Self Assessment and Review of Biochemistry Rebecca James Perumcheril
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1Amino Acids and Proteins
CHAPTERS
  1. Chemistry and Metabolism of Amino Acids
  2. Proteins
  3. Enzymes2

Chemistry and Metabolism of Amino Acids1

Topics Included
  • Chemistry of Amino Acids:
    • – Classification of Amino Acids
    • – Properties of Amino Acids
  • Metabolism of Amino Acids:
    • – General Amino Acid Metabolism
    • – Individual Amino Acid Metabolism
 
CHEMISTRY OF AMINO ACIDS
 
General Structure of Alpha Amino Acid
zoom view
Fig. 1.1: General structure of alpha amino acid
 
Alpha Amino Acid
  • Amino group and carboxyl group attached to the alpha carbon atom
  • Most of the amino acids are alpha amino acid.
 
Non Alpha Amino Acid
Unlike alpha amino acids either carboxyl group or amino group is not attached to the alpha carbon atom.
Non alpha amino acids present in tissues in free form are:
  • β Alanine
  • β Aminoisobutyrate
  • γ –Aminobutyrate
 
Imino Acid
  • In an imino acid amino group is not free
  • The nitrogen of amino group is seen inside the Pyrrolidine ring
  • Still it can form a peptide bond
  • Proline is an imino acid.
zoom view
Fig. 1.2: Structure of imino acid, proline
 
CLASSIFICATION OF AMINO ACIDS (VERY IMPORTANT TOPIC)
 
BASED ON VARIABLE SIDE CHAINQ
 
Aliphatic Amino Acid
  • Simple Amino Acid
    • GlycineQ
    • Alanine4
  • Branched Chain Amino AcidQ
    • Leucine
    • Isoleucine
    • Valine
  • Sulfur Containing Amino Acid
    • CysteineQ
    • MethionineQ
  • Amino Acid with Hydroxyl Group
    • SerineQ
    • ThreonineQ
  • Amino Acid with Amide Group
    • Asparagine
    • Glutamine
  • Acidic Amino Acid
    • Aspartic Acid (Aspartate)
    • Glutamic Acid (Glutamate)
  • Basic Amino Acid
    • Arginine (Most Basic Amino acid)Q
    • Lysine
 
Aromatic Amino Acid
  • PhenylalanineQ
  • TyrosineQ
With heterocyclic aromatic ring (Ring structure contain more than one type of atom.)
  • TryptophanQ
  • Histidine (Basic Amino Acid)Q.
 
Imino Acid
  • Proline
 
BASED ON SIDE CHAIN CHARACTERISTIC (POLARITY)Q
zoom view
Fig. 1.3: Classification of amino acid based on polarity
  • Polar Amino AcidsQ (Hydrophilic)
    • Charged
      • Acidic Amino acids-Aspartic Acid (Aspartate), Glutamic Acid (Glutamate)
      • Basic Amino Acids-Histidine, Arginine, Lysine
    • Uncharged
      • Aliphatic amino acid with hydroxyl group as side chain: Serine, Threonine
      • Aliphatic amino acids with amide group: Asparagine, Glutamine
      • Simple Amino acid: Glycine alone
      • Sulfur containing Amino acid: Cysteine alone.
  • Nonpolar Amino AcidQ (Hydrophobic)
    • Simple amino acid: Alanine alone
    • Sulfur containing amino acid: Methionine alone
    • Aromatic Amino acids except Histidine (Think as it is basic amino acid it is already included among polar amino acid)
    • All branched chain amino acids: Leucine, Isoleucine and Valine
    • Imino acid: Proline
 
BASED ON METABOLIC FATEQQQ
Classified into:
  • Ketogenic: Amino acids that are converted to Acetyl CoA and thereby to Ketogenic Pathway
  • Glucogenic: Amino Acids that enter into Glucogenic pathway
  • Both Glucogenic and Ketogenic: That can enter into both ketogenic and glucogenic pathway.
Classification of amino
Amino acid
Purely Ketogenic
LeucineQ
Both Ketogenic and Glucogenic
Phenylalanine
Isoleucine
Tyrosine
Tryptophan5
Lysine* (Predominantly Ketogenic)
Glucogenic
Any amino acid that do not belong to the above groups
 
BASED ON NUTRITIONAL REQUIREMENTQQQ
  • Essential: Those amino acids which cannot be synthesised in the bodyQ. Hence these amino acids are to be supplied in the diet.
  • Semiessential: Growing children require them in the food, but not essential in adults.
  • Nonessential: Amino acids which can be synthesised in the bodyQ, hence not required in the diet.
Essential
Semiessential
Nonessential
Methionine
Arginine
All the other amino acids
Threonine
Tryptophan
Valine
Isoleucine
Leucine
Phenylalanine
Lysine
Histidine
 
Special Groups Present in Amino Acids
Amino acid
Special group
Arginine
GuanidiniumQ
Phenylalanine
Benzene
Tyrosine
Phenol
Histidine
ImidazoleQ
Proline
Pyrrolidine
Methionine
Thioether linkage
Tryptophan
Indole
Cysteine
Thioalcohol (SH)
 
Conservative (Homologous) Substitution
One amino acid replaced by another amino acid of similar characteristics
Examples of homologous substitution is shown in the diagram given below.
 
Conservative Mutation
Hydrophilic, Acid
Asp
Glu
Hydrophilic, Basic
His
Arg
Lys
Polar, Uncharged
Ser
Thr
Gln
Asn
Hydrophobic
Ala
Phe
Leu
Ile
Val
Pro
 
Nonconservative (Nonhomologous) Substitution
One amino acid replaced by another amino acid of different characteristics.
 
ABBREVIATIONS OF AMINO ACIDS
Amino acids with unique first letter
Amino acid
Three letter Abbreviation
One letter Abbreviation
Cysteine
Cys
C
Histidine
His
H
Isoleucine
Ile
I
Methionine
Met
M
Serine
Ser
S
Valine
Val
V
Amino acids which do not have unique first letter
Abbreviated based on the commonly occurring amino acids
Amino acid
Three letter Abbreviation
One letter Abbreviation
Glycine
Gly
G
Alanine
Ala
A
Leucine
Leu
L
Proline
Pro
P
Threonine
Thr
T
Abbreviated based on phonetically sounding letters
Amino acid
Three letter Abbreviation
One letter Abbreviation
Arginine
Arg
R (aRginine)
Asparagine
Asn
N (asparagiNe)
Aspartatic Acid
Asp
D (asparDic acid)
Glutamic Acid
Glu
E (glutEmic acid)
Glutamine
Gln
Q (Qtamine)
Phenylalanine
Phe
F (Fenylalanine)6
Tyrosine
Tyr
Y (tYrosine)
Tryptophan
Trp
W (tWiptophan)
Abbreviated based on letter close to initial letter
Lysine
Lys
K (letter close to L)
 
DERIVED AMINO ACIDS
 
Derived Amino Acid seen in ProteinQ
4-Hydroxyproline
  • Found in Collagen
  • Vitamin C is needed for hydroxylation.
5-Hydroxylysine
Methyllysine
Found in Myosin
Gammacarboxy glutamate
  • Found in clotting factors, like Prothrombin that bind Ca2+
  • Vitamin K is needed for Gammacarboxylation.
Cystine
  • Found in proteins with disulphide bond.Q 2014 DNB
  • Two cysteine molecules join to form cystine, e.g. Insulin, Immunoglobulin
Desmosine
  • Found in ElastinQ AIIMS Nov 2014
 
Derived Amino Acid not seen in ProteinQ
Ornithine
Intermediates of Urea Cycle
Arginosuccinate
Citrulline
Homocysteine
Derived from MethionineQ
Homoserine
Product of Cysteine Biosynthesis
Glutamate-γ Semialdehyde
Serine Catabolite
 
PROPERTIES OF AMINO ACID
 
A Genetic Code Specifies an Amino Acid
More than 300 naturally occurring amino acids exist in nature out of which 20 amino acids constitute monomer units of proteins.
 
Amino Acid Exists in Three Charged State, Positive, Negative or Neutral
Depends on the two factors:
  1. Isoelectric pH of the amino acid.
  2. pH of the surrounding medium.
 
Isoelectric pH of Amino Acids
  • At pH = Isoelectric pH
  • At pH < Isoelectric pH
  • At pH > Isoelectric pH
At pH = Isoelectric pH (pI)
  • The amino acid carry equal number of positive and negative charge, i.e. NO NET CHARGE.
  • Amino acid exist as ZWITTER ION (AMPHOLYTE)
At pH less than isoelectric pH (pI)
  • Amino acid exists as protonated or positively charged.7
At pH greater than isoelectric pH (pI)
  • Amino acid exists as deprotonated or negatively charged.
 
Amino Acids Exhibit Isomerism
Amino acids have asymmetric (chiral) alpha carbon atom. The mirror images produced with reference to alpha carbon atom, are called D and L forms or enantiomers.
zoom view
Fig. 1.4: L and D amino acid
  • Almost all naturally occurring Amino Acids are L-Isomers
  • Some naturally occurring Amino acids are D Amino acids.
 
