Dr Ajayi Olulope Olufemi and Itepu Victor   (Published 2019)

Dr Olulope Olufemi
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Lecture Note

Department of Biochemistry
BCH 314: Amino acid, Protein and Nucleic acid Metabolism
Instructor: Dr. Olulope Ajayi, email: olulope.olufemi@edouniversity.edu.ng
Lectures: Tuesday (3-5 pm). LT6. Phone (+234) 8063737930
Office hours: Monday-Friday (8.00 am-4.00 pm). Office: New College of Medical Sciences and
Faculty of Engineering Office Block, 1st floor, Rm AD 82
Co-Instructor: Dr. Itepu E. Victor, email: itepu.victor@edouniversity.edu.ng
Lectures: Mondays, 2pm – 4pm, LT6.phone: (+234) 8067175111
Office hours: Mondays, 10am to 2pm, Office: College of Medicine building, 1st floor, Rm 85.
General overview of the Course
The course covers the following topic: Detailed treatment of metabolism of amino acids,
degradation and biosynthesis. Oxidative and non-oxidative deamination, transamination and
decarboxylation, transamidation. Disorders of amino acid metabolism. Inborn errors of
metabolism. Metabolism of inorganic nitrogen. Transport and toxicity of ammonia. The urea
cycle. Creatine metabolism. Polyamines. Nucleoside, nucleotide and nucleic acid synthesis and
degradation. One carbon metabolism. Transmethylation. Disorders of nucleotide metabolism.
Hyperuricemia and other inborn errors. Protoporphyrin synthesis in animals and plants. Hormone
and regulatory role inintermediary metabolism.
Intended Learning Outcomes
At the end of this aspect of the course, students should be able to
1. Discuss the metabolism of amino acids
2. Discuss the different processes involved in the metabolism of amino acids
3. Relate derangements in the metabolism of amino acids as well as inborn errors of
4. Discuss the transport and toxicity of ammonia.
5. Discuss the urea cycle
6. Discuss creatine biosynthesis
7. Discuss the metabolism of nucleoside, nucleotide and nucleic acids
8. The disorders of nucleotide metabolism
9. Explain one carbon metabolism
Assignments: We expect to have 5 individual homework assignments throughout the course in
addition to a Mid-Term Test and a Final Exam. Home works are due at the beginning of the class
on the due date. Home works are organized and structured as preparation for the midterm and
final exam, and are meant to be a studying material for both exams. There will also be 2 term
papers are expected to be written by individuals taking this course. This is aimed at broadening
students; knowledge of the course.
Grading: We will assign 10% of this class grade to home works, 10% for the term papers, 10%
for the mid-term test and 70% for the final exam. The Final exam is comprehensive.
Textbooks: The recommended textbooks for this class are as stated:
Title: Lehninger Principles of Biochemistry
Authors: David L. Nelson, Michael M. COX
Publisher: Freeman, W. H. and Company, Seventh Edition
ISBN- 13: 9787464126116
Year: 2017
Title: Textbook of Medical Biochemistry
Author(s): MN Chatterjea and RanaShinde.
Publisher: Jaypee Brothers Medical Publishers Ltd, Eighth Edition
ISBN: 978-93-5025-484-4
Year: 2012
Title: Textbook of biochemistry for Medical Students
Author(s): DM Vasudevan, Sreekumari S and KannanVaidyanathan.
Publisher: Jaypee Brothers Medical Publishers Ltd, Sixth Edition
ISBN: 978-93-5025-016-7
Year: 2011
Title: Lippincott’s Illustrated Reviews Biochemistry
Author: Denise R. Ferrier
Publisher: Lipincott Williams & Wilkins
ISBN: 978-1-4511-7562-2
Year: 2014
Title: Harper’s Illustrated Biochemistry. 28th edition
Authors: Robert K. Murray, Daryl K. Granner, Victor W. Rodwell
Publisher: McGraw Hill Lange
Title: Essential Cell Biology
Authors: Alberts Bray, Hopkin Johnson, Lewis Raff, Roberts Walter
Publisher: Garland Science
Year: 2004
Amino acid digestion
Most of the nitrogen in the diet is consumed in the form of protein, typically amounting to 70–
100 g/day in the diet. Proteins are generally too large to be absorbed by the intestine. An
example of an exception to this rule is that newborns can take up maternal antibodies in breast
milk. They must, therefore, be hydrolyzed to yield di- and tripeptides as well as individual amino
acids, which can be absorbed. Proteolytic enzymes responsible for degrading proteins are
produced by three different organs: the stomach, the pancreas, and the small intestine. In the
stomach, pepsin is the major proteolytic enzyme. It cleaves proteins to smaller polypeptides.
Pepsin is produced and secreted by the chief cells of the stomach as the inactive zymogen
Hydrochloric acid (HCl) produced by the parietal cells of the stomach causes a conformational
change in pepsinogen that enables it to cleave itself (autocatalysis), forming active pepsin.
Pepsin has a broad specificity but tends to cleave peptide bonds in which the carboxyl group is
contributed by the acidic amino acids, aromatic amino acids, or leucine. In the intestine, the
partially digested material from the stomach encounters pancreatic secretions, which include
bicarbonate and a group of proteolytic enzymes. Bicarbonate neutralizes the stomach acid,
raising the pH of the contents of the intestinal lumen into the optimal range for the digestive
enzymes to act.
Endopeptidases from the pancreas cleave peptide bonds within protein chains. Trypsin cleaves
peptide bonds in which the carboxyl group is contributed by arginine or lysine. Trypsin is
secreted as the inactive zymogen trypsinogen. Trypsinogen is cleaved to form trypsin by the
enzyme enteropeptidase (enterokinase), which is produced by intestinal cells. Trypsinogen may
also undergo autocatalysis by trypsin. Chymotrypsin usually cleaves peptide bonds at the
carboxyl group of aromatic amino acids or leucine. Chymotrypsinogen, the inactive zymogen, is
cleaved to form active chymotrypsin by trypsin.
Elastase cleaves at the carboxyl end of amino acid residues with small, uncharged side chains
such as alanine, glycine, or serine. Proelastase, the inactive zymogen, is cleaved to active
elastase by trypsin. Exopeptidases in the pancreas (carboxypeptidases A and B) cleave one
amino acid progressively from the C-terminal end of the peptide.
The carboxypeptidases are produced as inactive procarboxypeptidases, which are cleaved to their
active form by trypsin. Carboxypeptidase A cleaves aromatic amino acids from the C terminus.
Carboxypeptidase B cleaves the basic amino acids, lysine and arginine, from the C terminus.
Proteases produced by intestinal epithelial cells complete the conversion of dietary proteins to
peptides and finally to amino acids. Aminopeptidases are exopeptidases produced by intestinal
cells, cleaving one amino acid at a time from the N terminus of peptides. Dipeptidases and
tripeptidases associated with the intestinal cells produce amino acids from dipeptides and
Amino acid absorption
Amino acids resulting from protein digestion are absorbed from the small intestine by:
1. Passive transport mechanism (For D-amino acids).
2. Active transport mechanism (For L-amino acids and dipeptides), and this occurs via;
3. Carrier protein transport system
(sodium – amino acid carrier system).
4. Glutathione transport system
(?-glutamyl cycle)
Carrier protein transport system (sodium – amino acid carrier system)
This system transport the amino acids against its concentration gradient using energy derived
from Na/K+ pump. Here, amino acids are absorbed by specific carrier protein in the cell
membrane of the small intestinal cells. This carrier protein has one site for the amino acids and
another site for the Na+.
It transports them from the intestinal lumen across the cell membrane to the cytoplasm.
