Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

ESSENTIALS OF BIOCHEMISTRY

TOPIC 2 | BIOCHEMISTRY OF AMINO ACIDS

Senthil Raja Ayyannan, PhD

Associate Professor
Pharmaceutical Engineering & Technology
IIT (BHU) Varanasi
asraja.phe@iitbhu.ac.in

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 1

AMINO ACIDS | OVERVIEW

 What are Amino acids?
 Structure & Classification of Amino acids
 General properties of Amino acids
 Biosynthesis of Amino Acids
 Common Fate of Amino acids
 Metabolism of Important Amino acids
 Aliphatic | Gly, Ser, Asp, Glu, Cys, Met
 Aromatic | Phe, Tyr, Trp
 Disorders associated with Amino Acid Metabolism
 Summary & Recap
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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

WHAT ARE AMINO ACIDS?

 Amino acids are the small functional units of Proteins, the
molecules of prime importance.
 Polymerization of amino acids via peptide bonds leads to
formations of specific functional protein (Polypeptide)
 Amino acids consist of an amino group, acidic group & an
organic carbon (R) group attached to the same carbon atom.
 All natural amino acids are of L-configuration (S-Conformer)
 There are TWENTY amino acids commonly occur in Nature
 NINE amino acids are essential to Humans
 Val, Leu, Ile, Thr, Met, Lys, Phe, Trp, His
 ELEVEN are Non-essential & are biosynthesized in Humans
 Gly, Ala, Ser, Cys, Asp, Glu, Asn, Gln, Arg, Tyr, Pro
 His & Arg are semi-essential
Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 3

CLASSIFICATION OF AMINO ACIDS

 Aliphatic neutral amino acids | Neutral R group
Alkyl chain: Glycine G, Alanine A, Valine V, Leucine L, Isoleucine I
Hydroxyl derived: Serine S, Threonine T
Thiol derived: Cysteine C, Methionine M
 Aliphatic acidic | Acidic R group: Aspartic acid D, Glutamic acid E
 Aliphatic amide | Amide R group: Asparagine N, Glutamine Q
 Aliphatic basic | Basic R group: Lysine K, Arginine R
 Aromatic | Aryl R group: Phenylalanine F, Tyrosine Y
 Heterocyclic | Hetero R group: Tryptophan W, Histidine H
 Alicyclic | Cyclic amine: Proline P

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

STRUCTURE OF AMINO ACIDS | G A V L I S T

GLY | G ALA | A VAL | V LEU | L

ILE | I SER | S THR | T

OH O

H3C OH
NH2

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 5

STRUCTURE OF AMINO ACIDS | C M D E N Q K R

CYS | C ASP | D ASN | N LYS | K

MET | M GLU | E GLN | Q ARG | R

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

STRUCTURE OF AMINO ACIDS|F Y W H P

PHE | F TRP | W

PRO | P

TYR | Y HIS | H

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STRUCTURE OF AMINO ACIDS|UNUSUAL/OTHERS

Homoserine Homocysteine Cystine

O NH2 O
HS HO S
OH S OH
NH2 O NH2

Ornithine Citrulline

O O O

H2N OH H2N N OH
H
NH2 NH2

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

PROPERTIES OF AMINO ACIDS

General Properties of Amino acids
 Optical isomerism
 All natural amino acids are of L-conformation
 CO-R-N rule: clockwise D; counter-clockwise L

 Ionization | Amphoteric character

 Zwitter ion

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PROPERTIES OF AMINO ACIDS

General Properties of Amino acids | Chemical Identification tests
 Reaction of with Ninhydrin & Color reactions of Amino acids
Ninhydrin Test: To 1 mL amino acid solution, add 5 drops of 0.2%
ninhydrin solution in acetone & boil over a water bath for 2 min.
Allow to cool. Presence of amino
Blue colour
acid

Xanthoproteic Test: To 2 mL amino acid solution, add equal volume of Presence of Phe,
Yellow colour
concentrated HNO3 (a drop of H2SO4) and heat over a flame for 2 Tyr, Trp (Actd.
or ppt.
min. Cool the mixture & alkalinize by adding 40% NaOH. aromatic ring)

