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SFA 2073
Topic II
Amino Acid & Proteins
Nik Norma Nik Mahmood (PhD)
Faculty Science & Technology
Uni.Science Islam Malaysia
NILAI, N.Sembilan
OBJECTIVES
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To Classify amino acids according to their structures and
properties.
To explain the meaning of pKa and pI of amino acids
To understand the biochemical benefit of amino acids
To describe the importance of some amino acids in the
synthesis of important compounds
To understand the biochemical benefit of proteins
To Classify proteins according to their structures and
properties.
Relate the structure of proteins to their functions using
specific examples.
To understand the importance of amino acids & protein
in biochemical efficiency.
Discussion Order:
Structure & Function Of:
- Amino Acid
- Proteins
 Proteins :
- digestion and absorption
- metabolism
- metabolic disorder disease
 Amino Acid :
- absorption and metabolism
- metabolic disorder disease
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INTRODUCTION:
Expression of Concentration
(the various expressions of concentrations used).
At the end of this lecture, students should be able to:
 Differentiate molarity and molality
 Apply the units of concentration used in medicine (g%,
mmol, g/dl, IU/I etc.)
 Explain dilution, concentrated, saturated and
supersaturated solution
 Explain biological solution concentration ie hypertonic,
hypotonic and isotonic.
Solution
• I. There are several way to represent concentration of
solution:
a) Molarity (M) the number of moles of solute per liter
solution.
moles of solute (mol)
M =
Volume of solution (dm3 or liter)
Unit:
moldm-3 or
molL-1 or molar (M)
b) Molality (m) the number of moles of solute per kg of
solvent.
moles of solute (mol)
m =
mass of solvent (kg)
Unit: molal (m) or molkg-1
4.5
II. Units of concentration used in biological science:
a) Percent Composition by Mass (%)
Ratio of the mass of solute to the mass of solution multiply
by 100.
eg 20g NaCl in 100 g salt solution
20 x 100 = 20 % sodium chloride solution
100
b) mmol: millimol = 1X 10-3 mol or 1 mol= 103 millimol
c) g/dl : gdl-1 = g in 1 deciliter solution
10 dl = 1 L  1 dl = 10-1 L
d) IU/I : International Unit is a unit of measurement for the amount of a
substance, based on measured biological activity or effect.
The unit is used for vitamins, hormones, some medications, vaccines,
blood products, and similar biologically active substances.
IU is not part of the International System of Units used in physics and
chemistry.
IU should not be confused with the enzyme unit, also known as the
International unit of enzyme activity and abbreviated as U.
Mass equivalents of 1 IU
Insulin: 1 IU is the biological equivalent of about 45.5 μg pure
crystalline insulin (1/22 mg exactly)
 Vitamin A: 1 IU is the biological equivalent of 0.3 μg retinol, or of 0.6
μg beta-carotene
 Vitamin C: 1 IU is 50 μg L-ascorbic acid
 Vitamin D: 1 IU is the biological equivalent of 0.025 μg
cholecalciferol/ergocalciferol
 Vitamin E: 1 IU is the biological equivalent of about 0.667 mg d-alphatocopherol (2/3 mg exactly), or of 1 mg of dl-alpha-tocopherol acetate
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III. a) Making Dilutions
process of adding more solvent to a known
solution.
The moles of solute stay the same, moles = M x L
In solution: initial Mole of solute = final Mole of
solute
M1 V1 = M2 V2
III. b) concentrated solution
has less amount of water and more amount of the substance. For
example concentrated H2SO4 has 2% water and 98% H2SO4 and
dilute has less amount of substance and more amount of water
c) saturated solution
contains the maximum amount of a solute that will dissolve in a
given solvent at a specific temperature.
d) supersaturated solution
contains more solute than is present in a saturated solution at a
specific temperature.
e) biological solution: concentration is described as
hypertonic or hypotonic
Hypertonic solution contain a high concentration of solute relative
to another solution on the other side of the membrane. Water
from the other side will flow to this solution.
solution
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Few notes for weak acid:
pH is a direct measure of the H+ concentration.
Ka: is acid dissociation/extent of ionisation constant,
acidity constant.
pKa:The negative logarithm of Ka
pKb:The negative logarithm of the base protonation constant
Kb
the extent of ionization of a weak acid (the pKa) influences
the final concentration of H+ ions (the pH) of the solution. For
a weak acid there is a relationship between pH and its pKa.
This relationship is given by the Henderson–Hasselbalch
equation:
pKa = pH + log [HA] / [A-]
can be CH3CO2OR pH= pKa + log [A-] / [HA]
CH3 CZRCO2-
Derivation of Henderson–Hasselbalch equation
Ka = [H3O+] [CH3COO-]
[CH3COOH]
[H3O+] = Ka [CH3COOH]
[CH3COO-]
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X each by (- log) …… – log [H3O+] = – log Ka – log [CH3COOH]
[CH3COO-]
pH = pKa – log [CH3COOH]
[CH3COO-]
pH = pKa + log [CH3COO-]
[CH3COOH]
Henderson–Hasselbalch
equation.
Determination of pKa
Titration of 100 mL 0.1 M CH3CO2H with 50 mL 0.1M NaOH
CH3CO2H + NaOH
CH3CO2‾+Na +H2O
stoichiometric coefficient 1:1
Initial mole CH3CO2H = 0.01
Final mole CH3CO2ˉ =0.005
Unreacted CH3CO2H = 0.01- 0.005 = 0.005
pH value can be determined by using pH meter
Substituting all the values in the equation, can get pKa
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By varying the volume of 0.1M NaOH in each titration can get
the corresponding pH and pKa values
Relationship between amino acids and
protein:
 Amino acids are building units of protein
Protein
n
Peptide bonds
Different coloured balls
& box => Amino Acids
Amino Acid: Structure & Function
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Amino acid (a.a) 20 altogether = std aa
-
all aa share a general formula
R-CH-NH2
1 aa differ from the other by the feature of –R
Classified based on : i) structure
ii) side chain
-
COOH
• aliphatic aa
• non-polar
• dicarboxylic aa
• uncharge or nonionic polar
• charge or ionic
polar
• diamino aa
• aromatic aa
• heterocyclic aa
Aliphatic Non-polar Amino Acid
hydrophobicity
Properties:
- glycine and alanine are also found in
the free form.
Aromatic Amino Acid
Properties:
tryptophane
-Are non polar
- absorb ultraviolet light (to different degree)
- tyrosine has ionizable side chain
phenylalanine
Basic Amino Acid
Histidine
lysine
arginine
Properties:
- Are polar
- Are positively charged at pH values below their pKa’s
-Are very hydrophilic
- imidazole of histidine, at pH 7 exist predominantly in the neutral
form.
Acidic Amino Acid
Properties:
-are polar
- are negatively charge at physiological pH the –COOH of side chain can form amide
with an amino group.
- iii) Nutritional Requirement
• essential aa (8/9). Cannot be synthesized by the body
• non-essential aa (12/11). Can be synthesized by the body
Essential
Nonessential
Isoleucine
Alanine
Leucine
Asparagine
Lysine
Aspartate
Methionine
Cysteine*
Phenylalanine
Glutamate
Threonine
Glutamine*
Tryptophan
Glycine*
Valine
Proline*
Serine*
Tyrosine*
Arginine*
Histidine*
* Essential in certain
cases. Eg arginine &
histidine are growth
promoting factor there
fore become essential
in growing children
- Amino acid is a derivative of organic (weak) acid.
- Has 2 functional groups, carboxylic group (-COOH) and amino
group (-NH2).
Carboxylic (-COOH) and amine (-NH2) groups are capable of
ionization:
Can donate & accept H+
+
―COOH
―COO‾ + H (2< pKa1< 2.5) i.e amphoteric nature
aa are
―N+H3
―NH2 + H+ (9< pKa2< 9.5) therefore
ampholytes
( ―N+H3 is a weaker acid )
- All aa is affected by pH:
The net charge on the molecule in solution is affected by pH of their
surrounding and can become more positively or negatively
charged due to gain or the loss of protons (H+) respectively.
eg. At pH~2.0 the amino group will be as –NH3+, the carboxylic group
will remain as –COOH (aa will migrate towards the cathode).
As pH is increased, –COOH (from some fraction of aa) ionises.
When the pH is equal to the pKa1 the amino acid exists as a 50:50
mixture of the cationic and zwitter ionic forms.
As pH is further increased more cationic form converts to the
zwitterionic
- Adding more base results in continued ionization of the
carboxylic acid group until the zwitter ionic form is the
predominant form of the amino acid in solution. By the addition
of more base, the pKa of the amino group is reached and at this
point the amino acid exists as a 50:50 mixture of the zwitter ionic
form and the anionic form. As the pH is increased further the
amino group continues loses its proton and ultimately, at high
pH (pH ~ 12.0), the anionic form is the predominant form in
solution.
At pH>~9.6 the amino group will be as –NH2, the carboxylic
group will remain as -COOˉ (aa will migrate towards the anode).
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So at physiological pH 6.8 - 7.4, the –COOH group exist as
COO¯,
and the –NH2 as –NH3+. Therefore all aa are double-charged
structure or zwitterion in this pH region. The pH at which they
exist as “whole” zwitterion i.e the molecule carries no
electrical charge, or the negative and positive charges are equal
is called Isoelectric point (Ip) or Isoelectric pH .
aa Actual structure
CH3-CHCOOH
CH3CH COO¯
NH2
N+H3
Neutral un-charged
NOT THIS
High pH
region
Zwitterion. Neutral
but charge
Low pH
region
- Each aa has its Ip value. At Ip:
i) aa is double-charge (zewtterionic) i.e +ve & -ve, amount of positive
charge exactly balances the amount of negative charge so net
charge is 0 (electrically neutral).
ii) it does not move/migrate in electric current
iii) the molecule has minimum solubility.
iv) Ip of all aa lie in the range of pH 6.8 - 7.4
Isoelectric pH of an aa solution is given by:
pH = ½ (pK1 + pK2)
For aliphatic
aa
50% as cationic
50% as zwitterion
50% as anionic
50% as zwitterion
E.g
The pH profile of an acidic solution of alanine when
the solution is titrated with a strong base, NaOH.
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Physical properties:
- colourless crystalline; soluble in water/polar solvents.
Tyrosine is soluble in hot H2O
- have high m.pt >200oC
- have high dielectric constant and high dipole moment
- molecules have minimum solubility in water or salt solutions
at the Ip pH and often precipitate out of solution.Why? At Ip
aa is in zwitterionic form therefore non-polar. Hence no
interaction with polar water molecules
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Chemical properties: involve –COOH & involve –NH2
i) involve –COOH
• decarboxylation or formation of amine & CO2
eg. histadine
histamine + CO2
tyrosine
tyromine
+ CO2
tryptophan
tryptamine + CO2
lysine
cadaverine CO2
Glutamic
gamma amino butyric acid (GABA) +
CO2
•
Amide formation :
α-COOH of 1 aa reacts with α-NH2 of aa behind to form a peptide
bond or CO—NH bridge eg in peptides and proteins
Amide formation (at 2nd —COOH)
aspartic + NH3
asparagine
glutamic + NH3
glutamine (than N donated for N.A
synthesis)
ii) involve –NH2:
● formation of carbamino compound
–NH2 + CO2
–NH-CO2H
eg transport of CO2 by hemoglobin from tissue to lung
Hb–NH2
Hb–NH-CO2H
(carbamino-Hb)
