Lecture 8: Integration with Glycolysis & TCA cycle

what are carbon skeletons used for in muscle cells?

enter glycolysis or TCA to make ATP

what are carbon skeletons used for in liver cells?

synthesize fat or gluconeogenesis (synthesis)

the pathway that carbon skeletons take is dependent on _______ levels

nutrient

amino acids that are classified as ______, directly contribute to the production of glucose

glucogenic

amino acids that are classified as ______, directly contribute to the production of ketone bodies

ketogenic

which amino acids are ONLY ever used to make ketone bodies (only ketogenic)

leucine and lysine

what amino acids are degraded into acetyl-CoA

leu, lys, ile, thr

what amino acids are degraded into acetoacetate?

leu, lys, phe, trp, tyr

which amino acids are degraded into pyruvate?

ala, cys, gly, ser, thr, trp

which amino acids are degraded into oxaloacetate?

asp, asn

which amino acids are degraded into fumarate?

asp, phe, tyr

which amino acids are degraded into succinyl-CoA?

ile, met, val, thr

which amino acids are degraded into alpha-ketoglutarate?

glu, arg, gln, his, pro

amino acids that are used to make acetyl-CoA are NOT _______, because the carbons are released as _____ and not directly used to make _____

glucogenic; CO2, glucose

Arg and Met are essential amino acids because we ___________

cannot synthesize them in sufficient amounts

nonessential amino acids are ones that we can _________

synthesize ourselves

______ and _______ can provide building blocks for synthesis of ___ out of the 10 ______ amino acids

glycolysis; TCA; 9; non-essential

asparagine is made from _______ using the enzyme ______

oxaloacetate; asparagine synthase

what glycolysis intermediate is used to make serine?

3-phosphoglycerate

the first step of serine synthesis is _____ the ______ group into a _____ group

oxidizing; hydroxy; ketone

what is the oxidized form of 3-phosphoglycerate

3-phosphohydroxy-pyruvate

once 3-phosphohydroxy-pyruvate is made; _________ transfers an ______ group from ________ to 3-phosphohydroxy-pyruvate, making ________

PLP; amino; glutamate; 3-phosphoserine

what is the final step in serine synthesis?

release of phosphate from 3-phosphoserine to make serine

serine can be converted to cysteine by switching the ______ group for a ______

hydroxy; thiol

serine can be converted to glycine via an ________ reaction and ________ cofactor

a elimination; PLP

an alpha elimination breaks the bond between the _____ carbon and _______ carbon

alpha; beta

what cofactors are used in synthesis of serine?

NAD+, PLP

PLP can catalyze a reaction at the ____, _____, or ____ carbon

alpha, beta, gamma

reactions at the alpha carbon using PLP include _______, ______, and ______

transamination; decarboxylation; a-elimination

reactions at the beta or gamma carbons using PLP include:

elimination or replacement

why is PLP so versatile?

makes covalent adduct with substrate, stabilizing carbanions

what does stereo electric control mean?

enzyme determines which bond is broken by orientation of substrate

which bond will be cleaved depends on which _____ bond is oriented to be aligned with the ______ bonds

sigma; pi

formation of a _______ covalently links the amino acids to the cofactor

schiff’s base

to make an Cα-hydrogen cleavage, the ______ needs to be aligned with the pi orbitals

hydrogen

to make a Cα-CO2 cleavage, the _______ needs to be aligned with the pi orbitals

CO2 group

to make a Cα-Cβ cleavage, the ______ needs to be aligned with the pi orbitals

C-C bond

which cofactors are used in one carbon metabolism?

biotin, THF, SAM, Cobalamin

Biotin is involved in ________ and _______ (pathways)

fatty acid synthesis; gluconeogenesis

biotin always carries/transfers ______

CO2

what does THF stand for?

tetrahydrofolate

which metabolic pathways is THF involved in? (3)

amino acid metabolism, Met synthesis, and NA synthesis

What does SAM stand for?

S-adenosyl methionine

where is the 1 carbon unit carried on SAM?

sulfonium ion

which one carbon cofactor is the MOST reactive?

