Structure and Functions of Amino

Acids and Proteins

By: Endalamaw Tesfa

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Learning Objectives
At the end of this session students will be able to:
Explain the structures of AAs
Describe the functions of AAs
Identify the classification systems of AAs
Explain the structures of proteins
Describe the functions of proteins
List the factors that denature proteins

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Amino Acids (AAs)

More than 300 different AAs have been described in
nature but only 20 of them are coded by DNA
Organic acids that contain one or more amino (NH2)
group(s).
AA are structural units of proteins
Perform important functions in their free form.
It contains (COOH), (NH2) and side chain or Rgroup.
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Amphoteric electrolytes or ampholytes, i.e., react as

proton donor acid by COOH and as proton accepting

base by NH2 to get negative or positive charges.

Exceptions: Proline and hydroxyproline - have an
unionizable imino group (NH).

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Abbreviations for AAs

1. Unique First Letter:
If only one amino acid begins with a particular letter,
then that letter is used as its symbol.
e.g. I = isoleucine.

2. Most Commonly Occurring AAs Have Priority:

If more than one AA begins with a particular letter, the
most common of these AAs receives this letter as its
symbol.
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e.g., Glycine is more common than glutamate, so G =

glycine.

3. Similar Sounding Names:

Some one-letter symbols sound like the AA they represent.
e.g., F = phenylalanine, or W = tryptophan

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4. Letter Close to Initial Letter:

For the remaining AAs, a one letter symbol is assigned
that is as close in the alphabet as possible to the initial
letter of the amino acid, for example, K = lysine.
Furthermore, B is assigned to Asx, signifying either
aspartic acid or asparagine, Z is assigned to Glx,
signifying either glutamic acid or glutamine, and X is
assigned to an unidentified AA.

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Abbreviations for AAs

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Abbreviations of AAs cont

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Classification of amino acids

Amino acids are classified based on

1. Chemical nature of the AA

2. Biological importance of the AA
3. Metabolic fate of the AAs
4. Unusual/ modified AAs

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1. Chemical Classification of AAs

Based on their polarity of side chains (R groups) and
tendency to interact with water at biological pH
Amino acids classified into;
Nonpolar side chains (Ala, Gly, Pro, Val, Leu, Iso, and
Met)
Polar uncharged side chains (Ser, Thr, Cys, Asn & Gln )
Acidic side chains (Asp & Glx)
Basic side chains (Lys, His and Arg)
Aromatic side chains (Phe, Tyr and Try )
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Nonpolar, aliphatic R groups

Negatively charged R groups

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Positively charged R groups

Polar, uncharged R groups

Aromatic R groups

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2. Biological Classification of AAs

Based upon whether the AAs can be synthesized in human
body or not .
Indispensable or essential AAs - not synthesizable in the
body in adequate amounts and must be supplied in the diet
Dispensable or non-essential AAs - synthesizable in the
body and there is no diet dependency for them.
Biologically and nutritionally, the dietary deficiency of
any of the essential AAs leads to nutrition deficiency
disorders that affect both growth and health.
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3. Metabolic Classification of AAs

Based upon the catabolic fate of C skeleton of AAs .
A. Ketogenic AAs: Only two AAs are purely ketogenic viz. lysine
and leucine -catabolically give intermediates convertible into
acetyl-CoA or acetoacetyl-CoA.

B. Glucogenic AAs: 14 of the 20 protein AAs give rise to

intermediates of glycolysis or Krebs cycle and thus can be
converted to carbohydrates.
C. Mixed AAs: These are AAs, the C skeleton of which is
catabolized to produce the glycolytic intermediates as well
as the

acetyl CoA derivatives.

These
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4. Unusual/ Modified AAs

Some AAs after their incorporation into the proteins, are
modified by; hydroxylation, methylation or
carboxylation to form unusual AAs, e.g. hydroxylproline, hydroxyl-lysine, -carboxy glutamic acid.
Selenocysteine (Se) is the 21st AA of proteins formed
by substitution of S with Se Cys AAs.
Pyrrolysine: is the 22nd AA of protein and present in a
number of methyl-transferase enzymes.
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Non-Protein AAs
Some D-AAs have been found to play some role in
biological systems.
D-Ala and D-Glu are present in certain bacterial cell walls.
D-Asp and D-Ser have been isolated from brain tissue.
The AAs that do not exist in the proteins, perform very
important functions as biologically active molecules like
hormones or neurotransmitters, are important structural

components of biomolecules like CoA, Acyl carrier proteins

etc. or are intermediates in the metabolic pathways.
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Functions of Non protein AAs

-alanine

Part of vitamin pantotheinic acid, CoA and

Acyl carrier protein (FA synthesis)

-amino butyric acid

Inhibitory neurotransmitter

L-homocysteine

Metabolic intermediate of methylation

reactions

Ornithine

Intermediate in Urea cycle, Arg synthesis

Citrulline

Intermediate in Urea cycle, Arg synthesis

Dopa (3,4-dihydroxy Phe) Precursor of melanin

-amino laevulinic acid

(-ALA)

Intermediate in heme synthesis

S-adenosyl methionine

Active methionine a methyl donor

Sarcosine

Intermediate in AA synthesis

Tri-iodothyronine (T3)

Hormone from thyroid gland

Thyroxine
(T4)
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Hormone
from thyroid gland
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Functions of Amino Acids

Polymerized to form proteins
Stabilize in 3-D structure of proteins by forming H
and disulfide bonds
Presence of specific AAs at the active site of enzymes
is vital for catalytic activity
Some AAs (glucogenic) can be converted to CHOs
Cys and Met are sources of S in the body

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 Carbone skeleton and Nitrogen of AAs used for the

synthesis of purine and pyrimidine
Gly and Met help in the detoxification mechanisms
Met can act as a methyl group donor in methylation
reactions
Certain AAs give rise to biologically important
derivatives:
Gly is a precursor for heme of hemoglobin
Gly is also a precursor for creatine that acts as the mediator
of energy in muscles
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 Tyr is the precursor for a number of hormones & NTs

(T4, T3, epinephrine and nor-epinephrine) and melanin
Tryptophan can give rise to vitamin niacin and reduce
its dietary requirement
Tryptophan also gives rise to the NT, Serotonin.
Histidine can be converted to the mediator of allergic
reactions i.e. histamine

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Essential & non-essential AAs

Only 20 AAs are polymerizable into protein structure -

protein AAs
Those which do not occur in proteins - non-protein AAs
Essential AAs -can not be synthesized in our body
e.g. Val, Ile, Thr, Trp, Arg, Leu, Lys, Met, Phe, His
Non-essential AAs- can be synthesized in our body from
other AAs or metabolites
e.g. Glu, Gln, Asp, Asn, Gly, Ala, Pro, Tyr, Ser , Cys.
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Semi-essential amino acids

Two amino acids are grouped under semi-essential
AAs since they can be synthesized within the organism
but their synthesis is not in sufficient amounts.
In that they should also be provided in the diet.
Semi-essential AAs include; Arginine and Histidine.