● Transamination eg in metabolism pathway
RCHCOOH + R’CCOOH
RCCOOH + R’CCOOH
‼
‼
NH2
O
O
NH2
● oxidative Deamination eg. in metabolism pathway
RCHCOOH
RCCOOH
+ NH3
‼
NH2
O
Contributing properties from R groups
When R group is plain hydrocarbon (gly, ala, leu, isoleo, val)
the a.a interact poorly with water.
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* When R group have functional groups capable of hydrogen
bonding e.g -OH ( Ser, thr, tyr) ; -COOH (asp and glu),
these a.a are Hydrophilic or ‘water-loving’ so easily interact
with water.
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Ester Formation by –OH of serine
-OH + H3PO4
phosphoproteins
-OH + polysaccharide
O-glycoprotein
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* When R group have functional group –COOH ( asp , glu)
the a.a can exist as –ve molecule physiological pH and can
form ionic bonds with basic amino acids.
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When R group have functional group –NH2/ -NH (lys and
hist) , these a.a are +ve charged at physiological pH and can
form ionic bonds with acidic amino acids.
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The sulfhydryl group of cysteine is highly reactive.
-Oxidation of two molecules of cysteine forms cystine. The 2
molecules is linked by a disulfide bond/bridge. The reaction is
reversible oxidation
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Transmethylation
methyl group of methionine may be transferred to an
acceptor to become intermediates in metabolic pathway
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Formation of S-S bridge.
sulfhydryl (-SH) group of cysteine can form the S-S bond
with another cysteine residue intrachain or interchain
2 cysteines
cystine
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Function of R groups is also very significant in function of
peptides and Proteins.
Few examples:
a) The hydrophobic aa will generally be found in the interior
of proteins shielded from direct contact with water
b) The hydrophilic aa will generally be found in the exterior
& active centre of enzyme.
c) The imidazole ring of histidine acts as proton donor or
acceptor at physiological pH hence it is normally found in
active site of enzyme, in hemoglobin (RBC).
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Few aa are origin/starting molecules for important compounds or
amino acid derived molecules:
Glutamic acid
Gammaaminobutyric acid (GABA)
Tyrosine
dopamine.
these are neurotransmitters.
Histidine
histamine, a mediator of allergic reactions
Tyrosine
thyroxine, a thyroid hormone
Serine
cycloserine an anti-tuberculous;
azaserine, an anti-cancer molecule
Arginine
ornithine and citrulline, intermediates in urea
cycle
2. Structure and function of proteins
To enable to:
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Describe the formation of peptide bonds
Describe the four levels of protein organization with reference
to primary, secondary, tertiary and quaternary structure of
proteins using haemoglobin as example
Explain how structure of protein determines its function by
looking at examples
Differentiate between globular and structural proteins with
examples eg immunoglobulin, hemoglobin, collagen, keratin etc
Describe the functions of protein
Relationship between structural protein and its function in
health and disease.
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Proteins: Biological Functions
as biological catalysts of the chemical reactions that occur
within the cell examples:
i- starch
α-amylase
ii- protein
trypsin
iii- triglyceride
maltose + shorter chain starch
amino acids
lipase
+ peptide chain
f f a + mono + di
glycerides
iv- ATP
phosphatase
ADP +Pi
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As regulatory proteins. These proteins regulate the
activities of the cell and the ability of other proteins to carry
out their cellular function in regulating overall metabolism,
growth, development, and maintenance of the organism
eg peptide and protein hormones; allosteric enzyme; gene
inducers & repressors.
As transporter molecules eg. hemoglobin; GLUT,SGLUT
i- hemoglobin transport O2 from tissue to lungs; myoglobin
transport O2 intracellular
ii- GLUT transport glucose/galactose from intestinal to
blood,
iii- SGLUT transport glucose from intestinal to blood.
As storage proteins eg myoglobin, stores O2 in muscle
tissue
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A peptide bond (amide bond):
- feature bonds between amino acids (aa) in polypeptides
and proteins.
- is formed when the carboxyl group of one aa molecule
reacts with the amine group of the other aa molecule in
front of it, thereby releasing a molecule of water (H2O).
- this is a dehydration synthesis reaction or condensation
reaction,
- the resulting CO-NH bond is called a peptide bond, and
the resulting molecule is an amide. The four-atom
functional group -C(=O)NH- is called an amide group or
(in the context of proteins) a peptide group.
- living organisms employ enzymes to form peptide bonds.
eg. during translation process.
- When two amino acids are linked together, the product is
called a dipeptide and when the product is of three amino
acids then it is tripeptide
Peptide bond
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―C―N
O
H
feature bonds between amino acids (aa) in
polypeptides and proteins.
is a bond formed when a carboxylic group reacts with
an amino group instantaneously eliminating a
molecule of H2O
this is a dehydration synthesis reaction or
condensation reaction,
the resulting CO-NH bond is called a peptide bond,
and the resulting molecule is an amide.
The four-atom functional group -C(=O)NH- is called
an amide group or (in the context of proteins) a
peptide group.
living organisms employ enzymes to form peptide
bonds.
eg. during translation process.
When two amino acids are linked together, the product
is called a dipeptide and when the product is of three
amino acids then it is tripeptide
Structure organization in
proteins
Primary Structure (or primary level of
organization)
Definition. Is "The sequence of amino
acids in the polypeptide chain.",
The N-terminal on the left and C terminal
on the right.
 chain has 50 to 2000 amino acid
residues so it is a polypeptide
 The residues are joined by peptide
bonds
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Changes in the primary structure can
alter the proper functioning of the
protein.eg offcoded of 2 amino acid in
the protein of the glycoprotein in RBC
results in MN blood group
In actual chain these R
groups will be the
various side chains
N-terminal
Peptide bond
C-terminal
Effect of surrounding pH on the structure
At neutral pH
Protein with basic aa
will have overall positive
charge.
And
that with acidic aa will
have overall negative
charge
cont
Effect of surrounding
pH on the structure
Secondary structure: There are two types : the α -helix
and the β-pleated sheet.
 The attraction between the R groups can occur
within the same chain (case I) or between chains
lying next to one another (case II). Case I leads to
formation of weak bonds eg hydrogen bonds ; R-R
attraction etc. The hydrogen bonds is "Intrachain
Hydrogen Bonding" which is between the hydrogen
and oxygen atoms of the amino acid backbone.
These intrachain weak bondings can cause the
chain to twist into a "right handed" coil or α-helix.
Case II leads to formation of β-pleated sheet.
Such “secondary structure α -helix ” often
predominate in "globular proteins“ and β-pleated
sheet predominate in fibrous proteins.
Globular proteins are
(i) compactly folded and coiled somewhat spherical. The molecule’s
apolar a.a bound towards the molecule interior and the polar a.a
bound towards the molecule exterior allowing dipole-dipole
interaction with the solvent.
(ii) Soluble in aqueous medium giving colloidal solution
(iii) Play numerous functions, as:
i) enzymes eg esterases
ii) messengers/hormones eg. Insulin
iii) transporter of molecules across membran iv) storage eg myoglobin
** α-helix: "alpha" means, looking down the length of the spring, the
coiling is happening in a clockwise direction
β- pleated sheets: the chains are folded so they lie alongside each
other
H2 bond
β-pleated , anti-parallel
(arrows running in opposite
direction
Myoglobin
- first globular protein whose structure was analysed by Xray diffraction by protein crystals. The periodic repeats
characteristic of alpha helix were recognised, and the
structure shown to have 70% of the polypeptide is alphahelical.
- it is O2 storage site in muscle tissue.
- It is also intracellular transporter of O2.
- Its tertiary (3-D) structure consists of a 8 α-helices which
fold to make a compact globular protein.
- the side facing the interior having amino acids with
hydrophobic side-chains ie. hydrophobic groups are on
the inside of the protein. The side facing to outside
having polar side-chains ie. hydrophillic groups are on
the outside of the protein, facing the aqueous
environment.
Myoglobin Structure
Reference: J.Mol. Biol. 142, 531-554.
A representation of the 3D
structure of the myoglobin
protein. Alpha helices are shown
in colour, and random coil in
white,
Heme with
Fe2+/3+
β-pleated sheet
- the β-pleated sheet forms when the hydrogen atoms of the
amino group and the oxygen atoms of the carboxyl group of
amino acids on two chains (or more) lying side-by-side forms
hydrogen bond.
- Closely associate to structural/fibrous proteins
- the protein chains are in associate to form long fibers
- elongated or needle shaped
- possess minimum solubility
- resist digestion
- The β-pleated sheet
structure is often found in
many structural proteins, eg
"Fibroin", the protein in spider
webs; Keratin- a structural
protein found in hair and nails,
skin, and tortoise shells
Fibrous proteins are more filamentous or elongated, play only
structural funtions. Also known as scleroproteins. Found only
in animals. Are water-insoluble. Used to construct connective
tissues, tendons, bone matrix, muscle fibers. Examples are
keratin (hair; tough and hard bud not mineralized structure as
in reptiles) , collagen ( long chains, tied into bundles, has
great tensile strength). Its degradation leads to wrinkles that
accompanying aging.
"Tertiary" Structure: a 3 dimensional chain arrangement,
 the way the whole chain (including the secondary
structures) folds itself into its final 3-dimensional shape
 is held together by interactions between the side chains the "R" groups. Interactions such as: ionic; van der Waals
(hydrophobic-hydrophobic); H-bonds; S-S bridge OR
 When "proline", an oddly shaped amino acid occurs in the
polypeptide chain a "kink" in the a-helix develops. Kinks
can also be caused by repulsive forces between adjacent
charged R groups. These kinks create a 3 dimensional
chain arrangement
This 3 dimensional shape is also held together by weak
hydrogen bonds "disulfide" bonds between two amino
acids of cystine ("covalent") disulfide "bridges" (linkages)
cystine -- s -- s – cystine.
These strong covalent bonds hold the protein in its specific
3D shape. The 3D shape creates "pockets" or "holes' in the
surface of the protein which are very important in enzyme
function
Cystinyl
random coils
pleated sheets
α-helix
Quaternary Structure of Proteins

