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Can you write an oxidation number for nitrogen in different oxidation states?
Which nitrogen containing molecules do we eat that provides nitrogen for our body?
What is the oxidation state this nitrogen?

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Which nitrogen containing molecules do we eat that provides nitrogen for our body?
Which molecules do we excrete that contains nitrogen?
Can you state the sign of the nitrogen balance which is appropriate for good human nutrition
for normal adults (versus growing children)?

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Given that we eat founds with about 100 g of protein in our diet (typical of a 2000 Cal/day
diet) and 16% of this is nitrogen, how much nitrogen (in g) do we take in a day?
Nitrogen excretion is mainly through the kidney and appears in the urine. Often clinical
chemists determine total urine nitrogen (TUN) excretion in urine to measure nitrogen balance.
They add 3 g to TUN as a fudge factor to account for other losses. What other ways are there
to excrete nitrogen?
How much nitrogen do we excrete if our nitrogen balance is zero?
How does this compare to patients in ER with severe stress?
Which serum proteins are used to monitor nitrogen balance?
Why not use another serum marker like TG, cholesterol or glucose levels?

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Where does protein digestion start?
Which type of proteins are used in this process?
Are amino acids, small peptides, oligopeptides or proteins absorbed into serum?
Which type of amino acids are filtered out of serum and which are enriched?
Note: Certain tissues like muscle will have a strong preference of making ATP by catabolic
oxidation of the carbons derived from aliphatic branched amino acids!

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Can you list the essential amino acids for adults?
Can you list the extra amino acids that are essential for infants and young children?
If you eat a diet which is complete in every amino acid, do you anticipate that anabolic
pathways will be activated for the biosynthesis of nonessential amino acids?
If you eat a diet which is complete in every amino acid except one or two nonessential amino
acids, do you anticipate that anabolic pathways will be activated for the biosynthesis of the
dietary limited nonessential amino acids?
If you eat a diet which is complete in every amino acid except for one essential amino acid
(say lysine), do you anticipate that protein synthesis will occur?
Will you be in positive or negative nitrogen balance with the diet lacking an essential amino
acid(s)?
id( )?

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Can you write the reaction of glutamate dehydrogenase?
Which tissue is this enzyme present?
Can you list cosubstrates needed for this reaction?
Is this a near-equilibrium reaction or not?
Can you explain using the mechanism how nitrogen (ammonia) is fixed to form glutamate?
Which metabolic conditions favor the formation of glutamate over the formation of its alpha-
keto acid?

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Can you write the reaction of glutamine synthetase?
Which tissue is this enzyme present?
Can you list cosubstrates needed for this reaction?
Is this a near-equilibrium reaction or not?
If not what makes this reaction nonspontaneous? (Hint: Hydrolysis of R-C(O)-NH2 is ΔG ≈ -
15 kJ/mol and hydrolysis of ATP to ADP is – 30 kJ/mol)
Can you explain using the mechanism how nitrogen (ammonia) is fixed to form glutamate?
Which metabolic conditions favors the formation of glutamate over the formation of its alpha-
ketoacid?

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Can you write the reaction of an amino transferase?
Which tissue is this enzyme present?
Can you list cosubstrates needed for this reaction?
Which vitamin cofactors are needed?
Is this a near-equilibrium reaction or not?
Can you explain using the mechanism how nitrogen (ammonia) is fixed to form glutamate?

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Which two enzymes are used to assimilate ammonia into amino acids?
Which two enzymes are used to assimilate ammonia into glutamine?
Under which metabolic conditions will question 1 or 2 be active?
What is the name of the fourth enzyme listed on this slide?
Which role does it have in nitrogen metabolism of the liver?

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Can you name the alpha-ketoacids for formation of alanine, aspartate, glutamate, serine,
phenylalanine and tyrosine?

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Can you name the six families from which amino acids derive their carbon atoms?

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Can you name four amino acids synthesized from alpha-ketoglutarate?
Which of these amino acids is essential?
Which molecule is used as the nitrogen source for glutamate?
Which molecule is used as the nitrogen source for proline?
Which molecule is used as the nitrogen source(s) for glutamine?
Which molecule is used as the nitrogen source(s) for arginine?
Which enyzmes are needed for these nitrogen transfer? (Ignore arginine until next chapter)
Why would arginine be an essential amino acid in developing infants and young children?

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Can you name five amino acids synthesized from oxaloacetate?
Which of these amino acids is essential?
Which molecule is used as the nitrogen source for aspartate?
Which molecule is used as the nitrogen source(s) for asparagine?
Which molecule is used as the nitrogen source(s) for methionine?
Which molecule is used as the nitrogen source(s) for threonine?
Which molecule is used as the nitrogen source(s) for lysine?
Which enyzmes are needed for these nitrogen transfer?
Which molecule is used to transfer S to methionine?
Which molecule is used to donate the methyl group to methionine?

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Can you name three amino acids synthesized from glycerol-3-Pi?
Which of these amino acids is essential?
Which molecule is used as the nitrogen source for serine?
Which molecule is used as the nitrogen source for cysteine?
Which molecule is used as the nitrogen source(s) for glycine?
Which enyzmes are needed for these nitrogen transfer?
Which molecule transfer S to cysteine?
Which molecule is formed in the conversion of Serine to Glycine?
Which cosubstrate is needed in this reaction?

