Protein metabolism involves the breakdown of proteins into amino acids and their use and degradation throughout the body. Amino acids from food sources are broken down through digestion and absorbed. They are used for protein synthesis, forming hormones and other compounds, and undergo constant breakdown and renewal to replenish amino acid reserves. Excess amino acids have their nitrogen removed through transamination or oxidative deamination, producing ammonia. The liver plays a key role in nitrogen excretion by converting toxic ammonia into less toxic urea via the urea cycle, which is then excreted in urine.

1. Protein Metabolism:
Protein metabolism is an essential part of metabolism. Since
amino-acid metabolism is closely connected with the
metabolism of other nitrogen compounds, protein metabolism
is often included in the more general concept of nitrogen
metabolism. In autotrophic organisms—that is, plants (except
fungi) and chemo-synthesizing bacteria—protein metabolism
begins with the assimilation of inorganic nitrogen and
synthesis of amino acids and amides. In man and animals,
only a portion of the amino acids—the so-called nonessential
ones—can be synthesized in the organism from simpler
organic compounds. The other portion—the essential amino
acids—must be obtained from food, usually as protein.
Proteins contained in various foods are broken down by
cleavage under the action of such proteolytic enzymes as
pepsin, trypsin, and chymotrypsin into amino acids, which are
absorbed into the blood and carried to organs and tissues.

2. Plant tissues also contain proteolytic enzymes that
hydrolytically break up proteins. The succeeding
processes of protein metabolism in plants and animals
are essentially amino-acid metabolism.
A considerable portion of amino acids are used in the
formation and completion of various proteins in the
body, including functionally active proteins (enzymes,
hormones, antibodies, and so forth), plastic proteins,
structural proteins, and others. At the same time, the
body’s proteins undergo constant breakdown and
renewal, replenishing the reserve of free amino acids.
The other portion of the amino acids is used in the
formation of a number of low-molecular hormones,
biologically active peptides, amines, pigments, and
other substances necessary for the maintenance of
life. For example, the amino acid glycine is used to
form purine bases, and aspartic acid is used to
synthesize pyrimidine bases.

3. The mutual transformation of amino acids is, in
significant measure, produced by a process that is
widespread in all organisms—the enzyme process,
involving the transfer of amino groups. This
process, called transamination, was discovered by
the Soviet scientists A. E. Braunshtein and M. G.
Kritsman. Excess amino acids undergo enzyme
processes of decomposition.
The most common initial reaction of amino-acid
decomposition is deamination, primarily oxidative
deamination, after which the nitrogen-free
remainder of the amino-acid molecule degrades to
the end products—carbon dioxide, water, and
nitrogen that splits off in the form of ammonia.
In man and animals:

4. The transformation and fate of food proteins
from their ingestion to the elimination of their
excretion products:
Proteins are of exceptional importance to
organisms because they are the chief
constituents, aside from water, of all the soft
tissue of the body. Special proteins have
unique roles as structural and functional
elements of cells and tissues. Examples are
keratin of skin, collagen of tendons, actin and
myosin of muscle, the blood proteins, enzymes
in all tissues, and protein hormones of the
hypophysis.

5. Protein is digested to amino acids in the
gastrointestinal tract. These are absorbed and
distributed among the different tissues, where
they form a series of amino acid pools that are
kept equilibrated with each other through the
medium of the circulating blood. The needs for
protein synthesis of the different organs are
supplied from these pools. Excess amino acids
in the tissue pools lose their nitrogen by a
combination of transamination and
deamination. The nitrogen is largely converted
to urea and excreted in the urine. The residual
carbon products are then further metabolized
by pathways common to the other major
foodstuffs—carbohydrates and fats.

6. Protein digestion occurs to a limited extent in
the stomach and is completed in the
duodenum of the small intestine. The main
proteolytic enzyme of the stomach is pepsin,
which is secreted in an inactive form,
pepsinogen. Its transformation to the active
pepsin, initiated by the acidity of the gastric
juice, involves liberation of a portion of the
pepsinogen molecule as a peptide. Pepsin
preferentially hydrolyzes peptide bonds
containing an aromatic amino acid, and it
requires an acid medium to function.

7. The acid chyme is discharged from the
stomach, containing partially degraded
proteins, into a slightly alkaline fluid in the
small intestine. This fluid is composed of
pancreatic juice and succus entericus, the
intestinal secretion. The pancreas secretes
three known proteinases, trypsin,
chymotrypsin, and carboxypeptidase. All three
are secreted as inactive zymogens. Activation
starts with the transformation of the inactive
trypsinogen into the active trypsin. Trypsin, in
turn, activates chymotrypsin and
carboxypeptidase.