Naturally occurring D Amino Acid
  • Free D Aspartate and Free D Serine in brain tissue
  • D-Alanine and D Glutamate in cell walls of gram-positive bacteria
  • Bacillus subtilis excretes D-methionine, D-tyrosine, D-leucine, and D-tryptophan to trigger biofilm disassembly
  • Vibrio cholerae incorporates D-leucine and D-methionine into the peptide component of their peptidoglycan layer.
 
Potentially Toxic L-Amino Acids
  • Certain L α Amino acids present in the in plants can adversely affect human health
  • Present in the seeds of certain species of Lathyrus.
Examples of Toxic L-Amino Acids
L-Amino acids
Clinical implication
L-Homoarginine cleaved by Arginase to L Lysine and Urea
Causes Neurolathyrism in humans
β N Oxalyl Diamino Propionic Acid (β ODAP)
Neurotoxin
Causes Neurolathyrism in humans
β N Glutamyl Amino Propiono Nitrile (BAPN)
An Osteolathyrogen
2, 4-Diaminobutyric acid
Inhibits ornithine transcarbamylase, resulting in ammonia toxicity.
β-Methyl amino alanine (Present in Cycad seeds)
Possible risk factor for neurodegenerative diseases like
  • Parkinson's Disease
  • Amyotropic Lateral Sclerosis (ALS)
 
Amino Acid Absorb UV LightQ
Amino Acids which absorb 250–290 nm (Maximum at 280 nm) UV light are tryptophan, phenylalanine, tyrosine.
Maximum absorption of UV light by tryptophan.Q
zoom view
Fig. 1.5: Ultraviolet absorption spectra of aromatic amino acids
BETA–ALANINE (Very important topic for national board pattern exams)
  • Formed from Cytosine and UracilQDNB/AIPGMEE
  • Other sources of Beta Alanine is hydrolysis of Beta alanyldipeptides8
  • Beta Alanine is seen inQ DNB/AIPGMEE
    • Pantothenic Acid
    • Coenzyme A
    • Acyl Carrier Protein
    • Beta Alanyl Dipeptides.
  • Beta Alanyl Dipeptides are:
    • Carnosine [Histidine + Beta alanine]
    • Anserine [N methyl Carnosine] Both present in Skeletal muscle.
Uses of Carnosine
  • Activate Myosin ATPase
  • Chelate Copper
  • Enhance Copper uptake
  • Buffers the pH of anaerobically contracting muscle.
 
DECARBOXYLATION OF AMINO ACID
  • The amino acid undergo alpha decarboxylation to form corresponding Amines
  • PLPQ is the coenzyme for this reaction.
Examples of Amino Acid Decarboxylation
Amino acid
Biologic amines
Histidine
Histamine
Tyrosine
Tyramine
Tryptophan
Tryptamine
Lysine
Cadaverine
Glutamic AcidQ
Gamma Amino Butyric Acid (GABA)
Serine
Ethanolamine
Cysteine
Beta mercaptoethanol amine
 
COLOR REACTIONS OF AMINO ACIDS
 
Biuret Test
  • General test for proteins
  • Cupric ions in alkaline medium forms violet color with peptide bond nitrogen.
 
Ninhydrin Test
General test for all alpha Amino Acid
Amino acid + 2 mols of Ninhydrin -------> Aldehyde with 1 carbon atom less + CO2 + Purple Complex (Ruhemann's Purple)
Colour Reactions
Test answered by
Xanthoproteic Test (Conc HNO3 is a reagentQ)
Aromatic Amino Acid2014 DNB (Phenylalanine, Tyrosine, Tryptophan)
Millon's test
Tyrosine (Phenol)
Aldehyde test can be done in two methods:
  • Acree Rosenheim Test (Formaldehyde and Mercuric Sulfate is used)
  • Hopkin's Cole TestQ
  • (Glyoxylic Acid is used)
Tryptophan (Indole group)
Saka Guchi's test
ArGinine (Guanidinium group)
Mnemonic–G is common to all
Sulfur test
Cysteine
Cyanide Nitroprusside Test
Homocysteine
Pauly's Test
Histidine (Imidazole) Tyrosine (Phenol)
 
Buffering Action of Amino Acids
  • Buffers are solutions which can resist changes when acid or alkali is added.
Maximum buffering capacity is at pH = pKa. So amino acid which has pKa range near physiologic pH can act as an effective buffer.
 
pKa Range of Amino Acid
Dissociating group
pKa range
Alpha carboxyl group
3.2–4.1
Non alpha COOH of Asp and Glu
4.0–4.89
Imidazole group of histidine
6.5–7.4
SH group of Cysteine
8.5–9.0
OH group of Tyrosine
9.5–10.5
Alpha amino group
8.0–9.0
Guanidinium group of Arginine
> 12
 
DIGESTION OF PROTEINS
Native proteins are resistant to digestion because few peptide bonds are accessible to the proteolytic enzymes without prior denaturation of dietary proteins (by heat in cooking and by the action of gastric acid).
 
Enzymes Catalyze the Digestion of Proteins
There are two main classes of proteolytic digestive enzymes (proteases)
  1. Endopeptidases hydrolyze peptide bonds between specific amino acids throughout the molecule. They are the first enzymes to act, yielding a larger number of smaller fragments.
    • Pepsin in the gastric juice catalyzes hydrolysis of peptide bonds adjacent to amino acids with bulky side-chains (aromatic and branched-chain amino acids and methionine).
    • Trypsin, chymotrypsin, and elastase are secreted into the small intestine by the pancreas.
      • Trypsin catalyzes hydrolysis of lysine and arginine esters.
      • Chymotrypsin catalyzes hydrolysis esters of aromatic amino acids.
      • Elastase catalyzes hydrolysis esters of small neutral aliphatic amino acids.
  2. Exopeptidases catalyze the hydrolysis of peptide bonds, one at a time, from the ends of peptides.
    • Carboxypeptidases, secreted in the pancreatic juice, release amino acids from the free carboxyl terminal.
    • Aminopeptidases, secreted by the intestinal mucosal cells, release amino acids from the amino terminal.
    • Dipeptidases and tripeptidases in the brush border of intestinal mucosal cells catalyze the hydrolysis of di-and tripeptides, which are not substrates for amino-and carboxypeptidases.
The proteases are secreted as inactive zymogens; the active site of the enzyme is masked by a small region of the peptide chain that is removed by hydrolysis of a specific peptide bond.
Pepsinogen is activated to pepsin by gastric acid and by activated pepsin.
In the small intestine, trypsinogen, the precursor of trypsin, is activated by enteropeptidaseQ, which is secreted by the duodenal epithelial cells; trypsin can then activate chymotrypsinogen to chymotrypsin, proelastase to elastase, pro-carboxypeptidase to carboxypeptidase, and pro-aminopeptidase to aminopeptidase.
 
GENERAL AMINO ACID METABOLISM
 
Biosynthesis of Urea
Urea biosynthesis occur in four stages:
 
1. Transamination
Definition
  • Transfer of alpha amino group from one amino acid to a keto acid to form another pair of amino acid and keto acid.
  • Amino group from amino acids are concentrated in the form of Glutamate.
  • Because only Glutamate can undergo oxidative deamination to significant amount thereby releasing ammonia that enter into urea cycle.
zoom view
Fig. 1.6: Transamination
10
Examples of transamination
  • Alanine Amino Transferase (ALT) or Serum Glutamate Pyruvate Transaminase (SGPT)
    Alanine + α-Ketoglutarate → Pyruvate + Glutamate
  • Aspartate Amino Transferase (AST) or Serum Glutamate Oxaloacetate Transaminase (SGOT)
    Aspartate + α-Ketoglutarate → Oxaloacetate + Glutamate
 
2. Oxidative Deamination
  • The removal of amino group from amino acid is called deamination
  • Only glutamate can undergo significant oxidative deamination.
zoom view
Fig. 1.7: Oxidative deamination
zoom view
Fig. 1.8: L amino acid oxidase
Some examples of Nonoxidative DeaminationQ NBE pattern
  • Amino acid Dehydrases for amino acids with hydroxyl group (Serine, Threonine)
  • Histidase for histidine
  • Amino acid Desulfhydrases for amino acids with sulfhydryl group, Cysteine and Homocysteine
Transdeamination
Conversion of α Amino nitrogen to ammonia is by concerted action of amino tranferase and Glutamate Dehydrogenase is often termed as Transdeamination.
 