Millon’s Test: To 2 mL amino acid solution, add 1-2 drops of Millon’s

Brick red Presence of Tyr
reagent (Hg dissolved in Con HNO3). Warm the tube in a boiling
colour (Phenolic OH)
water bath for 10 min.
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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

PROPERTIES OF AMINO ACIDS

General Properties of Amino acids | Chemical Identification tests
Hopkin’s Cole Test: To a few mL of glacial acetic acid containing Purple colour
Presence of Trp
glyoxylic acid, add 1-2 drops of the amino acid solution. Pour 1-2 mL at the junction
(Indole ring)
H2SO4 down the side of the test tube. of two layers.

Lead-Sulfide Test: Boil 2 ml amino acid with a few drops of 40% NaOH Presence of Cys
Brown colour
for 2 min. Cool and add a few drops of sodium plumbate solution & cystine (SH
or ppt.
(prepared by heating 5 ml dilute NaOH and 2 ml dilute lead acetate). group)

Nitroprusside Test: Take 2 ml amino acid in a test tube, add 0.5 ml

Red colour!! Presence of Cys
nitroprusside solution, shake well & add 0.5 mL ammonium hydroxide.

Presence of Arg
Sakaguchi Test: Mix 1 ml NaOH with 3 ml amino acid (Arg) and 2 drops
Red colour (guanidine
of α-naphthol. Shake well and add 4-5 drops of bromine solution.
group)
Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 11

BIOSYNTHESIS OF AMINO ACIDS

How amino acids are biosynthesized in Microbes & Plants?
 Sources of ammonia (NH3)
Organic Nitrogenous
 Degradation of organic nitrogenous substances to compounds/Atm. N2
nitrogen/nitrite/nitrates!
 Fixation of atm. nitrogen in the form of ammonia – by
aerobic soil bacteria (Azotobacter), anaerobic soil bacteria
(Closteridium) and photosynthetic bacteria Ammonia (NH3)
 Reduction of nitrite & nitrate into ammonia – by
nitrosomonas, nitrobacter strains.
 Fixation of ammonia (NH3) into an organic compound
Ammonia fixation into
 Reductive amination of -ketoglutarate to Glu (E) the Carbon skeleton
 Formation of carbamoyl phosphate (CAP) (-keto acids) to form
AMINO ACIDS
 Amination of fumarate to Asp (D)
 Formation of Gln (Q) from Glu (E)
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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOSYNTHESIS OF AMINO ACIDS

How amino acids are biosynthesized in Microbes & Plants?
Glucose (C6)

 Biosynthesis of carbon skeleton (-keto acids) Glycolysis

 From Carbohydrates Glyceraldehyde-3-

phosphate (C3)
 Intermediates of Glycolysis – Pyruvic acid
 Intermediates of krebs cycle
 -Ketoglutarate, fumarate, OAA, etc. Pyruvate
(C3)

O O
 Transfer of amino group to alpha-keto acids R1 R1
OH OH
 Transamination pathway NH2 Transaminase O
Amino acid 1 Keto acid 1
(Reversible transfer of amino group) O
O
R2
R2 OH
HO Pyridoxal Pi
NH 2
O
Amino acid 2
Keto acid 2

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BIOCHEMISTRY | METABOLIC PATHWAYS

Amino Acid Metabolism in Humans | Overview
Overview of Metabolism | Journey of Nutrients inside the Body
Activation by
Dietary Proteins | Polypeptides Gastric juice
Pepsinogen Pepsin
(Must be hydrolyzed into AA in GIT for absorption)
Peptide
Endopeptidases – Pepsin in stomach at pH 2.0 | Cleaves at NH2 of Phe, Tyr
Acts within the Trypsin in intestine at pH 8.0 | Cleaves at acid of Lys, Arg
peptide chain Chymotrypsin in intestine at pH 8.0 | Cleaves at acid of Phe, Tyr, Trp
Activation by trypsin or
Simple Peptides
enterokinase
(Further hydrolyzed into AA) Trypsinogen Trypsin
Exopeptidases Carboxypeptidase breaks at carboxyl terminals Hexaeptide
– Acts at the Aminopeptidase breaks at amino terminals
end of chains Dipeptidase breaks dipeptides

