CC 103: BIOCHEMISTRY FOR MLS

College of Liberal Arts, Sciences and Education

Prepared by: DENNIS M. DIMARANAN, PhD
EIGENNN LOYOLA

MODULE 12
AMINO ACID METABOLISM

Brief Introduction or Description:

Amino acid metabolism is an important process that occurs within the human body
to assist in numerous biological reactions. This module covers the digestion of proteins,
amino acid absorption and transport, amino acid degradation, and the integration of
clinical applications to various concepts.

Learning Outcomes:
By the end of the module, you should be able to:
1. Explain the principles of amino acid metabolism.
2. Describe protein digestions in the body including the physical and chemical
process involved.
3. Explain the processes of amino acid absorption and transport.
4. Discuss the processes of amino acid degradation.
5. Determine clinical concepts applications of amino acid metabolism.

Before proceeding to the module, define first the following terms:

a. Protein
b. Amino acids
c. Pepsin
d. Chyme
e. Gastric Juices
f. Polypeptide
g. Absorption
h. Transport
i. Transamination
j. Urea

Lesson 1 Digestion of Proteins

How do the proteins from foods, denatured or not, get processed into amino acids that cells can
use to make new proteins? When you eat food the body’s digestive system breaks down the protein
into the individual amino acids, which are absorbed and used by cells to build other proteins and
a few other macromolecules, such as DNA. Let’s follow the specific path that proteins take down
the gastrointestinal tract and into the circulatory system. Eggs are a good dietary source of protein
and will be used as our example to describe the path of proteins in the processes of digestion and
absorption. One egg, whether raw, hard-boiled, scrambled, or fried, supplies about six grams of
protein.

From the Mouth to the Stomach

• Unless you are eating it raw, the first step in egg digestion (or any other protein
food) involves chewing. The teeth begin the mechanical breakdown of the large egg
pieces into smaller pieces that can be swallowed.
• The salivary glands provide some saliva to aid swallowing and the passage of the
partially mashed egg through the esophagus.
• The mashed egg pieces enter the stomach through the esophageal sphincter.
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EIGENN LOYOLA

• The stomach releases gastric juices containing hydrochloric acid and the enzyme,
pepsin, which initiate the breakdown of the protein. The acidity of the stomach
facilitates the unfolding of the proteins that still retain part of their three-
dimensional structure after cooking and helps break down the protein aggregates
formed during cooking. Pepsin, which is secreted by the cells that line the stomach,
dismantles the protein chains into smaller and smaller fragments. Egg proteins are
large globular molecules and their chemical breakdown requires time and mixing.
• The powerful mechanical stomach contractions churn the partially digested protein
into a more uniform mixture called chyme. Protein digestion in the stomach takes a
longer time than carbohydrate digestion, but a shorter time than fat digestion.
• Eating a high-protein meal increases the amount of time required to sufficiently
break down the meal in the stomach. Food remains in the stomach longer, making
you feel full longer.

Figure 1. Protein digestion requires the chemical actions of gastric juice and the
mechanical actions of the stomach

From the Stomach to the Small Intestine

• The stomach empties the chyme containing the broken down egg pieces into the
small intestine, where the majority of protein digestion occurs. The pancreas
secretes digestive juice that contains more enzymes that further break down the
protein fragments. The two major pancreatic enzymes that digest proteins are
chymotrypsin and trypsin. The cells that line the small intestine release additional
enzymes that finally break apart the smaller protein fragments into the individual
amino acids. The muscle contractions of the small intestine mix and propel the
digested proteins to the absorption sites. The goal of the digestive process is to
break the protein into dipeptides and amino acids for absorption.

• In the lower parts of the small intestine, the amino acids are transported from the
intestinal lumen through the intestinal cells to the blood. This movement of
individual amino acids requires special transport proteins and the cellular energy
molecule, adenosine triphosphate (ATP). Once the amino acids are in the blood, they
are transported to the liver. As with other macronutrients, the liver is the checkpoint
for amino acid distribution and any further breakdown of amino acids, which is very
minimal. Recall that amino acids contain nitrogen, so further catabolism of amino
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EIGENN LOYOLA

acids releases nitrogen-containing ammonia. Because ammonia is toxic, the liver

transforms it into urea, which is then transported to the kidney and excreted in the
urine. Urea is a molecule that contains two nitrogens and is highly soluble in water.
This makes it a good choice for transporting excess nitrogen out of the body.
Because amino acids are building blocks that the body reserves in order to
synthesize other proteins, more than 90 percent of the protein ingested does not
get broken down further than the amino acid monomers.