3. Transport of Ammonia (Very Important Topic PGMEE Exams)
Free ammonia is toxic to cells especially to brain. Excess ammonia generated has to be converted to nontoxic form Then transported to liver to enter into urea cycle.
  • Transport of Ammonia from most of the tissues including the brain
  • Transport of Ammonia from skeletal muscle.
Transport of Ammonia from most of the tissues including the brain.
  • As GlutamineQ with the help of the enzyme Glutamine Synthetase.11
Glutamine Synthetase
  • Ammonia formed in most tissues including the brain is trapped by Glutamate to form Glutamine
  • This is called first line trapping of ammonia
  • ATP is required for this reaction.
Glutaminase
  • In the liver, glutaminase removes the ammonia from Glutamine.
  • Ammonia enter into urea cycle in the liver.
zoom view
Fig. 1.9: Glutamine synthetase and glutaminase
Transport of Ammonia from skeletal muscle.
  • From Skeletal Muscle as AlanineQ
  • In skeletal muscle, excess amino groups are generally transferred to pyruvate to form alanine.
zoom view
Fig. 1.10A: Transport of ammonia from different organs
zoom view
Fig. 1.10B: Transport of ammonia from different organs
 
4. Disposal of Ammonia
  • The ammonia from all over the body reaches the liver. It is then detoxified to urea by liver cells, then excreted through kidney
  • UreaQ is the major end product of protein catabolism in the body.
Sources of UreaQ
zoom view
Fig. 1.11: Sources of nitrogen and carbon atoms of urea
 
UREA CYCLE (VERY IMPORTANT TOPIC)
The urea cycle is the first metabolic pathway to be elucidated by Sir Hans Krebs and a medical student associate, Kurt Henseleit hence as Krebs Henseleit Cycle.
  • Ornithine consumed in the reaction 2 is regenerated in the reaction 5. Hence called Ornithine Cycle.
 
Site of Urea Cycle
  • Organ: Takes place in liver.
  • Organelle: Partly mitochondrial and partly cytoplasmic.12
zoom view
Fig. 1.12: Reactions of urea cycle
 
Reactions of Urea Cycle
The first two reaction takes place in the mitochondria. The rest of the reactions takes place in the cytoplasm.
 
Carbamoyl Phosphate Synthetase–I (CPS-I)
  • Carbamoyl Phosphate is formed from the con-densation of CO2, Ammonia and ATP
  • Takes place in the mitochondria
  • CPS-I is the rate limiting (pacemaker) enzyme in this pathway.
  • Cytosolic CPS-II is involved in Pyrimidine synthesis
  • CPS-I is active only in the presence of N-Acetyl Glutamate, an allosteric activatorQ
  • This step require 2 mols of ATPs.
 
Ornithine Transcarbamoylase (OTC)
  • Transfer carbamoyl group of Carbamoyl Phosphate to Ornithine forming Citrulline
  • Takes place in the mitochondria
  • Subsequent steps takes place in the cytoplasm.13
 
Transporters of Urea Cycle
  • Ornithine Transporter: For entry of Ornithine
  • Citrulline Transporter: For exodus of Citrulline
 
Arginino Succinate Synthetase
  • Links amino nitrogen of aspartate to citrulline
  • Aspartate provides second nitrogen of Urea
  • This enzyme is a Ligase
  • This reaction requires ATP
  • Two inorganic phosphates are utilized.
 
Arginino Succinate Lyase
Cleavage of Argino succinate to Arginine and Fumarate. This enzyme is a Lyase
 
ArginaseQ
Hydrolytic cleavage of arginine, releases urea and reforms ornithine which reenter into mitochondria.
Arginase is a HydrolaseQ
 
Energetics of Urea Cycle
  • Urea cycle requires 4 high energy phosphates
  • Urea cycle requires 3 ATPSQ directly.
 
Urea Bicycle
Urea cycle is linked to TCA cycle through Fumarate and Aspartate. Hence this cycle is called urea bicycle.
 
CLINICAL CORRELATIONS: UREA CYCLE DISORDERS
 
Key Points of Urea Cycle Disorders
Characterized by
  • Hyperammonemia
  • Encephalopathy
  • Respiratory alkalosis.
 
Clinical Symptoms common to all Urea Cycle Disorders
In the neonatal period
Symptoms and signs are mostly related to brain dysfunction and are similar regardless of the cause of the hyperammonemia.
The affected infant is normal at birth but becomes symptomatic following the introduction of dietary protein.
  • Refusal to eat
  • Vomiting
  • Tachypnea
  • Lethargy
  • Convulsions are common
  • Can quickly progress to a deep coma.
In infants and older children
  • Vomiting
  • Neurologic abnormalities (ataxia, mental confusion, agitation, irritability, and combativeness)
 
BIOCHEMICAL DEFECT IN UREA CYCLE DISORDERS
Urea cycle disorders due to enzyme deficiency
Disorder
Enzyme defective
Hyperammonemia Type-I
Carbamoyl Phosphate Synthetase I (CPS-I)
Hyperammonemia type-II
Ornithine Transcarba-moylase (OTC)
Citrullinemia Type I (Classic Citrullinemia)
Argino succinate synthetase
Arginosuccinic aciduria
Arginosuccinate lyase
Hyperargininemia
Arginase
Urea cycle disorders due to transporter defect
Citrullinemia Type II
Citrin (transport aspartate and glutamate) defect
Hyperammonemia-hyperornithinemia-homocitrullinuria (HHH) syndrome
Ornithine transporter defect
14
 
HIGH YIELDING FACTS—UREA CYCLE DISORDERS
 
Hyperammonemia Type II (OTC Deficiency)
  • Most common Urea Cycle disorderQ
  • Disorder with X-linked partially dominant inheritance (All other Urea Cycle Disorders are Autosomal Recessive)
  • Urea cycle disorder with Orotic Aciduria
  • Marked elevations of plasma concentrations of glutamine and alanine with low levels of citrulline and arginine
  • Orotate may precipitate in urine as a pink colored gravel or stones.
 
Orotic aciduria in Hyperammonemia Type II
  • Ornithine Transcarbamoylase defective hence Carbamoyl Phosphate accumulate in the mitochondria
  • Carbamoyl Phosphate reaches the cytoplasm enter into Pyrimidine Synthesis
  • Orotic Acid, an intermediate in the Pyrimidine synthesis accumulates which leads to Orotic Aciduria.
 
Arginosuccinic Aciduria
  • Trichorrhexis nodosa (dry and brittle hair) is a common finding
 
Hyperammonemia-Hyperornithinemia-Homocitrullinemia (HHH) Syndrome
  • Autosomal recessively inherited disorder
  • Biochemical Defect is mutation in the ORNT 1 gene that encodes mitochondrial membrane Ornithine Permease
  • This results in defect in the transport system of ornithine from the cytosol into the mitochondria
  • This leads to accumulation of ornithine in the cytosol causes hyperornithinemia
  • Deficiency of ornithine in the mitochondria results in disruption of the urea cycle and hyperammonemia
  • Homocitrulline is presumably formed from the reaction of mitochondrial carbamoyl phosphate with lysine.
 
Citrullinemia Type II
  • The adult form (type II) is caused by the deficiency of a mitochondrial transport protein named citrin
  • Citrin (aspartate-glutamate carrier protein) is a mitochondrial transporter encoded by a gene (SLC25A13) located on chromosome 7q
  • One this protein's functions is to transport aspartate from mitochondria into cytoplasm
  • Aspartate is required for converting citrulline to argininosuccinic acid
  • So Citrulline accumulates.
 
Biochemical Investigation in a Case with Hyperammonemia
zoom view
Fig. 1.13: Biochemical investigation of hyperammonemia
 
Biochemical Basis of Treatment of Urea Cycle Disorder
  • Arginine:
    • Essential Amino Acid
    • Provide Ornithine
    • Arginine is an activator of N Acetyl Glutamate Synthase but contraindicated in Arginase Defect
  • Acylation therapy: The main organic acids used for this purpose are sodium salts of benzoic acid and phenylacetic acid.
Principle: Exogenously administered organic acids form acyl adducts with endogenous nonessential amino acids.
These adducts are nontoxic compounds with high renal clearances.
  • Sodium Benzoate: Benzoate forms hippuric acid with endogenous glycine in the liver. Each mole of benzoate removes 1 mole of ammonia as glycine.
Benzoic Acid + CoA → Benzoyl CoA + Glycine → Benzoyl Glycine [Hippuric Acid]
  • Sodium Phenylacetate: Phenylacetate conjugates with glutamine to form phenylacetylglutamine, which is readily excreted in the urine. One mole of phenylacetate removes 2 moles of ammonia as glutamine from the body
    Phenyl Acetic Acid + CoA → Phenyl Acetyl CoA + Glutamine → Phenyl Acetyl Glutamine.
 
INDIVIDUAL AMINO ACIDS
 
Phenylalanine and Tyrosine
 
Phenylalanine
  • Aromatic amino acid
  • Essential amino acid
  • Hydrophobic amino acid
  • Partly glucogenic partly ketogenic.
zoom view
Fig. 1.14: Phenylalanine
 
Tyrosine
  • Aromatic amino acid
  • Synthesized from phenylalanine
  • Nonessential
  • Partly glucogenic and partly ketogenic.16
zoom view
Fig. 1.15: Tyrosine
 
Synthesis of Tyrosine from Phenylalanine
zoom view
Fig. 1.16: Conversion of phenylalanine to tyrosine
 
Phenylalanine Hydroxylase
  • Enzyme belongs to Mixed Function Oxidase (Monooxygenase)
  • Require coenzymes Tetrahydrobiopterin, NADPH
  • One mol of oxygen is incorporated
  • Irreversible reaction.
 