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Acidic and Basic Properties of AAs

AAs in aqueous solution contain weakly acidic carboxyl groups and weakly basic -amino groups.
Acidic and basic AAs contains an ionizable group in its
side chain
Both free and combined AAs in peptide linkages can act
as buffers
The relationship between the pH of the solution and
concentration of a weak acid (HA) and its conjugate base
(A)
is described by the henderson-hasselbalch
equation
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Properties of AAs
Stereoisomerism:
-AAs (except glycine) have at least one asymmetric
(chiral) carbon
Show stereoisomerism due to differential orientation of

the amino and carboxylic groups in relation to the side

chain
All AAs (except glycine) are optically active, i.e., can
rotate plane polarized light
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L-form with NH2 on the left side of -carbon, is the

predominant form, the only form of AAs that occurs in
proteins and is metabolizable ; and the D-form, that is
unmetabolizable with NH2 on the right side of -carbon.
D-AAs are found in the peptides of bacterial cell walls

and certain antibiotics.

Aromatic AAs (Trp, Tyr and Phe) can absorb UV light
at 280 nm; a property utilizable for identification and
quantitation of AAs & proteins in solution.
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Stereoisomerism of AAs :
a) Ball and stick model b) Howarth projections

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Ionization and Isoelectric point

Carboxylic as well as the amino groups of AAs are ionizable.
In alkaline pH, the carboxylic COOH group of an AA gets
dissociated to release a proton and acquires a ve charge,
whereas, the NH2 group ionizes in acidic pH into +vely charged
amino NH3+.

R-COOH

R-COO- + H+

R-NH3+

R-NH2

+ H+

The ionization of all the groups is pH specific i.e. each functional

group is protonated or deprotonated at a particular pH called
pKa.
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At extremely alkaline pH, the AAs would carry a net

negative charge whereas, in acidic conditions, they will

be positively charged
Isoelectric pH: The specific pH at which an AA would
carry equal negatively charged COO- and positively
charged NH3+ groups is called isoelectric pH or
isoelectric point (pI).
In this state the molecule carries no net charge or is
isoionic and is called Zwitterion
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 Since at pI, the AAs are electrically neutral, they will

not migrate in electric field and are readily
precipitated
The pI is a specific characteristic for each AA or
protein, e.g., for alanine, it is 6.02 and for aspartic
acid, it is 2.98
This characteristic is utilized for protein separation by
electrophoresis and identification by isoelectrofocusing
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Titration of glycine: The ionic species of glycine at

different dissociation points

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Ionization Properties
The pH change from very low towards higher side follows a
sequential monophasic ionization of NH2 followed by
COOH phase
The ionization takes place at specific pKa of that group and
around this point, system resists the change in pH
At midpoint of each phase, the AA is half dissociated and
the specific pH inflection value (pKa) is equal to the
negative logarithm of the equilibrium constant for ionization

(Ka) of that group

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 For Gly, there will be two such inflections , first at 2.34

and second at 9.60 ; at pH 5.97, amino group exists as
NH3+ and carboxylic as COO The AA, at pH 5.97 (pI of glycine) carries equal -ve and
+ve charges and acts as a zwitterion
For an AA with only NH2 and COOH as ionizable groups
and an unionizable radical, pI is the arithmetic mean of the
two pKa values of NH3+ and COO-

For AAs with ionizable radical, e.g., Glu or His, there are
three phases of ionization.
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 In the peptide form, both COOH and NH2 groups

of internal AAs are consumed in peptide bond

formation.
Therefore, the acid-base behavior of a peptide is
predicted from its N-terminal free -amino and Cterminal -carboxyl groups but largely on the nature
and number of its ionizable R groups.
The AAs in proteins have different pKs compared to
free AAs.
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Peptides and Proteins

Proteins are the most abundant biological
macromolecules
Proteins contain elements like; C, O, H, N and also
contain S, P, non-protein organic groups and metal ions.
They are linear polymers made from 20 AAs linked
together by peptide linkages
It contain a wide range of functional groups like;
alcohols, thiols, thioethers, carboxylic acids,
carboxamides,
and a variety
ofT basic groups
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Proteins can interact with one another and with other

biological macromolecules to form complex assemblies.
Some proteins are quite rigid, whereas others display
limited flexibility

May be monomeric or polymeric

Simple proteins formed of AAs only
Some proteins have a non-proteinaceous moiety
attached covalently or non- covalantly to the polypeptide
chains Complex or conjugated proteins
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The 3-D shape of protein is determined by sequence

and nature of composite AAs because it provides the most

optimum self-folding conformation of the molecule

Function of proteins is based on the generation and
changes in the conformation of proteins particularly at
the specific active sites
Alteration in AA sequence of proteins change in the
conformation or stability of the proteins, thus
compromising their cellular function
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Such alterations originating at the genetic level lead to

clinical disorders known as inherited disorders
In the human body, there are about 100,000 different
proteins

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Functions of Proteins
Nutrition

Blood clotting factors

Catalytic

are proteins

Endocrine

Membrane transport

Defence

Structural

Osmotic Potential

Gene Regulation

Transport

Signal Transduction-

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Bonds participating in the protein structure

1. Peptide Bond:
The peptide bond is the strongest bond in protein
structure
AAs are polymerized to give rise to polypeptides or
proteins by formation of peptide bonds

