Protein degradation is accomplished by endopeptidases and exopeptidases that cleave peptide bonds within or at the ends of polypeptide chains. Pepsin, trypsin, and chymotrypsin, secreted in the stomach and pancreas, have different amino acid specificities and work together efficiently to digest proteins. Amino acids are oxidized in the liver to produce energy, carbon skeletons for gluconeogenesis, and ammonia. Excess ammonia is processed through the urea cycle where it is combined with carbon dioxide to form the non-toxic urea for excretion.

1. PROTEIN DEGRADATION

2. Proteinase and Peptidase
Endopeptidase:
‒ catalyzes the cleavage of peptide bonds
within a polypeptide or protein.
‒ pepsin, trypsin, chymotrypsin
Exopeptidase
‒ catalyzes the removal of an amino acid from
the end of a polypeptide chain.
‒ aminopeptidase
‒ carboxypeptidase

3. Reagent (biological source) Cleavage points
Pepsin (porcine stomach) Leu, Phe, Trp, Tyr (N)
Trypsin (bovine pancreas) Lys, Arg (C)
Chymotrypsin (bovine pancreas) Phe, Trp, Tyr (C)
Pepsin, trypsin and chymotrypsin
have different substrate specificities

4. A part of the human digestive tract
In stomach：gastrin (hormone)
→ gastric acid + pepsinogen
In small intestine:
 Pancreatic juice:
trypsinogen，
chymotrypsinogen，
procarboxypeptidases A
and B
 Mucous membrane of small
intestine:
aminopeptidase，
dipeptidase

5. Reagent (biological source) Cleavage points
Pepsin (porcine stomach) Leu, Phe, Trp, Tyr (N)
Trypsin (bovine pancreas) Lys, Arg (C)
Chymotrypsin (bovine pancreas) Phe, Trp, Tyr (C)
Protein digestion is accomplished very efficiently,
because pepsin, trypsin, and chymotrypsin have
different amino acid specificities.

6. AMINO ACID OXIDATION

7. Amino acid catabolism
• Carnivores can obtain (immediately following a
meal) up to 90% of their energy requirements from
amino acid oxidation, whereas herbivores may fill
only a small fraction of their energy needs by this
route.
• Most microorganisms can scavenge amino acids
from their environment and use them as fuel.
• Plants, however, rarely oxidize amino acids to
provide energy. Instead, they use amino acids to
produce metabolites for biosynthesis of proteins,
nucleic acids, and other molecules needed to
support growth.

8. • Leftover amino acids from normal protein
turnover
• Dietary amino acids that exceed body’s protein
synthesis needs
• During starvation or in uncontrolled diabetes
mellitus, when carbohydrates and fats are either
unavailable or not properly utilized, cellular
proteins are used as fuel.
When do amino acids undergo
oxidative degradation?

9. Overview of amino acid catabolism
Most amino acids are
metabolized in the liver.

10. Overview of amino acid catabolism
Amino acids lose their
amino groups to form
α-keto acids, the
“carbon skeletons” of
amino acids. The α-
keto acids undergo
oxidation to CO2 and
H2O or, often more
importantly, provide 3-
and 4-carbon units
that can be converted
by gluconeogenesis
into glucose - the fuel
for brain, skeletal
muscle, and other
tissues.

11. • Some of the
ammonia (NH4
+)
generated in this
process is recycled
and used in many
biosynthetic
pathways
• Excess NH4
+ is
either excreted
directly or
converted to urea or
uric acid for
excretion,
depending on the
organism.
Overview of amino acid catabolism

12. The liver plays a
major role in
nitrogen
processing in
animals
All other tissues
send amino acids
to the liver in the
form of glutamine
(all tissues),
alanine (muscles)
and all dietary
amino acids
(intestine).

13. aminotransferase
The liver plays a
major role in
nitrogen
processing in
animals
In the cytosol of
hepatocytes, amino
groups from most amino
acids are transferred to
α-ketoglutarate to form
glutamate, which enters
mitochondria and gives
up its amino group in the
form of NH4
+.

14. aminotransferase
The liver plays a
major role in
nitrogen
processing in
animals
Excess ammonia
(NH4
+) generated in
most other tissues
is converted to the
amide nitrogen of
glutamine, which
passes to the liver,
then into liver
mitochondria, and
gives up its amino
group in the form of
NH4
+.

15. • In these transamination
reactions, the α-amino group is
transferred to the α-carbon atom
of α-ketoglutarate, leaving behind
the corresponding α-keto acid
analog of the amino acid ↔
α-ketoglutarate becomes
aminated as the α-amino acid
is deaminated.
• The effect of transamination
reactions is to collect the amino
groups from many different amino
acids in the form of L-glutamate.
The glutamate then functions as
an amino group donor for
biosynthetic pathways.
Transamination

16. GPT: Glutamate - pyruvate transaminase
GOT: Glutamate - oxaloacetate transaminase
α-ketoglutarate
GPT
α-ketoglutarate
GOT
ALT (SGPT) & AST (SGOT) are important in the diagnosis of
liver damage
Two important aminotransferases: ALT (SGPT) & AST (SGOT)

17. Amino
acid CO2+ amine: decarboxylation
NH3+ α-keto acid: oxidative deamination
α-keto acid: transamination

18. Decarboxylation
RCHNH2COOH CO2 + RCH2NH2
amine
decarboxylase
PLP

19. Oxidative deamination
 In hepatocytes, glutamate is transported from the cytosol into
mitochondria, where it undergoes oxidative deamination catalyzed
by L-glutamate dehydrogenase.
 The glutamate dehydrogenase of mammalian liver is the only enzyme
that has the capacity to use either NAD+ or NADP+ as cofactor.
 The mammalian enzyme is allosterically regulated by GTP and ADP.