2 or more 3 dimensional tertiary proteins and sticking them together to form
a larger protein. Many enzymes and transport proteins are made of two or
more parts.
 only exists, if there is more than one polypeptide chain present in a complex
protein
 Hemoglobin: an oxygen carrying protein in red blood cells which is made of
4 parts.
Structural Level of Proteins
Denaturation or Loss of 3-D shape
denaturing agents: Temperature> 40oC; mineral acids; salts. eg.
when heated, protein can unfold or "Denature". This loss of
three dimensional shape will usually be accompanied by a loss
of the proteins function. If the denatured protein is allowed to
cool it will usually refold back into it’s original conformation.
Protein metabolism

denotes the various processes responsible for the
(i) biosynthesis of proteins from amino acids.
(ii) catabolism the breakdown of proteins by
/proteolysis liberating of amino acids.
That is, comprises of
I- Protein metabolism (synthesis and breakdown)
II-Amino Acid metabolism (synthesis and
breakdown)
WILL PROCEED WITH
Protein metabolism (synthesis and breakdown)
PROTEIN SYNTHESIS
proteins of one organ are similar but differ from
that of another organ. That is, each chain is
characterized by a specific sequence of a.a. How
is this special feature achieved?
 The sequence of a.a in a particular chain is
ensured through the following units and process:
translation; Codons; transciption tRNA; mRNA;
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Translation is “process of protein synthesis”. It is
translating genetic messages into the primary
sequence of a polypeptide. tRNA carries a specific
amino acid to the matching position along the
mRNA template. It can be divided into 4 stages:
Activation, Initiation, Elongation and Termination,
each regulated by a large number of proteins and
coactivators. It occurs in cytoplasm.
Codon: a sequence of 3 nucleotide in DNA that
codes a single a.a
transcription : synthesis of a single strand
messenger RNA (mRNA) by transcribing the
sequence of the nucleotide in the template
DNA/genom. The reaction is catalyzed by RNA
polymerase . The template DNA is “unzipped” by
enzyme helicase prior to the transcription.
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tRNA is transfer RNA that carries an a.a to the
mRNA to be incorporated into the peptide chain.
mRNA is a type of RNA that encoding the
sequence of the protein in the form of a
trinucleotide code . The specific sequence of the
nucleotide is accomplished through transcription.
The synthesis process/translation
Activation: the correct amino acid (AA) is joined
to the correct tRNA. The AA is joined by its
carboxyl group to the 3' OH of the tRNA by an
ester bond. The anti-codon determines the
correct AA.
 Initiation: involves the small subunit of the
ribosome binding to 5' end of mRNA with the help
of initiation factor (IF),
 Elongation occurs when the next aminoacyl-tRNA
(charged tRNA) in line binds to the ribosome
along with GTP and an elongation factor.
 Termination of the polypeptide happens when the
A site of the ribosome faces a stop codon (UAA,
UAG, or UGA).This activates release factor which
then causes the release of the polypeptide chain.
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TRANSLATION in diagrame :
LOADED tRNA
COMPONENTS PRESENT
IN THE PROCESS
Aminoacid
carried
anticodon
RIBOSOME
codon
mRNA
TRANSLATION
The newly made mRNA (transcription) leaves the nuceus and binds with the
ribosome in the cytoplasm.
ONE codon is exposed at site P and
another codon at site A
A tRNA with a complementary codon
in its anticodon site will bind with the
codon at site P, bringing an aminoacid.
1º AMINOACID:
Methionine (AUG)
in site P.
TRANSLATION
Even though every protein begins with the Methionine amino acid, not all
proteins will ultimately have methionine at one end. If the "start"
methionine is not needed, it is removed before the new protein goes to
work (either inside the cell or outside the cell, depending on the type of
protein synthesized)
TRANSLATION
2º AMINOACID:
Glycine (only in this case) in site A.
A
PEPTIDIC BOND IS FORMED
TRANSLATION
Growing polypeptide
STOP codon
NO aminoacid is added. Its the
END of the polypeptide!
PROTEIN CATABOLISM
Has various indication:
Comprises of Digestion and Absorption
 Is carried out via proteolysis
 is the directed degradation (digestion) of proteins
by cellular enzymes called proteases (various
kinds) releasing peptide/A.A
 The digestion of proteins from foods as a source
of amino acids (aas)
 The aas constituting “aa pool” are metabolized
further ( aa catabolism)

