BIOCHEM B

2 MAJOR PATHWAYS IN PROTEIN DEGRADATION

Protein Metabolism 1
Dra. Santos

The chemical transformations of amino acids are distinct

from those of carbohydrates or lipids in that they involve
the element, NITROGEN.
PROTEIN TURNOVER
It is the continuous degradation and resynthesis
of all cellular proteins.
Balance of proteins that undergo breakdown
and synthesis
1-2% of total body proteins (200-300grams) are
changed everyday
75-80% of the amino acids are reutilized/recycled
for protein synthesis
The nitrogen of the remaining 20-25% is now
converted to urea.
UREA final end product of protein metabolism
in the body
protein intake = urea excretion
HALF LIFE
Refers to the susceptibility of proteins to
degradation
Refers to the rate of degradation of proteins
Proteins with short half-lives usually have the PEST
SEQUENCE (used the 1-letter abbreviation)
P Proline
E Glutamate
S Serine
T Threonine
Proteins with long half-lives (over 100 hours)
include
o Aldolase (splitting enzyme in glycolysis)
o Lactate dehydrogenase (anaerobic
glycolysis; converts pyruvate to lactate)
o Cytochrome C (electron transport chain)
The most rapidly degraded enzymes are those
that occupy important metabolic control points.
o The more important the function of an
enzyme easier to degrade
o E.g. control enzymes, rate limiting
enzymes (have short half lives)
Enzymes with not that important functions has
longer half-lives
The rate of protein degradation also varies
according to the nutritional status.
food intake CHONS not easily degraded
o If you are nutritionally deprived or you will
not eat what will maintain your blood
sugar:
What maintains your blood sugar:
1ST DAY: Glycogen
Glycogen reserves maintain blood sugar in
the 1st 24 hours that you did not eat
2nd DAY:
On the 2nd day without food intake, you will
hydrolyze your fats.

Bernabe, Maria Katrina (2013)

Lysosomal Degradation
Lysosomes contain around 50 hydrolytic enzymes
including a variety of proteases.
Degrades proteins with KFERQ sequence. If you
have a protein with this sequence, it is easily
degraded by the lysosome.
K
Lysine
F
Phenylalanine
E
Glutamic Acid
R
Arginine
Q
Glutamine
Ubuiquitin
A 76-residue monomeric protein known for its
ubiquity and abundance.
If the N-terminal is:
Methionine or Serine cannot be degraded by
Ubiquitin (Retarded)
Aspartic or Arginine faster degradation
(Accelerated)
OVERALL SOURCES AND UTILIZATION OF AMINO ACIDS
2 sources of CHONs in the body:
1. Exogenous
o Diet after digestion of proteins
amino acids
2. Endogenous
o Amino acids synthesized by the liver,
which are the NON-essential amino acids
o Degradation of tissue proteins (protein
turnover) contributes to amino acid
pool
Functions of Amino Acids
1. The most important function of amino acids is for
you to use them to synthesize all the proteins that
you need (enzymes, hemoglobin, collagen,
plasma proteins, etc).
2. Synthesize essential non-protein nitrogenous
substances (these are not CHONs but needs
amino acids in order to be synthesized).
E.g.
Purines and pyrimidines require Asp, Gly and Gln
Gly gives C4 C5 N7
Gln gives N3 N9
Asp gives N1
Porphyrins need Glycine.
Some Vitamins require amino acids (Folic acid
requires Glu)
Creatine (tripeptide) Lys,Arg, Met
Glutathione Gly, Cys. Glu
PROTEIN DIGESTION
Mouth no enzyme acting on proteins
Stomach pepsin
Small intestines pancreatic enzymes (Trypsin,
Chymotrypsin, Carboxypeptidase, Elastase)