20. ? ?
Amino
acid CO2+ amine: decarboxylation
NH3+ α-keto acid: oxidative deamination
α-keto acid: transamination

21. Glutamine
(non-toxic)
1. Biosynthesis of AAs,
nucleotides, and amines
2. Convert to urea for
excretion
Alanine
(non-toxic)
Glucose – Alanine cycle
Ammonia (NH3) is toxic to animals
In most animals, much of the free ammonia is converted to a nontoxic
compound (glutamine, alanine) before export from the extrahepatic tissues
into the blood and transport to the liver or kidneys.

22. Ammonia could be transported safely from
tissues to liver in the form of glutamine
• Removal of excess ammonia requires reductive amination of α-
ketoglutarate to glutamate by glutamate dehydrogenase and
conversion of glutamate to glutamine by glutamine synthetase.
• Glutamine synthetase is found in all organisms, always playing
a central metabolic role.
COO
(CH2
)2
C
H NH3
COO
+
(CH2
)2
C
H NH3
COO
CONH2
+
glutamine
glutamate
NH3+ATP ADP+Pi
Mg 2+
Glutamine synthase

23. Alanine Transports
Ammonia from Skeletal
Muscles to the Liver
Alanine transports NH4
+ from
muscle to liver. When alanine
enters the liver cells, it gives up
its amino group and becomes
pyruvate which through
gluconeogenesis can be
converted to glucose and put into
blood for the muscles (and rest of
the body).

24. Glucose - Alanine cycle vs Cori cycle
https://www.memorangapp.com/flashcards/57286/4BC3+Urea+Cycle

25. NITROGEN EXCRETION AND
THE UREA CYCLE

26. Động vật sống trong nước bài tiết trực
tiếp NH4
+ vào môi trường nước nên
chúng được gọi là ammonotelic
Excretory forms of nitrogen
/jʊˌriəˈtɛlɪk/
/ˈjurɪkoʊˈtɛlɪk/
/ˌæmənoʊˈtɛlɪk/

28. Urea cycle: eliminate ammonia from the body
by converting it to urea

29. Urea cycle
or ornithine cycle
Amino acids come from
recycling (glutamine), muscle
glycolysis (alanine), and diet.
• The first nitrogen enters
from ammonia.
• The second nitrogen enters
from aspartate.

30. Begin in the Mitochondrion
?

31. Citrulline
Ornithine
Arginine

32. gluconeogenesis ←OAA
Fumarase
Fumarase
Malate DH
Malate DH
OAA
Some Krebs cycle enzymes such as fumarase
and malate dehydrogenase have both
cytosolic and mitochondria isozymes.
Krebs bicycle

33. Energetic cost of urea synthesis
Overall equation of the urea cycle is:
NH4
+ + HCO3
- + aspartate + 3 ATP
 urea + fumarate + 2ADP + AMP + 2Pi + PPi
Synthesis of one molecule of urea requires four high
energy phosphate groups
 Two ATP molecules to make carbamoyl phosphate
 One ATP to make argininosuccinate—the latter ATP
undergoing a pyrophosphate cleavage to AMP and
PPi, which is hydrolyzed to two Pi.

34. gluconeogenesis ←OAA
Fumarase
Fumarase
Malate DH
Malate DH
OAA
Krebs bicycle
The urea cycle also causes a conversion
of oxaloacetate to fumarate (via
aspartate), and the regeneration of
oxaloacetate produces NADH. Each
NADH molecule can generate up to 2.5
ATP during mitochondrial respiration,
greatly reducing the overall energetic
cost of urea synthesis.

35. Benzoate and
Phenylbutyrate
Given to Lower
Blood Ammonium
Treatment for genetic
defects in Urea Cycle
Excreted in Urine

36. Fate of the carbon skeletons of amino acid
• Used for synthesis of new amino acids
• Completely oxidized via TCA cycle
• Provide 3- and 4-carbon units that can be converted by
gluconeogenesis into glucose

37. Summary of Amino Acid Catabolism

38. • Glucogenic amino acids
– A glucogenic amino acid is an amino acid that
can be converted into glucose through
gluconeogenesis
• Ketogenic amino acids
– A ketogenic amino acid is an amino acid that can
be converted into ketone bodies through
ketogenesis

39. Major substance in kidney stones is the product
of glycine catabolism (calcium oxalate)

41. Tryptophan is the precursor for the biosynthesis of
nicotinate, indoleacetate và serotonin

42. Genetic defects in phenylalanine degradation
can result in phenylketonuria (PKU)
Phenylketouria results from
serum phenylalanine
(>20mg/dL) being converted
to phenylpyruvate.
Babies today are
immediately tested for this
just after birth. If they are
PKU babies, they have to be
on diet low in phenylalanine
to for the first 5-10 years of
life so that they do not
become mentally retarded.

44. Amino acid
CO2+ amine: decarboxylation
NH3+ α-keto acid: deamination
α-keto acid: transamination
Urea cycle
Alanine-glucose cycle
Krebs cycle