Amino acids are essential for every metabolic processes taking place in the

body. They can be acquired through the diet (essential) or through amphibolic
intermediates (non-essential) and, are used in various processes in the body e.g.
cellular repair, production of hormones, immunoglobulin synthesis and energy. When
the blood is saturated with amino acids, the liver will metabolize these units removing
the nitrogen component though different processes such as decarboxylation,
transamination, oxidative deamination, and urea formation. Therefore, excess amino
acids are not stored in the body as protein but are deaminated to form ammonia which
is then converted to urea by the liver. The carbon skeletons are then converted to either
glucose or ketone bodies dividing the amino acids into ketogenic (Leucine, Lysine), both
ketogenic and glucogenic (Phenylalanine Tryptophan, Tyrosine, Isoleucine, Threonine),
an glucogenic alone which includes the remaining amino acids. In addition, they can
also be catabolized to amphibolic intermediates that serve as energy for the
biosynthesis of carbohydrates and lipids. Amino acid metabolism is affected by several
factors such as diet, exercise, and age.

Urine Formation

Figure 3. Renal tubular transport mechanism

The process of urine formation, as shown in the figure above, involves a series of
filtration and reabsorption of water and solutes across the functional unit of the kidney-
the nephrons. The kidneys filter unwanted substances from the blood and produce urine
to excrete them. There are three main steps of urine formation: glomerular filtration,
reabsorption, and secretion. These processes ensure that only waste and excess water
are removed from the body. First, the glomerulus filters water and other substances
from the bloodstream. Each kidney contains over 1 million tiny structures called
nephrons. Each nephron has a glomerulus, the site of blood filtration. The glomerulus is
a network of capillaries surrounded by a cuplike structure, the glomerular capsule (or
Bowman’s capsule). As blood flows through the glomerulus, blood pressure pushes
water and solutes from the capillaries into the capsule through a filtration membrane.
This glomerular filtration begins the urine formation process. Second, the filtration
membrane keeps blood cells and large proteins in the bloodstream. Inside the
glomerulus, blood pressure pushes fluid from capillaries into the glomerular capsule
through a specialized layer of cells. This layer, the filtration membrane, allows water and
small solutes to pass but blocks blood cells and large proteins. Those components
remain in the bloodstream. The filtrate (the fluid that has passed through the
membrane) flows from the glomerular capsule further into the nephron. Third,
reabsorption moves nutrients and water back into the bloodstream. The glomerulus
filters water and small solutes out of the bloodstream. The resulting filtrate contains
waste, but also other substances the body needs: essential ions, glucose, amino acids,
and smaller proteins. When the filtrate exits the glomerulus, it flows into a duct in the
nephron called the renal tubule. As it moves, the needed substances and some water
are reabsorbed through the tube wall into adjacent capillaries. This reabsorption of vital
nutrients from the filtrate is the second step in urine creation. Lastly, waste ions and
hydrogen ions secreted from the blood complete the formation of urine. The filtrate
absorbed in the glomerulus flows through the renal tubule, where nutrients and water
are reabsorbed into capillaries. At the same time, waste ions and hydrogen ions pass
from the capillaries into the renal tubule. This process is called secretion. The secreted
ions combine with the remaining filtrate and become urine. The urine flows out of the
nephron tubule into a collecting duct. It passes out of the kidney through the renal
pelvis, into the ureter, and down to the bladder.

It should be noted that urine is 95% water. The percentage composition of salts,
ammonia, urea, water and other components of urine.The nephrons of the kidneys
process blood and create urine through a process of filtration, reabsorption, and
secretion. Urine is about 95% water and 5% waste products. Nitrogenous wastes
excreted in urine include urea, creatinine, ammonia, and uric acid. Ions such as sodium,
potassium, hydrogen, and calcium are also excreted.

Almost all amino acids are reabsorbed in the proximal tubule. However, excess amino
acids in the body which are deaminated to form ammonia, is then converted to urea by
the liver.

Amino acid metabolism and excretion

When amino acids are absorbed by liver cells a series of chemical reactions
begins. The amino acid is oxidized in the presence of an enzyme catalyst. At the same
time the amine group, -NH2, and a hydrogen atom, H, are removed from the main
structure of the amino acid. The important product of this reaction is ammonia. The
amine group is reduced to ammonia by the addition of a hydrogen atom. This process is
called deamination. The non-nitrogenous portion of the molecule is converted to
carbohydrates or fats.