Then, the amino acid passes to the blood down its concentration gradient, while the Na+ is
pumped out from the cell to the intestinal lumen by Na/K+ pump utilizing ATP as a source of
energy derived from Na/K+ pump.
Glutathione transport system (?-glutamyl cycle)
This transport system is for the transport of amino acids from the extracellular space to the
cytoplasm in the intestine, kidney, brain & liver (bile ductile cells).
An amino acid in the lumen reacts with glutathione (g-glutamyl-cysteinyl-glycine) in the cell
membrane, forming a g-glutamyl amino acid and the dipeptide cysteinyl-glycine.
The amino acid is carried across the cell membrane attached to g-glutamate and released into the
cytoplasm. The g-glutamyl moiety is used in the resynthesis of glutathione.
In infants, Ig A in the clostrum of milk is absorbed without digestion by pinocytosis, thereby
giving immunity to the babies.
Amino acid degradation
There are 3 common stages of amino acid degradation:
Deamination; the removal of amino group(s) which are converted into:
ammonia or the amino group of aspartate.
Incorporation of ammonia or aspartate nitrogen into urea for excretion.
Conversion of the amino acid carbon skeletons (i.e. the a-keto acids that result from
deamination) to the common intermediates.
The first step in amino acid breakdown usually is removal of an alpha-amino group and it is
achieved through the following processes;
1. Transamination
2. Deamination
3. Oxidative deamination
4. Non-oxidative deamination
5. Transdeamination
Specific methods of deamination, which applies to some specific amino acids.
It is the transfer of amino group from one ?- a.a. to ?- keto acid to form a new ?- amino acid & a
new ?- keto acid.
Transamination reactions are readily reversible and can be used in the synthesis or the
degradation of amino acids.
The process represents only an intermolecular transfer of NH2 group without the splitting out of
NH3. Ammonia formation does not take place by transamination reaction.
Enzymes involved:
Transaminases or aminotransferases
Coenzyme: PLP (Pyridoxal phosphate)
Transamination occurs in two stages:
Transfer of the amino group to the coenzyme pyridoxal phosphate (bound to the coenzyme) to
form pyridoxamine phosphate The amino group of pyridoxamine phosphate is then transferred to
a keto acid to produce a new amino acid and the enzyme with PLP is regenerated.
Transamination takes place in the cytosol or both the cytosol & the mitochondria of most cells
especially in the liver, kidney, heart and brain.
But the enzyme is present in almost all mammalian tissues and transamination can be carried out
in all tissues to some extent.
All amino acids except threonine, lysine, proline and hydroxyproline may undergo
transamination. As an example, amino group is interchanged between alanine and glutamic acid.
In almost all cases, the amino group is accepted by alpha ketoglutaric acid so that glutamic acid
is formed. ?-ketoglutarate& glutamate are often involved in transamination reactions.
Clinical importance of transamination
Function of transaminases:
Degradation of a.as to form ?- keto acids.
Synthesis of non essential a.as from CHO.
Diagnostic value:
Transaminases are normally intracellular enzymes. They are elevated in the blood when damage
to the cells producing these enzymes occurs.
Increased level of both ALT & AST indicates possible damage to the liver cells.
Increased level of AST alone suggest damage to heart muscle, skeletal muscle or kidney.
The removal of an amino group from the amino acids as NH3 is deamination.
Deamination results in the liberation of ammonia for urea synthesis. Simultaneously, the carbon
skeleton of amino acids is converted to keto acids.
Although transamination and deamination are separately discussed, they occur simultaneously,
often involving glutamate as the central molecule. For this reason, some authors use the term
transdeamination while describing the reactions of transamination and deamination, particularly
involving glutamate.
Deamination is of two types;
1. Oxidative deamination and
2. Non-oxidative deamination
Oxidative deamination
Oxidative deamination is the oxidation(removal of hydrogen) and deamination (removal of the
amino group which is liberated as free ammonia) giving ?- ketoacid and ammonia (reversible
reactions). Oxidative deamination takes place mostly in the liver and kidney. The purpose of
oxidative deamination is to provide NH3 for urea synthesis and ?-keto acids for a variety of
reactions, including energy generation.
Regulation: The direction of the reaction depends on:
Availability of the substrates:
--Relative concentration of (?-ketoglutarate&NH3) and (glutamate).
--Ratio of NADP : NADPH+H
Allosteric regulation:
--Activators : ADP or GDP.
-- Inhibitors : ATP ,GTP & NADH
D- & L- Amino acid oxidases :
Present only in the liver and kidney in minimal amounts.
They are of low activity in the mammalian tissue
N.B: L-amino acids: mammalian proteins are formed of only L-amino acids. D-amino acids are
found in plants and the cell wall of microorganisms but not used in the synthesis of mammalian
proteins. L-amino acid oxidase deaminates most of the naturally occuring amino acids. Damino
acid oxidase deaminates D-amino acids present in diet giving ?- keto acids that either
transaminated to the coressponding L-amino acid or converted to glucose or fatty acids or
catabolized to CO2 + H2O + energy.
Clinical importance of oxidative deamination
L-glutamate dehydrogenase enzyme is the only enzyme that undergoes oxidative deamination in
the mammalian tissue.
Oxidative deamination by L- glutamate dehydrogenase is an essential component of
So, it is important in deamination of most amino acids.
L-Amino acid oxidase and D-amino acid oxidase are flavoproteins, possessing FMN and FAD
respectively. They act on the corresponding amino acids (L or D) to produce a-keto acids and
NH3. In this reaction, oxygen is reduced to H2O2, which is later decomposed by catalase.
Non-oxidative deamination
There are certain amino acids, which can be non-oxidativelydeaminated by specific enzymes,
and can form NH3. These reactions do contribute to NH3 formation, but they do not fulfill a
major role in NH3 formation.
Examples of non-oxidative deamination include:
Deamination of histidine: Histidine is non-oxidativelydeaminated by the specific enzyme
Histidase to form NH3 and urocanic acid.
Amino acid dehydrases: The hydroxy amino acids viz serine, threonine and homoserine are
deaminated by specific enzymes, called amino acid dehydrases which requires Pyridoxal-P (B6-
P) as coenzyme. The enzymes catalyze a primary dehydration followed by spontaneous
Amino acid desulfhhydrases: S-containing amino acids, e.g. cysteine, and homocysteine are
deaminated by a primary desulfhydration (removal as H2S), forming an imino acid, which is
then spontaneously hydrolysed.
It is the combination of transamination & oxidative deamination.
It includes the transamination of most amino acids with ?– ketoglutarate to form glutamate, then
the glutamate is oxidativelydeaminated reforming ?– ketoglutarate and giving ammonia.
This provides a pathway by which the amino group of most amino acids is released in the form
of ammonia.
The amino group of most of the amino acids is released by a coupled reaction, transdeamination,
that is transamination followed by oxidative deamination.
Transamination takes place in the cytoplasm of all the cells of the body; the amino group is
transported to liver as glutamic acid which is finally oxidativelydeaminated in the mitochondria
of hepatocytes.
Thus, the two components of the reaction are physically far away, but physiologically they are
coupled. Hence, the term trans-deamination.
Decarboxylation is the reaction by which CO2 is removed from the COOH group of an amino
acid as a result an amine is formed.
The reaction is catalysed by the enzyme decarboxylase, which requires pyridoxal-P (B6-PO4) as
Tissues like liver, kidney, brain possess the enzyme decarboxylase and also by microorganisms
of intestinal tract.
The enzyme removes CO2 from COOH group and converts the amino acid to corresponding
amine. This is mostly a process confined to putrefaction in intestines and produces amines.