ABSORPTION OF AMINO ACIDS

Amino acids are absorbed from the intestinal

lumen in 3 ways, through:
1. Secondary active Na-dependent transport
2. Facilitated diffusion
3. Transport linked to the gamma-glutamyl
cycle
LIVER:
Any amino acid that is not used will undergo breakdown.
All the amino acids are metabolized in the liver EXCEPT
the branched-chain amino acids (Valine, Leucine,
Isoleucine) because they are metabolized in the brain
and muscles.
The liver will then use the amino acids to synthesize the
proteins and other nitrogen-containing compounds
(purines, pyrimidines, porphyrins, etc.)
The liver acts also as a supplier of amino acids to other
organs and this is where the non-essential amino acids
are synthesized. This is also where the catabolism or
breakdown of amino acids happens if they are not used.
CLASSIFICATION OF AMINO ACIDS FROM A NUTRITIONAL
POINT OF VIEW
Essential AA
Cannot be synthesized by the body
Must be provided in the diet
Try, Val, Met, Arg, Phe, His, iso, Leu, Lys, Thr
If all these amino acids are present in a protein, the
protein is COMPLETE (meat, milk, eggs)
If any one of the essential AA is lacking, the protein is
INCOMPLETE and cannot sustain life by itself (rice, corn).
LIMITING AMINO ACIDS
Refers to the amino acid that is lacking
Non-essential/Dispensable AA
Can be synthesized by the body
Doesnt need to be provided in the diet
Majority of the non-essential amino acids are
derived from the essential amino acids
There are 3 enzymes that are important for the synthesis
of amino acids:
1. GLUTAMATE DEHYDROGENASE
o Synthesizes glutamic acid
2. GLUTAMINE SYNTHETASE
o Synthesize glutamine
3. AMINOTRANSFERASE
o For transamination
o Can synthesize other amino acids

Bernabe, Maria Katrina (2013)

AMINO ACID CATABOLISM

When an amino acid is not used, it will just undergo
degradation or breakdown. If you remember there are 3
reactive parts of an amino acid: -NH2, COOH, -R. In order
to degrade or catabolise an amino acid, you just have to
remove the 3 reactive parts.
1. One-Carbon Transfer
2. Oxygenation
3. Decarboxylation
4. Removal of alpha amino group
a. Oxidative deamination
b. Non-Oxidative deamination
c. Transamination
1-CARBON TRANSFER
R group is removed
OXYGENATION
add oxygen
If you add Oxygen to Phe (essential), it is
converted to Tyr (non-essential). It is still
catabolism because Phe is converted to another
substance. This is an example of a non-essential
amino acid derived from an essential amino
acid.
DECARBOXYLATION
release of CO2
leads to the formation of amines
E.g.
Histamine derived from Histidine
Serotonin derived from Tryptophan
Epi, NE
derived from Phe & Tyrosine
REMOVAL OF THE AMINO GROUP
3 ways to remove the amino group:
a. Oxidative deamination
b. Non-Oxidative deamination
c. Transamination
Deamination

Amino acid NH2 NH3 + keto acid

Removal of the amino group
Each amino acid has its own corresponding keto
acid
This is reversible by reacting the keto acid to NH3
to get back the amino acid.

AMINO ACID
Ala
Glu
Asp
Gly
His

ITS CORRESPONDING
KETO ACID
Pyruvate
Alpha ketoglutarate
Oxaloacetate
Glyoxylic acid
Uroconic acid

Oxidative Deamination
Enzymes involved:
1. Glutamate dehydrogenase
Converts Glu to alpha ketogluratate
most active enzyme
o Glutamic acid is the MOST ACTIVE amino
acid
Found in almost all parts of the body
When you reverse the reaction, the alphaketoglutarate accepts the amino group to
form back the amino acid
o Alpha-ketoglurate is the MOST ACTIVE
amino group acceptor
2.

3.

L-amino acid oxidase

Will act on the other amino acids
E.g. Can act on
o Asp Oxaloacetate and can reverse
the reaction Oxaloacetate Asp
o Ala pyrutvate and reverse it.
D-amino acid oxidase
There are only 2 D-amino acids:
o D-aspartate
o D-serine
This enzyme is not used because we only
have 2 D-amino acids
This is an enzyme used by bacteria.

Zellwegger Cererohepatorenal Syndrome (CHRS)

Syndrome that results if L-amino acid oxidase is
deficient
Abnormalities in brain, liver, and kidneys
Could be a fatal disease
Abnormal neural development, generalized
aminoaciduria, absence of peroxisomes in a liver
biopsy
The aminoaciduria is due to deficient amino acid
oxidase activity
Non-Oxidative Deamination
Same equation as oxidative deamination but
using different enzymes
Enzymes involved:
1. Amino acid dehydrase
Will only act on the hydroxyl containing
amino acids (Ser, Thr, Tyr)
Co-enzyme: Pyroxidal PO4 or Vit B6 PO4

2.