Tetrahydrobiopterin
  • Resemble folic acid but is not a vitamin
  • Precursor of Tetrahydrobiopterin is Guanosine Triphosphate (GTP)
  • Rate limiting enzyme in the pathway is GTP Cyclohydrolase.
zoom view
 
CATABOLISM OF TYROSINE
zoom view
Fig. 1.17: Catabolism of tyrosine
 
Important Points in the Catabolism of Tyrosine
As phenylalanine is converted to tyrosine, the degradative pathway is the same for both Phenylalanine and Tyrosine.
Tyrosine Transaminase
PLP is the coenzyme for this reaction
Para Hydroxyphenylpyruvate Hydroxylase (4 Hydroxy-Phenylpyruvate Dioxygenase)
  • This enzyme belongs to Dioxygenase, i.e. incorporates both the atoms of oxygen
  • Cofactor for this enzyme is Copper
  • Ascorbic Acid is also needed for this reaction.
 
Homogentisate Oxidase
  • Belongs to Dioxygenase
  • Contains Iron at the active site.
 
Maleyl acetoacetate cis-trans isomerase
  • Belongs to Isomerase
  • Need Glutathione (GSH) as cofactor.
 
SYNTHESIS OF MELANIN
  • Takes place in the melanosome of melanocyte present in the deeper layers of epidermis.
  • Under the influence of MSH.
  • Melanin gives pigmentation to the skin and hair.
zoom view
Fig. 1.18: Melanin synthesis
Tyrosinase
  • Rate limiting step
  • Monooxygenase
  • Copper is the cofactor for this enzyme
  • Single enzyme catalyse two reactions.
 
SYNTHESIS OF CATECHOLAMINES
 
 
Catecholamines are:
  • Dopamine
  • Epinephrine
  • Norepinephrine
Catecholamines are compound which contain Catechol nucleus.
Site of Synthesis: Chromaffin cells of Adrenal Medulla and Sympathetic Ganglia.
  • In adrenal medulla major product is Epinephrine (80%)
  • In organs innervated by Sympathetic nerves major product is Norepinephrine (80%).
Conversion of Tyrosine to Epinephrine involves 4 sequential steps:
  1. Ring Hydroxylation
  2. Decarboxylation
  3. Side chain hydroxylation
  4. N-Methylation
zoom view
Fig. 1.19: Catecholamine
 
Important Points Catecholamine Synthesis
 
Tyrosine Hydroxylase
  • Rate limiting step in catecholamine synthesis
  • Similar to Phenylalanine hydroxylase
  • Monooxygenase
  • Require tetrahydrobiopterin.
 
Tyrosinase vs Tyrosine Hydroxylase
  • Both the enzymes convert Tyrosine to DOPA
  • Tyrosinase is expressed only in melanocyte where DOPA is used to synthesize Melanin
  • Tyrosine Hydroxylase is expressed only in the sites where catecholamines are synthesized, where DOPA utilized for Catecholamine synthesis
  • Tyrosinase is a monooxygenase containing Cu2+ in the active site
  • Tyrosine Hydroxylase is a monooxygenase with Tetrahydrobiopterin as the cofactor.
DOPA Decarboxylase
  • Present in all the tissues
  • PLP is the coenzyme for this enzymeQ.
 
DEGRADATION OF CATECHOLAMINES
  • The half life of catecholamines are very short, only 2–5 minutes
zoom view
Fig. 1.20: Degradation of catecholamines
18
  • Epinephrine and norepinephrine is catabolized by Catechol O Methyl Transferase (COMT)Q then by Monoamino Oxidase (MAO)Q
  • The major end product of epinephrine and norepinephrine is Vanillyl Mandelic Acid (VMA)Q
  • Normal level of VMA excretion in urine is 2–6 mg/24 hour
  • The major end product of Dopamine is Homo Vanillic Acid (HVA).
 
Synthesis of Thyroid Hormones
Thyroid hormones are synthesized on thyroglobulin, a large iodinated glycosylated protein. It contains. 115 tyrosine residues.
Tyrosine residues are iodinated to form Mono-Iodo–Tyrosine (MIT) and Di-iodo Tyrosine (DIT). Coupling of MIT and DIT on the thyroglobulin produce Thyroxine
  • MIT + DIT → Tri-iodothyronine (T3)
  • DIT+DIT → Tetra-iodothyronine. (T4) or Thyroxine.
 
CLINICAL CORRELATIONS (PHENYLALANINE AND TYROSINE METABOLISM)
 
Metabolic Disorders Associated with Catabolic Pathway of Phenylalanine and Tyrosine
zoom view
Fig. 1.21: Biochemical defects in the metabolism ofaromatic amino acids
 
PHENYLKETONURIA
 
Classic Phenylketonuria (Type I PKU)
  • Most common metabolic disorder concerned with amino acid
 
Biochemical Defect
  • Phenylalanine Hydroxylase Deficiency.
  • Phenylalanine could not be converted in to Tyrosine.
  • Phenylalanine in the blood rises.
  • Alternate metabolic pathways are opened.
zoom view
Fig. 1.22: Alternate metabolic pathways in PKU
 
Clinical Presentation of Phenylketonuria
  • The affected infant is normal at birth
  • Profound intellectual disability develops gradually if the infant remains untreated
  • Vomiting, sometimes severe enough to be misdiagnosed as pyloric stenosis
  • Older untreated children become hyperactive with autistic behaviors, including purposeless hand movements, rhythmic rocking, and athetosis
  • The infants are lighter in their complexion than unaffected siblings. (Phenylalanine not converted to Tyrosine, so decreased melanin synthesis)
  • These children have an unpleasant mousey or musty odor of phenylacetic acid.Q    JIPMER 2015
 
Lab Diagnosis of PKUQ
Guthries Test (Bacterial Inhibition Assay of Guthrie)
  • Rapid screening Test in the blood sample
  • First method used for this purpose19
  • Certain strains of Bacillus Subtilis need Phenylalanine as an essential growth factor
  • Bacterial growth is proportional to blood pheny-lalanine.
Ferric Chloride Test
  • Screening test in urine sample
  • Identifies Phenylketones in urine sample
  • A simple test for diagnosis of infants with develop-mental and neurologic abnormalities
  • Nowadays it has no place in any screening program especially in developed countries
  • These tests have been replaced by more precise and quantitative methods (fluorometric and tandem mass spectrometry).
Tandem Mass Spectrometry
  • The method of choice is tandem mass spectrometry, which identifies all forms of hyperphenylalaninemia.
Other methods
  • Molecular Biology Techniques like Phenylalanine Hydroxylase specific probes
  • Quantitative measurement of Blood Phenylalanine. (Blood level > 20 mg/dl in PKU)
  • Enzyme assay in dry blood spot also done.
 
Treatment of Classical PKU
  • A low–phenylalanine diet
  • Administration of large neutral amino acids (LNAAs) is another approach to diet therapy.
  • Sapropterin dihydrochloride (Kuvan), a synthetic form of BH4, which acts as a cofactor in patients with residual PAH activity, is approved by the FDA to reduce phenylalanine levels in PKU.
  • Preliminary trials with recombinant phenylalanine ammonia lyase have been encouraging and demon-strated reduced blood levels of phenylalanine during treatment.
 
Nonclassical Phenylketonuria
 
Biochemical Defect
Hyperphenylalaninemia due to Tetrahydrobiopterin defect
  • Due to Dihydrobiopterin ReductaseQ Defect (Type II and Type III PKU)
  • Due to defect in the enzymes that synthesize Tetrahydrobiopterin (Type IV & Type V PKU)
    • 6-pyruvoyltetrahydropterin synthase, (Most Common)
    • Guanosine Triphosphate (GTP) Cyclohydrolase.
Lab Diagnosis of Nonclassical PKU
  • Meausurement of Neopterin and Biopterin [Oxidative Product of Dihydrobiopterin and Tetrahydrobiopterin] level in urine
  • Tetrahydrobiopterin (BH4) loading test normalizes Plasma Phenylalanine level
  • Enzyme Assay in dry blood spots on filter paper
  • Genetic test: Mutation analysis and deletion/duplication studies are clinically available for all these enzyme defects and help to confirm the diagnosis.
 
Segawa Syndrome (Hereditary Progressive Dystonia)
  • Tetrahydrobiopterin deficiency due to defect in the enzyme GTP Cyclohydrolase
  • But interestingly no Hyperphenylalaninemia
  • Autosomal Dominant Inheritance
  • Dystonia with diurnal variation
  • Females are affected more than males.
 
Alkaptonuria
  • Autosomal recessive disorder
  • 1st inborn error detected.
  • Belongs to Garrod's Tetrad (Alkaptonuria, Albinism, Pentosuria, Cystinuria).
 
Biochemical Defect
  • Homogentisate oxidase deficiency
  • Accumulation of Homogentisic Acid (Homogentisate).which polymerizes to form Alkaptone bodies.
zoom view
Fig. 1.23: Biochemical defect alkaptonuria
20
 
Clinical Presentation of Alkaptonuria
  • Normal Life till 3rd or 4th decade
  • Urine Darkens on standing is the only manifestation in children
  • In adults ochronosis, i.e. Alkaptone bodies deposited in intervertebral disk, cartilage of nose, pinna, etc. leading to pigmentation.
  • Arthritis
  • NO MENTAL RETARDATIONQ.
 
Laboratory DiagnosisQ
  • Alkalanization increase darkening of urine
  • Benedicts test positive in urine because homogentisic acid is reducing agent
  • Ferric chloride test positive
  • Silver nitrate test positive.
 