8. Trypsin and chymotrypsin are endopeptidases;
that is, they cleave internal peptide bonds. The
so-called peptidases are exopeptidases; they
cleave terminal peptide bonds. Trypsin has a
predilection for those containing the basic
amino acid residues of lysine and arginine.
These two proteinases perform the major share
in hydrolyzing proteins to small peptides.
Digestion to amino acids is completed by the
exopeptidases. Carboxypeptidase acts on
peptides from the free carboxyl end;
aminopeptidases from the free amino end.
Other peptidases act on di- or tripeptides, or
peptides containing such special amino acids
as proline.

9. The amino acid digestion products of the
proteins are absorbed by the small
intestine as rapidly as they are liberated.
The absorbed amino acids are carried by
the portal blood system to the liver, from
which they are distributed to the rest of
the body. Small amounts of the peptides
formed during digestion escape further
hydrolysis and may also enter the
circulation from the intestine. This is
shown by a rise in the peptide nitrogen in
the blood.

10. Figure 25.17 The
Postabsorptive State
Figure 25.17

12. PROTEIN IS
• A major component of foods. It is digested
firstly in the stomach, and then in the
duodenum to dipeptides and amino acid.
• Absorbed using symport active transport
with sodium.
• Stored in liver and muscles.

13. Uses
• Protein synthesis : The synthesis of new
proteins is very important during growth. In
adults new protein synthesis is directed
towards replacement of proteins as they are
constantly turned over.
• Synthesis of a variety of other compounds :
Examples of compounds synthesized from
amino acids include purines and pyrimidines
(components of nucleotides), catecholamines (
adrenaline and noradrenalin) &
neurotransmitters (serotonin)

14. Amino acid catabolism
The other biological fuels discussed (
carbohydrates & fats) contain only the
elements carbon, hydrogen and oxygen.
Amino acids contain nitrogen as well. The
first step in amino acid catabolism is the
removal of the nitrogen (the amino group).

15. Nitrogen rreemmoovvaall ffrroomm aammiinnoo aacciiddss
Transamination
Oxidative
deamination
Urea cycle
Aminotransferase
PLP

16. Transamination
it is a process of transferring amino groups from one
molecule to another. There is no formation and no
exceretion of ammonia, thusly no net change in the
nitrogen amount of body. It is a process involved in amino
acids in which the amino group is transferred from the
amino acid to a certain α-ketoacid with the consequant
formation of a second α-ketoacid and amino acid. The
reaction is catalyzed by the enzyme aminotranferase (aka
transaminase) which requires pyridoxal phosphate as a
prosthetic group. All transaminases contain this prosthetic
group which derives from pyridoxine a water soluble
vitamin also known as vitamin B6. The amino group from
amino acids is temporarily uptaken by the pyridoxal
phosphate as pyridoxamine phosphate prior to its donation
to an α-ketoacid. All aminoacids except lysine, threonine,
proline and hydroxyproline participate in transamination
process.

17. Deamination
it is a process of removing amino groups from one
molecule in order to reduce the amount of nitrogen of the
body through ammonia synthesis and elimination. It is a
process occurring in the liver during the metabolism of
amino acids. The amino group is removed from the amino
acid and converted to ammonia-NH3 whose toxic activity is
canceled by conversion into urea which is eventually
excreted. The glutamate dehydrogenase-GDH enzyme
occupies a central role in nitrogen metabolism. Glutamate
amino acid is cleaved into α-ketoglutarate and ammonia a
reaction catalyzed by GDH in a process called
deamination. Glutamate is the only amino acid that
undergoes oxidative deamination at a relatively high rate.
The formation of ammonia from the amino group thusly
occurs mainly via the amino group of glutamate.

18. Once the amino groups have all been "collected"
in the form of the one amino acid, glutamate, this
amino acid has its amino group removed (termed
"oxidative deamination"). This reaction reforms
alpha-ketoglutarate with the other product being
ammonia (NH4 +).
Ammonia is toxic to the nervous system and its
accumulation rapidly causes death. Therefore it
must be detoxified to a form which can be readily
removed from the body. Ammonia is converted to
urea, which is water soluble and is readily
excreted via the kidneys in urine.

19. Unlike glucose, there is no
storage form of amino acids.
Amino acids are degraded into
free ammonia (NH4+) and the
carbon skeleton. Living
organisms excrete excess
nitrogen as ammonia, uric acid,
and urea.