Simple amino acids (Esp. 8 EAA) Transported to the tissues and

(readily absorbed into the liver) metabolized (incorporated into proteins,
catabolized to keto acids, ammonia, CO2)

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

AMINO ACIDS | COMMON METABOLIC PATHWAYS

Amino Acid Metabolism in Humans | Overview
 Removal of amino group, yielding -Keto acid
 Deamination
 Transamination
 Decarboxylation – Removal CO2
 Fate of amino group - Ammonia  Fate of carbon skeleton (-Ketoacids)
 Synthetic pathway -  Synthesis of new amino acids
 New amino acid formation  Glucogenic pathway
 Purine and Pyrimidine biosynthesis  Formation of Ala - pyruvate, Asp
 Storage pathway – Gln formation - OAA & Glu - -KG
 Excretory pathway – Urea biosynthesis  Ketogenic pathway
 Direct excretion as ammonia  Leu, Ile, Phe, Tyr forms acetate
and acetoacetate

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 15

AMINO ACIDS | COMMON METABOLIC PATHWAYS

Removal of amino group; yielding -Keto acid
1. Deamination (Three types) | Formation of Ammonia

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

AMINO ACIDS | COMMON METABOLIC PATHWAYS

Removal of amino group; yielding -Keto acid
2. Transamination | Reversible transfer of amino group

 Glu serves as amino group donor

O O
R1
 Oxaloacetate, Pyruvate are amino group
R1
OH OH acceptors
Transaminase
NH2 O
Keto acid 1
 Liver Transaminases (Pyridoxine coenzyme)
Amino acid 1
O O  SGOT (Serum Glutamate-Oxaloacetate Transaminase)
R2
HO
R2 Pyridoxal Pi OH  Glu ---> OAA
O NH2  SGPT (Serum Glutamate-Pyruvate Transaminase)
Keto acid 2 Amino acid 2
 Glu ---> Pyr
 The level of these enzymes in the liver
goes up during disease conditions (LFT)

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AMINO ACIDS | COMMON METABOLIC PATHWAYS

2. Transamination | Transaminase-Pyridoxal catalyzed Mechanism
O
R1 O
OH R1
OH
NH2 H2O
O H2O O
Amino acid 1 O
R1 Keto acid 1
R1 OH
OH
H O N NH2
H N
HO P HO P HO P
O HO P O O
O
H3C N H3C N H3 C N H3C N
H2O
O
R2 O
OH O R2 O
H2 O R2
OH
R2
NH2 OH N HO
H N
Amino acid 2 HO P O
O
HO P
H O O Keto acid 2
H3C N
HO P H3C N
O

H3C N

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

AMINO ACIDS | COMMON METABOLIC PATHWAYS

O
Fate of Amino group | Ammonia HO
O NH3
HO
OH OH
 Synthetic pathway - New amino acid formation O O NH2
Asp
 Reductive Amination: Glu + Ammonia ----> Gln NH3

 Amination of Fumarate to Asp & then to Asn H2N

O

OH
O NH2
 Excretory pathway – Urea biosynthesis Asn
O
 Formation of CAP, entry to Urea cycle ATP
Pi
NH3 CO2 Ureogenesis
H2N O

 Purine and Pyrimidine biosynthesis CAP

Asp
 Formation of CAP (Pyrimidine bases) O
 Glu to Gln which supplies N to Purines CAP HN NH2
Asp N
N
O N Asp
 Storage pathway – Gln formation Ribose-5-Pi N N
Ribose-5-Pi
 Direct excretion as Ammonia Gln

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 19

AMINO ACIDS | COMMON METABOLIC PATHWAYS

Decarboxylation | Removal of Carbonyl group
 Amino acids loss CO2 to yield corresponding amines
 Catalyzed by amino acid decarboxylases and Pyridoxal Phosphate (co-enzyme)
O
R1 R1
OH
H2O H2 O
NH2 O NH2
Amino acid 1 R1
OH
Decarboxylase R1