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2. Disulfide Bond:
The side chain SH of two cysteine residues of a
protein join with the removal of two H atoms to form
a disulfide bond
It may be intra-chain or inter-chain
Weaker than peptide bond in strength

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3. Hydrogen Bond:
Weak partial electrostatic attraction between polar
molecules through the participation of H atom
The presence of H-bonds in large number plays critical role
in stabilizing specific secondary structures in proteins as
well as NAs
H bond is formed when H atom is shared between two
highly electronegative atoms (e.g. N, O, or P)
Polarization of H bonds confers polarization to the
molecules that become consequently hydrophilic
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4. Electrostatic Interactions:
Large differences in electronegativity of participating
atoms generates weaker non-covalent electrostatic /
ionic /salt bond due to unequal sharing of electrons
In biomolecules, there are a number of ionizable
moieties that can acquire a positive or a negative
charge
Strength of ionic bonds varies depending on overall
electronegativity of participating atoms
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5. Van der Waals Interactions:

The weakest type of bonds
Within each molecule, atoms are surrounded with
charges that vary asymmetrically and temporally in
distribution
Asymmetricity within the molecule induces similar
changes in neighboring molecules that creates dipolar
interactions between them known as the van der Waal
forces
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 Such nonspecific forces could be attractive, when

molecules are an optimal van der Waal distance apart
or could be repulsive, when molecules are too close to
each other
Although weak, they play important role in intra-

and inter-molecular proteins stability

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6. Hydrophobic Interactions:
The nonpolar groups, e.g. hydrocarbon side chains of
AAs, in an aqueous environment tend to cluster tightly
to minimize the hydrophobic surface so as to avoid
interaction with polar water molecules
The water hating property of non-polar molecules
rather than their affinity to one another holds them

together

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 An advantage for the non-covalent bonds being weak is that

they break and reform easily under normal, physiological

conditions allowing dynamic conformational reshaping of

proteins, to adapt for different biochemical activities
The stability of protein structure is due to contribution from
all the above type of interactions
Majority of the proteins are amphipathic molecules
This property enables them to interact with other molecules
or solvents having either polar or nonpolar characteristics
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Levels of Organization of Protein Structure

1. Primary Structure of Proteins

Specifies total number of AAs; the linear sequence of
AAs connected by peptide bonds

Also specifies possible position of intra- and intermolecular disulfide bonds, if present
Conventionally, peptide sequence is written left to
right

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 N-terminal in the left side and C- terminal in the right

end
There is colinearilty between gene DNA, mRNA and
the peptide sequences
The mutational changes in DNA sequence are reflected
on the peptide sequence and final conformation and
hence its function

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2. Secondary Structure of Proteins

Specifies the fine conformation of peptide backbone
created by spatial arrangements and interactions
of AA residues that are near one another in the linear
sequence
Restricted rotation around peptide bond and steric
hindrance due to side chains of AAs primary
driving force for the local folding of peptide into
several types of periodic structures
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e.g., helix, -pleated sheet, turns and readiness for

triple helix formation from several polypeptides such as

collagen
Clustering of different types of secondary structures at a
domain of the peptide forms super-secondary structure
-Helix: Most common secondary structure ,about of
all AA residues in polypeptides are found in -helices.
The -Helix model given by Pauling and Corey

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-Helix showing peptide backbone

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Characteristics of -Helix
Polypeptide backbone is tightly wound around an
imaginary axis drawn longitudinally through the
middle of the helix
A single turn extends about 0.54 nm and each helical
turn includes 3.6 AA residues
The rise per AA is 0.15 nm
R groups of AA residues protrude outward from the
helical backbone
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 The right handed helix formed from L-AAs is much

more stable than the left handed helix
Interactions between AA side chains can stabilize or
destabilize the helical structure
The bulk and shape of Asn, Ser, Thr, and Cys residues

can destabilize an -helix if they are close together

The amino or carboxylic groups in proline are fixed at
angle unsuitable for helix formation , hence known as
helix breaking AA
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-pleated sheets& - bends

-pleated sheets:
Polypeptides (2-5 chains) run in-line with each other and
H- bonding stabilizes the structure
When the polypeptide chains run in parallel direction to
each other, called parallel -pleated sheets and when
they run in opposite direction to each other, called antiparallel -pleated sheets
The polypeptide chains forming the sheets may not be
adjacent
in the primary structure
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-Bends or Reverse Turns:

Proteins have to be flexible to accommodate a number of

secondary structures
There have to be regions where it is important for the
polypeptide to take a sharp turn and then continue with a
helix or a sheet
These intermediate regions are called -bends or reverse
turns
The AAs pro and hydroxyproline have natural bend in
their structure, so exist more frequently at the -bends
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Another way to form -bends is to form a tight loop in

which the carbonyl of one peptide bond is H- bonded to
the NH group of AA 3 residues ahead of it

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Triple helix & super- secondary structure

Triple helix:
Seen in collagen fibers which are rich in pro and
hydroxyproline along with Lys
The 3 polypeptide strands are wound around each
other
The triple helices running parallel are cross linked
to form very stable structures
The triple helix is stabilized by inter chain H
bonds as well as non-covalent interactions
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Super- secondary structures:

A number of proteins show the formation of super secondary structures by combination of more than one
type of secondary structures
-- units: Two units separated by an -helix
The Greek key: A number of sheets join to form a
structure often found on classical Greek pottery items
-meander: 5 polypeptides with -pleated sheet structures

joined by -turns run antiparallel to each other to form meander

The -sheets are stabilized
byT extensive H bonding
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A. -- unit
B. -Meander
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3. Tertiary Structure of Proteins

Tertiary structure defined as the 3- dimensional

arrangement and interrelationship of various regions/
domains of a protein

Specifies the final functional 3- D structure of a protein

formed by complicated folding and super-folding of the
peptide chain into globular or fibrous form of different size
Stabilized by interactions through R-groups of composite
AAs utilizing, H bonding, disulfide bonds, ionic

interaction, hydrophobic, and van der Waals

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 A monomeric protein composed of only a single peptide

chain has no quaternary structure but only tertiary

organization
Tertiary structure is dictated by primary structure i.e.
linear AA sequence
As it is the biologically active conformation of the
polypeptide, is the most labile to denaturation
Example of tertiary structure is myoglobin