Amino acid desulfhydrase

Will act on the sulphur containing amino
acids (Cysteine, Methionine, Homocysteine)
Co-enzyme: Pyroxidal PO4 or Vit B6 PO4

Transamination
Major process for removing nitrogen from amino
acids
Transfer of amino group from the original amino
acid to keto acid
*Keto acid is a substance without amino group.
Keto acid + amino group = AMINO ACID
Amino acid Amino group = KETO ACID
Every transamination, there is formation of a new
amino acid
Enzymes for transamination: AMINOTRANSFERASE
or TRANSAMINASES
o When these enzymes are used, new
amino acids can be synthesized
depending on the acceptor of the
amino group.
The usual acceptor is ALPHA-KETOGLUTARATE;
therefore, the usual amino acid formed is GLU.
The transfer of amino group requires a carrier.
Pyridoxal PO4/VitB6 PO4
o PLP
o carrier of the amino group or the coenzyme for transamination

AMMONIA

ABSENT as a product in transamination because

the removed amino group is immediately
incorporated to the keto acid. There is NO free
ammonia release.
PRESENT as product in oxidative and nonoxidative deamination
TOXIC if it accumulates in the body
Hyperammonemia ammonia intoxication

Manifestations of Ammonia Intoxication:

Initially (NH3 is still not that high):
Headache
Nausea
Vomiting
As the NH3 level in the blood increases:
Blurring of vision

Slurring of speech

Convulsive seizures

Unconsciousness

Comatose

Death

**This is also what happens when you have Hepatitis B.

Bernabe, Maria Katrina (2013)

Because Ammonia is not released during transamination,

the body prefers to do transamination always.
But there are amino acids that do NOT undergo
transamination:
Lysine
Threonine
Proline
Hydroxyproline

UREA CYCLE/KREBS-HENSELEIT CYCLE

Most important pathway in the detoxification of

ammonia in the liver
Involves both cytosol and mitochondria

Ways of Detoxifying Ammonia

1.

Reversal of glutamate dehydrogenase reaction

Using
ammonia
to
convert
alpha
ketoglutarate to glutamic acid

2.

Glutamine formation
Major means by which the BRAIN detoxifies
ammonia.
BRAIN: most sensitive to ammonia
Once Ammonia reaches the brain, it will
react with the glutamic acid in the brain
Glutamine (through the enzyme Glutamine
synthetase) goes to the kidney once in
the kidneys, it will be converted back to
glutamic acid + NH3 (through the enzyme
Glutaminase) NH3 will go out in the urine.
There are vitamins with glutamic acid (e.g.
Glutafoss). There is no need to take in these
because the body can already synthesize
Glu unless you have a disease that consumes
that consumes Glu.

Q: What is the most common source of NH3

excreted in the urine?
A: GLUTAMINE
Q: Where did the NH3 excreted in the urine come
from?
A: BREAKDOWN OF GLUTAMINE
3.

4.

Urea formation
Major means by which the LIVER detoxifies
ammonia.
Most ACTIVE way of detoxifying NH3
Form majority of NH3 in the liver
Aspargine formation
Asn formation is comparable to
formation by just changing Glu to Asp

Bernabe, Maria Katrina (2013)

Gln

REACTION 1:
Mitochondria
2 ATPs, CO2, NH3 and H2O reacts to form
Carbamoyl phosphate
ENZYME: Carbamoyl phosphate synthetase 1
(CPS1)
CPS 1
Urea Cycle
Mitochondria
Requires an activator
(N-AGA
or
N-Acetyl
Glutamic Acid)

CPS 2
Pyrimidine Metabolism
Cytosol
Does
not
require
activator

an

REACTION 2:
Ornithine reacts with carbamoyl PO4 to form
Citrulline
The ornithine that reacted with carbamoyl PO4
came from the Cytosol
ENZYME: Ornithine Transcarbamoylase
REACTION 3:
Citrulline will go out into cytosol and reacts with
one more NH3, entering as Aspartic Acid to form
Argininosuccinate
Note: the 2nd ammonia that will be detoxified
enters as aspartic acid.
ENZYME: Argininosuccinate Synthetase

