met to substitute a sulfur for side chain oxygen
What is tetrahydrofolate?
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
What are the groups carried by tetrahydrofolate?
methyl -CH3(most reduced)

methylene -CH2- (intermediate)

formyl -CHO
formimino -CHNH
Methenyl -CH=
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.
What's the major source of 1-carbon units?
3-PG --> Ser --> Gly + N5,N10-methyleneTHF

So thus 1 carbon units can be derived from carbohydrates
What is SAM?
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
What makes SAM activated?
positive charge on adjacent S when adensoyl group is added

Wants to get rid of that methyl group
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
What is the activated methyl cycle?
methyl groups enter when homocysteine is converted to Met and then the addition of the AMP activates the S to make SAM
What is nitrogen fixation?
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
Why are glutamate and glutamine valuable in amino acid biosynthesis?
They add the NH4+ into the equation

Glu adds a-amino group

Gln adds side chain N
What is the reaction that Glu dehydrogenase catalyzes?
NH4+ + a-ketoglutarate (a-KG) + NADPH + H+ --> Glu + NADP+ + H2O
What is the reductant in biosynthesis of Glu?
NADPH
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)
What reaction does Gln synthetase catalyze?
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
Name the essential amino acids?
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
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
What residue provides the N for the PMP transamination reaction for the synthesis of Asp Ala and Glu?
Lysine residue of transaminase.

Glu comes in and makes it PMP
HWhat is the key thing to remember about the conversion of Asp to Asn?
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.
what's the difference between mammals and prokaryotes about where the N comes from for making Asn?
In bacteria comes from ammonia

in mammals N comes from Gln (no exposure to toxic NH4+ in cell)
How is Pro made from Glu?
Glu + ATP-->high energy acyl Pi intermediate-->glutamic y-semialdehyde-->cyclization to ^1-pyrroline-5-carboxylate
How is Arg made from Glu?
Glu + ATP-->high energy acyl-Pi intermediate-->glutamic y-semialdehyde + Glu -->ornithine + a-KG and from the ornithine you get Arg
What is the precursor to Ser?

What is the intermediate?
3-phosphoglycerate

3-phosphohydroxypyruvate
Explain how Ser is made?
3-Phosphoglycerate gets oxidized to 3-Phosphohydroxypyruvate. This a-Kacid is transaminated with Glu to produce 3-phosphoserine which gets hydrolyzed to Ser
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
What are the 3 oxidation states of THF?
most reduced
Methyl N-5

intermediate
methylene -CH2-

most oxidized
formyl -CHO, formimino -CHNH, methenyl -CH=

CO2=biotin
What is the role of THF?
versatile carrier of activated one carbon units
What are the 2 ways Gly can be synthesized?
Ser hydroxymethylaseferase or Gly synthase (CO2 + N5-N10 THF)
What is the major source of one carbon units?
carbohydrates

3PG-->Ser-->Gly + N5, N10-methylene THF
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
What does Met synthase do?
regenerates Met from getting a methyl from N5 THF to add to the homocysteine.
What is homocysteine a precursor to?
Met (add N5 THF and Met synthase)

Cys (condense with Ser and cystathionine B-synthase & cystathioniase)
When making Cys from homocysteine where does the S and where does the carbon skeleton come from?
S is from homocysteine

Carbon skeleton is from Ser
What are the key elements that we need to know for E coli's biosynthesis of Phe, Tyr and Trp?
PEP, Erythrose 4-Phosphate
stuff
stuff
stuff
Chorismate-->Phe, Tyr, Trp
Describe the prephenate branch for the formation of Phe.
chorismate
mutase
prephenate
(dehydration / decarboxylation)
phenylpyruvate
+ Glu
=
Phe
Describe the prephenate branch for formation of Tyr.
chorismate
mutase
prephenate
(oxidative decarboxylation)
p-hydroxyphenylpyruvate
+ Glu
=
Tyr
Describe the anthranilate branch to form Trp
Chorismate
Gln amidation
loss of pyruvate=
anthranilate
5-phosphoribisoyl-1-PPi (PRPP)
stuff
stuff
stuff
indole
Ser
=
Trp
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
Describe regulation of 3 phosphoglycerate dehydrogenase.
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
describe how branched pathways require more sophisticated regulation
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
What is reversible covalent modification?
attachment of AMP to hydroxyl group of Tyr residue in subunit of Gln synthetase
How is Gln Synthetase regulated?
Cumulative feedback
Trp, His, carbamoyl-Pi, CTP, AMP all inhibit

reversible covalent modificaiton
adenylated = less active and more susceptible to cumulative feedback inhibition
what is adenylyl transferase?
the enzyme that either adenylates Gln synthetase or deadenylates it.

has 2 forms
Pa=adenylates
Pd=deadenylates
What is uridylyl transferase?
covalently converts Pa to Pd in adenylyl transferase

ATP and a-KG stimulate UT

Gln inhibits UT
Why do high levels of a-KG and ATP signal the uridylation of Pa form of Adenylyl Transferase?
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.
What is the amino acid precursor to NO?

What's the catalytic enzyme?
Arg

nitric oxide synthase
What are the cofactors that you need to make NO from Arg?
NADPH and O2
How do you make porphyrins in mammals?
Succinyl CoA + Gly

d-aminolevulinate synthase