The overall equation for deamination of an amino acid in the liver is:

2 NH2CHRCOOH + O2      2 CROCOOH + 2 NH3

Figure 4. Deamination of Amino Acids

The amino acids serine and threonine can be deaminated directly. For example,
serine     pyruvate + NH4+

Ammonium ions exist in aqueous solution in dynamic equilibrium with ammonia

molecules
NH3 + H2O     NH4+ + OH-

Ammonia is highly toxic in the body and therefore cannot be allowed to accumulate.
With the help of specific catalysts in the liver cells carbon dioxide reacts chemically with
the ammonia molecule, NH3. The less toxic nitrogenous compound urea is produced
together with water.

CO2 + 2NH3     (NH2)2CO + H2O

This series of reactions is called the ornithine cycle. The urea and water are
released from the liver cells to the bloodstream and transported to the kidneys where
the blood is filtered and the urea is passed out of the body in the urine. Urea is very
soluble and a small molecule, so it is relatively easily passed out by the kidneys as a
solution in water.
 Disorders of amino acid metabolism are usually accompanied with signs and
symptoms at a young age, thus, the significance of newborn screening. The most
commonly known disorders are phenylketonuria (phenylalanine buildup), maple syrup
urine disease (unable to breakdown branched-chain amino acids), homocystinuria
(cystathionine beta synthase deficiency; buildup of homocysteine and derivatives), and
tyrosinemia (tyrosine buildup).

Urine Analysis

Urine analysis is one of the methods used to provide information regarding amino
acid wasting and aberrant metabolism associated with cofactor insufficiencies. In the
experiment, amino acid metabolism was assessed in the urine of a well-rested subject
that has taken a high carbohydrate meal. The following parameters were assessed:
urine pH, urine specific gravity, urine protein concentration, urine nitrogen
concentration, and urine glucose concentration.

Figure X. Urine test strip

The dipstick test was used to assess the urine (Fig X). A urine test strip or dipstick test
is a basic diagnostic tool used to determine pathological changes in a patient’s urine in
standard urinalysis. A standard urine test strip may comprise up to 10 different chemical
pads or reagents which react (change color) when immersed in, and then removed
from, a urine sample. The test can often be read in as little as 60 to 120 seconds after
dipping, although certain tests require longer. Routine testing of the urine with
multiparameter strips is the first step in the diagnosis of a wide range of diseases. The
analysis includes testing for the presence of proteins, glucose, ketones, haemoglobin,
bilirubin, urobilinogen, acetone, nitrite and leucocytes as well as testing of pH and
specific gravity or to test for infection by different pathogens.

Urine pH

Urine pH represents the relative acidity or alkalinity of urine. It is normally acidic

to maintain the alkalinity of the blood. The acidic urine is due to the presence of urine
acidifying methionine. Freshly voided urine is usually with pH of ~6 with the normal
range between 4.8 and 7.5. It varies with the time of day and diet. High acidity is
present in acidosis, fevers, and high protein diets. Furthermore, a healthy adult usually
produces a more alkaline pH after a meal, a phenomenon called alkaline tide. Other
factors that can increase urine pH includes exercise, high protein intake, some drugs
that acidify urine, and more.

The subject has a urine pH of 6.0 which indicates that the subject has normal pH
urine. Since the patient has an intake of high carbohydrate meal, a more acidic pH is
not expected. Due to the normal functioning of the Na+/ H+ exchanger, the pH was
maintained at normal levels. Well-rested individuals are expected to have a physiologic
acidic urine pH which is only due to the normal physiologic processes in the kidney.
However, the fasting of the individual can contribute to the acidity due to an increase
metabolism of protein that increases the ammonium concentration, but this is well-
compensated by the high carbohydrate meal before fasting.

The principle of pH testing is shown in the figure below:

Figure X. pH test principle

Urine specific gravity

Urine specific gravity is the ratio of weight of a volume of urine to the weight of an equal
volume of water. Measuring specific gravity is important in determining the ability of
renal tubules to concentrate or dilute the glomerular filtrate. Specific gravity is increased
if there is urine concentration or presence of proteins or glucose. As a homeostatic
response to varying dietary intake, the body will still be able to maintain the urine
specific gravity. The normal urine specific gravity ranges from 1.000-1.035. It is
important to note that urine will always have a value greater than 1.000 under normal
circumstances due to the solutes it contains.

The subject has a urine specific gravity of 1.030. This is still in the normal range.
Theoretically, the patient with high carbohydrate intake but is well-rested should have a
normal specific gravity of urine due to the absence of factors that can further increase
the specific gravity of urine such as glucose, protein, or other electrolytes. High specific
gravity may indicate damage in the tubular walls or it may also be due to dehydration.