Treatment
  • New Drug is Nitisinone [NTBC] which inhibit para Hydroxylphenylpyruvate hydroxylase which leads to the accumulation of homogentisic acid
  • Symptomatic treatment.
 
Tyrosinemia
There are three types of Tyrosinemias Type I, Type II and Type III
 
Type I (Hepatorenal Tyrosinemia, Hereditary Tyrosinemia)
Biochemical defect:
  • Fumarylacetoacetate hydrolase deficiency
  • Organs affected are liver, kidney, and peripheral nerves
  • Organ damage is believed to result from accumulation of metabolites of tyrosine degradation, especially fumarylacetoacetate and succinylacetone
  • Cabbage like odor due to Succinylacetone.
Diagnosis
  • Plasma tyrosine value less diagnostic value. Because it is dependent on diet
  • Elevated Succinylacetone in urine and blood is more diagnostic.
Treatment
  • Diet low in Phenylalanine and Tyrosine
  • New Drug is Nitisinone [NTBC].
 
Type II Tyrosinemia (Oculocutaneous Tyrosinemia, Richner-Hanhart Syndrome)
Biochemical defect
  • Tyrosine transaminase deficiency.
Clinical manifestations
  • Palmar and plantar hyperkeratosis
  • Herpetiform corneal ulcers
  • Intellectual disability.
 
Type III (Neonatal Tyrosinemia)
Biochemical defect
Parahydroxylphenylpyruvate Hydroxylase (4 Para Hydroxyphenylpyruvate Dioxygenase 4-HPPD deficiency.
 
Hawkinsinuria
  • Hawkinsinuria is inherited as an autosomal dominant trait
  • Certain missense mutations in the gene for Para hydroxylphenylpyruvate hydroxylase) (4 Para Hydroxyphenylpyruvate Dioxygenase)
  • This results in an abnormal enzyme activity
  • The mutant enzyme, incapable of normally oxidizing 4-hydroxyphenylpyruvate to homogentisic acid
  • Instead it forms an intermediate that reacts with cysteine to form the unusual organic acid hawkinsin
  • Hawkinsin named after the first affected family secondary glutathione deficiency may occur
  • An unusual odor (described as like that of a swimming pool).
 
Pheochromocytoma
Symptomatic catecholamine-producing tumors, in adrenal and extraadrenal retroperitoneal, pelvic, and thoracic sites.
Clinical Presentation
The classic triad of Pheochromocytoma:
  • Episodes of palpitations
  • Headaches
  • Profuse sweating are typical and constitute a classic triad
  • All three symptoms are associated with hypertension.21
Biochemical Testing of Pheochromocytoma and paraganglioma
Elevated plasma and urinary levels of:
  • Catecholamines
  • Metanephrines
  • Vanillyl Mandelic acid
Biochemical methods used for pheochromocytoma and paraganglioma diagnosis
Diagnostic method
Sensitivity
Specificity
24 hour Urinary Testing
1. Vanillylmandelic acid
++
++++
2. Catecholamines
+++
+++
3. Fractionated metanephrines Q
++++
++
4. Total metanephrines
+++
++++
Plasma Tests
1. Catecholamines
+++
++
2. Free metanephrines
++++
+++
 
Albinism
Disorder associated with deficiency of Tyrosinase enzyme which synthesize Melanin, the pigment of skin and eye.
 
TRYPTOPHAN
  • Aromatic amino acid
  • Essential amino acid
  • Special group present is indole group
  • Glucogenic and ketogenic.
 
Catabolic Pathway Tryptophan (Kynurenine -Anthranilate Pathway)
  • Major metabolic fate of Tryptophan is to be oxidized by tryptophan pyrrolase
 
Tryptophan Pyrrolase (Tryptophan Oxygenase)
  • Dioxygenase
  • Iron Porphyrin Metalloprotein (i.e. it is a heme containing Protein).
 
Kynureninase
  • Coenzyme is PLP.
 
Clinical Correlation-Kynurenine Anthranilate Pathway
Pellagra like symptoms in PLP deficiency
  • Decreased Kynureninase leads to decreased NAD+ pathway
  • Hence Niacin deficiency, which lead to Pellagra like symptoms.
Xanthurenate is excreted in urine in PLP deficiency
  • This is because PLP deficieny leads to decreased Kynureninase activity
  • Hence Kynurenine accumulate which is converted to Xanthurenate.
zoom view
Fig. 1.24: Metabolic pathways of tryptophan
 
Nicotinic Acid Pathway of Tryptophan
  • 3% of Trptophan enter this pathway
  • 60 mg Tryptophan is converted to 1 mg of NiacinQ
  • Quinolinate Phosphoribosyl Transferase is the rate limiting step in this pathway.22
 
Serotonin (5 Hydroxytryptamine)
Synthesized in the Argentaffin cells in the intestine, mast cells, platelets and in the brain.
Functions of Serotonin
  • Neurotransmitter in the brain
  • Mood elevation
  • GI motility
  • Temp regulation
  • Potent vasoconstrictor.
 
Melatonin
Synthesized in the Pineal gland.
 
Functions of Melatonin
  • Diurnal variation
  • Biological rhythm
  • Sleep wake cycle
zoom view
Fig. 1.25: Specialized products from tryptophan
 
Important Enzymes in the synthesis of Serotonin
 
Tryptophan Hydroxylase
  • Rate limiting step in the serotonin and melatonin synthesis
  • By this enzyme tryptophan is converted to 5 hydroxytryptophan
  • Tetrahydrobiopterin is the coenzyme for this enzyme monoxygenase.
 
Amino Acid Decarboxylase
  • 5 OH Trytophan is decarboxylated to 5 OH Tryp-tamine, or Serotonin.
 
CATABOLISM OF SEROTONIN
  • Mono amino oxidase is the enzyme
  • 5 Hydroxy indole acetic acid (5HIAA) is the degradatory product of Serotonin
  • Normal urinary excretion of 5 HIAA is < 5 mg/day.
 
SYNTHESIS OF MELATONIN
  • N Acetylation of serotonin followed by N-methylation in the pineal body forms Melatonin
  • Methyl donor is S-Adenosyl Methionine (SAM)
 
Excretory Product of Tryptophan
Normal excretory product of Tryptophan in Urine is 5 Hydroxy Indole Acetate and Indole 3 Acetate.
 
Carcinoid Tumor [Argentaffinoma]
  • Belongs to gastrointestinal neuroendocrine tumors
  • Tumor of Argentaffin Cells that secrete Serotonin.
  • Increased Synthesis of Serotonin
 
Clinical Symptoms
  • Most common symtoms are Intermittent Diarhea (32–84%) and Flushing (63–75%)
  • Sweating
  • Fluctuating hypertension
  • Pellagra like symptoms
 
Diagnosis
  • Serum serotonin increased
  • Urinary 5 HIAA increased
  • Neuroendocrine markers used for diagnosis are:
    • Chromogranin A
    • Neuron specific enolase
    • Synaptophysin
23
 
Typical and Atypical Carcinoid
 
Typical Carcinoid
  • Is caused by a midgut carcinoid tumor
  • Increased synthesis of 5 Serotonin
  • Expanded serotonin pool size, increased blood and platelet serotonin
  • Increased urinary 5-hydroxyindolacetic acid (5-HIAA).
 
Atypical Carcinoid
  • Foregut carcinoids are the most likely to cause an atypical carcinoid syndrome.
Biochemical Defect
  • Due to a deficiency in the enzyme aromatic amino acid decarboxylase
  • 5-Hydroxy Tryptophan (5 HTP) cannot be converted to 5-Hydroxytryptamine (5HT) (serotonin)
  • 5-Hydroxytryptophan is secreted into the bloodstream
  • Plasma serotonin levels are normal
  • Characteristically, urinary 5-Hydroxytryptophan and 5-Hydroxytryptamine (5-HTP is converted to 5-HT in the kidney) are increased
  • But urinary 5-HIAA levels are only slightly elevated.
zoom view
 
Hartnup Disorder
  • Autosomal Recessive Condition
  • Named after first family in which the disorder identified.
 
Biochemical Defect
  • Defective absorption of tryptophan and other neutral amino acid from intestine and renal tubules
  • The transporter protein for these amino acids (B0AT1) is encoded by the SLC6A19 gene
  • Two chemically close transcription factors, angiotensin-converting enzyme (ACE2) in the intestine and renal tubules, and collectrin in the renal tubules, are required for expression of B0AT1 transporter protein by the SLC6A19 gene
  • The mutated gene in patients with Hartnup disorder, unable to interact with the above transcription factors, results in deficiency of B0AT1 protein either in the intestine or in the renal tubules or in both.
 
Clinical Features
  • Asymptomatic
  • Cutaneous Photosensitivity is the most common presenting complaint
  • Intermittent Ataxia manifested as unsteady wide based gait
  • Pellagra like symptoms.
Laboratory diagnosis of hartnup disease
  • Obermeyer Test (Test for indole compounds in the urine) positive.
Treatment
  • Lipid-soluble esters of amino acids and tryptophan ethyl ester
  • Treatment with nicotinic acid or nicotinamide (50–300 mg/24 hr) and a high-protein diet.
 