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4. Quaternary Structure of Proteins

Specifies the nature of association of more than one
polypeptides in a defined geometric positional
configuration to make a functional protein

The polypeptides in a quaternary protein could act in

synergy, suppress or stimulate the function(s) of each
other

Many proteins contain 2, 3, 4 or more subunits:

dimeric, trimeric, tetrameric or oligomeric proteins
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 Polymeric proteins could be hetero-oligomers or

homo-oligomers
Oligomeric proteins are very common among enzymes
Quaternary structure stabilized by; hydrogen bonds,
ionic bonds, and hydrophobic interactions and is the
most sensitive to denaturation
Many times the protein structure alternates between
two functional states that may get interchanged upon
binding to other proteins or allosteric low MW effectors
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 Such proteins are allosteric proteins, e.g., Hb and

changes its conformation upon binding with O2 or CO
Cooperativity : one of the major characteristics of
quaternary structure
The different subunits of oligomeric proteins exchange
information and affect the functional characteristics of
each other
The protein has +ve cooperativity if the activity is
increased by the binding of a modulator and -ve
cooperativity if the activity
isT decreased
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The proteins, at their final tertiary or quaternary

conformation, may be aggregated into functional

macro-molecular complexes
In such superstructures, abnormality in one or more of
the composite proteins affects the whole structurefunction efficiency

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Digestion of Proteins
About 95-99% of ingested proteins are digested and
absorbed in GIT
No protein digestion in the mouth as saliva lacks any
protease
Gastric parietal cells secrete HCl into the gastric lumen
that makes the stomach highly acidic (pH 1-3)
Gastric juice contains 3 digestive enzymes for protein:
rennin, pepsin and gelatinase
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 These cells contain enzyme carbonic anhydrase

which splits carbonic acid (H2CO3) into H+ and
bicarbonate ions
Protons are actively transported by ATPase
transporter into the lumen of the stomach
Bicarbonate returns to the blood in exchange with
Cl- ions which pass onto the gastric lumen to
associate with H+ to form HCl

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Functions of HCl:
A. Denatures native proteins into easily digestible
acid-proteans due to disruption of the secondary
bonds
B. Destroys most microorganisms that enter GIT
C. Creates optimum pH required for gastric
proteolytic enzymes
D. Activates proenzymes into active enzymes e.g.
pepsinogen into pepsin
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Formation of HCl in parietal cells

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 Pepsin (optimum pH: 1.6-2.5 , inactive at pH

5.0 or higher):
Major protease secreted by the chief cells of the
stomach body into the lumen in an inactive
proenzyme form - pepsinogen (362 AAs)
Gastric HCl activates pepsinogen to pepsin
It is also activated by autocatalysis by the activated
pepsin into pepsin (320 AA residues), 5 small inactive
peptides and a short polypeptide with pepsin
inhibitory activity

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Does not hydrolyze keratins, mucoproteins, or basic

proteins
Endopeptidase i.e. acts on peptide bonds inside the
polypeptide chains, particularly those formed by COOH of aromatic AAs ( Tyr, Phe, Trp) and -NH2 of
aromatic or dicarboxylic acids ( Glu, Asp)
Releases large peptides as proteoses, peptones,
polypeptides and a few free AAs from dietary proteins

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Hydrolyses casein of milk into paracaseinate and whey

protein (a proteose)

Paracaseinate is precipitated as calcium paracaseinate that

is hydrolyzed further by pepsin into peptones

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Rennin (Optimum pH = 4)
Present in infant's stomach but disappears slowly from
the stomach of adults
Important for infants because it coagulates milk in the
stomach to prevent its rapid passage to the intestine
This gives the baby the satiety and sensation of
fullness
Secreted as inactive pro-rennin that is activated by
proteolysis and by association with Ca2+ ions into active
rennin
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Digests casein into paracaseinate which combines

with Ca+2 ions to form insoluble Calcium-paracaseinate

(milk clot), which is then acted upon by pepsin to release

smaller peptides (peptones).

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Gelatinase: A component of gastric juice that works

at acidic pH and hydrolyzes gelatin
The partially digested food bolus enters the duodenum

and is met by enzyme rich pancreatic juice that carries

vary potent proteolytic enzymes.

Pancreatic enzymes:
Trypsin, chymotrypsin, carboxypeptidase,
elastase ,collagenase.
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Trypsin (Optimum pH = 7.9)

Secreted as trypsinogen and proteolytically activated
into trypsin by enterokinase (a glycoprotein secreted by
intestinal mucosa with an optimum pH of 5.5) and by
autocatalysis
Calcium enhances the activation process
Raw egg white, soybeans and blood contain strong
trypsin inhibitors

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Endopeptidase
Hydrolyzes the peptide bonds having -COOH group of
basic AAs (Lys, Arg) in native proteins and polypeptides
including trypsinogen and chymotrypsinogen to activate
them into trypsin and chymotrypsin, respectively
Releases smaller peptides and more free AAs
Converts fibrinogen into fibrin to clot blood

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Chymotrypsin (Optimum pH = 7-8):

Secreted as chymotrypsinogen that is activated by
trypsin and chymotrypsin into chymotrypsin and two
inactive peptides.
Actions: Endopeptidase that hydrolyses peptide bonds
with -COOH of aromatic AAs, Met, His, Leu and Asn.
Products of trypsin and chymotrypsin digestion are
mixtures of proteoses, peptones , polypeptides and free
AAs
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Carboxypeptidase (Optimum pH 7.5): Metallo-enzyme

(contains Zn2+), secreted in inactive pro-carboxypeptidase
form that is activated by trypsin and itself.
Actions: Hydrolyzes the C-terminal AA of polypeptide
chains. It releases one AA at a time from the C-terminal.
Two types of carboxypeptidases have been documented:
Carboxypeptidase-A: Prefers Tyr, Phe or Trp as terminal
AAs.
Carboxypeptidase-B: Prefers Arg and Lys as terminal
AAs
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Elastase:
Secreted as pro-elastase that is activated by trypsin
and breaks peptide bonds with -COOH of neutral
aliphatic AAs.
Hydrolyzes yellow connective tissue fibers (elastin).