Examples of biogenic amines are Histamine (from histidine), GABA (from glutamic acid),
ethanolamine (from serine), taurine (from cysteic acid), putrescine (from ornithine)
Polyamines are putrescine, spermidine and spermine.
They are aliphatic amines.
They are synthesized from Ornithine. Ornithine in addition to its role in urea cycle, serves as the
precursor of ubiquitous mammalian and bacterial polyamines, spermidine and spermine. It
requires ‘active’ methionine.
The key enzyme of polyamine synthesis is ornithine decarboxylase (ODC). It requires pyridoxal
phosphate, and is induced by steroid hormones.
The enzyme,ODC has pyruvate (not PLP) as the prosthetic group; it is the only mammalian
enzyme, known to contain bound pyruvate
Biochemical Functions of Polyamines
They have been implicated in diverse physiological processes and are involved in cell
proliferation and growth. Putrescine is best “marker” for cell proliferation.
They are required as ‘growth factors’ for cultured mammalian and bacterial cells.
They have been implicated in the stabilisation of intact cells, sub-cellular organelles and
As Polyamines have multiple +ve charges, they can associate readily with Polyanions such as
DNA and RNAs and have been implicated in such fundamental processes as stimulation of DNA
and RNA biosynthesis, DNA stabilisation and packaging of DNA in bacteriophages.
Polyamines also exert diverse effects on protein synthesis.
They act as inhibitors of enzymes that include Protein kinases.
Polyamines added to cultured cells induce synthesis of a protein antienzyme that binds to
ornithine decarboxylase and inhibits putrescine formation.
Spermidine has been claimed to be best “marker” of tumor cell destruction.
In Pharmacologic dosage Polyamines have been found to be hypothermic and hypotensive.
Transport of ammonia
NH3 is absorbed from the intestine into portal venous blood which contains relatively high
concentration of NH3 as compared to systemic blood.
Under normal conditions of health, Liver promptly removes the NH3 from the portal blood, so
that blood leaving the liver is virtually NH3-free. This is essential since even small quantities of
NH3 are toxic to CNS.
Two mechanisms are available in humans for the transport of ammonia from the peripheral
tissues to the liver for its ultimate conversion to urea.
The first uses glutamine synthetase to combine ammonia with glutamate to form glutamine, a
nontoxic transport form of ammonia. The glutamine is transported in the blood to the liver where
it is cleaved by glutaminase to produce glutamate and free ammonia. The ammonia is converted
to urea.
The second transport mechanism involves the formation of alanine by the transamination of
pyruvate produced from both aerobic glycolysis and metabolism of the succinyl coenzyme A
(CoA) generated by the catabolism of the branched-chain amino acids isoleucine and valine.
Alanine is transported by the blood to the liver, where it is converted to pyruvate, again by
The pyruvate is used to synthesize glucose, which can enter the blood and be used by muscle, a
pathway called the glucose–alanine cycle.
Thus, glutamic acid acts as the link between amino groups of amino acids and ammonia.
The concentration of glutamic acid in blood is 10 times more than other amino acids.
Glutamine is the transport forms of ammonia from brain and intestine to liver; while alanine is
the transport form from muscle.
Glutamine removes the toxic effect of NH3 in the brain. Then the glutamine goes via the blood
to the kidneys where it become hydrolyzed by glutaminase into glutamic acid and NH3 which is
excreted in urine (This accounts for 60% of the NH3 excreted in urine)
NH3 produced from a.a. deamination in the kidney is directly excreted in urine (This accounts
for 40% of NH3 excreted in urine)
N.B. NH3 produced from amino acid deamination in the kidney especially glutamine regulates
acid base balance and preserve cations.
Toxicity of ammonia
An increase in blood NH3 concentration has adverse effect on the brain, as it produces the
symptoms such as
Slurred speech, Blurred vision, Flapping tremor. Under severe states, coma and even death.
The reaction catalyzed by glutamate dehydrogenase probably explains the toxic affect of NH3 in
brain. Accumulation of NH3 shifts the equilibrium to the right with more glutamate formation,
hence more utilization of ?-ketoglutarate. ?- Ketoglutarate is a key intermediate in TCA cycle
and its depleted levels impair the TCA cycle. The net result is that production of energy (ATP)
by the brain is reduced. The toxic effects of NH3 on brain are therefore, due to impairment in
ATP formation. Another reason is the fact that increased NH3 concentration enhances glutamine
formation from Glutamate and thus reduces ‘braincell’ pool of glutamic acid. Hence there is
decreased formation of inhibitory neurotransmitter GABA (?-aminobutyric acid).
Urea cycle
The ammonium ion, the end product of amino acid degradation, is toxic if it is allowed to
accumulate. The urea cycle converts ammonium ions to urea, which is transported to the
kidneys to form urine. The urea cycle in the liver cells consists of reactions that occur in the
mitochondria and cytosol. detoxifies ammonium ions from amino acid degradation. begin with
the conversion of ammonium ions to carbamoyl phosphate using energy from two ATP. The
enzymes that catalyze the reactions are located partly in the mitochondria and partly in the
The reactions of urea cycle can be studied in five sequential enzymatic reactions.
Reaction 1: Synthesis of carbamoyl-phosphate
Reaction 2: Synthesis of citrulline
Reaction 3: Synthesis of argininosuccinate
Reaction 4: Cleavage of argininosuccinate
Reaction 5: Cleavage of arginine to form ornithine and urea
The urea cycle is a cyclic process and the five reactions involve ornithine, citrulline, arginine and
aspartic acid.
Urea formation takes place in liver in mammals and all of the enzymes involved have been
isolated from Liver tissue.
Reaction 1: Synthesis of Carbamoyl-P (Mitochondrial)
In this reaction, HCO3– , NH4+ and phosphate derived from ATP reacts to form carbamoyl-P
(also called Carbamyl-P). The reaction is catalysed by the mitochondrial-enzyme Carbamoyl
phosphate synthetase 1. Mitochondrial carbamoyl phosphate synthetase I catalyses the ATPdependant
conversion of HCO3– and NH4+ to the energy-rich, mixed anhydride carbamoyl
Reaction 2: Synthesis of Citrulline: (Mitochondrial)
In reaction 2, the enzyme, Ornithine transcarbamoylase which is also known as ornithine
carbamoyltransferase is found associated with carbamoylphosphatesynthetase I in the
mitochondrial matrix. It catalyses the nucleophilic addition of ornithine to the carbonyl group of
carbamoyl-P to produce Citrulline. During this reaction, the ?-NH2 group of ornithine attaches to
the carbonyl group of carbamoyl-P and the phosphate group (Pi) is released. It is important to
note that Ornithine which is used up at this stage of the reaction, is regenerated in cytosol in the
5th reaction and transported into the mitochondrial matrix by a specific transport protein in the
inner mitochondrial membrane.
Reaction 3: Synthesis of Argininosuccinate: (cytosolic):
In reaction 3, the Citrulline which is produced in mitochondrial matrix in reaction 2, is
transported across the inner mitochondrial membrane to the cytosol by a specific transport
protein. It then condenses with Aspartate to form argininosuccinate in an ATP-dependant
reaction catalysed by argininosuccinatesynthetase. During this reaction, transfer of an “adenylyl”
group from ATP to citrulline generates the activated intermediate “Citrullyl-AMP”. Formation
of the citrullyl- AMP intermediate facilitates removal of the ureido oxygen (carbonyl oxygen) of
citrulline. The isoureido carbon of citrullyl-AMP is subjected to nucleophilic attack by the ?-
NH2 group of aspartate. The isoureido oxygen leaves with the departing AMP, and
‘argininosuccinate’ is formed
Reaction 4: Cleavage of Argininosuccinate: (Cytosolic)
In this reaction of urea cycle, the enzyme argininosuccinase also known as
ArgininosuccinateLyasecatalyses conversion of Argininosuccinate to arginine and fumarate.