DIGESTION & ABSORPTION
Digestion:
Source of proteins that come in the diet:
- animal eg milk, dairy products, meat, fish, eggs, liver
- vegetable sources eg cereals, pulses, peas, nuts and beans
 In mouth: no proteolytic enzyme so the proteins are
unchanged but the size(food) becomes smaller due to
mastication and chewing. Food bolus travels down and
reaches stomach and meet gastric juice
 In stomach ( pH 1-2 maintains by HCl) : attack by pepsin,
renin, gelatinase and gastricin ( enzymes in the gastric juice).
All these enzymes attack internal peptide bonds.
- Pepsin( a endoproteinase) acts on :
Proteins
proteoses + peptones
Casein(milk)
paracasein + proteos (whey proteins)
paracasein + Ca 2+
calcium paracasein (insoluble)
- gastricin ( a proteinase)
- gelatinase: gelatine
polypeptide
In small intestine : duodenum, jejunum, ileum
- Duodenum:
Food bolus meet pancreatic juices.
Enzymes in pancreatic juices :
Trypsin ( a proteolytic enzyme)
Chymortypsin
Carboxy peptidases
( 2 types: A and B) are exopeptidases;
splits one amino acid at a time fr free end.
Elastases : a serine protease
Collagenases act on protein present in collagen/connective tissue
yielding peptide