H N H N H O
H O
HO P HO P HO P
HO P O CO2 O O
O
H3C N H3C N
H3C N H3C N

 Asp produces Alanine O

O O
 Glu produces GABA Glu. Decarboxylase
HO
 His produces Histamine HO OH
NH2 NH2
 Ser produces Ethanolamine Pyridoxal Phosphate
GABA – Inhibitory
 DOPA produces Dopamine Neurotransmitter
 5-OH Trp produces Serotonin
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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

AMINO ACIDS | COMMON METABOLIC PATHWAYS

Fate of Carbon skeleton (-Ketoacids)
The carbon skeleton of amino acids is utilized in the
 Formation of Pyruvate (Ala), Oxaloacetate (Asp) & -Ketoglutarate (Glu)
 Synthesis of new amino acids (non-essential) – Ala, Asp, Glu, etc
 Glucogenic pathway – Biosynthesis of Glucose (Glucogenic amino acids)
 Ketogenic pathway (Leu, Ile, Phe & Tyr forms Acetate & Acetoacetate)
O O O O
H3C HO
Removal of OH OH HO OH
O amino group O O O O O
R1 R1 O O O O
OH OH H3C HO
NH2 Deamination/ OH OH HO OH
O NH2 O NH2 NH2
Transamination
H OH
O O O HO
HO
HO H
H OH
H3C OH H3C OH H OH

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AMINO ACIDS | METABOLISM

Metabolism of Important Amino acids

 Ser & Gly

 Asp & Glu

 Phe & Tyr

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

Metabolism of Glycine & Serine - Overview

 Biosynthesis of Serine  Catabolism/Fate of Glycine

 Metabolism of Serine  Deamination/transamination
 Ser – Gly inter-conversion  Formation of Hippuric acid (Glycine
conjugation)
 Decarboxylation
 Biosynthesis of Glutathione (Glu-Cys-Gly)
 Biosynthesis of Glycine
 Biosynthesis of Creatine
 Shemin Cycle
 Biosynthesis of Porphyrins (Hb)
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BIOCHEMISTRY | METABOLIC PATHWAYS

 Biosynthesis of Serine | From Glucose
 During Glycolysis 6C Glucose is converted into 2 mols. of 3-Phospho
glyceric acid.
 Phosphoglycerate serves a precursor for the formation of Serine with the
help of dehydrogenase, transaminase and phosphatase enzymes.

Dehydrogenase Transaminase Phosphatase

H OH OH OH
OH NADH+H + OH NH3 H 2O
O
HO Glycloysis NAD+ O
HO O O NH2
HO H NH2
H OH O
OH Few steps
H OH Pi OH
O Pi
O Pi O Pi
Alpha-D-Glucopyranose 3-Phosphoglyceric acid 3-Phosphohydroxy O-Phosphoserine SERINE
pyruvic acid

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

 Ser – Gly inter-conversion by a “misnomer” enzyme
O OH
Serine O
O Transhydroxymethylase O
OH
Pyridoxal phosphate N
OH OH H O
HO
NH2 OH CH2 N
NH2
N
N
H-CHO N5-N10 methylene THFA
FH4 H2O H2N N N H
H
O OH
O
OH
N
H O
OH H HN
N
N
THFA: H4-Folic acid (Pteroyl glutamic acid)
H2N N N H
H

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BIOCHEMISTRY | METABOLIC PATHWAYS

O
Metabolism of Serine O Serine decarboxylase O O R1

 Decarboxylation HO OH HO R2 O O
O P OH
NH2 NH2
OH
CO2 O DAGP
 Biosynthesis of Glycine O O R1
R2 O O
N-Formyl FH4 O P NH2
NH2 OH
N SAM
N SAM Phophatidyl ethanolamine
HO O CH3 SAM
NH2 N N
HO S
O O 3 SAHC
NH2 H H
HOH OH
H O
3 N-Me THFA
FH4 O O R1
R2 O O
DAGP: Diacylglycerol phosphate FH4 CH3
O P N
FH4 CH
FH4: Tetrahydro folic acid OH CH3 3
- CH3 O
O HO CH3
SAM: S-Adenosyl methionine N N
CH O O R1
O CH3 3 CH
CH3 3 R2 O O
SAHC: S-Adenosyl homocysteine Betaine Choline O P OH
OH
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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

