Before we leave the amino acids I want to look at some related processes, the first of which, Nitrogen fixation, is restricted to prokaryotes.
Nitrogen is one of the four most common elements in all living organisms. The problem is that although nitrogen is very common in its elemental form, the N2 molecule is very stable - the triple bond has an energy of 945 kJ/mol (vs. around 350 kJ/mol for single bonds) and is kinetically stable as well, and is thus unavailable to most organisms. Conversion of elemental nitrogen to usable forms, e.g. NH3 or NO3- (nitrogen fixation) occurs to a limited extent via lightning discharges (about 10% of naturally fixed N2) and via a complex process carried out by some bacteria and cyanobacteria.
All biological nitrogen fixing systems have 5 basic requirements:
Nitrogen fixation is a biologically expensive process, costing 16 ATP's and 8 electrons per N2, as seen in the reaction stoichiometry:
(Note the obligatory production of H2 by nitrogenase, which increases at low [ATP].)
The electron flow in this process is diagramed as follows:
Glutamate dehydrogenase. Once ammonia has been formed the nitrogen can be incorporated via one of two major pathways. The first is familiar - Glutamate dehydrogenase found in mitochondria (or bacteria). Note that the equilibria will allow the reaction to go either direction, depending on substrate concentrations. (You may also note the enzyme will accept either NADH or NADPH, the only enzyme known to be non-specific!)
In animals ammonia is quite toxic, so its concentration is kept quite low, and glutamate DH is not a major source of nitrogen incorporation.
Glutamine Synthetase. Glutamine is a major storage form of nitrogen and a source of nitrogen in various synthetic pathways. It has the advantage over glutamate dehydrogenase of a much lower Km - that is it can incorporate ammonia into biomolecules at much lower concentrations. Glutamine is made from glutamate and ammonia with energy supplied by ATP:
Glutamine's central position in nitrogen metabolism makes control of its biosynthesis essential.
FYI –Glutamine Synthase Regulation
All cell proteins are turned over, with half-lives commonly ranging from minutes to hours. Generally the proteins used for basic cell operations ("housekeeping proteins, e.g. glycolytic enzymes) have relatively long half-lives, while those involved in adaptation (e.g. gluconeogenesis, ketone body synthesis) have short half-lives. Two well known systems are used by eukaryotic cells to degrade proteins:
The lysosomal system is generally non-selective in well nourished cells, but becomes more selective with starvation. Thus proteins with the KFERQ sequence (lys-phe-glu-arg-gln) are preferentially degraded, shortening their half-lives.
The second system is specific to eukaryotes and is based on the degredation of proteins which have had the protein ubiquitin covalently attached to them. Ubiquitin itself is a highly conserved protein (i.e. identical in humans and fruit flys), possibly because it is recognized by a number of other proteins. Ubiquitin is attached to a "condemned" protein in a three stage process:
The ubiquinated protein is then broken down by the proteosome, a large 28 subunit, 6182 aa, 700 kD, barrel -shapped, protein. The proteosome breaks proteins down to octapeptides, which are released to the cytosol for further degredation. The ubiquitin is recycled, not degraded.
Triglycerides are synthesized from DHAP (cytosol) or glycerol-3-P (mitosol) and fatty acyl CoA (activated fatty acid) via the pathway outlined in your text. Note that either starting reactant leads first to the monacylglycerol phosphate, Lysophosphatidate:
A second fatty acyl CoA is then added to give Phosphatidic acid, which is then hydrolyzed to the diacylglycerol and a third fatty acyl CoA to give the final product. Note that 2-monoacylglycerol from the intestinal track may also be used to make triglycerides by adding two fatty acyl CoA's.
These phospholipids generally tend to have a saturated fatty acyl group on the C1 position while they mostly have an unsaturated fatty acyl group on the C2 position. The biosynthesis of phosphatidylethanolamine and phosphatidylcholine (lecithin) are outlined in your text. For phosphatidylcholine:
Choline + ATP Phosphocholine + ADP
Phosphocholine + CTP CDP-choline + PPi
CDP-choline + Diacylglycerol Phosphatidylcholine + CMP
Phosphtidylserine is made by exchanging serine (using the side chain -OH group) for ethanolamine on a phosphatidylethanolamine.
The Glyoxylate Cycle
As we've seen fats are only used in biosynthesis for lipids in animals. Plants, on the other hand can use fats for biosynthesis of carbohydrates, amino acids, etc. Of course plants don't generally store lots of energy as fat, except in their mobile forms, such as seeds. Seeds then use this fat, which is a dense form of energy storage, to manufacture the carbohydrate and protein needed to sprout. So how do seeds use fat for biosynthesis?
Plants add two new enzyme activities to the set seen in the TCA Cycle to create a new pathway, the Glyoxylate Cycle or Pathway. The stoichiometry of this pathway is:
The pathway can be represented by a simple cycle with two acetyl-CoA's added with succinate as the product, the Glyoxylate Cycle.
In actuality, the pathway is broken up into two parts by being compartmentalised in the mitochodria and a specialized organelle, the Glyoxysome. The two new reactions occur in this organelle:
The acetyl-CoA required for this synthesis is generated in the glyoxysome from fatty acids via a modified -oxidation pathway using NAD+ and molecular oxygen (instead of FAD) as oxidants.
Begin with a review of the Stages of Catabolism. Recall the major branch point at pyruvate and the decision point when making acetyl-CoA which is now committed to energy production or lipid biosynthesis. Note also the entry of glucose by facilitated diffusion, which is then committed to the cell by phosphorylation by Hexokinase - the net effect is an active transport, since G-6-P cannot escape the cell.
Biosynthesis of fatty acids from glucose requires the integration of a number of pathways. Glucose can ultimately provide carbons, energy equivalents, and reducing equivalents:
As an exercise in the integration of metabolic systems we can look at how the body responds to "carbohydrate stress," the situation occurring when blood glucose levels fall below the normal homeostatic level of about 5 mM. This commonly occurs during a fasting state.
Before following the development of a fasting state and its metabolic consequences, let's set some baselines by noting the potential available fuel in humans as represented by a 'typical' male, as shown in Table 1, below:
Next let's look at the normal and fasting fuel usage of various tissues in Table 2:
For humans the brain uses about 20% of resting energy, regardless of whether its user is "vegging out" or studying like crazy. In the fed state the brain uses about 4 g/hr of glucose while the anaerobic tissues (e.g. red blood cells) use about 1.5 g/hr. This is a particular problem because the brain is quite restricted in what fuels it can use, while the anaerobic tissues are restricted to glucose alone.
© R. A. Paselk 2010;
Last modified 6 May 2013