Collagenase: Hydrolyzes white connective tissue

fibers

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1. Aminopeptidase (Optimum pH 5-7):

The enzyme is a metallo-enzyme (contains Zn2+, Mg2+,
and Mn2+) and acts as an amino-exopeptidase , releasing
one AA at a time but can not hydrolyze tripeptides any
further

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2. Enteropeptidase (enterokinase, optimum pH 5.5):

A glycoprotein secreted by duodenal mucosa ,
hydrolyzing peptide bonds with Lys residues, particularly
in trypsinogen to activate it
Calcium activates the enzyme and bile salts free it into
intestinal lumen

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3. Tripeptidase & Dipeptidases:

Require Zn2+, Co2+, and Mn2+ as cofactors and secreted
in an active form from duodenal mucosa
They complete the digestion of tripeptides and
dipeptides into free AAs in the intestinal lumen or inside
the mucosa cells after absorption
The digestion of proteins is dependent upon the
availability of the gastric, pancreatic and intestinal juices.
The secretion from these glands is regulated by GI
hormones
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Gastrin: Secreted from gastric antrum and duodenum

mucosal cells in response to the entry of food bolus into the
stomach and stimulates secretion of pepsinogen and the
intrinsic factor from gastric mucosa.
Cholecystokinin (CCK): Released from duodenum and
jejunum and activates pancreatic proenzyme secretion.
Secretin: Located in duodenum and jejunum and
stimulates secretion of bicarbonate-rich pancreatic juice.

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Absorption of Amino Acids

Site of Absorption: Most of the absorption of AAs takes
place in jejunum by active transport or by passive
diffusion
A.

Normally in infants where -globulins (antibodies)

present in colostrum are absorbed to acquire passive
immunity by the baby

B.

Abnormally in adults in certain diseases that lead to

allergic reaction e.g. urticaria

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Mechanisms of Absorption of AAs:

The absorption of AAs is mostly active where

energy is directly or indirectly required

Active transport also requires pyridoxal phosphate

A number of carries (transporters) mediate the

passage of AAs through the mucosal membrane

D-AAs are absorbed by passive diffusion that needs

no energy

A specific -glutamyl cycle also operates in the

intestines

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Carrier Protein Transport System:

L-AAs are absorbed by specific carrier proteins

present in small intestine; the carrier has one site for
AA and another site for Na+

The AAs are co-transported with Na+

Na+ ions are then pumped out of the mucosal cells in

exchange with K+ by Na+-K+-ATPase pump.

For each AA, one ATP molecule is utilized

3 or more different AA carrier systems; each carrier

transports a group of structurally related AAs

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Classification of Proteins
Protein classification is based on two criteria:
Depend on their Structure or Function
From structural point of view proteins can be
subdivided based on composition, solubility or presence
of prosthetic group
Taking composition as a yard stick proteins may be
subdivided into simple or conjugated proteins.

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Simple proteins are molecules that yield AAs on

hydrolysis
Conjugated proteins are proteins that are either
chemically linked to or physically complexed with non
AA units
Further more, proteins may be subdivided based on
number of AAs per molecule
In these context they are subdivided into peptide,
polypeptide or proteins if they are made up of 2-10, 10-40,
>40
AAs respectively
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Simple Proteins
Simple proteins are sub-classified into smaller
groups on the basis of their solubility
Accordingly, proteins of animal origin are
subdivided into two sets Albumins and Globulins
are water soluble proteins that exist in cellular and
ECFs.
On the other hand scleroproteins, sclero (G), hard
are fibrous proteins like tendon, hair, horn, etc
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Albumins and globulins perform several functions

including transport of elements, vitamins, and hormones,
immune function and maintenance of blood osmosis
Protamines Simplest natural proteins with MW >3.0
KD They are basic proteins, pI 7.4 , rich in Arg ( up to
90% ).
Triprotamines: Contain Lys and His beside Arg.
Diprotamines: Contain Lys and His only
Monoprotamines: Containing Arg only
Protamines
do not contain
Cys,
Trp and Tyr
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Scleroproteins
1. Elastins:
The yellow fibers of connective tissues in lungs,
uterine wall, arteries, tendons and ligaments
Rich in Ala, Leu, Val and Pro but deficient in
Cys, Met, Lys and His
Hydrolysable by prolonged boiling in strong acids
or strong alkalis or by elastase
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2. Collagens:
Major constituent of white fibrous connective tissues
body wide and in tendons and bones
~ 33% Gly; rich in Pro and hydroxy proline; the three
of them constitute 2/3 of the total contents of AAs.
Resistant to peptic and tryptic digestion
Prolonged boiling of collagen in water, dilute acids or
alkalis denatures, partially hydrolyzes and solubilizes
into the easily digestible gel forming gelatin
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 Collagen and gelatin are deficiency in Trp and Cys

Different tissues contain different combination of the
19 types of collagen formed of triple combinations of
30 types of polypeptide subunits

3. Reticulins:
The connective tissue network of reticular tissues
e.g., spleen, liver and lymph glands ; properties

common with elastin and collagen

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4. Keratins:
Highly insoluble in regular solvents
Resistant to peptic and tryptic digestion
Hydrolyzable by prolonged boiling with alkalis and in
barium sulfide
High content of Cys (~14%) and disulfide bonds
confers resistance, stability and insolubility of hairs,
nails and superficial layer of the skin
Contain His, Lys and Arg at 1:4:12 molar ratio
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Fibrous & Globular Proteins

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Conjugated Proteins
1. Phosphoproteins:
Conjugated proteins with replicable phosphate
prosthetic groups attached to -OH groups of Ser, Tyr or
Thr, e.g. milk casein, egg yolk
Phosphorylation- dephosphorylation as a major
posttranslational covalent modification of proteins
plays a major role for integration of protein-mediated
signal transduction and activities
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2. Lipoproteins in cellular and subcellular membranes

and plasma are protein-lipids conjugates
They carry structural, regulatory and transport
function particularly for plasma water insoluble lipids

3. Glycoproteins are those conjugated with N- or Oattached CHOs in varying amounts as short or long
chains on outer surface of cell membrane and in
intracellular components.
CHO moiety may confer the specific antigenicity and
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4. Metalloproteins are conjugates with metals,

e.g., iron bound to ferritin - the intracellular
iron-binding protein, transferrin - the iron-binding
transport plasma protein, Hb and Mb - the O2

binding proteins
Zn in SOD, carbonic anhydrase and insulin; and
Cu in the copper transporting antioxidant plasma
ceruloplasmin
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5. Chromoproteins are conjugates with a color

conferring prosthetic group

e.g., haem of Hb, Mb and cytochromes, and

riboflavin in the yellow flavoproteins
6. Nucleoprotein conjugates with NAs
particularly contain basic histone and non-histone
regulatory proteins
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Protein

Composition

Nucleoprotein

DNA- Protein Complex.