Blue Diaper Syndrome (Drummond syndrome)
  • Tryptophan is specifically malabsorbed
  • The defect is expressed only in the intestine (unlike Hartnup Disease) and not in the kidney.
 
SIMPLE AMINO ACIDS
 
Glycine
  • Simplest amino acid
  • Nonessential
  • Glucogenic
  • Optically inactive amino acid.Q
 
Biosynthesis of GlycineQ
  • Glycine Amino transferase catalyse the synthesis of Glycine from Glyoxylate, Glutamate and AlanineQ
  • From Serine by Serine hydroxymethyltransferase. This is a reversible reaction
zoom view
Fig. 1.26: Conversion of serine to glycine
24
  • By Glycine Synthase System in Invertebrates
  • From Threonine by Threonine Aldolase.
 
Catabolism of Glycine
By Glycine Cleavage systemQ
Present in liver mitochondria.
Glycine cleavage system consists of three enzymes and an H Protein that has covalently attached Dihyrolipoyl moiety. The three enzymes are:
  • Glycine Dehydrogenase
  • Aminomethyltransferase
  • Dihydrolipomide Dehydrogenase
  • The overall reaction is
Glycine + THFA + NAD+CO2 + NH3 + N5, N10 Methenyl THFA + NADH + H+
 
Glycine as Conjugating Agent
  • Conjugation of Bile acid (Glycocholic Acid, Glyco-chenodeoxy Cholic Acid)
  • Conjugation of Benzoic Acid
Glycine + Benzoyl CoA → Benzoyl Glycine (Hippuric Acid)
 
Glycine as Neurotransmitter
  • Both excitatory and inhibitory neurotransmitter.
 
Glycine is the recurring Amino acid present in the Collagen
  • Every third amino acid in Collagen is Glycine.
 
CREATININE
  • Synthesized from 3 Amino Acids (Glycine, Arginine and Methionine Q)
 
Steps of Synthesis of Creatinine
Step I Glycine Arginine Amido Transferase
  • First step in the kidney
  • Guanidino group of Arginine is transferred to Glycine to form Guanidinoacetic Acid.
Step II Guanidinoacetate Methyltransferase
  • Second step in the Liver
  • Creatine is formed
  • S Adenosyl Methionine is the methyl donor
Step III Creatine Kinase
  • Third step in the muscle
  • Creatine phosphate is formed.
Step IV
  • Occur spontaneously
  • Creatinine is formed.
zoom view
Fig. 1.27: Synthesis of creatinine
 
Heme
  • Succinyl CoA + Glycine → Heme
  • In the liver and erythroid precursor cells.
 
Formation of Purine Ring
  • C4, C5, N7 of Purine ring is contributed by Glycine.
Remember glycine do not contribute to Pyrimidine Ring.Q
 
GLUTATHIONEQ
  • Is otherwise called Gamma Glutamyl Cysteinyl Glycine
  • TripeptideQ from three Amino Acids: Glutamic Acid, Cysteine and Glycine
  • PseudopeptideQ
  • Abbrevated as GSH
  • Business part of Glutathione is Sulfhydryl group of Cysteine.
 
Functions of GlutathioneQ
  • Meister's Cycle or Gamma Glutamyl Cycle
    • Absorption of neutral amino acids in the intestine, kidney tubules and brain.
    • 3 mols of ATP utilized for the transport of amino acid.25
  • Free Radical Scavenging
    • Especially in the RBC, hence responsible for RBC membrane integrity.Q
      zoom view
      Fig. 1.28: Free radical scavenging
  • Reduction of MethemoglobinQ
    • Keep the iron in the heme in the ferrous state by reduced glutathione.
  • Conjugation reactions in Phase II Xenobiotic reactions
    • Glutathione S transferase is the enzyme.
  • Acts as coenzyme for some reactions.
 
Primary Hyperoxaluria Type I
  • The most common form of primary hyperoxaluria.
    zoom view
    Fig. 1.29: Biochemical defect in hyperoxaluria
  • It is due to a deficiency of the peroxisomal enzyme alanine-glyoxylate aminotransferase, (expressed only in the liver peroxisomes and requires pyridoxine (vitamin B6) as its cofactor).
  • Protein targeting defect.
 
Primary Hyperoxaluria Type II (Glyceric Aciduria)
  • Due to a deficiency of D-glycerate dehydrogenase (glyoxylate reductase enzyme complex).
 
Secondary Hyperoxaluria
  • Pyridoxine deficiency (cofactor for alanine-glyoxylate aminotransferase)
  • After ingestion of ethylene glycol
  • High doses of vitamin C
  • After administration of the anesthetic agent methoxyflurane (which oxidizes directly to oxalic acid)
  • In patients with inflammatory bowel disease or extensive resection of the bowel (enteric hyperoxaluria).
 
Nonketotic Hyper Glycinemia
  • Due to a defect in the Glycine Cleavage System.
 
ALANINE
  • Simple amino acid
  • Nonessential amino acid
  • Principal glucogenic amino acid.
  • Transports amino group from skeletal muscle.Q
  • Participate in glucose-alanine cycle (Cahill cycle).
 
Biosynthesis of Alanine
  • From Pyruvate by Transamination.
 
SERINE
  • Hydroxyl group containing amino acid
  • Glucogenic amino acid
  • Nonessential amino acid
  • Polar amino acid
 
Biosynthesis of Serine
  • From glycine by serine hydroxymethyl transferase. PLP is a coenzyme in this reaction
  • From glycolytic intermediate 3 Phosphoglycerate.
 
Metabolic Functions of Serine
  • Primary donor of one carbon group26
    zoom view
    Fig. 1.30: Conversion of serine to glycine
  • Serine is used for formation of cysteine
    • Serine + homocysteine cysteine + homoserine
  • For phospholipid synthesis
    • Phosphatidyl serine
  • Serine analogs as drugs
    • Cycloserine: Antituberculous drug
    • Azaserine: Anticancer drug
  • Serine is used for:
    • Ethanolamine Synthesis
    • Choline (Trimethylethanolamine) synthesis
    • Betaine (Trimethylglycine) synthesis
      zoom view
      Fig. 1.31: Synthesis of betaine
  • Serine is the precursor of SelenocysteineQDNB/AIPGMEE
  • Serine used for Glycoprotein Synthesis-O Glycosylation takes place at Serine and Threonine residues
  • Most common sites for Phosphorylation are Serine and Threonine
  • Serine and Palmitoyl CoA are the starting material for the synthesis of Sphingosine, thereby Ceramide
 
SULfUR CONTAINING AMINO ACIDS
They are Methionine and Cysteine
 
Methionine
  • Sulfur Containing Amino Acid
  • Essential Amino Acid
  • Glucogenic Amino Acid.
 
Cysteine
  • Nonessential Amino Acid
  • Glucogenic Amino Acid.
 
The Amino Acids that Decreases Aging
  • Cysteine, hence aging is otherwise called Cysteine deficiency Syndrome
  • Taurine.
 
The Amino Acid that Accelerate Ageing
  • Homocysteine.
 
METABOLISM OF SULfUR CONTAINING AMINO ACIDS
 
Steps of Methionine metabolism
  • Conversion of Methionine to S-Adenosyl Methionine (SAM) and Transmethylation reactions
  • S Adenosyl Methionine to Homocysteine
    zoom view
    Fig. 1.32: Metabolism of sulfur containing amino acid
    27
  • Two fates of Homocysteine:
    1. Synthesis of Cysteine
    2. Resynthesis of Methionine
  • Degradation of Cysteine.
 
Step I Methionine Adenosyl Transferase (MAT)
  • Methionine converted to S-adenosyl Methionine, the principal methyl donor of the body
  • ATP donates the Adenosyl group to methionine
  • 3 Isoenzyme QDNB forms for MAT are MAT-I, MAT-II and MAT-III
  • MAT-I and MAT-III in the liver. MAT-II in the extrahepatic tissue.
 
Step II Fates of Homocysteine
  1. Resynthesis of Methionine
    • By transferring a methyl group to Homocysteine, Methionine is resynthesized
    • N5 Methyl THFA and Vitamin B12 is involved. Folate trap is discussed below.
  2. Synthesis of Cysteine (Trans sulfuration reactions) Cystathionine Beta synthase
    • Homocysteine condenses with Serine to form Cystathionine by removing a H2O by the enzyme Cystathionine Beta Synthase
    • PLP is the coenzyme.
Cystathionase
  • Cystathionine to Cysteine and Homoserine by Cystathionase
  • PLP is the coenzyme
  • By further reactions Homoserine is converted to Propionyl CoA then to Succinyl CoA.
 
Functions of S-Adenosyl Methionine
  • Transmethylation reactions
  • DNA Methylation
  • Polyamine Synthesis.
 