O
Fate of Glycine HOOC OH
THFA
N-Formyl THFA
1C transfer
DNA Synthesis
H-CHO
(UMP to TMP)
O Co-A-SH
Alpha-KG
CO2

TCA Cycle CO2 COOH

O
HOOC HOOC ATP
O
H CoA-SH
OH
HN
CoA-SH: Coenzyme A COOH CO-S-CoA O OH
HCHO
O

Deamination
CO-S-CoA
UMP: Uridine monophosphate NH3 Hippuric acid
Shemin Cycle (Non-toxic metabolite)
THFA: Tetrahydro folic acid HOOC HOOC
SH
O O O
SAM: S-Adenosyl methionine TA O Glu-Cys H
N
O O HO N OH
OH
SAHC: S-Adenosyl homocysteine O H2N
H O
H NH2 CoA-SH CO2 NH2 Arg Glutathione (GSH)
Hb: Hemoglobin Gluteraldehyde Delta-Amino Detoxifying peptide
Levulinic acid NH
Porphyrin Ornithine C NH2
Biosynthesis 2H2O

COOH HN COOH SAM

NH
ATP H
HOOC C N Pi
Hb SAHC N COOH
N ADP
H3C
several steps
NH2 H Creatine Phosphate
Mobilisable energy reserve
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BIOCHEMISTRY | METABOLIC PATHWAYS

Metabolism of Aspartic Acid (Asp, D) | Overview

 Biosynthesis of Asp from OAA  Metabolism/Fate of Asp

O O
 Deamination to Fumarate
HO HO
OH OH
 Transamination to OAA
O O O NH2
SGOT
OAA
Asp  Decarboxylation to -Alanine/-Alanine
O
O  Biosynthesis of Asn
R2 Pyridoxine Pi R2
HO OH  Ureogenesis
NH2 O
Amino acid 1 Keto acid 1  Biosynthesis of pyrimidine nucleotide
(UMP)
 Biosynthesis of AMP from IMP

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

Fate of Aspartic Acid (Asp, D)
O TCA Cycle
NH2 Gluconeogenesis
1 Asp deaminase HO
N OH
N O
2 Transaminase O O
Fumarate HO
N N OH H3C
3 Asp alpha or Ribose-5-Pi O O OH
beta-decarboxylase NH3
Adenosine Oxaloacetate O
1 2
4 Asn synthase KA
O AA O
IMP H3C NH3
HN O OH
CAP 3
HO NH2
O N OH Ala
O NH2 HO
Ribose-5-Pi ATP CO2
UMP
4 O NH2
Citrulline Gln AMP+PPi
UMP: Uridine monophosphate O Beta-Ala
Ornithine
Urea Cycle Glu H2N
IMP: Inosine monophosphate OH
Urea Arginine Arginosuccinate
O NH2 Asn
CAP: Carbamoyl phosphate
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BIOCHEMISTRY | METABOLIC PATHWAYS

Fate of Aspartic Acid (Asp, D) | Ureogenesis
O

Site: Mitochondrial membrane HO

OH
H2N O NH2 Asp
O
HN HO O
1 CAP Synthase 3 O
H2N
NH3 CO2 Pi ATP
AMP+Pi N OH
2 Ornithine carbamoyl transferase ATP HN
1 H2N
3 Arginosuccinate synthase 2 O Arginiosuccinate
HO
O Citrulline
H2N H2N
4 Pi
Arginosuccinase H2N O O
Urea Cycle HO
CAP
5 Arginase O
4
H2N
H2N OH
O
HO NH
Ornithine HO
HN
CAP: Carbamoyl phosphate O Fumarate
NH2 NH 5