The latter is mainly histones

Lipoproteins

Lipids-proteins complex. They are transport

form of lipid & membrane molecules

Proteolipid

Proteins that carry covalently attached lipid

Metalloprotein

Proteins that contain tightly bound metal Ions.

The latter is retained on dialysis

Chromoproteins Proteins that contain covalently held prosthetic

group such as porphyrin, corrin ring, etc.

Glycoproteins

Proteins with covalently held oligosaccharide

unit (the carbohydrate composition is app.<5%)

Mucoproteins

Proteins with covalently held carbohydrate such

that the carbohydrate content is >5%.

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Functional Classification of Proteins

Proteins play several important functions.
It follows from the above proteins may be sub-

classified on the basis of these function.

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Protein

Function

Enzymes
Hormones
Receptors

Proteins that catalyze Biological reactions

Regulates extraccellular processes
Intracellular or Membrane proteins that selectively
recognize hormones, immunoglabulins, etc.
Immunoglob Proteins that recognize and selectively react with and
ulins
neutralize target molecules
Detoxifiers
Proteins such as Albumins, Metalothionines that
sequester heavy metals
Toxins
Proteins that poison organisms (eg. snake venom).
Transporters Proteins that transport gasses (eg. Hgb) and ions.

Contractile
Structural
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Proteins that convert chemical energy to Mechanical

energy (eg.Myosin)
Proteins that provide shape and protection to various
organs (eg. Collagen of skin)
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Proteins-Denaturation
Loss of native form with disruption of Secondary,
Tertiary & Quaternary structure changes in
physical and chemical characteristics & loss of
biological activity
No hydrolysis of peptide bonds, primary structure
preserved
Factors disrupting weak secondary bonds
responsible for maintaining protein structure
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1. Physical Manipulations:
Shaking
High temperature
Ionizing irradiations,

2. Some Biological Factors

e.g. insulinase that disrupts interchain disulfide
bond of insulin and inactivates it
Viruses can change physical, chemical &
biological nature of proteins
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3. Chemical Factors:
loss of bonds, (hydrogen, hydrophobic and
electrostatic bonds).
This makes denatured proteins antigenically and

immunologically distinct from their native form

Impairment of structure-function relationship loss
of enzymatic, hormonal and other biological activities.

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Advantages of Denaturation
Proteins denatured by cooking are more easily digested
than native proteins
Denaturation is used for detection of urinary albumin
Measurement of specific analytes in biological samples
such as uric acid and glucose requires removal of
proteins that could interfere with the estimation
For the scientific study to investigate new AAs in the
sequence of proteins
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 So the blood/serum sample is first treated with

alkaloidal reagents to denature and precipitate the
proteins
Several traditional medical approaches for stoppage
of bleeding and treatment of burns are based on
precipitation and denaturation of a superficial
protein
Denaturing conditions in electrophoresis are used to
separate the proteins on basis of MW
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Amino Acid Catabolism

Most AAs catabolized in liver but for met and branchedchain AAs, other organs also participate
Transamidation : Transfer of NH2 from AA amide,
e.g., Gln to a sugar for synthesis of sugaramines
Amidation is the addition of NH3 to non--COOH
group to give the amide of AA, e.g., Asn and Gln
Deamidation: is the removal of that amide amino group
of these amide AAs as free NH3
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Decarboxylation: Removal of CO2 from an AA

amines. Amines are physiological and pathological
effectors in the body
Transmethylation: Transfer of a CH3 from methyl
donors (methyl-FH4 or SAM) to methyl acceptors
methylated form; catalyzed by O- or N-methyl transferase.

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Transamination
Occurs mainly in liver, kidney, brain ,heart.
First step in the catabolism of AAs.
No net loss of NH2 or N
Only transfer of NH2 to -KGA to form Glu.
Metabolic function of transamination: to collect all the
N(amino groups) from AAs into Glu.
Glu then functions as an NH2 donor for biosynthetic
pathways or for excretion pathways that lead to the
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All AAs are transaminable except Lys, Thr, Pro and

Hydroxyproline.

Mechanism: Catalyzed by group of enzymes known as

transaminases or aminotransferases.

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They are intracellular enzymes, i.e., their appearance in the

blood indicates presence of cellular damage somewhere in the
body
Transaminases require pyridoxal phosphate (PLP) as a
coenzyme
The covalently linked PLP is an intermediate acceptor of
NH2 from the AA to be aminated into pyridoxamine phosphate
and liberating a new -keto acid.
Then, it transfers NH2 to the -keto acid converting it into
a new -amino acid and regenerating PLP
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Functions of Transaminases
Transfer of NH2 from most AAs to -KGA to form Glu.

This is very important since Glu is the only deaminable

AA that can release free NH3 suitable for urea synthesis.

Synthesis of non-essential AAs, through reactions of keto acids with Glu.

Transamidation to form amide of AAs, sugaramines and
nitrogenous bases and conversion of C skeleton of AAs
into ketone bodies or Glucose for energy production
during starvation.
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1. Aspartate Transaminase:
Present in both cytosol and mitochondria of the cells of
myocardium and liver.
Muscles, pancreas and kidneys also have the enzyme.
Catalyzes the transfer of amino group from Asp to -KGA
to form Glu and OAA in a reversible reaction.