The urea cycle is linked to the TCA cycle through the production of fumarate. Amino acid
catabolism, is therefore directly coupled to energy production. The fumarate is converted to
oxaloacetate (OAA) via the fumarase and malate dehydrogenase reactions and then
transaminated to regenerate aspartate to participate in the cycle.
Reaction 5: Cleavage of Arginine to Ornithine and Urea
The last reaction of the urea cycle completes the cycle. It is catalysed by the enzyme arginase,
which is found only in the liver cells. Arginase catalyses hydrolysis of the guanidine group of
arginine, releasing urea and regenerating ornithine. Ornithine now enters mitochondrion through
inner mitochondrial membrane by a specific transport protein. Ornithine and lysine are potent
inhibitors competitive with arginine.
Highly purified arginase from mammalian liver cells is activated by CO++ and Mn++.
Bioenergetics of the urea cycle
Urea cycle consumes four "high-energy" phosphate bonds (3 ATP hydrolyzed to 2 ADP and one
1 ATP ADP + Pi
1 ATP ADP + Pi
1 ATP AMP + Pi + Pi
However, One NADH+H molecule is produced by oxidative deamination of glutamate to NH3
and ?-ketoglutarate. Glutamate provides the NH3 used in the initial synthesis of carbamoyl
phosphate. Also fumarate in the cycle may be converted to malate in the cytosol . Malate then
oxidized to oxaloacetate gives 1 NADH+H equivalent to 3 ATP obtained from 3ADP,
So the net energy expenditure is only one high energy phosphate. The two NADH+H produced
can provide energy for the formation of 5 ATP, a net production of one high energy phosphate
bond for the urea cycle. However, if gluconeogenesis is underway in the cytosol, the latter
reducing equivalent is used to drive the reversal of the glyceraldehyde 3-p dehydrogenase step
instead of generating ATP. So the net energy expenditure is only one high energy phosphate .
Regulation of the urea cycle
The first reaction catalysed by carbamoyl phosphate synthase l is the rate limiting reaction or
committed step in urea synthesis.
Carbamoyl phosphate synthase I is allosterically activated by N-acetylglutamate which is
synthesized from glutamate and acetyl CoA by synthase and degraded by a hydrolase.
The rate of urea synthesis in liver is correlated with the concentration of N-acetylglutamate and
this could be directly affected by:
Intake of protein-rich diet. Concentration of arginine
Excretion of urea
After the formation of urea in the liver, it diffuses into blood and is transported to the kidneys for
excretion. However, a small proportion of the urea produced, enters the intestine and is degraded
to carbon dioxide and ammonia by an intestinal bacterial enzyme called urease. The resultant
ammonia is either lost in the faeces or absorbed into the blood. Patients with renal failure have
problems excreting urea, hence there is a buildup of urea in the blood. A condition known as
uremia. In uremia, there is diffusion of more urea into the intestine with resultant breakdown to
ammonia. This results in elevated blood ammonia (hyperammonemia)
Consequently, renal failure patients are administered oral antibiotics to kill the intestinal bacteria.
Clinical significance of urea
The normal blood urea concentration in a healthy adult is 10-40mg/dl. However, this value could
increase within normal range with high protein intake.
About 15-30 g of urea (7-15 g nitrogen) is excreted in urine per day.
Blood urea estimation is widely used as a screening test for the evaluation of renal function.
Elevation in blood urea may be broadly classified into three categories:
Prerenal causes:
These are conditions associated with increased protein breakdown or reduced plasma
volume/body fluids with resultant negative nitrogen balance. Examples include
Salt and water depletion, diabetic coma, severe and prolonged diarrhoea, thyrotoxicosis, pyloric
stenosis with severe vomiting, Haematemesis, Haemorrhage and shock; shock due to severe
burns, Ulcerative colitis with severe chloride loss. Severe and protracted vomiting as in pyloric
and intestinal obstruction,
Renal causes
The blood urea can be increased in all forms of kidney diseases:
In acute glomerulonephritis.
In early stages of type II nephritis (nephrosis) the blood urea may not be increased, but in later
stages with renal failure, blood urea rises.
Other conditions are
malignantnephrosclerosis, chronic pyelonephritis and
mercurial poisoning.
In diseases such as hydronephrosis, renal tuberculosis; small increases are seen but depends on
extent of kidney damage.
Postrenal causes
These lead to increase in blood urea, when there is obstruction to urine flow. This causes
retention of urine and so reduces the effective filtration pressure at the glomeruli; when
prolonged, produces irreversible kidney damage. Causes include:
Enlargement of prostate, Stones in urinary tract, Stricture of the urethra, Tumours of the bladder
affecting urinary flow.
Inborn errors of amino acid metabolism
Inborn errors of metabolism result from the synthesis of abnormal proteins, specifically enzymes
which are often caused by mutant genes.
If an error occurs in the gene that codes for the enzyme a FAULT occurs.
Subsequently, the enzyme is not produced and the pathway breaks down.
Inborn errors of metabolism are uncommon but complicated medical conditions involving
abnormalities in complex biochemical and metabolic pathways
The inherited defects may be expressed as a total loss of enzyme activity or, more frequently, as
a partial deficiency in catalytic activity. Examples of such are:
Tyrosinosis or Tyrosinemia type I
Tyrosinemia type II
Maple syrup urine disease
Phenylketonuria( PKU) is the most common metabolic disorder in amino acid metabolism.
The name phenylketonuria was derived from the metabolite, phenylpyruvate which is a keto acid
(C6H5CH2-CO-COO-) excreted in urine in high amounts in PKU. lt is due to the deficiency of
the hepatic enzyme, phenylalanine hydroxylase, caused by an autosomal recessive gene. This
enzyme deficiency impairs the synthesis of tetrahydrobiopterin required for the action of
phenylalanine hydroxylase. The net outcome in PKU is that phenylalanine is not converted to
tyrosine. Phenylketonuria primarily causes the accumulation of phenylalanine in tissues and
blood, and results in its increased excretion in urine. Due to disturbances in the routine
metabolism, phenylalanine is diverted to alternate pathways, resulting in the excessive
production of phenylpyruvate, phenylacetate, phenyllactate and phenylglutamine. All these
metabolites are excreted in urine in high concentration in PKU. Phenylacetate gives the urine a
mousey odour.
Clinical features
Elevated phenylalanine:
Phenylalanine is present in high concentrations (ten times normal) in tissues, plasma, and urine.
Phenyllactate, phenylacetate, and phenylpyruvate
Central nervous system symptoms:
Severe intellectual disability, developmental delay, microcephaly, and seizures are characteristic
findings in untreated PKU.
Patients with untreated PKU may show a deficiency of pigmentation (fair hair, light skin color,
and blue eyes).
By estimation of plasma Phenyl alanine level.
By screening for the presence of phenyl pyruvate with FeCl3 (In urine).
Administration of phenyl alanine to a phenylketonuric patient should result in prolonged
elevation of the level of this amino acid in blood (“phenyl alanine tolerance test”).
Most natural protein contains phenylalanine, an essential amino acid, and it is impossible to
satisfy the body’s protein requirement without exceeding the phenylalanine limit when ingesting
a normal diet. Therefore, in PKU, blood phenylalanine level is maintained close to the normal
range by feeding synthetic amino acid preparations free of phenylalanine, supplemented with
some natural foods.