Transmethylation Reactions
Acceptor of methyl group
Methylated compound
Guanidinoacetate
Creatine
Norepinephrine
Epinephrine
Epinephrine
Metanephrine
Ethanolamine
Choline
Carnosine
Anserine
Acetyl Serotonin
Melatonin
 
POLYAMINE SYNTHESIS
Polyamines are organic compounds having multiple amino groups. They are:
  • Cadaverine derived from decarboxylation of Lysine
  • Putrescine derived from decarboxylation of Ornithine
  • Spermidine derived from Ornithine and Methionine
  • Spermine derived from Ornithine and Methionine.
zoom view
Fig. 1.33: Synthesis of polyamines
 
Steps of Polyamine Synthesis
  • Ornithine is decarboxylated to form Putrescine, by the enzyme ornithine decarboxylase. Ornithine decarboxylase is the rate limiting step of Polyamine synthesis
  • S adenosyl Methionine is decarboxylated to form Decarboxylated SAM
  • Decarboxylated SAM donates 3 carbon atom and 1 α amino group to Putrescine to form Spermidine
  • Decarboxylated SAM donates 3 carbon atom and 1 α amino group to Spermidine to form Spermine.
 
Significance of Polyamines
  • They bear multiple positive charges, they associate readily with DNA and RNA
  • Function in cell proliferation and growth
  • Act as growth factors for cultured mammalian cells
  • Stabilize intact cells and membranes and orgenelles
  • Role in carcinogenesis.
28
 
Vitamins in the metabolism of Sulfur containing Amino Acids
  • Three vitamins needed are Vitamin B12, Folic Acid and Vitamin B6
  • Vitamin B12 and Folic Acid for Methionine Synthase reaction.
  • Vitamin B6 for Cystathionine Beta Synthase (Transsulfuration reaction) and Cystathionase.
 
Folate Trap (THFA Starvation)
zoom view
Fig. 1.34: Folate trap (THFA Starvation)
 
Classic Homocystinuria
Most common inborn error of methionine metabolism.
Biochemical defect
  • Due to deficiency of Cystathionine Beta Synthase.
  • Homocysteine is not converted to Cysteine, so there is cysteine deficiency
  • More homocysteine is available for methionine synthesis, so there is hypermethioninemia.
 
Clinical Features
  • Normal at birth.
  • Symptoms during infancy are nonspecific and may include failure to thrive and developmental delay.
  • The diagnosis is usually made after 3 years of age, when subluxation of the ocular lens (ectopia lentis) occurs. This causes severe myopia and iridodonesis (quivering of the iris).
  • Progressive intellectual disability is common.
  • Skeletal abnormalities resembling those of Marfan syndrome tall and thin, with elongated limbs and arachnodactyly scoliosis, pectus excavatum or carinatum, genu valgum, pes cavus, high-arched palate, and crowding of the teeth are commonly seen.
  • These children usually have fair complexions, blue eyes, and a peculiar malar flush.
  • Thromboembolic episodes involving both large and small vessels, especially those of the brain, are common and may occur at any age.
 
Diagnosis
  • Elevations of both methionine and homocystine (or homocysteine) in body fluids are the diagnostic
  • Cystine level is low in the plasma
  • Screening test for Homocystinuria-Cyanide Nitroprusside TestQ in freshly voided urine as homocystine is highly unstable
  • Enzyme analysis in liver biopsy specimen or cultured fibroblasts
  • DNA mutation analysis can be done
  • Prenatal diagnosis by Enzyme assay of cultured amniotic cells or chorionic villi or by DNA analysis.
 
Treatment
  • High doses of vitamin B6 (200–1,000 mg/24 hours) causes dramatic improvement in most patients
  • Some patients do not respond to Vitamin B6, may be due to Folate depletion. For them folic acid (1–5 mg/24 hours) has been added to the treatment regimen
  • Restriction of methionine intake in conjunction with cysteine supplementation is recommended for patients who are unresponsive to vitamin B6
  • Betaine (trimethylglycine) lowers homocysteine levels in body fluids by remethylating homocysteine to methionine
  • Administration of large doses of vitamin C (1 g/day) has improved endothelial function.
29
 
Nonclassic Homocystinuria
Can be due to:
  • Defects in Methylcobalamin formation
  • Deficiency of Methylene tetrahydrofolate Reductase (MTHFR).
Homocystinuria due to defect in Methylcobalamin formation:
  • Methylcobalamin is the cofactor for the enzyme methionine synthase, which catalyzes remethylation of homocysteine to methionine
  • Homocysteine cannot be remethylated to Methionine
  • Homocysteine accumulate
  • Methionine level decreases.
Laboratory findings
  • Megaloblastic anemia: The presence of megaloblastic anemia differentiates Methylcobalamin formation defects from homocystinuria due to methylenetetrahydrofolate reductase deficiency
  • Homocystinuria
  • Hypomethioninemia.
Treatment
Vitamin B12 in the form of hydroxycobalamin (1–2 mg/24 hours) is used to correct the clinical and biochemical findings.
Homocystinuria Caused by Deficiency of Methylenetetrahydrofolate Reductase
Due to Deficiency of Methylenetetrahydrofolate Reductase (MTHFR)
  • This enzyme reduces N5, N10-methylenetetrahydrofolate to form 5-methyltetrahydrofolate
  • N5 Methyl THFA provides the methyl group needed for remethylation of homocysteine to methionine
  • Hence Hypomethionemia
  • Homocystinemia and Homocystinuria
  • Absence of megaloblastic anemia (Unlike Methyl-Cobalamin formation defect).
Treatment
  • Combination of folic acid, vitamin B6, vitamin B12
  • Methionine supplementation (Because Methionine is not resynthesized)
  • Betaine (early treatment with betaine seems to have the most beneficial effect).
 
Cystathioninuria
Cystathionase Deficiency
Mental retardation, anemia, thrombocytopenia.
Cyanide nitroprusside test negative.
 
Cystinuria
  • Included in Garrod's Tetrad (Cystinuria, Albinism, Pentosuria, Alkaptonuria)
  • Defect in Dibasic Amino Acid Transporter
  • Defective reabsorption of Cystine, Ornthine, Lysine and Arginine (Remember-COLA)
  • Cystine, Ornithine, Lysine and Arginine (COLA)Q in urine
  • Cystine Stones in urine
  • Cyanide Nitroprusside Test Positive
  • Treated with ample hydration and alkalinization of urine.
 
Oasthouse Syndrome
  • Malabsorption of Methionine and other Neutral Amino Acid.
 
Primary Hypermethioninemia
  • Due to deficiency of hepatic Methionine Adenosyl Transferase (MAT I and III)
  • MAT II present in other tissues are not defective
  • Peculiar smell of Boiled Cabbage.
 
Cystinosis
  • Lysosomal Storage Disorder
  • Systemic disease caused by a defect in the metabolism of cystine
  • Caused by mutations in the CTNS gene, which encodes a novel protein, cystinosin
  • Cystinosin is a H+ driven lysosomal cystine transporter
  • Results in accumulation of cystine crystals in most of the major organs of the body:
    • Kidney
    • Liver
    • Eye
    • Brain.
Diagnosis
  • Detection of cystine crystals in the cornea
  • Confirmed by measurement of increased leukocyte cystine content.
Treatment
  • Specific therapy is available with cysteamine, which binds to cystine and converts it to cysteine30
  • This facilitates lysosomal transport and decreases tissue cystine
  • Kidney transplantation is a viable option in patients with renal failure.
 
BRANCHED CHAIN AMINO ACIDS
Branched chain amino acid
Metabolic fate
Valine
Glucogenic
Leucine
Ketogenic
Isoleucine
Both Ketogenic and Glucogenic
 
Three Common Steps in the Metabolism of Branched Chain Amino Acids
Reaction
Enzyme
Coenzyme
1. Transamination
Branched Chain Amino Acid Transaminase
PLP
2. Oxidative Decarboxylation
Branched Chain Keto Acid Dehydrogenase
Thiamine Pyrophosphate, FAD, NAD+,
Lipomide and CoA
3. Dehydrogenation
Acyl CoA Dehydrogenase
FAD
 
After the First Three Common Steps
zoom view
 
MAPLE SYRUP URINE DISEASE
Biochemical defect
  • Deficiency of the enzyme Branched Chain Ketoacid Dehydrogenase
  • Defective reaction is Defective Decarboxylation.
Components of Branched Chain Ketoacid dehydrogenase Complex and defective components in MSUDQ
Gene
Component
MSUD types
E1α
Branched Chain α Ketoacid decarboxylase (contains TPP)
Type I A MSUD
E1β
Branched Chain α Ketoacid decarboxylase
Type I B MSUD
E2
Dihydrolipoyl Transacylase (contains Lipomide)
Type II MSUD
E3
Dihydrolipomide Dehydrogenase (Contains FAD)
Type III MSUD
Clinical features
  • Affected infants who are normal at birth develop poor feeding and vomiting in the 1st week of life.
  • Lethargy and coma, convulsions may ensue within a few days
  • Metabolic Acidosis
  • Physical examination reveals hypertonicity and muscular rigidity with severe opisthotonos
  • Periods of hypertonicity may alternate with bouts of flaccidity manifested as repetitive movements of the extremities (boxing and bicycling)
  • The peculiar odor of maple syrup (burnt sugar) found in urine, sweat, and cerumen
  • Mental Retardation.
Lab diagnosis
  • Plasma shows marked elevation of leucine, isoleucine, valine, and alloisoleucine (a stereoisomer of isoleucine not normally found in blood)
  • Urine contains high levels of leucine, isoleucine, and valine and their respective ketoacids
  • Ketoacids are detected by Dinitrophenylhydrazine (DNPH) Test
  • Rothera's Test
  • Enzyme analysis in leukocytes and cultured fibroblast
  • Tandem Mass Spectrometry.
Treatment
Restrict Branched Chain Amino Acid
Give high doses Thiamine.31
 
Isovaleric Aciduria
Biochemical defect
  • Defective Leucine metabolism
  • Defective Enzyme is Isovaleryl CoA Dehydrogenase
  • Characteristic odor of Sweaty FeetQ is present.
 
