Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:


The One-Carbon Pool, cont.

One-Carbon Uses, cont.


Choline is synthesized by methylating ethanolamine on Phosphatidyl ethanolamine three times using S-Adenosylmethionine as the source of methyl groups:

Choline synthesis

The phosphatidyl choline can then be used as a membrane lipid, or choline can be hydrolyzed off to give the free molecule for acetyl choline synthesis. The phosphatidyl ethanolamine is derived from phosphatidyl serine (via a PLP catalyzed decarboxylation). Since serine can be synthesized from glucose, choline can be biosynthesized de novo.

FYI - For your curiosity and entertainment:

S-Adenosylmethionine is obviously an important source of carbon groups in biosynthesis. There are two main pathways for regenerating it from S-Adenosylhomocysteine. First it may be regenerated by homocysteine methyltransferase (coenzyme B12-dependent) using 5-methyl H4-folate as a methyl group source. In this case glucose may thus serve as the ultimate source of the methyl group:

homocysteine methyltransferase  reaction

Alternatively it can be regenerated using choline as the source of the methyl group:

Pathway for regenerating S-Adenosylmethionine using choline as methyl source

The N,N-dimethyl glycine can be oxidized further to give two formaldehydes and glycine.

S-Adenosyl homocysteine may also be irreversibly degraded. Adenosine is first hydrolyzed off. The thiol group of the resulting homocysteine then attacks the alpha–methyl carbon of serine displacing the hydroxyl group to give water and cystathionine (catalyzed by cystathionine synthase, requires PLP). Hydrolysis by beta–cystathionine gamma-lyase (PLP requiring)

Nucleotide Metabolism

Nucleoside = nitrogenous base + ribose

Nucleotide = nitrogenous base + ribose + phosphate

We have already seen how important the nucleotides etc. are to life as the monomer residues in nucleic acids (DNA & RNA), energy transfer cofactors, components of essential cofactors (e.g. NADH, CoA), and secondary messengers (e.g. cAMP) etc.

Today we want to look at their anabolism and catabolism.

Recall the basic structures:

Structural diagrams for the Purine and Pyrimidine rings

Purines are synthesized via IMP:

Structural diagram of IMP

Pyrimidines are synthesized via UMP:

Structural diagram of UMP

the other nucleotides are then obtained by modification of IMP and UMP.

The two initial nucleotides are biosynthesized by two quite different strategies:

Structural diagram showing the origins of the atoms in the Purine ring

Structural diagram showing the origins of the atoms in the Pyrimidine ring

The strategies also differ for subsequent modification. Thus for the purines the monophosphate is modified and then phosphorylated:

Flow diagram for the conversion of IMP to GTP & ATP

while for the pyrimidines the monophophate is first phosphorylated, and then modified:

Orotate + PRPP right arrow OMP right arrow CO2 + UMP right arrow UDP right arrow UTP

dTMP is derived from dUMP which in turn is modified from dUTP.

Purine Biosynthesis

Purines are synthesized in a multi-step process outlined in the Purine Biosynthesis Pathway in your packet.

Note the strategy: Start with PRPP (phosphoribosyl pyrophosphate synthesized from ribose-5-P, then add atoms one at a time to build ring system with the exception of a three atom group from glycine.

Recall the origins of the purine ring system:

Structural diagram showing the origins of the atoms in the Purine ring

Structural diagram of the reactions converting IMP to AMP

Structural diagram of the reactions converting IMP to GMP


Regulation of Purine Biosynthesis

Purine regulation demonstrates a couple of different strategies reflecting different growth and evolutionary strategies.


Flow diagram of PRPP to ATP and GTP with feedback control loops for mammals

E. coli

Regulation in E. coli is more complex, reflecting the primacy of this synthesis in growth and replication:

Flow diagram of PRPP to ATP and GTP with feedback control loops for E. coli

In addition GTP is required as a co-substrate for the synthesis of adenylosuccinate from IMP, while ATP is a required co-substrate for synthesizing GMP from XMP. This cross-over between the two pathways tends to keep the [ATP] = [GTP] as needed in nucleic acid synthesis for cell replication.

FYI — A couple of enzyme regulatory mechanisms are in play: AMP and GMP are competitive inhibitors in their own biosynthesis from IMP, while the first commited step of IMP biosynthesis from PRPP is regulated by two allosteric sites, one binding the adenylates and the other the guadenylates. These sites operate independently but synergistically to regulate IMP production.

Pyrimidine Biosynthesis

Unlike purine biosynthesis, where all of the enzymes are in the cytosol, in pyrimidine synthesis the enzyme localization is split, and the enzymes are mostly in complexes.

1. Carbamoyl phosphate synthetase II (which synthesizes carbamoyl P using glutamine instead of ammonia as a nitrogen source - carbamoyl phosphate synthetase I is the mitochondrial enzyme used in Urea biosynthesis from ammonia), Aspartate transcarbamoylase (ATCase) and Dihydrooratase are in a single cytosolic complex. The reactions are outlined below:

Structural diagram of the reactions for the synthesis of Dihydroorotate from glutamine and bicarbonate

2. Dihydroorotate dehydrogenase is localized in the mitochondria (on the outer surface of the inner membrane).

Structural diagram of the reaction catalysed by dihydroorotate DH

3. Orotate phosphorybosyl transferase and OMP decarboxylase are in a second cytosolic complex.

Structural diagram of the reactions of Orotate phosphorybosyl transferase and OMP decarboxylase

UMP is then phosphorylated twice using ATP (catalyzed by nucleoside mono- and diphophate kinases. respectively) to give UTP. CTP is then synthesized from UTP as below:

Structural diagram of the reaction onverting UTP to CTP


Regulation of Pyrimidine Biosynthesis

The regulation of pyrimidine biosynthesis in mammals is outlined below:

Flow diagram for pyrimidine biosynthesis with feedback control loops for mammals

Degradation of Nucleotides

In muscle tissue the Purine Nucleotide Cycle (or AMP cycle) is important to fill the TCA cycle in muscle, since muscle is lacking most anapleurotic enzymes for the TCA cycle. In effect it deaminates aspartate to fumerate which can then be used as a TCA intermediate, allowing higher TCA activity.

Structural diagram of the reactions of teh Purine Nucleotide Cycle

The Purines themselves are catabolized to a variety of products. depending on the organism. Thus most mammals degrade the purine to allantoin, a soluble product, which is excreted in the urine. On the other hand, primates excrete uric acid, a sparingly soluble molecule, as do birds and reptiles. The over all pathway of purine degradation is given in the handout.




Pathway iconPathway Diagrams

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© R. A. Paselk 2010;

Last modified 3 May 2013