Tyrosinosis or Tyrosinemia type I
Tyrosinosis is a rare inherited disorder that is characterised by accumulation of metabolites that
adversely affect the activities of several enzymes and transport systems. In tyrosinosis, there is
lack of the enzyme Fumaryl acetoacetate hydrolase and possibly also Maleyl acetoacetate
Tyrosinosis could be acute or chronic.
In acute tyrosinosis, infants exhibit diarrhoea, vomiting, a “cabbage”-like odour. They do not
thrive well, and there is usually associated Liver damage. Infants die from liver failure.
Untreated acute tyrosinosis cases do not survive and death occurs within 6 to 8 months.
In chronic tyrosinosis:
Clinical features are similar but milder symptoms and course. Children survive and in untreated
cases leads to death by the age of 10 years. In both types plasma tyrosine levels are elevated: 6 to
12 mg/dl. There also occurs increase in plasma methionine level.
Involves a diet low in phenyl alanine and tyrosine and sometimes also low in methionine.
Tyrosinemia II
This disorder is also known as Richner-Hanhart syndrome and it is due to a defect in the enzyme
tyrosine transaminase.
This results in a blockade in the routine degradative pathway of tyrosine. This results in the
accumulation and excretion of tyrosine and its metabolites, namely p-hydroxyphenylpyruvate, phydroxyphenyllactate,
phydroxyphenylacetate, N-acetyltyrosine-and tyramine are observed.
Clinical findings include:
Mental retardation, which may be mild to moderate.
Skin lesions (dermatitis) and eye lesions.
Some infants may exhibit self-mutilation and disturbances in fine co-ordination
There is an elevation of plasma tyrosine level
Tyrosine as well as the metabolites, tyramine and N-acetyltyrosine are excreted in urine
Involves a diet low in phenyl alanine and tyrosine
Neonatal Tyrosinemia
Neonatal tyrosinemia is caused by the deficiency of the enzyme phydroxyphenylpyruvatedioxygenase.
It may be seen in premature infants.
Blood levels of tyrosine and phenyl alanine are elevated.
Urinary excretion of tyrosine, tyramine, p-OH-Phenyl acetate, and N-acetyl tyrosine are
Involves feeding a diet low in protein, specially with low phenyl alanine and tyrosine.
Neonatal tyrosinemia is mostly a temporary condition and usually responds to ascorbic acid
especially in premature infants.
It is explained that the substrate inhibition of the enzyme is overcome by the presence of ascorbic
Alkaptonuria is also known as the black urine disease. A rare inborn error or hereditary defect in
metabolism of Phenyl alanine and Tyrosine. It is due to the deficiency of homogentisate oxidase.
Homogentisate accumulates in tissues and blood, and is excreted into urine. Homogentisic acid
like many derivatives of tyrosine is readily oxidised to black pigments (alkapton). Hence, the
urine of alkaptonuric patients when exposed to air slowly turns black from top to bottom.
Alkapton deposition occurs in connective tissue, bones and various organs (nose, ear etc.)
resulting in a condition known as ochronosis. Many alkaptonuric patients suffer from arthritis
and this is believed to be due to the deposition of pigment alkapton (in the joints), produced from
Alkaptonuria is not a life-threatening condition. Hence, no specific treatment is required.
However, consumption of protein diet with relatively low phenylalanine content is
Albinism refers to a group of conditions in which a defect in tyrosine metabolism results in a
deficiency in the production of melanin.
The most common cause of albinism is a defect in tyrosinase, the enzyme most responsible for
the synthesis of melanin.
These defects result in the partial or full absence of pigment from the skin, hair, and eyes.
There are various forms of the disease. But can be divided into two major groups:
Oculocutaneous albinism
Ocular albinism
Clinical features:
The most important function of melanin is the protection of the body from sun radiation. Lack of
melanin in albinos makes them sensitive to sunlight.
Increased susceptibility to skin cancer (carcinoma) is observed.
Photophobia (intolerance to light) is associated with lack of pigment in the eyes. However, there
is no impairment in the eyesight of albinos.
Maple syrup urine disease
Maple syrup urine disease (MSUD) is a rare autosomal recessive disorder in which there is a
partial or complete deficiency in branched-chain ?-keto acid dehydrogenase (BCKD), a
mitochondrial enzyme complex that oxidativelydecarboxylatesleucine, isoleucine, and valine.
The name originates from the characteristic smell of urine (similar to burnt sugar or maple sugar)
due to excretion of branched chain keto acids.
Clinical features:
Disease starts in the first week of life.
It is characterized by convulsions, severe mental retardation, vomiting, acidosis, coma and death
within the first year of life.
Treatment is achieved by the ingestion of diet low in branched chain amino acids.
However, a milder form of the disease called intermittent branched chain ketonuria responds to
high doses of thiamine. This is because the decarboxylation of the BCKA requires thiamine.
Liver transplantation has been successfully tried in some cases of MSUD.
Homocystinuria type I
The homocystinurias are a group of disorders involving defects in the metabolism of
homocysteine. These autosomal-recessive diseases are characterized by high plasma and urinary
levels of homocysteine and methionine and low levels of cysteine.
Homocystinuria type I is the classical form of homocystinuria.
lt is due to a defect in the enzyme cystathionine synthase and results in the accumulation of
Plasma level of homocystine increases and excreted in urine. In some cases, S-adenosyl
methionine is also excreted.
Clinical features
Mental retardation thrombosis
Hepatomegaly osteoporosis
Atherosclerosis Most of the patients
show abnormal EEG.
Ectopialentis (dislocation of lens of the eye)
Two forms of type I homocystinurias are known, one of them can be corrected with vitamin B6
supplementation (B6 responsive) while the other does not respond to B6. The treatment includes
consumption of diet low in methionine and high in cystine
The other homocvstinurias are associated with enzyme defects in the conversion of
homocysteine to methionine by remethylation.
Homocystinuria II
Homocystinuria II is autosomal recessive.
In homocystinuria II, there is deficiency of the enzyme N5-methyl-Tetrahydrofolatehomocysteine
methyl transferase.
Clinical features
Mental retardation
No ectopialentis or thrombotic episodes seen.
There is increased plasma level of homocysteine.
Homocysteine is excreted in urine.
Responds to folic acid administration.
Homocystinuria III
Homocystinuria III is autosomal recessive.
In homocystinuria III, there is deficiency of the enzyme N5, N10-methylene tetrahydrofolate
Clinical features
Mental retardation
No ectopialentis or thrombotic episodes seen.
There is increased plasma level of homocysteine.
Homocystine is excreted in urine.
Responds to folic acid administration.
Creatine biosynthesis
Three amino acids are required in the biosynthesis of creatine:
Methionine (as S-adenosylmethionine)
Site of biosynthesis:
Step 1: Kidneys
Step 2: Liver
Distribution of body creatine
From liver, creatine is transported to other tissues
98% of creatine are present in skeletal and heart muscles
In Muscle, it gets converted to the high energy source creatine phosphate (phosphocreatine)
Creatine phosphate is a high-energy phosphate compound
It acts as a storage form of energy in the muscle
Provides a small but, ready source of energy during first few minutes of intense muscular
The amount of creatine phosphate in the body is proportional to the muscle mass
Creatine degradation
Creatine and creatine phosphate spontaneously form creatinine as an end product
Creatinine is excreted in the urine
Serum creatinine is a sensitive indicator of kidney disease (Kidney function test)
Serum creatinine increases with the impairment of kidney function
Urinary creatinine
A typical male excretes about 15 mmol of creatinine per day
A decrease in muscle mass due to muscular dystrophy or paralysis leads to decreased level of
creatinine in urine
The amount of creatinine in urine is used as an indicator for the proper collection of 24 hours
urine sample.