- Jejunum-ileum
Food remnant meet intestinal juice.
Enzymes in intestinal juices:
Amino peptidase: peptides tripeptides
Enteropeptidase/Enterokinase
Prolidase: acts at terminal proline
Di and tri-peptidase: Di and tri-peptide
 amino acids
Absorption Of Amino Acids
Absorption is by active transport
 Site of absorption is
- ileum and distal jejunum: amino acids
- duodenum and proximal jejunum: di and tri-peptides
 After absorption, amino acids and di and tri-peptides (if any)
are carried by portal blood to liver, partly :
i- are taken up by liver cells
ii- enter the systemic circulation (made up part of aa pool),
diffusing throughout body fluid & taken up by tissue cells.
( The body's circulatory system has three distinct parts:
pulmonary (the lungs) circulation, coronary (the heart)
circulation, and systemic (the rest of the system) circulation.
Each part works independently in order for them to all work
together)

The aa will be used to synthesize:
tissue proteins; enzyme; hormones
3 states relates to aa pool -cell :
i- dynamic equilibrium amnt of aa taken-up = amnt of aa
loss
ii- cell waste  amnt of aa taken-up < amnt of aa loss
iii- cell grows  amnt of aa taken-up > amnt of aa loss
Regulatory of Amino Acid


If amino acids are in excess of the body's biological
requirements, they are metabolized to glycogen or fat
and subsequently used for energy metabolism.
If amino acids are to be used for energy their carbon
skeletons are converted to acetyl CoA, which enters the
Krebs cycle for oxidation, producing ATP
Summary: Digestion & Absorption
Aas available for use in metabolic processes come from
dietary protein and breakdown of tissue protein by
proteolysis.
 Digestion (dietary protein) occurs in stomach as well as
intestine.
In stomach, digested by pepsin, in intestine and duodenum
by a group of enzymes, protease (trypsin. Chymotrypsin
and carboxypeptidase)
These liberated aas are absorbed into cells and are
collectively referred as “aa pool”

## Amino acids are transported into cell by various
transport mechanisms involving membrane-bound
transport proteins.
Ingested protein→ digested → aa → absorbed (aa pool)
Assimilation of Amino Acids
Dietary protein
Tissue protein
enzymic proteolysis
OUTSIDE CELL
e.g trypsin/pepsin
A A pool
synthesis
─NH2
INSIDE CELL
─ C skeleton
protein
Excreted as
urea & uric
acid
energy
New AA
N containing
molecules
Healthy & in young subject
Precursors
for other
molecules
>> aa breakdown
Amino acid synthesis