AMP: Adenosine monophosphate H2N O H2N OH Arginine

H2N
Urea Iso-urea H2O O
HO

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

Fate of Aspartic Acid (Asp, D) | De novo Biosynthesis of UMP
O O
Gln ATP
HN 6 HN
1 CAP synthase
OH
2 Glu O N O N
Aspartate transcarbamoylase
NH3 CO2 O
CO2
3 Dihydro-orotase UMP Ribose-5-Pi OMP Ribose-5-Pi
ATP
4 Dihdro-orotic acid dehydrogenase 1
Pi O PPi
O
5 Orotate-phosphoribosyl transferase 5
O Pi Pi
O OH OH
6 OMP decarboxylase CAP
Pi PRPP
H2N O O
O O
O
2 4 HN
3 HN
HO HO OH
NH2 OH O N
O O N H
H2N OH O
CAP: Carbamoyl phosphate O N H O NAD+ NADH+H+
OH H
PRPP: Phosphoribosyl pyrophosphate O Orotic acid
Carbamoyl Asp Dihydro-orotic acid
OMP: Orotidine monophosphate
UMP: Uridine monophosphate
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BIOCHEMISTRY | METABOLIC PATHWAYS

Fate of Aspartic Acid (Asp, D) | Biosynthesis AMP

O OH O OH
O O
H2N OH HN OH NH2
OH
GTP GDP+Pi N
N 2
De novo N 1 N N
N
Purine N
Biosynthesis N N N N
N H2 O Fumarate Ribose-5-Pi
Ribose-5-Pi Ribose-5-Pi

Ionosine Monophosphate Adenylosuccinic acid Adenosine Monophosphate

1 Adenylosuccinate synthase
2 Adenylosuccinate lyase

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

Metabolism of Glutamate (Glu, E) & Gln (Q)
 Biosynthesis of Glu from -Ketoglutarate (TCA)
 Biosynthesis of Glu from Gln by Glutamate synthase

Fate of Glu
 Nitrogen Metabolism | Biosynthesis of Gln (Glutamine synthase)
 Transamination to -Ketoglutarate (-KG) | IM of TCA cycle
 Decarboxylation to GABA | Inhibitory neurotransmitter
 Biosynthesis of Glutathione (GSH) | Detoxifying agent
 Biosynthesis of Folic acid |Cofactor of Vitamin BH
 Biosynthesis of AA | Formation of Ornithine and Pro
 Biosynthesis of Purine nucleotide (IMP) | RNA & DNA
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BIOCHEMISTRY | METABOLIC PATHWAYS

Metabolism/Fate of Glu O O
O OH
O
OH HO OH
N O O
H O
O Alpha-KG
OH HN H2N OH
N
N
Pteroic acid
AA
NH3 Gln NH2
H2N N N H 1
Folic acid KA 2

OH Cys Gly
several steps O O 3 4
N Glu-Cys Glutathione
N
HO OH (GSH)
N N NH2 5
Ribose-5-Pi CO2 O
1 Transaminase Ionosine monophosphate NADH+H+
(IMP) 6 HO GABA
2 Gln synthase NAD+ NH2
NADH+H+ NAD+
3 Gamma Glu-Cys synthase O NH3
O O OHC O few steps
4 GSH synthase H2N Urea
H2N OH Cycle
N N OH H2N OH
5 Glu decarboxylase OH
H H2O Glu-delta-semialdehyde
Pro Ornithine
6 Glu dehydrogenase

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

Fate of Glutamic Acid (Glu, E) | De novo Biosynthesis of Purine nucleotide (IMP)
Gln NH2
Pi O Pi O
2 Pi O NH2
O 1 O O
HO O
OH O Pi Pi
OH OH OH OH PPi OH OH 3
ATP AMP H2O Glu ADP+Pi
PRPP PRPP
1 PRPP synthase ATP NH2
N10-formyl O
2 PRPP glutamyl amidotransferase O THFA Pi O NH
THFA O O
Fumarate H2N
3 Dihydro-orotase N
H2N
10 N N5-N10
OH OH
4 Formyl transferase 9 H2N OHC
Pi O N N Methenyl H2O
O Pi O HO N THFA
5 Formylglcinamidine RP synthase 11 4