The normal concentration of creatine and creatinine in human serum and urine are as follows:
Serum: Creatine - 0.2 – 0.6mg/dl Creatinine – 0.6 – 1mg/dl
Urine: Creatine – 0 – 50mg/day Creatinine – 1 – 2g/day
Estimation of serum creatinine (along with blood urea) is used as a diagnostic test to assess
kidney function.
Serum creatinine concentration is not influenced by endogenous and exogenous factors, as is the
case with urea.
Hence, some workers consider serum creatinine as a more reliable indicator of renal function.
lncreased output of creatine in urine is referred to as creatinuria. Creatinuria is observed in
muscular dystrophy, diabetes mellitus, hyperthyroidism, starvation etc.
Introduction to Purine and Pyrimidine Metabolism
Purines and pyrimidines are heterocyclic structures that contain carbon and nitrogen. They are
referred to as organic bases. Purines: adenine and guanine. Pyrimidines: cytosine, uracil and
thymine. Purines and pyrimidines are synthesized from amphibolic intermediates in human
tissues. Ingested nucleic acids and nucleotides are degraded in the intestinal tract to
mononucleotides, which may be absorbed or converted to purine and pyrimidine bases. The
purine bases are then oxidized to uric acid, which may be absorbed and excreted in the urine
Nucleosides are derivatives of organic bases; purine and pyrimidine that have a sugar linked to
the nitrogen atom of a purine or pyrimidine. D-ribose is the sugar moiety in ribonucleosides
while 2-deoxy-D-ribose is the sugar moiety in deoxyribonucleosides. These sugars are linked to
the heterocycle by a –N-glycosidic bond, usually to the N-1 of a pyrimidine or to N-9 of a
Nucleotides are phosphorylated nucleosides. The phosphoryl group is esterified to a hydroxyl
group of the sugar. Examples are adenine monophosphate, guanine monophosphate. All forms of
life excluding parasitic protozoa synthesize purine and pyrimidine nucleotides.
Catabolism of Purines
Adenosine and guanosine are catabolized into uric acid. Adenosine is first converted to inosine
by adenosine deaminase.
Abnormalities of Purine Catabolism
Lesch-Nyhan Syndrome: An overproduction of uric acid (hyperuricaemia). It is caused by a
deficiency in the activity of hypoxanthine-guanine phosphoribosyl transferase.
Von Gierke Disease: It is caused by glucose-6-phosphatase deficiency. This results in purine
overproduction and hyperuricaemia.
Hypouricaemia: this is caused by xanthine oxidase deficiency as a result of genetic defect or to
severe liver damage. This often result in increased excretion of hypoxanthine and xanthine
Adenosine Deaminase deficiency: this is associated with immunodeficiency in which both
thymus-derived lymphocytes (T cells) and bone-marrow-derived lymphocytes (B cells) are
sparse and dysfunctional. Patients therefore suffer from severe immunodeficiency- probne to
Purine nucleoside phosphorylase deficiency: this is associated with severe deficiency of T cells
but apparently normal B cell function. This results in ummune dysfunctions
Catabolism of Pyrimidines
The end products of pyrimidine catabolism are water soluble: NH3, CO2, alanine and
aminoisobutyrate. Excretion of aminoisobutyrate increases leukaemia.
Abnormalities of Pyrimidine Catabolism
Disorders of alanine and aminoisobutyrate metabolism arise from defects in the enzymes of
pyrimidine catabolism.
Hydroxybutyric aciduria: caused by the deficiency of dihydropyrimidine dehydrogenase
Uraciluria-thyminuria: There is presence of uracil and thymine in the urine
Synthetic Analogues of Nucleotide
Synthetic analogs of purines, pyrimidines, nucleosides and nucleotides have various applications
in medicine. They are used in the management of cancer. Examples are 5-fluoro- or 5-iodouracil,
3-deoxyuridine, 6-thioguanine and 6-mercaptopurine, 5- or 6- azauridine, 5- or 6-azacytidine,
and 8-azaguanine. They are incorporated into DNA prior to cell division. They are also used in
the treatment of Gout. Allopurinol (an analog of purine) is used in treatment of hyperuricemia
and gout. It inhibits purine biosynthesis and xanthine oxidase activity. They are also used in
organ transplantation. Azathioprine is used in organ transplantation. It is catabolized to 6-
mercaptopurine. It suppresses immunologic rejection
Intended Learning Outcomes
At the end of the lecture, students should be able to
1. Explain the chemical composition of the DNA
2. Relate the DNA, gene and chromosome
3. Discuss the denaturation and renaturation of DNA
The DNA consists of the organic bases i.e. adenine (A), guanine (G), cytosine (C) and thymine
(T). These bases are held in linear array by phosphodiester bonds through the 3’ and 5’ positions
of adjacent deoxyribose moieties. The DNA is organized into two strands by the pairing of bases
A to T and G to C. The two complementary chains are held by hydrogen bonds between the base
portions of the nucleotide. The chemical polarity of DNA strand is maintained by the unique way
the nucleotide subunits are linked. There are 3.2 x 109 base pairs of DNA in humans organized
into 23 chromosomes.
The DNA carries the genes. A gene is a segment of the DNA that encodes the information
required to produce a functional biological product. The complexity of an organism correlates
with the number of genes in its genome. For example, the total number of genes ranges from less
than 500 in a bacterium to about 30,000 in humans.
The nucleic acid molecules are the repository of an organism’s genetic information. They are the
largest molecules in a cell and may contain thousands of genes as well as considerable tracts of
intergenic DNA. Chromosomes are linked with proteins involved in gene expression, DNA
replication and repair
In eukaryotic cells, each chromosome consists of a single, very long linear DNA molecule
associated with proteins that fold and pack the DNA into a more compact structure. The
packaging of DNA generates a series of coils and loops that provide higher levels of organization
that prevents the DNA from becoming an unmanageable tangle.
A DNA molecule performs other functions in addition to carrying genes; it must be able to
replicate, the replicated copies must be separated and partitioned reliably into daughter cells at
each cell division. These processes occur through an ordered series of stages, known collectively
as the cell cycle.
There are two important stages of the cell cycle; interphase and mitosis.
Interphase: This is the period between one mitotic (M) phase and the next. It encompasses the
remaining three phases of the cell cycle; synthesis (S) phase, gap (G1) phase and G2 phase. The
following events occur in the interphase; duplication of chromosomes and protein synthesis.
Mitosis: chromosomes are distributed to the two daughter nuclei in this stage of the cell cycle.
DNA Replication
This is a process by which a DNA molecule is duplicated. At each cell division, a cell must
accurately copy its genome. DNA replication produces two complete double strands from the
original DNA molecule. Each new DNA helix is identical in nucleotide sequence to the parental
DNA double helix. DNA replication is initiated by DNA polymerase.
Denaturation of DNA
This is the process of separating the double-stranded structure of the DNA into two component
strands in a solution. This is done by increasing the temperature and decreasing the salt
concentration. This separates the two stacks of bases. The bases unstack while still connected in
the polymer by the phosphodiester backbone. Denaturation of the DNA increases the optical
absorbance of the purine and pyrimidine bases. This is called hyperchromicity of denaturation.
DNA rich in G-C pairs (with 3 hydrogen bonds) melts at a higher temperature than that rich in
A-T pairs (with 2 hydrogen bonds)
Renaturation of DNA
This is a process whereby separated DNA strands re-associate under normal physiologic
temperature and salt conditions. The rate of re-association depends on the concentration of the
complementary strands. Example: the re-association of the two complementary DNA strands of a
chromosome after transcription.