is the set of metabolic pathways /processes by which the
various amino acids are produced from direct incorporation/
combination
(I) of –NH2 group OR
(II) of ammonium ion NH4+ with other compounds found in
the organism’s diet or growth media
I –NH2 group is incorporated into α-keto acid through 2 types
of reactions:
i- non-reductive transamination
i) glutamate/aspartate as –NH2 donor
ii) glutamine/asparagine as –NH2 donor
iii) branch chain aa as –NH2 donor
ii- reductive transamination
ammonium ion NH4+ is incorporated α-keto acid. through
- Reductive amination
- non-reductive amination
II-
Non-reductive transamination characteristics:Reaction of Glutamate (or Aspartate) and an α-keto acid or BCAA.
 -NH2 is transferred from Glutamate/ Aspartate to an α-keto acid.
( Glutamate/ Aspartate/asparagine is -NH2 group donor;
α-keto acid supplies C-skeleton)
** glutamate as -NH2 group donor is more regular
 Reaction is catalysed by i) enzyme aminotransferase or
transaminase ;
ii) required co-enzyme pyridoxal-5’-phosphate (PLP)
O
R1—C—C--O‾ +
O O
Acceptor α-ketoacid
R1—CH—C--O‾
+NH
+ α-ketoglutarate
3
New AA
referred as pair
Non-reductive transamination: Examples
i) Glutamate and an α-keto acid (pyruvate)
NH2
CH3
OOC-CH2-CH2- CH
+
C=O
COOH
Glutamate
CH3
HC─NH2 + OOC-CH2-CH2C=O
COOH
COOH
pyruvate
alanine
COOH
α-ketoglutarate
pair
ii) Aspartate and an α-keto acid (pyruvate)
NH2
OOC-CH2-- CH
COOH
aspartate
CH3
+
C=O
CH3
HC─NH2 +
COOH
COOH
pyruvate
alanine
OOC--CH2C=O
COOH
oxaloacetate
iii- asparagine and an α-keto acid (pyruvate)
COOˉ
CO-CH2-CH
NH2
NH3+
Asparagine
CH3
COOˉ
+ C=O
COO-CH2-CH
COO
+
CH3
CH-NH2
NH3+
Pyruvate
Aspatate
COOˉ
Alanine
Transaminase
** Aspartate transaminase or aspartate
aminotransferase is an enzyme
associated with liver parenchymal cells.

Non-reductive transamination (in skeletal muscle).
enzyme: glutamine synthase (GS)
Glutamate + BCAA → glutamine + α-keto acid
( BCAAs are comprised of valine, leucine, and isoleucine)
COO
COO
OOC-CH2-CH2-CH + (CH3)2CH-CH
NH2
Glutamate
NH2
valine
COO
COO
O=C-CH2-CH2-CH + (CH3)2-CH-C
NH2
NH2
glutamine
O
BC α-oxoacid
Enzyme Transaminase/Aminotransferase
requires co-enzyme pyridoxal-5’-PO4 ,
abbreviated (PLP).
a derivative of vitamin B6

R of Lysine
PLP attaches to the active site of enzyme by noncovalent
interaction and a Schiff base aldimine ( condensation of εamino of lysine residue and aldehyde group of PLP) is
formed.
 amino acid substrate becomes bound to PLP via the αamino group in an imine exchange reaction.
 bond 1 breaks leaving –NH2 on the co-enzyme to be
transferred to an α-keto acid,
[ Vitamin B6 is involved in the metabolism (especially
catabolism) of amino acids, as a cofactor in transamination
reactions. This is the last step in the synthesis of
nonessential amino acids and the first step in amino acid
catabolism.
Vitamin B6 is a mixture of pyridoxin derivatives. PLP is 1 of
them].

Glutamate in transamination:
(pyruvate/alanine pair)
NH2
OOC-CH2-CH2- CH
CH3
+
COOH
Glutamate
C=O
COOH
pyruvate
CH3
HC─NH2 + OOC-CH2-CH2C=O
COOH
alanine
COOH
α-ketoglutarate
(oxaloacetate/aspartate)
NH2
OOC-CH2-CH2- CH
COOH
Glutamate
CH2 COO
+
C=O
COOH
oxaloacetate
CH2COO
HC─NH2 +
COOH
aspartate
GS
OOC-CH2-CH2C=O
COOH
α-ketoglutarate
**(in skeletal muscle) Glutamate + BCAA → glutamine + α-keto acid
BCAAs are comprised of valine, leucine, and isoleucine
Reductive Transamination
Glutamine, asparagine transfer the amide
nitrogen to oxo (or keto) acid to form a new
amino acid.
 2-oxoglutarate is –NH2 receptor and glutamine is
–NH2 donor
 The enzyme GOGAT is NADPH dependent

glutamine + 2-oxoglutarate + NADPH + H+ ---> 2 glutamate
+ NADP+
GOGAT
GOGAT: enzyme glutamine oxoglutarate amidotransferase
II-
Incoporation of NH4+ ion:
i) Reductive amination
 reaction of α-ketoglutarate with NH4+ leading to
formation of glutamate (in mitochondria &
cytoplasm).
α-ketoglutarate is –NH2 acceptor
 catalysed by glutamate dehydrogenase, the
enzyme is NADH dependent
 reaction is reversible  i.e the reverse pathway is
a primary means of producing NH4+ for N
excretion.
 The enzyme is driven toward right when excess
NH4+ is present
 NH4+ is from oxidative deamination of glutamate
(in extrahepatic tissue)
+ NH4+ + NADH + H+
GD
Enzyme: Glutamate Dehydrogenase
+ NAD+ + H2O
NH3 + H+
Reductive Amination : left - right
(Oxidative Deamination : right  left)
ii) Non-reductive amination or amidation
Glutamate or aspartate react with NH4+ to form
glutamine, (asparagine)
 catalyze by glutamine/ asparagine synthetase
respectively.
 Sites : liver, brain , kidney, muscles & intestine
 This rxn forms the path by which cell rid off
excess NH4+.
** NH4+ at high conc may be toxic to certain cell
e.g brain cell. Glutamine is non toxic.