The principle of specific gravity testing is shown in the figure below:

Figure X. Specific gravity test principle

Urine protein concentration

Proteins normally can’t pass through the glomerular filtration barrier unless acted upon
by certain factors like exercise and fever. However, small proteins can pass through the
glomerular filtration barrier but are immediately reabsorbed in the proximal convoluted
tubule through endocytosis. Normally, protein component of urine is 0 or negative or
minute traces. Albumin is the major serum protein found in normal urine Other proteins
include: small amounts of serum and tubular microglobulins, Tamm- Horsfall protein.
Proteinuria or high levels of protein in urine, usually in the form of albumin, is due to
endothelial damage in the filtration barrier of the walls of the nephrons. This may be due
to a persistent and uncontrolled hypertension and/or diabetes mellitus. Furthermore,
microalbuminuria is the presence of albumin in urine above the normal level but below
the detectable range of conventional urine dipstick methods. This is an indicator of early
and possibly reversible glomerular damage. The Microalbumin test or micral test may
be useful in detecting early development of renal failure or diabetic nephropathy
(Strasinger & Di Lorenzo, 2014.)

The subject has a negative result for the test of urine albumin which agrees theoretically
since the subject had no damaged in the filtration barrier, nor was induced with a high
amount of protein. Also, glucose is protein-sparing. The absence of protein indicated
that proteins are more consumed for tissue building and maintenance instead of being
used as an emergency source of energy.
The principle of urine protein testing is shown in the figure below:

Figure X. Urine protein test principle

Urine nitrogen concentration

Excess amino acids are degraded to form ammonia which will then undergo urea cycle
to form urea. Figure X below shows the urea cycle.

Figure 2. Urea cycle

Of concern in protein metabolism is the ammonia formed as its byproduct. This is

processed in the liver through the urea cycle, which converts it to urea, which is soluble
in urine. In the kidneys, urea is partly reabsorbed in the proximal tubules. As an
effective osmole, it could affect the movement of water and solutes. It builds the
osmolality in the medullary interstitium as well as serve as an osmole in renal tubular
fluid. Its transport across the renal tubule is affected with hormonal regulation, in
particular the antidiuretic hormone. The pathway below shows the summary of the urea
cycle.
 α-amino nitrogen is transferred to α-ketoglutarate via transamination à
glutamate à oxidative phosphorylation à ammonia à excreted by kidneys
OR amidation of ammonia with glutamate à glutamine à glutaminase à
glutamate and ammonia à urea cycle à urea

Normal urine nitrogen is 12-20 grams per 24 hours. However, in the

experiment, the subject only has trace amount of urine nitrogen, this may
be due to the precision in the measurement of nitrogen using the dipstick
as the tool. Sensitivity of the dipstick to a certain amount of nitrogen can
be consider as a factor for the deviation of the subject’s nitrogen to the
range of values. Since the subject is in fasting state, the urine nitrogen is
expected to increased. However, the glucose from the high carbohydrate
meal compensated to prevent the use of protein as an alternative energy
source.

Urine glucose concentration

Glucose is almost completely reabsorbed in the renal proximal tubule which explains for
no glucose component in urine. The presence of detectable amounts of glucose in
urine is termed glycosuria which occurs whenever the glucose level in the blood
surpasses the renal tubule capacity for reabsorption, usually blood glucose level of
greater than 180–200 mg/dL. Diabetic patients usually present glycosuria as a
preliminary sign of diabetes.

The subject has negative glucose in the urine. This indicates that the subject has a
normal glucose absorption in the proximal tubule. Even though the subjected has taken
a high carbohydrate meal before the test, normal physiologic functions worked on the
subject to preserve the excess glucose through glycogenesis and glucogenolysis.
Therefore, the normal subject who took a high carbohydrate meal, although well rested,
agreed theoretically that no trace of glucose was found in the urine.

The principle of urine glucose testing is shown in the figure below:

Figure X. Urine glucose test principle

 To summarize, in a high carbohydrate diet yet well rested state, the subject is
expected that all the parameters the urinalysis would be in the normal ranges due to the
capacity of the kidneys to reabsorb glucose in the proximal tubules via the sodium-
glucose transporters. Since it is reabsorbed early on in urine formation, there should be
no traces of glucose in the urine output. Albumin should also present a negative result
as it is not filtered into the ultrafiltrate when blood passes through the glomerular
capillaries.