Topic: The RNA
Intended Learning Outcomes
At the end of the lecture, students should be able to
1. Discuss the classes of RNA
2. Distinguish between DNA and RNA
The RNA consists of ribose sugar linked with organic bases and phosphoryl group. The bases in
RNA includes; adenine (A), uracil (U), cytosine (C) and guanine (G). Thymine is not found in
RNA. Adenine pairs with uracil, cytosine pairs with guanine. It is synthesized from a DNA
template by a process called transcription. It entails the transfer of information from DNA where
it is stored into RNA which can be transported and interpreted. RNA synthesis is catalysed by
RNA polymerase.
Ribonucleotide sequence in RNA molecule is complementary to the deoxyribonucleotide
sequence in a strand of DNA molecule
Template Strand: the strand that is transcribed into RNA molecule.
Non template (coding) strand: the non template strand.
Transcription unit: the region of DNA that includes the signals for transcription
Classes of RNA
Eucaryotic cells have four major classes of RNA
1. Messenger RNA (mRNA)
2. Ribosomal RNA (rRNA)
3. Transfer RNA (tRNA)
4. Small nuclear RNA (snRNA) and micro nuclear RNA (miRNA)
mRNA, rRNA and tRNA are involved in protein synthesis
Messenger RNA (mRNA)
This is the most heterogenous class of RNA in; abundance (likely varies over 104 fold range),
size and stability. Every member of this class of RNA functions as messenger conveying the
information in a gene to the protein synthesizing machinery. It serves as a template on which
specific sequence of amino acids is polymerized to form a specific protein molecule.
Transfer RNA (tRNA)
Transfer RNA serves as an adapter for the translation of information in the sequence of mRNA
into specific amino acids. It varies between 79 and 95 nucleotides in length. There are about 20
species of tRNA in every cell. The nucleotide sequence of tRNA molecules allows extensive
folding and intra-strand complementarity to generate a secondary structure
Ribosomal RNA (rRNA)
This class of RNA is located in the ribosome. It is made from pre-ribosomal RNA. Ribosomal
RNA is involved in protein synthesis. It represents about 70% of cellular RNA.
Short Nuclear (snRNA) and Micro Nuclear (miRNA)
They are important in gene regulation and mRNA splicing
Differences between DNA and RNA
1. DNA is double-stranded, RNA is single-stranded
2. There is a difference in the pyrimidine component of DNA and RNA. DNA contains
adenine, thymine, guanosine and cytosine RNA contains adenine, uracil, guanosine and
3. The sugar moiety of RNA is ribose. The sugar moiety of DNA is deoxyribose.
4. Since the RNA molecule is a single strand complementary to only one of the two strands
of a gene, its guanine content does not necessarily equal its cytosine content, nor does its
adenine content necessarily equal its uracil content
5. RNA can be hydrolyzed by alkali to 2',3' cyclic diesters of the mononucleotides,
compounds that cannot be formed from alkali-treated DNA because of the absence of a
2'-hydroxyl group. The alkali lability of RNA is useful both diagnostically and
Topic: Metabolism of one carbon units
Intended Learning Outcomes
At the end of the lecture, students should be able to
1. Discuss the absorption and bioavailability of folic acid
2. Discuss the catabolism and excretion of folic acid
3. Reactions involving folate
Folic Acid
Folic acid serves as a carrier of one carbon groups in many metabolic reactions. It is required for
the biosynthesis of compounds such as purines, serine, glycine, choline and deoxythymidine
monophosphate (dTMP). Folic acid or folate function as a coenzyme. They are derived from
pteroic acid to which one or more molecules of glutamic acid are attached.
Multiple forms of folic acid occur with substitutions of functional groups such as methyl, formyl,
methylene, hydroxymethyl etc at nitrogen atoms in the pteroic acid residue usually N5 or
bridging N5 and N10. 5-methyltetrahydrofolate is the principal form of folic acid in the human
serum and other body fluids.
Dietary Sources
The principal food sources of folate are liver, spinach and other dark green leafy vegetables,
legumes such as kidney and lima beans, orange juice etc
Absorption and Bioavailability
Folate is absorbed from dietary sources mainly as reduced methyl and formyltetrahydropteroylpolyglutamates.
The bioavailability of folate from food sources is variable and
depends on factors such as;
1. Incomplete release from plant cellular structure,
2. Entrapment in food matrix during digestion,
3. Inhibition of deglutamation by other dietary constituents Possibly the degree of
The bioavailability of supplemental folic acid is greater than that of food folate. It can be as high
as 100% for folic acid supplements taken on an empty stomach compared with about 50% for
food folates. Polyglutamate forms of folate present in food are first converted to monoglutamates
by pteroylpolyglutamate hydrolase in the intestinal mucosa. Thereafter, most of the folate is
reduced and methylated and enters the circulation as 5-methyltetrahydrofolate (5-MTHF),
circulating loosely bound to albumin or to folate-binding protein. Once within the cell, 5-MTHF
is demethylated and converted to the polyglutamyl form by folypolyglutamate synthase which
helps to retain folate within the cell, this is because it is unable to cross cell membranes.
The polyglutamates are reconverted to monoglutamates by polyglutamate hydrolase before they
are released into the circulation. Folic acid and vitamin B12 metabolism are linked by the
reaction that transfers a methyl group from 5-MTHF to cobalamin. In cases of cobalamin
deficiency, folate is trapped as 5-MTHF and is metabolically dead.
It cannot be recycled as tetrahydrofolate (THF) back into the folate pool to serve as the main
one-carbon unit acceptor for many biochemical reactions. Eventually, cellular depletion of
MTHF ensues, causing a reduction in thymidylic acid synthesis, which in turn results in
megaloblastic anaemia and neuropathies.
Protein-free plasma folate is filtered at the glomerulus and most is reabsorbed by the proximal
renal tubules. Therefore, intact urinary folate is only a small percentage of intake. Folate is
predominantly excreted by catabolism following cleavage of the C9-N10 bond to produce paminobenzoylpolyglutamates
which are then hydrolyzed to monoglutamates and N-acetylated
before excretion.
Functions of Folate
1. Folate coenzymes as well as coenzymes derived from vitamins B12, B6 and B2 are
essential for one carbon metabolism.
2. Biochemically, a carbon unit from serine or glycine is transferred to tetrahydrofolate
(THF) which is then used in the synthesis of thymidine which is incorporated into DNA
oxidized to formyl-THF for use in the synthesis of purines precursors of RNA and DNA
or reduced to methyl-THF which is necessary for the methylation of homocysteine to
3. Much of this methionine is converted to S-adenosylmethionine, a universal donor of
methyl groups to DNA, RNA, hormones, neurotransmitters, membrane lipids and
Anaemia is a condition in which the blood has a lower than normal concentration of
haemoglobin, which results in a reduced ability to transport oxygen.
Nutritional anaemia
This is caused by inadequate intake of one or more essential nutrients. It can be classified
according to the size of the red blood cells (RBCs) or mean corpuscular volume (MCV) observed
in the individual.
Nutritional anaemia can be divided into microcytic and macrocytic anaemias
Microcytic anaemia: This is caused by lack of iron. It is the most common form of nutritional
anaemia. The MCV is below normal.
Macrocytic anaemia: It results from a deficiency in folic acid, or vitamin B12. The MCV is
above normal. Macrocytic anaemias are commonly called megaloblastic because a deficiency of
either vitamin (or both) causes accumulation of large, immature RBC precursors, known as
megaloblasts, in the bone marrow and the blood. The normal mean corpuscular volume (MCV)
for people older than age 18 is between 80 and 100 ?m3
Folate and Anaemia
Inadequate serum levels of folate can be caused by increased demand (for example, pregnancy
and lactation), poor absorption caused by pathology of the small intestine, alcoholism, treatment
with drugs that are dihydrofolate reductase inhibitors. E.g. methotrexate.
