Microbes and Metabolism - Environmental Biotechnology: Theory and Application - page 27

Proteins
The first catabolic step in protein degradation (see Figure 2.5) is enzymatic
hydrolysis of the peptide bond formed during protein synthesis resulting in the
release of short pieces, or peptides, and eventually after further degradation,
amino acids. The primary step in amino acid catabolism is to remove the amino
group thus producing an -keto acid. This is usually achieved by transfer of

the amino group to the TCA cycle intermediate,

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-ketoglutarate, resulting in the
amino acid, glutamate. Amino groups are highly conserved in all organisms due
to the small number of organisms able to fix atmospheric nitrogen and so the
source of an amino group is usually by transfer from another molecule. How-
ever, eventually, nitrogen is removed by oxidative deamination and is excreted
in a form which depends upon the organism. Ammonia is toxic to most cells,
but if an organism lives in an aqueous habitat, it may release ammonia directly
into its surroundings where it is diluted and so made harmless. However, even in
such an environment, if dilution should prove insufficient, ammonia concentration
will increase, likewise the pH, consequently, the well-being of the organism will
be compromised. Organisms which cannot make use of dilution, rid themselves
of ammonia by converting it first into a less toxic form such as urea in the case of
mammals and the fairly insoluble uric acid in the case of birds and most reptiles.
Bacteria may then convert the excreted ammonia, urea or uric acid into nitrite
and then oxidise it to nitrate which may then be taken up by plants. From there it
is included in anabolic processes such as amino acid synthesis to produce mate-
rial ingested by higher animals and the whole procedure of amino group transfer
repeats itself. This is the basis of the nitrogen cycle which forms a central part
of much of the sewage and effluent treatment described in Chapters 6 and 7.
The

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-keto acid resulting from deamination of the amino acid is degraded by
a series of reactions, the end product being dependent on the original amino
acid, but all will finally result as a glycolysis or TCA cycle intermediate. A
fascinating story of catabolism showing collaboration between mammals and
bacteria resident in the gut, is the degradation of haemoglobin, the component
of blood which carries oxygen and carbon dioxide. Haemoglobin comprises the
protein, globin, into which was inserted during synthesis, the haem ring system
where the exchange between binding of oxygen or carbon dioxide takes place in
circulating blood. The first step of haemoglobin degradation, performed in the
mammalian system, is removal of the haeme ring structure releasing globin which
is subject to normal protein degradation. Haeme has its origins in the amino acids
in that the starting point for the ring structure is the amino acid, glycine. The
degradation pathways start with removal of iron and release of carbon monoxide
to produce the linear structure, bilirubin. This is eventually excreted into the
gut where enteric (gut) bacteria degrade the bilirubin to urobilinogens which are
degraded further, some being excreted in the urine and others, such as stercobilin,
are excreted in the faeces. All these products are further metabolised by microbes,
for example in the sewage treatment plant.

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