Non-reductive amination or amidation
From excess aa pool
COO-
COOCOO-CH2-CH2- CH
CO-CH2-CH2- CH + ADP
NH2
NH3+
+ Pi
Glutamine
Glutamine Synthetase (GS)
+ ATP + NH4+
NH3+
Glutamate
COO-
COOCOO-CH2- CH
+ ATP + NH4+
NH3+
Asparagine Synthetase
Aspartate
CO-CH2-CH + ADP
NH2
NH3+
+ Pi
Asparagine
www.rcsb.org/pdb/explore/pubmed

Glutamine synthetase (GS) catalyzes the ligation of
glutamate and ammonia to form glutamine, with
concomitant hydrolysis of ATP. In mammals, the activity
eliminates cytotoxic ammonia, at the same time
converting neurotoxic glutamate to harmless glutamine;
there are a number of links between changes in GS
activity and neurodegenerative disorders, such as
Alzheimer`s disease.
glutamate
GD
Reductive amination
NH4+
NADH
Oxidative deamination
glutamate
α-keto acid
transamination
New aa
α-ketoglutarate
C skeleton of all non-essential aa are derivatives of:
 Glycerate -3-phosphate
 Pyruvate
 Α-ketogluterate
 Oxaloacetate
But Tyrosine from essential aa phenylalanine
On basis of common precursor Ξ similarities in their synthetic
Pathway, aa can be grouped into 5 families.
glutamate family= synthesis of glutamate,
glutamine, arg, pro.
- C skeleton derive fr α-ketoglutarate

serine family = synthesis of serine, glycine,
cystein
- C skeleton derive fr glycerate-3-phosphate

aspartate family = synthesis of aspartate,
lysine, methionine, asparagine, threonine
- C skeleton derive fr oxaloacetate

pyruvate family = synthesis of alanine, valine,
leucine, isoleucine
- C skeleton derive fr pyruvate

aromatic family = synthesis of *phenylalanine,
tyrosine, *tryptophan *EAA

Glutamate family
- key substrate is αketoglutarate fr TCA
-Glutamate is produced by
GD and is the principle rxn of
fixation of NH3 in bactria
- glutamine is produced by
ATP-requiring +n of NH3 to
glu and the rxn fnc as a
major means of assimilating
of NH3 fr environment
-Regulation of this family is
controlled by repression of
mRNA and feedback
inhibition: by prolin and arg
Regulatory of Amino Acid


If amino acids are in excess of the body's
biological requirements, they are metabolized
to glycogen or fat.
If amino acids are to be used for energy their
carbon skeletons are converted to acetyl CoA,
or other metabolites intermediates (pyruvate,
oxaloacetate, Succinyl-coA ) which then
enters the Krebs cycle for oxidation,
producing ATP.
Catabolism of AA
Generally involves :
Removal of amino group
- Disposal of amino group to final compounds
urea([NH2]2CO) and ammonia (NH3); also
incoporated into other molecules
- Utilization of C skeleton by channeling into TCA
through which they are converted to final
products carbon dioxide (CO2), water (H2O), ATP,
or degraded into a variety of metabolite
intermediates which then enter synthesis
pathway of other compounds
- Decarboxylation
- one carbon metabolism

-
Removal of amino group
 Occurs by
- transamination
- oxidative deamination (only happens with glutamate )
catalyses by glutamate dehydrogenase
glutamate + NAD+ −− NH+4 + α-ketoglutarate
Transamination ( largely occurs in cytosol of liver cells)
is the transfer of the nitrogen (the amino) group of
an L-a.a to α-ketoglutarate forming L-glutamate.
The reaction is catalysed by transaminase and it
requires co-enzyme pyridoxal-5’-PO4(see earlier
section for detail mechanism). Glutamate may
undergo another transamination, transfering –NH2
to another α-ketoacid i.e glutamate becomes -NH2
carrier
Oxidative Deamination
Oxidative Deamination (O.xdn)




reaction is prevalent when proteinintake> proteinsynthesis
=> aa from“aa pool” undergoes degradation. The Nin aa is removed by deamination rxn and converted
to ammonia which is toxic, therefore need to be
detoxified and excreted.
Is :L-glutamate + NAD+ −− NH+4 + α-ketoglutarate
happens only with glutamate
catalyses by glutamate dehydrogenase GD.
It occurs in liver & in most extrahepatic tissue.
* N of amino group made available for excretion by rxn .
In muscle cell ( no GD) any excess aa transfer its -NH2 to αketoglutarate to form L-glutamate (transamination). Lglutamate undergoes transamination with pyruvate catalyse
by alanine transaminase to give alanine + α-ketoglutarate.
Alanine carries by blood to liver, (alanine cycle) . In liver,
alanine + α-ketoglutarate react catalysed by alanine
transaminase reforming L-glutamate + pyruvate as alanine
transaminase rxn is reversible. Then L-glutamate undergoes
Oxidative deamination.
Pyruvate can be diverted to gluconeogenesis. This process is
refered to as the glucose-alanine cycle and NH+4 moves onto
urea cycle which is also known as ornithine cycle, be
converted to urea.

Urea is transferred through the blood to the kidneys
and excreted in the form of urine.
Alanine Cycle
-NH2 in Muscle
Transported to liver for
Oxidative deamination
NH4+ (liver)
glutamate
alanine
New α-keto
acid
Alanine transamination
transamination
pyruvate
alanine
Liver
excess aa
α-ketoglutarate
glutamate
Alanine transamination
α-ketoglutarate
pyruvate
GD
H2O +
NAD+
NH4+
+ NADH
To urea
cycle
α-ketoglutarate
•Deamination is also an
oxidative reaction
•occurs under aerobic
conditions in all tissues but
especially the liver. During
oxidative deamination, an
amino acid is converted into
the corresponding keto acid by
the removal of the amine
functional group as ammonia
and the amine functional group
is replaced by the ketone
group.
• The reaction is catalysed by
glutamate dehydrogenase
which is allosterically
controlled by ATP and ADP. ATP
acts as an inhibitor whereas
ADP is an activator.
The ammonia eventually goes
into the urea cycle.
Oxidative deamination occurs
primarily on glutamic acid
because glutamic acid was
the end product of many
transamination reactions.
GD
The glutamate dehydrogenase (GD) is
allosterically controlled by ATP and ADP. ATP
acts as an inhibitor whereas ADP is an
activator.
Summary of Urea Cycle
 Occurs in liver cells
 Is a 5 steps cycle: 1 step in mitochondria 4 steps
in cytosol
 Main substrates: NH3, CO2 and Aspartate.
 In the matrix of mitochondria occurs CPS I and
OTC catalysed rxn,
CPS rxn uses 2ATP and reaction is irreversible
 Citrulline Ornithine occur in cytosol, in 4 steps
-Citrulline is tranported across the inner membrane
by a carrier neutral aa.
- enzymes are arginosuccinate synthase,
arginosuccinate lyase and arginase
 Urea transferred to kidney through blood and
excreted as urine
Fate of A.A Nitrogen