COOH H2O
6 Aminoimidazole RP synthase OH OH
OH OH
THFA
CH2 O NH
O
7
Aminoimidazole carboxylate HN O O
RP synthase Pi O NH
COOH N HN O H
Aminoimidazole succinyl AMP N
8 H2N N
carboxamide RP synthase Pi O
O
N
N
OH OH
Pi O
O
9 Adenylo succinase Glu
OH OH GMP Gln
IMP ADP+Pi
10 Formyl transferase ADP+Pi
OH OH
5 ATP
O
8 NH
11 IMP cyclohydrolase -
O O
Asp HN
N CO2 N NH
Pi O H
ATP 6 O
H2N H2N N
Pi O N 7 Pi O
O O
OH OH

Senthil Raja A, IIT (BHU) Varanasi OH OH OH OH 3 February 2021 35

BIOCHEMISTRY | METABOLIC PATHWAYS

Precursors of Pyrimidine & Purine Skeletons | Asp, Gln, Gly, CAP
CO2
Gly
O
Asp H
CAP HN C N N5-N10
Asp N C
CH Methenyl
O N N10-formyl HC C N
N THFA
Ribose-5-Pi Glucose THFA H

Gln (Amide N)

Purine Bases | UMP, CMP, TMP Purine Bases | AMP, GMP

The common fate of aromatic amino acids will follow...

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

Metabolism of Aromatic Amino Acids

Phe | Tyr | Trp | His

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 37

BIOCHEMISTRY | METABOLIC PATHWAYS

Metabolism of Phe & Tyr
 Biosynthesis of Tyr
 Metabolism of Tyr
 Biosynthesis of Biogenic Amines (Adr & Nor-Adr) & Melanines
 Normal & Abnormal Catabolism of Tyr
Phenyl pyruvic acid If absent, Phenyl ketonuria
 Biosynthesis of Tyr from Phe Phenyl lactic acid Mental disorder
Phenyl acetic acid
Phe Hydroxylase O
O
O=O H2O OH
OH
NH2
NH2 HO
FH4 FH2
Tyr
Phe
NADP NADPH+H+

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 38

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

Metabolism of Phe & Tyr
 Biosynthesis of Biogenic Amines | Adrenaline & Nor-Adrenaline
O
Phe Hydroxylase O
O Tyrosinase HO
O=O H2O (Misnomer) OH
OH
OH NH2
NH2 HO
NH2 HO
FH4 FH2 Dihydroxy Phenylalanine
Tyr (DOPA)
Phe
NADP NADPH+H+

DOPA
CO2 Decarboxylase

OH OH
NA Methylase Dopamine
HO HO HO
beta-hydroxylase
HN NH2 NH2
HO CH3 HO HO
SAHC SAM Dopamine
Adrenaline Nor-Adrenaline (Neurotransmitter)
(Neurotransmitter) (Neurotransmitter)

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 39

BIOCHEMISTRY | METABOLIC PATHWAYS

Metabolism of Phe & Tyr
 Biosynthesis of Melanines | Black pigments of the Skin & Hairs (Except in
Albinos, due to the absence of melanocytes or tyrosinase enzyme)
O
Phe Hydroxylase O
O Tyrosinase HO
O=O H2O (Misnomer) OH
OH
OH NH2
NH2 HO
NH2 HO
FH4 FH2 Dihydroxy Phenylalanine
Tyr (DOPA)
Phe
NADP NADPH+H+
H Oxidase
N O

O O O O
Decarboxylase
O Polymerizn. COOH Cyclase O
OH
O N O N
H H NH2
O N O
H CO2 2-Carboxy-2,3-dihydro-
Indole-5-6-dione Indole-5-6-dione Dopaquinone
Melanines

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 40

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

Metabolism of Phe & Tyr Thyroglobulin
Tyr
 Biosynthesis of Thyroid Hormones (T3 & T4)
I2
 Thyroid gland produces the amine hormones T3 & T4
DIT T4
from Tyrosine MIT MIT
Coupling
T4 MIT