• Very little protein makes it to the large intestine if you are not eating excessive
amounts. If you have smelly flatulence, this may be a sign you are eating too much
protein because the excess is making it to the colon where you gut microbes are
digesting it and producing smelly gas.

Protein Absorption

In adults, essentially all protein is absorbed as tripeptides, dipeptides or amino acids and this process
occurs in the duodenum or proximal jejunum of the small intestine. The peptides and/or amino acids
pass through the interstitial brush border by facilitative diffusion or active transport. Active transport
sodium and ATP to actively transport the molecule through the cell membrane. The R group determines
the type of transporter used. Once passed through the membrane, the amino acids or peptides are
released into the intestinal blood stream and are transported to the liver by the hepatic (liver) portal
vein. This is known as the enterohepatic circulation.

In the liver, 50-65% remain and are used to synthesize protein, nitrogen containing compounds and
form purine/pyrimidine bases. In some cases, they may be converted to energy. The liver regulates
the amino acid levels in the blood. The amino acids that do not stay in the liver, pass through and are
transported to the rest of the body to be taken up and utilized by other cells. Most branch chain amino
acids pass through the liver.

Nitrogen Metabolism Overview

Amino acids are unique because they contain nitrogen. Several things can happen to the nitrogen.
First, it can remain on the molecule and be incorporated into the product that cell is making, for
example, a polypeptide. The nitrogen may be transaminated, in other words, the amine group (NH 2)
is transferred to another carbon skeleton to form a new amino acid. An example would be the
transfer of the amine from the non-essential amino acid, alanine, to alpha-ketoglutaric acid to make
glutamic acid, another non-essential amino acid. The water-soluble vitamin B6 is needed for this
process.

The amine group may be removed from the amino acid in a process known as deamination. This
process is used for the excretion of the nitrogen, and the carbon skeleton is used to produce energy.
Again, vitamin B6 is needed for this process.

The nitrogen removed from amino acids is excreted via several different routes. The most familiar
path is urine where most of the nitrogen is in the form of urea. Nitrogen is also excreted in the feces,
skin, hair, and nails. In skin, hair, and nails the nitrogen is bound to protein as this is the building
block of each.

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EIGENN LOYOLA

Amino Acids Are Recycled

Just as some plastics can be recycled to make new products, amino acids are recycled to make
new proteins. All cells in the body continually break down proteins and build new ones, a
process referred to as protein turnover. Every day over 250 grams of protein in your body are
dismantled and 250 grams of new protein are built. To form these new proteins, amino acids
from food and those from protein destruction are placed into a “pool.” Though it is not a literal
pool, when an amino acid is required to build another protein it can be acquired from the
additional amino acids that exist within the body. Amino acids are used not only to build
proteins, but also to build other biological molecules containing nitrogen, such as DNA and
RNA, and to some extent to produce energy. It is critical to maintaining amino acid levels within
this cellular pool by consuming high-quality proteins in the diet, or the amino acids needed for
building new proteins will be obtained by increasing protein destruction from other tissues
within the body, especially muscle. This amino acid pool is less than one percent of total body
protein content. Thus, the body does not store protein as it does with carbohydrates (as
glycogen in the muscles and liver) and lipids (as triglycerides in adipose tissue).