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2. Alanine Transaminase (ALT)

Reversibly catalyzes transfer of NH2 from Ala to
-KGA to form Glu and pyruvate.
ALT transports NH2 to the liver in a non-toxic form via
glucose-alanine cycle.
In muscle and other tissues that degrade AAs for fuel,
NH2 collected as glu by transamination.
Glu then transfers NH2 to pyruvate by ALT.
The Ala so formed passes into the blood and travels to
liver.
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In the cytosol of hepatocytes, ALT converts this NH2 to

glu which then releases N as NH3 by GDH for urea

synthesis.

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3. Glutamate Transaminase
Scavenger of the amino nitrogen from a variety of AAs.
Cytosolic as well as mitochondrial enzyme that catalyzes
NH2 transfer from any transaminable AA to -KGA producing
Glu & - keto- acid.
Transamination is not restricted to the -amino N of AAs; amino of ornithine is readily transaminated to form glutamate-semialdehyde.

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Deamination
Irreversible removal of NH2 from AAs as free NH3.
Most AAs are deaminable , undergo deamination in
liver/ kidneys.
Oxidative and non-oxidative deamination of amino
N has an important contribution to the over all N
metabolism.

Routes for Deamination:

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1. Oxidative Deamination:
Irreversible removal of NH2 as NH3 secondary to
dehydrogenation of AA.
-AA -keto acid.
Autooxidizable flavoproteins, have FMN or FAD as
prosthetic groups.
Reduced flavin nucleotides produced in the reaction are
reoxidized directly by molecular O2 forming H2O2 without
transferring hydrogen to cytochromes or other electron
carriers.
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H2O2 is detoxicated into O2 and H2O by catalase.

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2. Non-oxidative Deamination:
Deamination reactions that are very specific for the AA and allow
removal of amino group without oxidation or addition or removal of
water.
It takes place during processes such as putrefaction in large
intestine.

Example: Histidase reaction, that removes the amino group of

histidine to form urocanic acid without any accompanying reactions.

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3. Hydrolytic Deamination:
Removal of free NH3 by addition of H2O molecule

Important for deamination of nitrogenous bases:

purines and pyrimidines

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4. Reductive Deamination:
Occurs in the processes of putrefaction in the large

intestine and abscesses due to effect of bacteria.

NH3 is removed by addition of two hydrogen atoms to
the AA to form the corresponding carboxylic acid
(i.e., fatty acid)

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Transdeamination
The process of transamination + oxidative deamination
of Glu : transdeamination
Transamination of most of AAs channels their amino
nitrogen into L-Glu
GDH carries out oxidative deamination of Glu into KGA and liberates NH3 that enters urea cycle
Glu links metabolism of AAs to synthesis of urea, so
central position in nitrogen metabolism
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GDH: Aaerobic dehydrogenase located in the matrix

Metalloenzyme containing Zn2+

Allosteric enzyme, with 6 identical subunits

Only enzyme that can use either NAD+ or NADP+ as
coenzyme
Widely distributed in mammalian tissues
Has high activity.
Since transdeamination is a reversible process, it is used
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synthesis
of non-essential AAs
NH3 and -keto acids

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Clinical Importance of Transdeamination

Accumulation of NH3 as in liver disease pushes the reaction
towards Glu causing depletion of -KGA from Krebs cycle
causing its inhibition.
This leads to energy failure in the NH3 -sensitive tissues
such as the brain, a cause of hepatic coma.
Mutations at the allosteric GTP binding site of GDH cause
permanent activation of the enzyme leading to a human
genetic disorder called hyperinsulinism-hyperammonemia

syndrome characterized by hyperammonemia and

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Blood Ammonia
NH3: toxic nitrogenous compound
NH3 intoxication causes symptoms like peculiar flapping
tremor, slurring of speech, blurring of vision .
In severe cases can lead to coma and eventually death.
Normal range of NH3 in blood: 10 - 80 g/dL.
Rapidly removed from circulation by the liver & converted
either to Glu, Gln or urea.
In liver disorders like alcoholic liver disease or cirrhosis,

NH3 not converted into urea and rises in blood, a toxicity

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condition
known as hyperammonemia.

135

NH3 passes directly to systemic blood through collateral

arteries and exposes brain tissue to the toxic
concentrations.
The brain detoxifies NH3 into Gln that depletes -KGA
of Krebs' cycle
This leads to energy failure in the brain cells
Moreover, an abnormal -transamidation reaction of
NH3 with -KGA produces the toxic -ketoglutaramate

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Sources of Blood Ammonia

Main source: transamination & deamination of AAs.
Deamination of purines and pyrimidines and monoamines.
Intestinal bacterial activity on dietary proteins, urea secreted
in GI juice, and deamination of other nitrogenous bases.
This becomes significant source in constipation, GI
hemorrhage and high protein diet.
It is very important to be prevented in liver diseases;
otherwise NH3 intoxication would be worsened.

Intestinal antiseptic antibiotics and enema are very

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in such cases .

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Sources of Blood Ammonia

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Disposal of Blood NH3: Anabolic Fates

Free NH3 removed by deamination enters the NH3 pool of the
body and may be used for:
1.

Synthesis of urea

2.

Synthesis of non-essential AAs

3.

Synthesis of purines, pyrimidines, and sugaramines

4.

Synthesis of Porphyrins have 4 Gly molecules

incorporated in their ring structure.

5.

Glutamine Synthesis

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Glutamine Synthesis (Gln):

Gln acts as a reservoir or carrier of N and provides a

mechanism for detoxification of NH3 in extra-hepatic
tissues particularly brain, kidney, retina and muscles.

Glu reacts with NH3 in presence of ATP, Mg2+ and the

mitochondrial glutamine synthetase to produce Gln.

Gln is transported through blood from various tissues to

the kidney and liver where it is hydrolyzed by
glutaminase into Glu and NH3 .

Glutaminase is present in liver, kidneys, brain as well as

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Normal blood Gln level is 6 - 12 mg/dL and can rise

above 30 mg/dL during hepatic coma.

Glutamine cycle: Gln serves as a transport vehicle for

NH3 from brain to kidneys or liver

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Functions of Glutamine
Transamination
Detoxification by conjugation
Purine and pyrimidine synthesis
Synthesis of Trp and His
NH3 released by glutaminase in liver is converted to urea and
excreted in urine

In kidneys, NH3 excretion acts as an excretory vehicle for H+.

