Biomolecules are the products of organic chemistry in cells – the chemistry of carbon (C) compounds.  The core structure of a biomolecule is its C skeleton.

Other atoms required for life – hydrogen, oxygen, nitrogen, phosphorus, sulphur (H, O, N, P, S) – are attached to C skeletons to make the variety of biomolecules needed for cells and organisms to work.

Enzymes, the essential catalysts of living systems, are proteins.  Proteins also have important structural roles in cells and tissues.  Proteins are long chains of individual amino acid units.  And amino acids in turn are C skeletons with N attached.

The relationship between N and the C skeletons of amino acids and proteins is globally significant.  It’s where C and N cycles within and outside the biosphere interact with profound biological and environmental consequences.

N gets into plants primarily as inorganic nitrate which is converted to ammonium and attached to C skeletons provided by photosynthesis.  A series of transfers and interconversions generates the full set of twenty or so different kinds of amino acids needed to make all the proteins necessary for life.

The picture on the left represents the C skeletons of amino acids as squiggles and ring structures, decorated with N(itrogen) and O(xygen) - and, in the case of cysteine and methionine, S(ulphur) too.

How amino acids are put together in the right order to make all the different proteins required by the living cell is the familiar story of the DNA sequences of genes transcribed into RNA which in turn is translated into protein structure.

By contrast with their synthesis, we understand relatively little about how proteins are broken down, even though it’s an essential step in the N cycle.

Enzymes that cut up proteins into their amino acid structural units are called proteases, or proteinases, or peptidases and the protein-dicing activity is called proteolysis.  Biological detergents contain proteinases (usually of microbial origin, but sometimes plant enzymes such as papain are found too), which attack the protein component of fabric stains and improve accessibility to the surfactant.

A grazing animal ingests plant protein and breaks it down to amino acids which it absorbs and uses to build the proteins of its own tissues or milk.  Because of the issue of energy availability and the need to synchronise processes in the rumen, it’s best if as little proteolysis as possible happens there.

Ideally, carbohydrates and lipids in the diet should meet all the energy requirements of rumen microorganisms.  But forages may contain high levels of amino acids, often because, in response to grazing damage, plant proteinases are activated and attack the plant’s own proteins.

Read more about plant proteolysis here.

Faced with the choice between getting C from relatively inaccessible cell walls and membranes on the one hand, or the products of proteolysis on the other, rumen microbes will preferentially ferment the C skeletons of amino acids, releasing ammonia.

Ammonia is poorly utilized by the animal and emerges in the form of malodorous high-N slurries and emissions, with dangerous consequences for air, soil and water quality.

There’s a more sinister side to this as well.  N emitted in this way is N that could have been captured as meat or milk, and thus contributes to low economic efficiency.  In intensive production systems the remedy may be to supplement forage with extra protein; but if the additional protein is of animal origin…well, the BSE story is too well known to require further telling here.

The release of inorganic N when amino acids are respired was understood long ago by plant scientists such as A Chibnall and WO James (Chibnall 1939), and led ultimately to determination of the metabolic pathway that separates C skeletons and ammonia.

On a global scale, everywhere you look, the making and breaking of C-N associations seems to mean trouble.  It may be a bit of an exaggeration to reduce huge issues like BSE, agricultural emissions and intensification to the breaking of one “bad” chemical bond; but as someone once said, inside every big intractable problem is a small approachable problem trying to get out.

And it suggests ways in which plant genetics and breeding could contribute solutions.  For example, can we develop forage varieties that are less predisposed to break down their own proteins when harvested or eaten?

There certainly seems to be plenty of heritable variation for intrinsic proteolytic activity in forage grasses.  Research carried out by Mike Humphreys and Alison Kingston-Smith has identified the regions of genome responsible for this trait and demonstrated the possibility of transferring them into new genetic backgrounds.

More about animals and agriculture here.

AC Chibnall (1939) Protein metabolism in the plant.  OUP.

AH Kingston-Smith, MK Theodorou (2000) Post-ingestion metabolism of fresh forage. New Phytologist 148: 37-55.

AH Kingston-Smith, RJ Merry, DK Leemans, H Thomas, MK Theodorou (2005) Evidence in support of a role for plant-mediated proteolysis in the rumens of grazing animals. British Journal of Nutrition 93: 73-79.

H Thomas (1978) Enzymes of nitrogen mobilization in detached leaves of Lolium temulentum during senescence. Planta 142: 161–169

U Feller, A Fischer (1994). Nitrogen metabolism in senescing leaves. Critical Reviews in Plant Science 13: 241-273.