SAM

where are is the 1 carbon unit carried on THF

N5 and N10

where is CO2 carried on biotin?

carboxyl group

the synthesis of Serine and Glycine is the primary link to _________

one carbon metabolism

which cofactors are required to synthesize glycine from serine?

PLP and THF

what enzyme converts serine to glycine?

serine hydroxy-methyltransferase (SHMT)

______ cofactor stays bound to the enzyme, but _____ dissociates

PLP; N5-N10-methylene-THF

the conversion of serine to glycine removes a ______, which is transferred onto ______

methylene; THF

what does THF become once a methylene is added?

N5-N10-methylene-THF

THF is derived from ______, and its conversion is catalyzed by the enzyme ________

folate; dihydrofolate reductase

how’s folate converted to THF?

2 reductions with NADPH

bacteria are able to synthesize their own _____, while humans must get from their diet; this lead to the use of ________ as an antibiotic (which inhibits synthesis)

folate; sulfanilamides

once a 1 carbon unit is added to THF to make N5-N10-Methylene-THF, it can carry 1-carbon units in many different oxidation states, including…(4)

N10-formyl-THF; methenyl-THF, N5-formimino-THF, and N5-methyl-THF

what is the more reduced version of N5,N10-methylene-THF?

N5-methyl-THF

oxidizing N5,N10-methylene-THF leads to _______ forms; while reducing leads to an ______ form

reversible; irreversible

what form of THF is NOT reversible

N5-methyl-THF

methylation is facilitated by the ________ cofactor

SAM

we generate SAM via the _____

methyl cycle

the goal of the methyl cycle is to _______ and ______

generate SAM; regenerate THF

the methyl cycle begins by adding a _______ group to ______ to make _______

methyl; homocysteine; methionine

what is the enzyme that adds a methyl to homocysteine?

methionine synthase

what cofactors are used the methylation of homocysteine?

N5-methyl-THF and coenzyme B12

where does the methyl come from in the formation of methionine?

N5-methyl-THF

how is SAM made from methionine?

addition of methionine to adenosyl group of ATP

what is the adenosyl group in ATP?

sugar and adenine groups (everything but phosphates)

when SAM transfers its methyl group to a target, how is it regenerated?

remove adenosyl group (adenosine) to reform homocysteine

what is the main way that the body is able regenerate THF from N5-methyl-THF?

methyl cycle

vitamin B12, aka:

cobalamin

what are the 4 main structural components of cobalamin

Cobalt, Corrin ring, ribose-P, benzimidazole

humans require cobalamin for only ___ reactions

2

The 2 reactions that require cobalamin are:

1. conversion of _____ to _______ (_____ cycle)

2. rearrangement of ______ to ______ (____ oxidation)

homocysteine; methionine; Methyl; methyl-malonyl-CoA; succinyl-CoA; fatty acid

which amino acids are degraded through propionyl-CoA?

Ile, Val, Met, Thr

what 2 pathways make propinoyl-CoA which can feed into TCA?

B-oxidation of odd chain fatty acids; degradation of certain amino acids

when propionyl-CoA is produced, a _____ is added by a ____ cofactor, which produces _____

CO2; biotin; methyl-malonyl-CoA

methylmalonyl-CoA undergoes a rearrangement by the enzyme _______, with help from the cofactor _______, which makes _______

methyl-malonyl-CoA mutase; Cobalamin; succinyl-CoA

succinyl-CoA produced from methylmanlonyl-CoA can be used in the _______

TCA cycle

what happens if you are deficient in methyl-malonyl-CoA mutase?

can’t convert to succinyl-CoA, builds up and breaks down to acidic form

what condition is a direct result of Methyl-Malonyl-CoA mutase deficiency?

methyl-malonyl acidemia

the methyl cycle is heavily linked to ________

one carbon metabolism

the N5-Methyl-THF generated in _______ is made back into THF via the _______

1-carbon metabolism; methyl cycle

a B12 deficiency means that ______ with accumulate and ___ will deplete

N5-methyl-THF; THF

What condition is caused by a B12 deficiency?

pernicious anemia

can we make SAM if the body is unable to make methionine?

yes, we can get methionine from the diet (levels will just be slightly lower)