 Thyroid gland consists of thyroid follicles surrounded by Thyroglobulin

Tyr
Thyroglobulin
Tyr
follicular epithelial cells that contains Thyroglobulin DIT
DIT
T4
DIT
MIT T3
protein (TGP, rich in Tyr) and Iodide.
 Thyroid peroxidase generated Iodine by oxidizing Iodide I O
HO I
ions and couples the generated Iodine to Tyr residues OH
present in Thyroglobulin, thus yielding Moniodo Tyr O
NH2

(MIT) and Diodo Tyr (DIT) I

3,5,3'-triodothyronine (T3)
 T3 is generated by coupling MIT & DIT while T4 is
I O
produced (20 times more than T3) by combining two HO I
DITs OH
NH2
I O
 TGP is endocytosed in the gland and broken down by
I
lysosomes (TSH) to release the hormones T3 & T4. 3,5,3', 5'-triodothyronine (T4)

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 41

BIOCHEMISTRY | METABOLIC PATHWAYS

Catabolism of Phe & Tyr 4-Hydroxy
Phenyl lactic acid
In Scurvy, this enzyme is
inactivated. Treated with Vit C.
O O
O OH
Tyr transaminase Oxidase
OH OH
OH
O 2+
O
NH2 HO Cu HO
HO NH3 Quinol
 Normal Catabolism Tyr
4-Hydroxy Phenyl pyruvic acid

yields glucogenic & TCA Cycle (Glucogenic)

Transposition

ketogenic products. OH
O
HOOC
COOH OH
 Abnormal HOOC
HO
COOH Fumarate O
catabolism leads to O O
2,5-Dihydroxy
phenyl pyruvic acid
H3C
some disorders Keto form
COOH
O
CO2
(indicated in the Acetoacetate (Ketogenic)

Fig.) COOH OH
Oxidase O
Isomerase O O
HOOC HO OH
COOH
HO OH Fe2+
OH OH
Homogentisic acid
Fumaryl acetoacetic acid (trans) Maleyl acetoacetic acid (cis) (Alcaptone)

If absent, Alcaptonuria
Brown pigmentation of urine
Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 42

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

BIOCHEMISTRY | METABOLIC PATHWAYS

O
 Metabolism of Trp
OH
NH2
N
H
HO HO
O Trp Hydroxylase HO
O AA Decarboxylase Monoamine oxidase
OH O=O H2O COOH
NH2 OH NH2
N N N
H NH2 H H
N CO2
H 5-Hydroxy Tryptamine (5-HT)
Trp 5-Hydroxy Indole acetic acid
5-Hydroxy Trp Serotonin (5HIAA)
Acetyl Co-A
Trp dioxygenase
(TDO) 5-HT N-acetyltransferase
H3CO
O HO
O-Methyltransferase
OH
HN CH3
O NH2 N HN CH3
NH H N
CHO O H
O
Melatonin
(Sleep inducer, N-Acetylserotonin
N-Formyl Kynuranine
Hormone of darkness)

Formylase

O COOH
Several steps
OH
O NH2 N
NH2
Nicotinic acid
Kynuranine (Niacin, Vitamin B3)

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 43

BIOCHEMISTRY | METABOLIC PATHWAYS

 Metabolism of His
O
N OH
NH2
N
H
 Biosynthesis of Histamine from His
 Histamine induces Gastric secretion, helps in the contractions of smooth
muscles of stomach, lungs, uterus, lowers BP
O
His Decarboxylase N
N OH
NH2
NH2 N
N H
H
His CO2 Histamine

Senthil Raja A, IIT (BHU) Varanasi 3 February 2021 44

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Lecture Notes L3-7 | Amino Acids | SR 03-Feb-21

SUMMARY & RECAP

 What we have covered? (5 Lectures)
 Amino Acids
 Chemistry | Structure and Classification
 Essential & Non-essential amino acids
 Common Pathways of Amino acid Metabolism
 Biosynthesis & Metabolism of Important Amino Acids
 Ser & Gly
 Asp & Glu | Asn & Gln
 Phe & Tyr; Trp & His
 Major Disorders associated with Amino Acid Metabolism
 What NEXT? (5 Lectures)
 Biochemistry of Carbohydrates | Classification & Metabolism
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