REACTION 4:
Argininosuccinate is cleaved to Fumarate and
Arginine
Arginine is still an essential amino acid despite
that it can be synthesized by the body. Strictly
speaking, Arginine should be termed as SEMIESSENTIAL because it can be synthesized by the
body and yet, it should be provided in the diet; it
can both non-essential and essential.
ENZYME: Arigininosuccinase
Q: Why is Arginine considered semi-essential?
A: Because it can be synthesized by the body
through the urea cycle and yet, you have to
provide it in the diet because the arginine that is
synthesized in the urea cycle cannot be used for
CHON synthesis because it is immediately
converted to urea and ornithine. The Arginine
used for CHON synthesis should be provided in
the diet.
REACTION 5:
Arginine is converted to Urea and Ornithine
ENZYME: Ariginase
For every turn of the urea cycle, you are detoxifying
2 MOLES of Ammonia.
comes out in the urine
Is solid (increases specific gravity of urine)
Considered to be a diuretic (increases the
volume of urine)

CHON diet

urea
excretion

urine
sp.gravity &
volume

If it is ATP + Pi, there is no 4th ATP.

For this reaction you produce Fumarate, which can enter
the Krebs.
KREBS BICYCLE
Krebs + Urea Cycle
Connects the two pathways (Krebs and Urea
cycle)
Before ornithine enters the mitochondria, it needs a
transport system. The transporter has genes. There is a
gene for the ornihtine transporter.
HHH SYNDROME
Mutation of the ornithine transporter gene.

Mutation of the Ornithine Transporter Gene

It will be destroyed

inability to transport Ornithine inside mitochondria

UREA CYCLE STOPS

NH3 will no longer be detoxified

NH3 accumulation

Hyperammonemia
Rate Limiting Steps (Control Points of Urea Cycle):
1. Synthesis of Carbamoyl PO4 with CPS1 (R#1)
2. Synthesis
of
Citrulline
with
Ornithine
transcarbamoylase (R#2)
3. Cleavage of Arginine with Arginase (R#5)
If you want to stimulate/stop the cycle, stimulate/inhibit
the control points.
Q: Do you produce ATP through the urea cycle?
A: NO. ATP is used. This is an endergonic reaction.
Q: How many ATPs are used?
A: 4 ATPS; 2 on the 1st step, 1 on the 3rd step and 1 more
because of the PPi (PPi 2 Pi 1 ATP.
Normally when ATP undergoes degradation or hydrolysis,
the products are ADP+Pi. But when you look at the
hydrolysis of ATP in the urea cycle, there is ATP + AMP +
PPi (pyrophosphate). The PPi should be converted to 2 Pi
in order for the reaction to be complete. And that will
yield 1 more ATP.

Bernabe, Maria Katrina (2013)

AMMONIA INTOXICATION
H1: Hyperammonemia
Because the urea cycle stops there will be
Increase in ammonia
H2: Hyperornithinemia
Ornithine cannot enter so it will accumulate in
the blood
H3: Homocitrullinuria
Because the urea cycle cannot
Citrulline will come out of the urine.

proceed,

INBORN ERRORS OF THE UREA CYCLE

If anyone of these enzymes is deficient, you come up with

inborn errors of the urea cycle.
INBORN ERROR
Hyperammonemia Type I
Hyperammonemia Type 2
Citrullinemia
Argininosuccinate Aciduria
Arginemia

ENZYME DEFICIENT
Carbamoyl PO4 synthetase
Ornithine
transcarbamoylase
Argininosuccinate
synthetase
Argininosuccinase
Arginase

All the inborn errors will lead to ammonia intoxication.

BEST TREATMENT: Treat the cause.

Replace any intermediate that is missing.

Q: What kind of disease can easily give you severe NH3

intoxication?
A: Liver diseases
Because it is in the liver where you have the UREA
CYCLE which is the primary cycle that detoxifies
your NH3.