Figure 2. Amino Acids are Recycled

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 CC 103: BIOCHEMISTRY FOR MLS
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EIGENN LOYOLA

Lesson 2 Absorption and Transport of Amino Acid

It is an active process that needs energy derived from hydrolysis of ATP. It occurs in small
intestine.
Mechanisms of amino acids absorption

It is the main system for amino acid absorption. It is an active process that needs energy
derived from ATP. Absorption of one amino acid molecule needs one ATP molecule. There are 7
carrier proteins; one for each group of amino acids. Each

carrier protein has two sites one for amino acid and one for Na +. It co-transports amino acid
and Na+ from intestinal lumen to cytosol of intestinal mucosa cells. The absorbed amino acid
passes to the portal circulation, while Na+ is extruded out of the cell in exchange with K + by
sodium pump

Figure 3. Carrier Protein Transport System

Glutathione transport system (−Glutamyl cycle)

Glutathione is used to transport amino acids from intestinal lumen to cytosol of intestinal mucosa
cells. It is an active process that needs energy derived from ATP. Absorption of one amino acid
molecule needs 3 ATP molecules. Glutathione reacts with amino acid in the presence of −glutamyl
transpeptidase to form −glutamyl amino acid. −−glutamyl amino acid releases amino acid in the
cytosol of intestinal mucosa cells with formation of 5-oxoproline that is used for regeneration of
glutathione to begin another turn of the cycle.

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EIGENN LOYOLA

Clinical Applications

1. Oxoprolinuria: The deficiency of the enzyme 5-oxoprolinase leads to accumulation of 5-

oxoproline in blood and hence excreted in urine. It is associated with mental retardation.
2. The allergy to certain food proteins (milk, fish) is believed to result from absorption of
partially digested proteins.
3. Defects in the intestinal amino acid transport systems are seen in inborn errors of
metabolism such as cystinuria
4. Partial gastrectomy, pancreatitis, carcinoma of pancreas and cystic fibrosis may affect the
digestion and absorption of proteins.
5. Protein losing enteropathy: There is an excessive loss of proteins through the
gastrointestinal tract.

Figure 4. The −Glutamyl cycle

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EIGENN LOYOLA

Amino Acid Pool

The amount of free amino acids distributed throughout the body is called amino acid pool. Plasma
level for most amino acids varies widely throughout the day. It ranges between 4–5 mg/dl.
Following a protein containing meal, the amino acid levels rise to 45 to 100 mg / dl.

Tissue Amino Acids

• The amino acids are transported into tissues actively. Pyridoxal-P (B6-P) is one of the
requirement for this active transport. Tissue uptake is also favoured by hormones:
o Insulin, growth hormone and testosterone favour the uptake of amino acids by
tissues (anabolic hormones).
o Estradiol stimulates selectively their uptake by uterus.
o Epinephrine and glucocorticoids: Stimulate the uptake of amino acids by the
Liver.

Sources of Amino Acid Pool

• Dietary protein
• Breakdown of tissue proteins
• Biosynthesis of amino acids in liver (except essential amino acid)

Fate of Amino Acid Pool

• Biosynthesis of structural proteins e.g. tissue proteins.

• Biosynthesis of functional proteins e.g. haemoglobin, myoglobin, protein hormones and
enzymes
• Biosynthesis of small peptides of biological importance e.g. glutathione, and Thyrotropin
releasing hormone (TRH)
• Biosynthesis of non-protein nitrogenous compounds (NPN) as urea, uric acid, creatine,
creatinine and ammonia
• Catabolism of amino acids to give ammonia and -keto acids. Ammonia is transformed
mainly into urea

The -keto acids that remain after removal of ammonia from amino acids are called the
carbon skeleton.

• Energy production: oxidation

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EIGENN LOYOLA

Figure 5. Sources and utilization of amino acids

Lesson 3 Degradation of Amino Acid

The liver is the principal site of amino acid metabolism, but other tissues, such as the kidney, the
small intestine, muscles, and adipose tissue, take part. Generally, the first step in the breakdown
of amino acids is the separation of the amino group from the carbon skeleton, usually by a
transamination reaction. The carbon skeletons resulting from the deaminated amino acids are
used to form either glucose or fats, or they are converted to a metabolic intermediate that can be
oxidized by the citric acid cycle. The latter alternative, amino acid catabolism, is more likely to
occur when glucose levels are low—for example, when a person is fasting or starving.