20. EExxccrreettoorryy ffoorrmmss ooff nniittrrooggeenn
a) Excess NH4
+ is excreted as ammonia (microbes,
aquatic vertebrates or larvae of amphibia),
b) Urea (many terrestrial vertebrates)
c) or uric acid (birds and terrestrial reptiles)

21. Nitrogen rreemmoovvaall ffrroomm aammiinnoo aacciiddss
Step 1: Remove amino group
Step 2: Take amino group to liver for
nitrogen excretion
Step 3: Entry into mitochondria
Step 4: Prepare nitrogen to enter urea cycle
Step 5: Urea cycle

22. SStteepp 11.. RReemmoovvee aammiinnoo ggrroouupp
• Transfer of the amino group of an amino acid to an a-
keto acid Þ the original AA is converted to the
corresponding a-keto acid and vice versa:

23. • Transamination is catalyzed by transaminases
(aminotransferases) that require participation of
pyridoxalphosphate:
amino acid
pyridoxalphosphate Schiff base

24. SStteepp 22:: TTaakkee aammiinnoo ggrroouupp ttoo lliivveerr ffoorr
nniittrrooggeenn eexxccrreettiioonn
Glutamate
dehydrogenase
Glutamate releases its amino
group as ammonia in the liver.
The amino groups from many of
the a-amino acids are collected in
the liver in the form of the amino
group of L-glutamate molecules.
The glutamate dehydrogenase of
mammalian liver has the unusual capacity
to use either NAD+ or NADP+ as cofactor

25. 1. Glutamate
NNiittrrooggeenn ccaarrrriieerrss
transferres one amino group WITHIN cells:
Aminotransferase → makes glutamate from a-ketogluta-rate
Glutamate dehydrogenase → opposite
2. Glutamine
transferres two amino group BETWEEN cells →
releases its amino group in the liver
3. Alanine
transferres amino group from tissue (muscle) into the
liver

26. Move within cells
SynthAtase = ATP
In liver
Move between cells

27. Glucose-alanine cycle
Alanine plays a special role in
transporting amino groups to liver.
Ala is the carrier of ammonia and of the carbon
skeleton of pyruvate from muscle to liver.
The ammonia is excreted and the pyruvate is
used to produce glucose, which is returned to
the muscle.
According to D. L. Nelson, M. M. Cox :LEHNINGER. PRINCIPLES OF BIOCHEMISTRY Fifth edition

28. SSoouurrcceess ooff aammmmoonniiaa ffoorr tthhee uurreeaa ccyyccllee::
• Oxidative deamination of Glu, accumulated in the liver by the action of
transaminases and glutaminase
• Glutaminase reaction releases NH3 that enters the urea cycle in the liver (in
the kidney, it is excreted into the urine)
• Catabolism of Ser, Thr, and His (nonoxidative deamination) also releases
ammonia:
Serine - threonine dehydratase
Serine →→ pyruvate + NH+
4
Threonine →→ a-ketobutyrate + NH4
+
• Bacteria in the gut also produce ammonia.

29. Review:
• Nitrogen carriers  glutamate, glutamine, alanine
• 2 enzymes outside liver, 2 enzymes inside liver:
– Aminotransferase (PLP) → a-ketoglutarate →
glutamate
– Glutamate dehydrogenase (no PLP) → glutamate →
a-ketoglutarate (in liver)
– Glutamine synthase → glutamate → glutamine
– Glutaminase → glutamine → glutamate (in liver)

30. Step 3: entry of nitrogen to mitochondria

31. Step 4: prepare nitrogen to enter urea cycle
Regulation

32. The urea cycle takes place in the
mitochondria and the cytosol.
There are four enzymes involved,
three of which are cytosolic and
one is mitochondrial.

33. Step 5: Urea cycle aspartate
OOrrnniitthhiinnee
ttrraannssccaarrbbaammooyyllaassee
AArrggiinniinnoossuucccciinnaattee
ssyynntthhaassee
AArrggiinniinnoossuucccciinnaattee
llyyaassee
AArrggiinnaassee 11

34. Oxaloacetate → aspartate
OOA

35. UUrreeaa ccyyccllee –– rreevviieeww
((SSeeqquueennccee ooff rreeaaccttiioonnss))
• Carbamoyl phosphate formation in mitochondria is a
prerequisite for the urea cycle
– (Carbamoyl phosphate synthetase)
• Citrulline formation from carbamoyl phosphate and
ornithine
– (Ornithine transcarbamoylase)
• Aspartate provides the additional nitrogen to form
argininosuccinate in cytosol
– (Argininosuccinate synthase)
• Arginine and fumarate formation
– (Argininosuccinate lyase)
• Hydrolysis of arginine to urea and ornithine
– (Arginase)