Folate and neural tube defect
Folic acid supplementation before conception and during the first trimester has been shown to
significantly reduce neural tube defects (NTDs). Example: Spina bifida
All women of childbearing age are advised to consume 0.4 mg/day of folic acid to reduce the
risk of having a pregnancy affected by NTDs and ten times that amount if a previous pregnancy
was affected. Adequate folate nutrition must occur at the time of conception because critical
folate-dependent development occurs in the first weeks of foetal life. This is a time when many
women are not yet aware of their pregnancy.
Topic: Metabolism of Inorganic Nitrogen
Intended Learning Outcome
At the end of this lecture, students should be able to
1. Explain the metabolism of inorganic nitrogen in living systems
Amino acid catabolism is part of the larger process of the metabolism of nitrogen containing
molecules. Nitrogen enters the body in a variety of compounds present in food, the most
important being amino acids contained in dietary protein. Nitrogen leaves the body as urea,
ammonia, and other products derived from amino acid metabolism. The role of body proteins in
these transformations involves two important concepts: The amino acid pool and protein
The amino acid pool
Free amino acids are present throughout the body, such as in cells, blood, extracellular fluids.
These amino acids can be said to belong to a single entity called the amino acid pool. This pool
is supplied by three sources:
1. Amino acids provided by the degradation of endogenous (body) proteins, most of which
are reutilized;
2. Amino acids derived from exogenous (dietary) protein
3. Non essential amino acids synthesized from simple intermediates of metabolism.
Conversely, the amino pool is depleted by three routes:
1. Synthesis of body protein.
2. Consumption of amino acids as precursors of essential nitrogen-containing small
3. Conversion of amino acids to glucose, glycogen, fatty acids and ketone bodies or
oxidation to CO2 + H2O. Although the amino acid pool is small (comprising about 90–
100 g of amino acids) in comparison with the amount of protein in the body (about 12 kg
in a 70 kg man).
Protein turnover
The total amount of protein in the body of a healthy adult remains constant because the rate of
protein synthesis is just sufficient to replace the protein that is degraded. This process, called
protein turnover, leads to the hydrolysis and re-synthesis of between 300 and 400 g of body
protein each day.
The rate of protein turnover varies widely for individual proteins.
Short-lived proteins (for example, many regulatory proteins and mis-folded proteins) are rapidly
degraded, They have half-lives measured in minutes or hours. Long-lived proteins, with halflives
of days to weeks, constitute the majority of proteins in the cell. Structural proteins, such as
collagen, are metabolically stable and have half-lives measured in months or years
Protein degradation:
There are two major enzyme systems responsible for degrading proteins:
1. Ubiquitin–proteasome proteolytic pathway
2. Chemical signals for protein degradation
Ubiquitin–proteasome proteolytic pathway
Proteins selected for degradation by the cytosolic ubiquitin-proteasome system are first modified
by the covalent attachment of ubiquitin (Ub), a small, globular, nonenzymic protein that is highly
conserved across eukaryotic species. Ubiquitination of the target substrate occurs through
isopeptide linkage of the ?-carboxyl group of the C terminal glycine of Ub to the ?-amino group
of a lysine on the protein substrate. This occurs by a three-step, enzyme-catalyzed, ATPdependent
process. Enzyme 1 (E1, or activating enzyme) activates Ub, which is then transferred
to E2 (conjugating enzyme). E3 (a ligase) identifies the protein to be degraded and interacts with
The consecutive addition of four or more Ub molecules to the target protein generates a
polyubiquitin chain. Proteins tagged with Ub are recognized by a large, barrel-shaped,
macromolecular, proteolytic complex called a proteasome.
The proteasome unfolds, deubiquitinates, and cuts the target protein into fragments that are then
further degraded by cytosolic proteases to amino acids, which enter the amino acid pool. Ub is
recycled. It is noteworthy that the selective degradation of proteins by the ubiquitinproteosome
complex unlike simple hydrolysis by proteolytic enzymes) requires energy in the form of ATP.
Chemical signals for protein degradation
Because proteins have different half-lives, it is clear that protein degradation cannot be random
but, rather, is influenced by some structural aspect of the protein. For example, some proteins
that have been chemically altered by oxidation or tagged with ubiquitin are preferentially
The half-life of a protein is also influenced by the amino (N)-terminal residue. For example,
proteins that have serine as the N-terminal amino acid are long-lived, with a half-life of more
than 20 hours, whereas those with aspartate at their N-terminus have a half-life of only 3
minutes. Additionally, proteins rich in sequences containing proline, glutamate, serine, and
threonine are rapidly degraded and, therefore, have short half-lives.
Digestion of protein
On entering the small intestine, large polypeptides produced in the stomach by the action of
pepsin are further cleaved to oligopeptides and amino acids by a group of pancreatic proteases
that include both endopeptidases (cleave within) and exopeptidases (cut at an end).
Abnormalities in protein digestion
Digestion and absorption of fat and protein are incomplete in individuals with a deficiency in
pancreatic secretion which could be due to
1. Chronic pancreatitis
2. Cystic fibrosis
3. Surgical removal of the pancreas
This results in the abnormal appearance of lipids in the faeces (a condition called steatorrhea) as
well as undigested protein.
The Urea Cycle
Urea is the major disposal form of amino groups derived from amino acids. It constitutes about
90% of the nitrogen-containing components of urine. A nitrogen of the urea molecule is supplied
by free ammonia and the other nitrogen by aspartate. Glutamate is the immediate precursor of
both ammonia (through oxidative deamination by glutamate dehydrogenase) and aspartate
nitrogen (through transamination of oxaloacetate by AST). The carbon and oxygen of urea are
obtained from CO2 (as HCO3
–). Urea is produced by the liver and then is transported in the blood
to the kidneys for excretion in the urine.
Fate of urea:
Urea diffuses from the liver and is transported in the blood to the kidneys, where it is filtered and
excreted in the urine. A portion of the urea diffuses from the blood into the intestine and is
cleaved to CO2 and NH3 by bacterial urease. This ammonia is partly lost in the faeces and is
partly reabsorbed into the blood. In patients with kidney failure, plasma urea levels are elevated,
promoting a greater transfer of urea from blood into the gut. The intestinal action of urease on
this urea becomes a clinically important source of ammonia, contributing to the
hyperammonemia often seen in these patients. Oral administration of antibiotics reduces the
number of intestinal bacteria responsible for this NH3 Production
Summary and Conclusion
This course has informed students on genome organization, organic bases (purines and
pyrimidines), nucleosides and nucleotides as well as abnormalities in their metabolism. The
metabolisms of nucleic acids, one carbon units and inorganic nitrogen were also discussed.
Interactions and Questions
1. Discuss the metabolism of protein
2. Discuss the urea cycle
3. What are inborn errors of metabolism
4. Draw the structure of Thymidine
5. Discuss the classes of RNA
6. Distinguish between DNA and RNA
Bibliography/ further reading
1. Harper’s Illustrated Biochemistry. 28th edition
2. Lippincot Illustrated Reviews Biochemistry. 6th edition
3. Essential Cell Biology
4. Textbook of Medical Biochemistry

Item Type: Lecture note(non-copyrighted)
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Copyright: Creative Commons LicenseCreative Commons license
Department: Natural Science
Field of Study: Biochemistry
Uploaded By: Uwaifo Ferdinand
Date Added: 04 Feb 2019 8:00am
Last Modified: 04 Feb 2019
Lecture URL: https://www.edouniversity.edu.ng/oer/lecturenotes/amino_acid_protein_and_nucleic_acid_metabolism_20182019

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