Transamination

Transamination is an exchange of functional groups between any amino acid (except lysine,
proline, and threonine) and an α-keto acid. The amino group is usually transferred to the keto
carbon atom of α-ketoglutarate, converting the α-keto acid to glutamate. Transamination reactions
are catalyzed by specific transaminases (also called aminotransferases), which require pyridoxal
phosphate as a coenzyme.

In an α-keto acid, the carbonyl or keto group is located on the carbon atom adjacent to the
carboxyl group of the acid.

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EIGENN LOYOLA

Figure 6. Two transamination reactions. In both reactions, the final acceptor of the
amino group is a an α-ketoglutarate, and the final product is glutamate

Another important example of a transamination reaction is the formation of aspartate, which is

used during urea formation. In this case, the acceptor of the amino group is oxaloacetate. For
example, aspartate can be obtained from another amino acid such as alanine:

Figure 7. A transamination reaction in which aspartate is formed. In this case,

oxaloacetate is the amino group acceptor.

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EIGENN LOYOLA

Oxidative Deamination

In the breakdown of amino acids for energy, the final acceptor of the α-amino group is α
ketoglutarate, forming glutamate. Glutamate can then undergo oxidative deamination, in which it
loses its amino group as an ammonium (NH ) ion and is oxidized back to α-ketoglutarate (ready
to accept another amino group):

This reaction occurs primarily in liver mitochondria. Most of the NH ion formed by oxidative
deamination of glutamate is converted to urea and excreted in the urine in a series of reactions
known as the urea cycle.

The synthesis of glutamate occurs in animal cells by reversing the reaction catalyzed by glutamate
dehydrogenase. For this reaction nicotinamide adenine dinucleotide phosphate (NADPH) acts as
the reducing agent. The synthesis of glutamate is significant because it is one of the few reactions
in animals that can incorporate inorganic nitrogen (NH ) into an α-keto acid to form an amino acid.
The amino group can then be passed on through transamination reactions, to produce other amino
acids from the appropriate α-keto acids.

The Fate of the Carbon Skeleton

Any amino acid can be converted into an intermediate of the citric acid cycle. Once the amino
group is removed, usually by transamination, the α-keto acid that remains is catabolized by a
pathway unique to that acid and consisting of one or more reactions. For example, phenylalanine
undergoes a series of six reactions before it splits into fumarate and acetoacetate. Fumarate is an
intermediate in the citric acid cycle, while acetoacetate must be converted to acetoacetyl
coenzyme A (CoA) and then to acetyl-CoA before it enters the citric acid cycle.

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EIGENN LOYOLA

Figure 8. Fates of the Carbon Skeletons of Amino Acids

Those amino acids that can form any of the intermediates of carbohydrate metabolism can
subsequently be converted to glucose via a metabolic pathway known as gluconeogenesis. These
amino acids are called glucogenic amino acids. Amino acids that are converted to acetoacetyl-CoA
or acetyl-CoA, which can be used for the synthesis of ketone bodies but not glucose, are called
ketogenic amino acids. Some amino acids fall into both categories. Leucine and lysine are the only
amino acids that are exclusively ketogenic. Figure 4 summarizes the ultimate fates of the carbon
skeletons of the 20 amino acids. The table below summarizes the Glucogenic and Ketogenic Amino
Acids.

Figure 9. Glucogenic and Ketogenic Amino Acids

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The Urea Cycle

Ammonia can be produced by the break-down of amino acids, or by the gut bacteria in humans.
If the level of ammonia in the blood becomes too high, then it becomes toxic to the brain.
The urea cycle removes ammonia from the blood and makes urea, which is eventually excreted
as urine. This cycle is carried out by the cells of the liver, and, as the name suggests, the last step
of the process feeds into an earlier step of the cycle.

Figure 10. The Urea Cycle

Summary of the Urea Cycle

Ammonia is formed by the breakdown of amino acids/gut bacteria.
The mitochondrial stage:

• Carbamoyl phosphate is formed from ammonia and bicarbonate, by carbamoyl

phosphate synthetase (CPS).
• Ornithine transcarbamoylase (OTC) condenses carbamoyl phosphate and ornithine to
form citrulline.
• Citrulline is then transported to the cytosol by SLC25A15.