Severe liver disease

Urea cycle stops

TREATMENT OF AMMONIA INTOXICATION

Go on a low CHON diet but HIGH in quality

(complete proteins).
Because NH3 comes from CHONs limit CHON
intake (but see to it that what you eat are
complete CHONs so all the needed amino acids
are still present).
You CANNOT completely remove proteins in your
diet because there are substances that are very
important in your body that require proteins
(Hgb, Myoglobin, Enzyme synthesis). Without
CHONs, it will stop all the pathways in the body.

Give LEVULLOSE/LACTULOSE

NH3 accumulation in the liver

NH3 spills out into the systemic circulation

NH3 will now invade the diff. organs in the

body

NH3 reaches brain (very sensitive to NH3)

Brain detoxifies NH3

This is given to promote excretion of NH3 in the

stools because it prevents the absorption of NH3.

Give ANTIBIOTICS (e.g. Neomycin)

This is given to kill the normal bacterial flora. The
normal bacteria in the intestines will not cause a
disease but normally, they produce NH3 by
FERMENTATION.
There is no need to give very expensive
antibiotics because what is being killed are only
the normal bacteria (which produces NH3) and
there is currently no infection.

Give compounds that will combine with NH3

Every amino acid has ammonia. When the amino
acid binds with the compound, it will be
excreted in the urine (excreting 1 NH3 per amino
acid).
E.g.
Benzoic acid + Gly Hippuric Acid
If glycine exits as hippuric acid, 1 NH3 is also
excreted.
Phenylacetate + Gln Phenylacetylglutamine

Bernabe, Maria Katrina (2013)

NH3 is converted to Glutamine

(through Glutamine Synthetase)

Glutamine will go to the kidneys

Glutamine will be converted to Glutamic

acid + NH3

Excretion in urine

If you have a liver disease, the level of NH3 is so much

because the liver is unable to detoxify it. So the NH3 that
reaches the brain is so much also. Until such time that all
the Glutamic acids are already used up, NH3 still
continues to enter BRAIN DAMAGE.
Best source of Glutamic Acid: ALPHA KETOGLUTARATE

In
the
presence
of
the
enzyme
Glutamate
dehydrogenase + NH3, that can be converted to
Glutamic acid.
Glutamate dehydrogenase is a very active enzyme that
is present in almost all parts of the body. Therefore, it is
also present in the brain. If all the glutamic acids are used
up, it will convert alphaketoglutarate + NH3 (in the
presence of Glutamate dehydrogenase) to Glumatic
Acid.
But Alpha-ketoglutarate is taken from the Krebs cycle
(major ATP producing pathway) deplete Krebs cycle
of alpha-ketoglutarate Krebs cycle stops no ATP
production No ATP in the brain coma.
Q: What is the immediate cause of coma when you have
a severe liver disease?
A: depletion of alpha-ketoglutarate in the Krebs cycle.
Q: How to prevent the coma?
A: Prevent the depletion of alpha-ketoglutarate by giving
alpha-ketoglutarate to the patient. But there is no
preparation of a-ketoglutarate that can be given to the
patient because it is corrosive to the veins. So you give
GLUTAMIC ACID.
A-ketoglutarate is depleted because there is
shortage of Glutamic acid.
If there is an external source of glutamic acid,
then there is no need to give a-ketoglutarate.
All the previously mentioned interventions are all
supportive treatments and do not treat the actual cause
of the disease.
Main treatment: TREAT THE CAUSE! (give external
Glutamic Acid)
What will happen to the other product, KETO ACID?

Can be converted to an amino acid by reversing

the reaction, combining it again with NH3
amino acid

It can enter the gluconeogenesis pathway to be

converted to glucose

Can be converted to ketone bodies

METABOLIC FATES OF KETOACIDS
Each amino acid has a miscellaneous pathway
depending where the amino acid goes (can become
glucose/ketone body),
Purely Ketogenic Amino Acid
Can become a ketone body but NOT glucose
Leucine, Lysine
Both Ketogenic and Glycogenic AA
can be become glucose or ketone bodies)
Ile, Phe, Tyr, Trp
Purely Glycogenic AA
The rest of the amino acids

Bernabe, Maria Katrina (2013)