The NH4+ions in kidneys are excreted in exchange for Na+, hence
NH3 helps in the retention of base and excretion of acid, thereby
providing a mechanism for resistance to the change in pH in acidosis
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Gln gives its amide NH3 to purines (N3 and N9),

pyrimidines (N3), fructose-6-phosphate to give glucosamine6-phosphate, -keto acids to give AAs, and asp to give Asn.
Gln formation in the brain removes excess NH3.
Gln is used in detoxication of phenyl acetate and other toxic
metabolites. Glutamine then goes through the blood to the
kidney where it is hydrolyzed by glutaminase (deamidation of
CO-NH2) to give free NH3 that passes to urine and Glu that is
recycled to the brain.
It is a major source for energy for cells of the immune
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Functions of Glutamine

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Regulation of Glutamine Synthesis

Synthesis of gln has to be regulated because it saps the
glu as well as -KGA from metabolism which might slow
down the Krebs cycle.
The enzyme glutamine synthetase is regulated by
polyadenylation 12 adenylate units are covalently
attached by adenyl transferase to the enzyme to inactive it.
Removal of these adenylate units by deadenylase enzyme
reactivates it .
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Feedback inhibition of glutamine synthetase is

provided by accumulation of Carbamoyl-P, Glucosamine-

6-P, AMP, CTP as well as Trp and His.

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Urea Cycle (Krebs-Henseleit Cycle)

Elucidated by Krebs and Henseleit (1932).
A five-reaction cyclic cascade that utilizes two amino
groups and a CO2 to synthesize urea, the nitrogenous
waste of our body.
Major pathway of nitrogen excretion
80-90% of the protein nitrogen released as NH3 is
excreted in man as urea
Urea is synthesized in the liver, diffuses freely into the
blood and is cleared through
the kidneys.
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Sites of Urea Synthesis:

1. Urea synthesizes in liver from NH3 & CO2
2. The cycle operates in mitochondria & cytoplasm
3. Kidney and brain have an activity urea cycle enzymes
4. Kidneys operate urea cycle up to the formation of Arg but
enzyme arginase is absent, so urea is not synthesized but
the cycle provides a source of Arg in the kidneys.

5. Brain tissue lack the enzyme ornithine transcarbamoylase,

i.e., can not form citrulline. Rest of the enzymes are
present, hence brain tissue can synthesize urea if citrulline
is provided.

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Steps of Urea Cycle

1.Synthesis of carbamoyl-phosphate:
Condensation of one mole of NH3, one mole of CO2 and
one mole of phosphate (derived from ATP) leads to the
formation of carbamoyl phosphate.
Enzyme: carbamoyl phosphate synthetase I
Cofactors: Mg2+ or Mn2+ ;
Allosteric activator: N-acetyl glutamate (NAG)
NAG increases the affinity of carbamoyl phosphate
synthetase I for ATP.
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The second type of this enzyme the cytosolar liver

carbamoyl phosphate synthetase II is utilized in
pyrimidine biosynthesis and does not require NAG as an
allosteric regulator.

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2. Synthesis of Citrulline:
Transfer of the carbamoyl residue from carbamoyl
phosphate into ornithine to form citrulline with
liberation of phosphate.
Enzyme: Mitochondrial ornithine carbamoyl transferase
(ornithine transcarbamoylase).
Citrulline goes to cytosol to complete the cytosolar
component of the urea cycle, where, the rest of the
reactions take place.
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 Ornithine carbamoyl transferase is clinically utilized

to check for liver function

The level of this enzyme in blood is increased in

many diseases, e.g., liver metastasis from breast
cancer and malignant lymphomas.

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3. Synthesis of Argininosuccinate:
Citrulline is condensed into the amino group of Asp to form
argininosuccinate with liberation of H2O.
Enzyme: argininosuccinate synthetase
Cofactors: ATP and Mg2+.
Citrullyl-AMP is an active intermediate formed during the
reaction.

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4. Cleavage of Argininosuccinate:
Enzyme: Argininosuccinase found in liver and
kidney
Fumarate formed by this cleavage joins Krebs' cycle

to replenish its intermediates.

Fumarate is also converted into oxaloacetate that
could be transaminated into asp to return the N into the
urea cycle, thus, closing a fumarate-aspartate loop.

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The AST transamination reactions are also as

important as the transdeamination reactions through

Glu in excretion of AA nitrogen.

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5.Cleavage of Arginine into Urea and Ornithine:

Liberation of urea is brought about by cleavage of Arg
catalyzed by arginase.
The ornithine returns to mitochondria.
Arginase present mainly in the liver of all ureotellic
organisms.
Smaller quantities also occur in testes, skin and mammary
gland.

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Link Between Urea Cycle and TCA Cycle:

Fates Of Oxaloacetate:
1. Transamination to Asp, which can then feed back into

the urea cycle;

2. Condense with acetyl CoA to form citrate which then
continues on round in TCA cycle
3. Conversion into glucose via gluconeogenesis
conversion into pyruvate.

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Link Between Urea Cycle and TCA Cycle

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Regulation of Urea Synthesis

Urea formation increases during increased rate of
protein breakdown under conditions like starvation and
lack of energy.
High protein diet in non-growing individuals also
increases urea synthesis.
Therefore, urea cycle responds to the N flush from
proteins or AAs in the form of NH3.

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Key regulatory step for the regulation of urea cycle is

the condensation reaction catalyzed by carbamoyl
phosphate synthetase I.
The enzyme shows allosteric regulation by N-acetylglutamate, which increases the affinity of the enzyme for
ATP.
The carbamoyl phosphate synthetase reaction is
determined by the availability of substrate NH3.

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The major source of NH3 in liver is the transdeamination

reactions of GDH, which channels NH3 from all transaminable
AAS to carbamoyl phosphate synthetase I.
The dehydrogenase reaction is reversible but is pulled in the
forward direction by rapid removal of NH3 from the matrix.
ATP is another activator of the cycle it stimulates GDH
enzyme unidirectionally in the forward direction, i.e., liberation
of NH3.
The availability of NH3 then triggers the carbamoyl
phosphate synthetase activity.
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Urea Cycle & Inherited Disorders

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