36. TThhee oovveerraallll cchheemmiiccaall bbaallaannccee ooff tthhee
bbiioossyynntthheessiiss ooff uurreeaa
NH3 + CO2 + 2ATP → carbamoyl phosphate + 2ADP + Pi
Carbamoyl phosphate + ornithine → citrulline + Pi
Citrulline + ATP + aspartate → argininosuccinate + AMP + PPi
Argininosuccinate → arginine + fumarate
Arginine → urea + ornithine
Sum: 2NH3 + CO2 + 3ATP  urea + 2ADP + AMP + PPi + 2Pi

37. NNiittrrooggeenn bbaallaannccee
Tissue proteins
Dietary
proteins
Amino acid
pool
Purines, heme, etc.
Energy
Excretion
as urea and
NH+
4
The amount of nitrogen ingested is balanced by the excretion of an
equivalent amount of nitrogen. About 80% of excreted nitrogen is in
the form of urea.

38. Ammonia is rendered harmless in animals through the
synthesis of urea (which in man, mammals, and
several other animals forms in the liver and is
discharged with urine) or uric acid (in birds, reptiles,
and insects) and is partially given off in the form of
ammonium salts.
In plants and some bacteria, inorganic ammonium nitrogen may
be reutilized, that is, used again in the synthesis of amino acids
and amides and then of proteins. In these processes the amides
of aspartic and glutamic acids play an important role, being the
most important reserve compounds of nitrogen in plants. These
compounds play an important role in animal organisms as well.
Urea is also found in a number of plants; its essential role in
rendering ammonia harmless in fungi, bacteria, and higher plants
has been established. In contrast to processes in animals, urea in
plants may be used again in the processes of protein synthesis
when a sufficient quantity of carbohydrates is formed.

39. Thus, the principal difference between protein
metabolism in animals and plants is that plants
synthesize protein, first forming amino acids
and amides from inorganic substances, and
the ammonia that is formed in the deamination
of amino acids is again used (through
glutamine, asparagine, and urea) in the
resynthesis of protein.
Animals and man synthesize proteins from
amino acids that are obtained from food and
that are partially formed as a result of
transamination; the cleavage products of
amino acids are discharged by the body.
Intermediate stages of protein metabolism in
plants and animals have much in common.

40. The remainder of the amino acid is
referred to as the "carbon skeleton".
Depending on the particular amino
acid being catabolised, its carbon
skeleton will be converted to :
acetyl CoA.
Those carbon skeletons which end up
as acetyl CoA are committed to energy
production. They will either be
immediately oxidised via the citric acid
cycle or they may be converted to
ketone bodies. Because the amino
acids whose carbon skeletons yield
acetyl CoA are potentially a source of
ketone bodies they are referred to as
ketogenic amino acids
or pyruvate
or a citric acid cycle intermediate.

41. Glycine is the principal source for the
formation of the pigmented grouping of
hemoglobin. The hormones of the thyroid
gland (thyroxin and its derivatives) and of the
adrenal glands (epinephrine and
norepinephrine) are formed from the amino
acid tyrosine. Tryptophan serves as the source
for the formation of biogenic amines and also
(in part) of nicotinic acid and its derivatives. A
number of other nitrogenous substances of the
animal organism, such as glutathione,
carnosine, anserine, and creatine, are products
of the union or transformation of amino acids.
Alkaloids in plants are also formed from amino
acids.

42. Amino acid synthesis
Amino acids are divided into two
classes depending on whether they
can be synthesised in the human
body or whether they must be
supplied in the diet. The former group
are referred to as non-essential and
the latter group as essential. The
table below shows which of the
twenty are in each group. Note that
there are ten in each of the two
groups

44. Non-essential amino acids are synthesised from the
products of their catabolism - i.e. acetyl CoA,
pyruvate or the relevant Krebs cycle intermediate.
The amino group is donated by glutamate and added
by the reverse of the transamination discussed
above. The essential amino acids are synthesised in
micro-organisms (bacteria and yeasts) and passed
through the food chain until they reach us in our diet.
One of the pathways essential to life which is carried
out by bacteria is the "fixation" of atmospheric
nitrogen initially as inorganic nitrate and ultimately as
amino groups in amino acids. Higher organisms
cannot perform this function.

45. 1.Biosynthesis
2.Urea cycle
Fumarate
Oxaloacetate
Overview of amino acid catabolism in mammals