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Can you name four amino acids synthesized from pyruvate?
Which of these amino acids is essential?
Which molecule is used as the nitrogen source for alanine?
Which molecule is used as the nitrogen source for valine?
Which molecule is used as the nitrogen source(s) for leucine?
Which molecule is used as the nitrogen source(s) for isoleucine?
Which enyzmes are needed for these nitrogen transfer?
Which cofactor is needed for the synthesis of branched chain amino acids?

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Can you name the amino acid synthesized from ribose-5-Pi?
Is this amino acid essential for adults?
Is it essential for children?
Which molecule is used as the nitrogen source for histidine’s alpha amino group?
Which molecule is used as the nitrogen sources for histidine’s imidazole ring?
Since ribose has 5 carbons and histidine has 6 carbons, where does the extra carbon come
from in the metabolism?
Which species is produced in the branch point of the biosynthesis of histidine?
Which metabolism is the intermediate used for.
Could this information help explain why histidine is an essential amino acid for growing
youth?

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Can you name three amino acids synthesized from PEP and erythrose-4-Pi?
Which of these amino acids is essential?
Which molecule is used as the nitrogen source for phenylalanine?
Which molecule is used as the nitrogen source for tyrosine?
Which molecule is used as the nitrogen source(s) for tryptophan’s alpha amino group?
Which molecule is used as the nitrogen source(s) for tryptohphan’s indole nitrogen?
Which enyzmes are needed for these nitrogen transfer?
Why is phenylalanine an essential amino acid but tyrosine is not?
Which intermediate in this pathway is used to synthesize aromatic molecules?

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Can you name the cofactor derived from folate?
Which type of reaction is used to convert folate to THF?
Which cosubstrate is needed for this reaction?

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Can you name four forms of THF?
Can you name in which metabolism these activated cosubstrates are used as reactants in C1
transfer reactions?
Can you rank the forms of THF in terms of the oxidation of the C1 unit?
How is methylene-THF
methylene THF formed? OR Which metabolism forms methylene-THF?
methylene THF?

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Can you write the reaction which synthesizes SAM?
How much chemical energy or reducing power is needed for SAM synthesis?
Can you write a reaction of SAM with a methyl acceptor?
How much chemical energy or reducing power is needed for methyl transfer?

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Can you follow (i.e., name the intermediates) the hydroxylmethylene group from serine to
methyl-THF (in the THF cycle)?
Can you follow the methyl group on methyl-THF to the methylated products in the SAM
cycle?
Which molecule is needed to accept the methyl group for methyl
methyl-THF
THF an form methionine?
Homocysteine and homoserine are homologs of cysteine and serine. Homologs are
structurally similar molecules that differ by one carbon (often a methylene) that is not a
functional group. Knowing the one structure will help you define its homolog structure. Can
you do this for homocysteine (or homoserine)?

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Can you name purines and pyrimidines?
Can you number their rings?
Can you write their names using substituents on each ring system (e.g., Which nucleotide is
2-amino-6-oxo-purine?)

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Can you name all NMPs listed and name their rings?

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Can you write the reaction that generates PRPP?
Can you name the enyzme type responsible for mediating this reaction?
How much chemical energy is needed in this reaction?

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Can you name the source of the nitrogen/carbon atoms for each atom in the purine?

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Can you list the 10 reactions that add carbons or nitrogens to the purine ring to form IMP from
PRPP?
Do you know which reactions requires ATP?

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Can you write the reaction for the conversion of Ribose-5-Pi to IMP?
How many formyl-THF are used?
How many and which type of nitrogen sources are used?
How much chemical energy is needed to form this nucleotide?

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Can you name the source of the 6-amino group of AMP?
Can you describe the chemical changes that occur in the formation of GMP from IMP?

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Can you name the source of the nitrogen/carbon atoms for each atom in the pyrimidine?

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Can you list the 6 reactions that add carbons or nitrogens to the pyrimidine ring to form UMP?
Do you know which reactions requires ATP?
Do you know which reactions NAD+ or NADH?
How is UMP converted to UTP?
How is UTP converted to CTP?

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Can you write the reaction for the conversion of bicarbonate and other carbon sources to
UMP?
What are the carbon sources for this pyrimidine nucleotide?
How many and which type of nitrogen sources are used?
How much chemical energy is needed to form this nucleotide?

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Can you write the chemical reaction for reduction of the ribose ring to its 2’-deoxyribose form
in deoxynucleotide biosynthesis?
Which enzyme is used to mediate this synthesis?
Is the enzyme nucleic base specific (ATP preferred over GTP)?
Is the enzyme specific for the phosphorylation level of nucleotides (AMP preferred over
ATP)?

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Can you write the net reaction for the conversion of dUMP to dTMP?
Can you name the enyzme which mediates this transformation?
Which reaction describes the regeneration of dihydrofolate to THF?
Which enzyme is used in this metabolism?

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Can you list four different nitrogen sources in biosynthesis?
Can you list at least one example of each nitrogen transfer?

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