The cytosolic stage:

• Argininosuccinate synthetase (AS) condenses citrulline and aspartate to

form argininosuccinate.
• Argininosuccinate is broken down into arginine and fumarate by argininosuccinate
lyase (AL).
• Arginine is broken down into urea and ornithine by arginase.

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• Ornithine translocase transports ornithine into the mitochondria

The Mitochondrial Stage

The first two steps of the urea cycle occur in the mitochondria of the cell. First, the enzyme
CPS takes ammonia and bicarbonate and forms carbamoyl phosphate with the use of
adenosine triphosphate (ATP). This is the step in the cycle that determines how fast the
cycle progresses. N-acetylglucosamine is also required for CPS to function, and functions as
a regulator for the formation of urea.
OTC then condenses carbamoyl phosphate and ornithine, which forms citrulline. This
citrulline is then moved out of the mitochondria into the cytosol of the cell by the transporter
SLC25A15.

The Cystolic Stage

AS takes the citrulline formed in the mitochondrial stage and condenses it with aspartate
to form argininosuccinate. This occurs by the formation of an intermediate, citrulline-AMP.

Argininosuccinate is then broken into arginine and fumarate by AL. Fumarate is then
incorporated into another metabolic cycle, the tricarboxylic acid (TCA) cycle. The TCA cycle,
which is also known as the citric acid cycle or the Krebs cycle, can then reform aspartate,
which is used by AS.

Arginine is then further broken down into urea and ornithine by arginase. Arginine can
also be acquired from the diet, and this can also be taken in by the liver cells and broken
down into urea and ornithine by arginase.

The ornithine is then transported into the mitochondria by ornithine translocase. There, it
is used by OTC again to form citrulline. The citrulline is then processed to form urea and
ornithine again, and the cycle continues. During the cycle, urea is the only new product
which is formed, while all other molecules used in the cycle are recycled.

Clinical Applications

If there is a problem with the urea cycle, then the level of ammonia in the blood will rise,
causing hyperammonemia. Ammonia is able to cross the barrier between the bloodstream
and the brain. Once it enters the brain, it can stop the TCA cycle by depleting one of the
metabolites, α-ketoglutarate. This means that these brain cells cannot make energy,
ultimately leading to their death. This eventually will lead to neurological problems, which
can be as severe as irreversible brain damage.

Problems can arise as a redsult of damage to the liver (cirrhosis) or by an inherited defect
in one of the above enzymes. In both cases, the level of ammonia rises with the potential
consequences previously detailed.

Inherited urea cycle defects are part of “inborn errors in metabolism”, and are known as
“urea cycle disorders.” Symptoms usually present in newborns around 24-48 hours after
birth. The most severe symptoms are seen in newborns with a defect in CPS.
Treatment for hyperammonemia consists of removing protein from the diet, removing the
excess ammonia and supplementing with molecules of the urea cycle which are missing.
Also, sodium benzoate and sodium acetate can be used to form ammonia-containing
compounds that can be excreted through feces.

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The sugar lactulose has been shown to reduce the production of ammonia by the gut
bacteria, as well as promote the excretion of ammonia through the feces. Alternatively,
antibiotics can be used to eliminate the ammonia-forming gut bacteria.

Uric Acid

Humans also excrete a second nitrogenous waste, uric acid. It is the product of nucleic acid, not
protein, metabolism. It is produced within peroxisomes, and it is excreted in the urine, or
reabsorbed by kidneys to regulate blood levels. Uric acid is a potent antioxidant and thus can
protect cells from damage by reactive oxygen species (ROS). In human blood plasma,
the reference range of uric acid is typically 3.4–7.2 mg per 100 mL for men, and 2.4–6.1 mg per
100 mL for women. Uric acid concentrations in blood plasma above and below the normal range
are known as, respectively, hyperuricemia and hypouricemia.

Uric acid is only slightly soluble in water and easily precipitates out of solution forming needle-like
crystals of sodium urate. These contribute to the formation of kidney stones and produce the
excruciating pain of gout when deposited in the joints.