Excreted in the form of urea (urine)
 Transferred to specific α-keto acids (of the TCA
intermediates) to form new a.a. This can be represented
in the form of α-keto acids / aa pair eg:
α-ketoglutarate/glutamate; pyruvate/alanine;
aspartate/oxaloacetate pair.
 Incorporated into skeleton of non amino acid molecules
=> aa derived compound
Derived AA Compounds
What are derived amino acid compounds?
They are compounds that contain N- atom, S- atom or
part of aa structure as part of their molecular
structure .Can be divided into 2 groups: alkaloids (in
plants) & animal related.
Animal related and specific parent aa eg. Glutathione
(GSH), Serotonin and Histamine, Heme, GABA , DNA
bases
 Why the synthesis occurs?
These molecules are synthesized because they are
important to the body.
 The synthesis process

Parent aa
glutamate
derived compd
Glutathione(GSH)
Parent aa
derived compd
tyrosine
Dopamine
melanine
GABA
tyroxine
Epinephrine/
norepinephrine
Serine
ethanolamine
Choline
Leucine
β-OH-βmethylglutaryl-CoA
Lysine
carnithine
Histidine
Histamine,
Carnosine,
anserine
Betaine
tryptophan
Serotonine,
melatonine
serotonin



Fncn to influence the functioning of the cardiovascular,
renal, immune, and gastrointestinal systems
Any disruption in the synthesis, metabolism or uptake of
this neurotransmitter has been found to be partly
responsible for certain manifestations of schizophrenia,
depression, compulsive disorders and learning problems.
Synthesis:
Function of some AA derived compounds
 As neurotransmitter : GABA, dopamine, serotonin,
 Sleep inducing : melatonin
 Carrier : carnithine
 As hormone: tyroxine,
 Dilating/constriction of blood vessel: histamine
 Exhibit multifunctions: GSH
- acts as reducing agent in NA and eicosanoids synthesis
- maintain the sulfahydryl grp of enzymes & other
molecules in reduced state
- promotes aa transport
- protect cells fr radiation, O2 toxicity and environmental
toxins
Utilization of the C-skeleton
The C-skeleton of the standard amino acids are
degraded to seven common metabolic
intermediates such as Acetyl-coA; Acetoacetyl-CoA;
pyruvate; Oxaloacetate, α-ketoglutarate,
Succinyl-CoA and fumerate.
Those aa are referred to different names depending
to the class to which the final product are
classified:
i) degraded to acetyl-CoA and AceAcetyl-CoA are
referred to as KETOGENIC because the
intermediates lead to either fatty acids or ketone
bodies.eg Lys and Leu
ii) degraded to pyruvate; α-ketoglutarate, SuccinylCoA, Oxaloacetate, and fumerate are referred to
as GLUCOGENIC because they are intermediates
of gluconeogenesis. All except Lys and Leu are
pure or partly glucogenic
Those that yield acetyl-CoA are divided into 2
groups.
a) Those that yield pyruvate as intermediate: Ala,
Cys, Gly, Ser and Thr
b) Those that do not yield pyruvate as
intermediate: Phe, Lys, Leu Trp and Tyr
utilization of the C-skeleton
Decarboxylation of amino acid
•is effected by decarboxylase enzyme, PLP dependent
•Products are alkylamine + CO2 . The alkylamine are
neurotransmitters
•There are 4 aa decarboxylase enzymes:
Aromatic L-amono acid decarboxylase (is a group of
enzymes); L-glutamate decarboxylase (GAD); lysine
decarboxylase (LDC); histidine decarboxylase (HDC)
HDC
HOOC-CH2-CH2-CH(NH2)-COOH ───→ CO2 + HOOC-CH2-CH2-CH2NH2
GAD
GABA is a neurotransmitter in brain
(GABA)
Aromatic L-aa decarboxylase synonyms to DOPA
decarboxylase, tryptophan decarboxylase, 5hydroxytryptophan decarboxylase, AAAD.
tryptophan ───→ tryptamine + CO2
Tryp D
A.As Metabolic Disorder Diseases
Are diseases resulted from disorders of a.as
processing/metabolism due to
Inherited/genetic defects that cause deficiency
of certain enzymes for
i) the breakdown of amino acids or
ii) the body's ability to get the amino acids into
cells or
iii) Amino acid Transport
- Symptoms of disease appear early in life
- Generally are autosomal recessive that is why
only small number of man suffers.
-
Inherited metabolic disorder ( I.M.D) :
 Oculocutaneous albinism
 Tyrosinemia
of tyrosine
 Alkaptonuria





Phenylketonuria
Hyperalaninemia
of phenylalanine
Leucinosis or maple syrup urine disease – of
branched-chain a.a
homocystinuria – of methionine
Nonketotic hyperglycinemia – of glycine
PROTEIN CATABOLISM
Has various indication:




Is carried out via proteolysis
is the directed degradation (digestion) of proteins
by cellular enzymes called proteases (various
kinds) releasing peptide/A.A
The digestion of proteins from foods as a source
of amino acids (aas)
The aas constituting “aa pool” are metabolized
further (refer to aa catabolism)
Muscle-cell
aa1
Aa
aminotransferase
+
α-ketoglu
glutamate
Ala.aminotransferase
blood
+ pyrv
alanine
Ala.aminotransferase
glutaminase
glutamine
+ α-ketoglu
glutamate
NH+4
Oxidatv
deamintn/GD
NH+4 + α-ketoglu
glutamine
Glutamate +ATP
Glutmine
synthetase
Non-redtv
amination
NH+
4
liver
+ α-ketoglu
Non-liver cell
Oxidatv deamintn/GD
glutamate
.
One Carbon Metabolism
http://seqcore.brcf.med.umich.edu/mcb500/folm
etov.html
source of Diagram on next slide