Uric acid is only slightly soluble in water and easily precipitates out of solution forming needle-like
crystals of sodium urate. These contribute to the formation of kidney stones and produce the
excruciating pain of gout when deposited in the joints. The concentration of uric acid is 100-times
greater in the cytosol than in the extracellular fluid. So when lethally-damaged cells release their
contents, crystals of uric acid form in the vicinity.

So the risk of kidney stones and gout may be the price we pay for the antioxidant protection
provided by uric acid.

Most mammals have an enzyme - uricas - for breaking uric acid down into a soluble product.
However, during the evolution of great apes and humans, the gene encoding uricase became
inactive. A predisposition to gout is our legacy.

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Amino Acid Synthesis

In humans, only half of the standard amino acids (Glu, Gln, Pro, Arg, Asp, Asn, Ala, Gly, Ser, Tyr, Cys)
can be synthesized, and are thus classified the nonessential amino acids.

Most amino acids are synthesized from α-ketoacids or α-hydroxy acids (3-phosphoglycerate), and
later transaminated from another amino acid (usually glutamate). The enzyme involved in this reaction
is an aminotransferase. Glutamate is usually the amino group donor for this reaction: α-ketoacid +
glutamate ⇄ amino acid + α-ketoglutarate.

Glutamate itself is regenerated by the amination of α-ketoglutarate, catalyzed by Glutamate

dehydrogenase:

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The carbon skeletons used for the synthesis of amino acids are intermediates of the glycolysis
pathway and the citric acid cycle (see table below)

Source of carbon skeleton used for the synthesis of non-essential amino acids.

Tyrosine is another amino acid that depends on an essential amino acid as a precursor.
In this case, phenylalanine hydroxylase oxidizes phenylalanine to produce tyrosine:

Phenylketonuria is a genetic disorder that results in low levels of

the enzyme phenylalanine hydroxylase. This results in the buildup of dietary
phenylalanine to potentially toxic levels. Untreated, PKU can lead
to intellectual disability, seizures, behavioral problems, and mental disorders. It may also
result in a musty smell and lighter skin.

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Learning Tasks:

1. Make a concept map showing the digestion of proteins from the mouth to the small
intestine. Include the parts of the digestive system, the processes and enzymes involved.

2. Answer the following questions:

a. Amino acids are not stored in the body. Describe how excess amino acids are
processed in the cell.
b. Release of trypsin and chymotrypsin in their active form can result in the digestion of
the pancreas or small intestine itself. What mechanism does the body employ to
prevent its self-destruction?
c. Write the equation for the transamination reaction between alanine and oxaloacetate
and name the products that are formed.
d. What is the purpose of oxidative deamination? What is its role in the amino acid
degradation.
e. What is the relationship between urea cycle and uric acid formation in humans?
f. Explain how some amino acids are considered as non-essential? Write the various
chemical reactions involved in their synthesis.

3. Summarize the urea cycle by writing the various chemical equation involved in the series
of chemical reactions in the cycle.

4. List ten (10) amino acid disorders in humans caused by errors or abnormality in amino
acid metabolism. Use the table below.

Amino Acid Description Amino Acid Mode of diagnosis

Disorder Involved

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5. Offline and Online Quiz in SILID

References:
Chua, J.M.T (2022). Biological chemistry. Lorimar Publishing House Inc.

Stoker, S. H (2017). General, Organic and Biochemistry. Houghton Mifflin College Div; 4th edition
https://med.libretexts.org/Courses/American_Public_University/APUS%3A_An_Introduction_to_Nutrition_(B
yerley)/APUS%3A_An_Introduction_to_Nutrition_1st_Edition/05%3A_Proteins/5.04%3A_Protein_Digestion_
Absorption_and_Metabolism
https://uomustansiriyah.edu.iq/media/lectures/2/2_2021_09_27!11_30_32_AM.pdf
https://www.news-medical.net/health/The-Urea-Cycle-Step-by-Step.aspx
https://chem.libretexts.org/Courses/Brevard_College/CHE_301_Biochemistry/10%3A_Metabolism_of_Amino_
Acids/10.03%3A_Urea_Cycle

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