Intermittent Branched Chain Ketonuria
  • Retains some activity of Branched Chain α Ketoacid decarboxylase.
 
BASIC AMINO ACID
 
Lysine
  • Represented by the letter K
  • Essential Amino Acid
  • Saccharopine is an intermediate in the Lysine Catabolic pathway
  • Amino Acid deficient in Cereals
  • Predominantly Ketogenic.
 
Functions of Lysine
  • Hydroxy Lysine is important in Covalent Cross links in Collagen and Desmosine crosslinks in Elastin
  • ε Amino group of Lysine forms Schiff's bases
  • Lysine along with Methionine (SAM is the methyl donor) are the precursors of Carnitine
  • Bacterial Putrefaction (Decarboxylation) of Lysine forms Cadaverine
  • Histone Proteins are Lysine rich.
zoom view
Fig. 1.35: Metabolism of arginine
 
Arginine
  • Glucogenic
  • Semiessential Amino Acid
  • L Glutamate Semi aldehyde to α Keto Glutarate to Glucogenic pathway.
 
Metabolic Functions of Arginine
  • Nitric Oxide Synthesis
  • Agmantine
  • Arginine splits to Ornithine and Urea. (Terminal step in Urea Cycle)
  • Creatine.
 
Nitric Oxide
  • Uncharged molecule having an unpaired electron, so it is highly reactive, free radical
  • Very short half-life (0.1 seconds)
  • Formerly called Endothelium Derived Relaxing Factor
  • Gaseous molecule
  • Second messenger is cGMP.
 
Functions of Nitric Oxide
  • Potent Vasodilator
  • Involved in Penile erction
  • Neurotransmitter in brain and Peripheral Nervous System
  • Low level of NO involved in Pylorospasm in Congenital Hypertrophic Pyloric Stenosis
  • Inhibit adhesion, activation and aggregation of Platelets.
 
Therapeutic uses of Nitric Oxide
  • Inhalation of Nitric Oxide in the treatment of Pulmonary Hypertension
  • Treatment of Impotence (Sildenafil inhibit cGMP Phosphodiesterase)
  • Glyceryl Nitrite which is converted to Nitric Oxide is used in Angina Pectoris.
 
Synthesis of Nitric Oxide
zoom view
Fig. 1.36: Synthesis of nitric oxide
 
Nitric Oxide Synthase
  • Cytosolic Enzyme
  • Mono oxygenase
Five Redox Cofactors are:
  1. NADPH
  2. FAD
  3. FMN
  4. Heme
  5. Tetrahydrobiopterin
 
Three Major Isoforms of Nitric Oxide Synthase
Subtype
Name
Characteristics
Deficiency leads to
1.
nNOS
First identified in the neurons
Activated by increase in Ca2+
Pyloric Stenosis Aggressive Sexual Behavior32
2.
iNOS
Prominent in macrophages
Independent of elevated Ca2+
More susceptible to certain types of infection
3.
eNOS
First identified in endothelial cells.
Activated by Ca2+
Elevated mean blood pressure.
 
Mechanism of Action of Nitric Oxide
zoom view
 
Agmatine
  • Derived from Arginine by decarboxylation
  • Properties of Neurotransmitter
  • May have Antihypertensive Properties.
 
HISTIDINE
  • Semi essential amino acid
  • Contains Imidazole ring
  • Maximum buffering capacity at physiological pH.
 
Metabolism of Histidine
zoom view
Fig. 1.37: Metabolism of histidine
Important points of the histidine metabolism pathway
  • Urocanate is a derivative of Histidine
  • FIGLU is Formimino Glutamic Acid
  • FIGLU is derived from Histidine
  • In Folic Acid deficiency FIGLU is excreted in Urine.
 
Histidine Load Test
  • To identify Folic Acid deficiency.
  • FIGLU excreted in urine is measured following a Histidine load.
Biologically important compounds derived from Histidine
  • Histamine from histidine by decarboxylation. PLP is a coenzyme
  • Carnosine (Beta Alanyl Histidine)
  • Anserine (Methyl Carnosine)
  • Homocarnosine (Gamma Amino Butyryl Histidine)
  • Ergothionine
Function of Histamine and receptor responsible for its action
Type of receptor
Effect
H1
Smooth muscle contraction. Increased vascular permeability.
H2
Gastric HCl secretion.
H3
Synthesis and release of histamine in the brain.
  • Metabolic error due to deficiency of Histidase is histidinemia.
 
ACIDIC AMINO ACIDS
 
Glutamic Acid (Glutamate)
  • Nonessential Amino Acid
  • Glucogenic Amino Acid
  • Central role in metabolism of Amino Acid
  • Amino group of all Amino Acids are concentrated as GlutamateQ by transamination.
 
Biosynthesis of Glutamate
By reductive amidation of α Ketoglutarate catalyzed by Glutamate dehydrogenase.
zoom view
Fig. 1.38: Biosynthesis of glutamate
33
 
Metabolic Functions of Glutamic Acid
  • Synthesis of N-Acetyl Glutamate
    Positive regulator of Carbamoyl Phosphate synthetase-1 of urea cycle
    Glutamic Acid + Acetyl CoA → N-Acetyl Glutamate + CoASH
  • Synthesis of Glutathoine (Gamma Glutamyl Cysteinyl Glycine)
  • Synthesis of Gamma Amino Butyric Acid (GABA)
    • Glutamic Acid on decarboxylation gives GABA.
    • PLP is the coenzyme.
 
Glutamine
Biosynthesis of Glutamine
Glutamine synthesized from Glutamic Acid by Glutamine Synthetase.
zoom view
Fig. 1.39: Biosynthesis of glutamine
Metabolic functions of glutamine
  • Converts inorganic ammonium ions into the α amino nitrogen of amino acid. This reaction is called first line trapping of Ammonia
  • Carry amino group from Brain and most other tissues
  • N3 and N9 of Purine ring derived from Glutamine.
  • N3 of Pyrimidine is derived from glutamine.
  • Source of NH2 group of Guanine and Cytosine
  • Glutamine is a conjugating agent
  • Source of Ammonia excretion for Kidney, which has a role in renal regulation of acid base balance.
 
Aspartic Acid (Aspartate)
  • Nonesssential
  • Glucogenic amino acid.
 
Synthesis of Aspartate
Transamination of Oxaloacetate forms Aspartate.
 
Functions of Aspartate
  • Contribute its alpha amino group for Urea Synthesis.
  • Contributes to Purine Synthesis
  • Contributes to Pyrimidine Synthesis.
 
Canavan Disease
  • Autosomal recessive disorder
  • More prevalent in individuals of Ashkenazi Jewish descent than in other ethnic groups.
Biochemical defect
  • Deficiency of aspartoacylase, leads to Canavan disease
  • N-Acetylaspartic acid, a derivative of aspartic acid, is synthesized in the brain
  • The exact function of N-acetylaspartic acid is unknown, but it may serve as a reservoir for acetate, which is needed for myelin synthesis
  • Aspartoacylase, cleaves the N-acetyl group from N-acetylaspartic acid.
Characterized by
  • Leukodystrophy
  • Excessive excretion of N-acetylaspartic acid.
Diagnosis
  • Aspartoacylase deficiency can be determined in skin fibroblasts
  • Increased excretion of N-acetylaspartic acid in the urine.
 
Asparagine
 
Synthesis of Asparagine
Aspartate is converted to Asparagine by Asparagine Synthetase.
zoom view
Fig. 1.40: Biosynthesis of asparagine
 
Asparagine Synthetase
  • Asparagine Synthetase is analogous to Glutamine Synthetase
  • In Asparagine Synthetase, Glutamine rather than ammonium ions, provides nitrogen
  • Hence cannot fix ammonia like Glutamine Synthetase.
  • Bacterial Asparagine Synthetase can however, also use ammonium ion.
 
Catabolism of Glutamate, Glutamine, Aspartate and Asparagine
  • Glutamine and Glutamate forms Alpha Keto GlutarateQ
  • Asparagine and Aspartate forms Oxaloacetate.Q
34
zoom view
Fig. 1.41: Catabolism of asparagine
zoom view
Fig. 1.42: Catabolism of glutamine
 
AMINO ACIDS ENTER INTO TCA CYCLE AT DIFFERENT LEVELS
 
To Alpha Ketoglutarate
Arginine, Histidine, Glutamine, Proline to Glutamate. This is transaminated to Alpha Ketoglutarate.
 
To Succinyl CoAQ
  • Valine
  • Isoleucine
  • Methionine
  • Threonine
  • Remember VIM to Succinyl CoA.
 
To FumarateQ
  • Tyrosine
  • Phenylalanine
  • Aspartate.
 
To OxaloacetateQ
Asparagine to Aspartate, which is transaminated to Oxaloacetate.
zoom view
Fig. 1.43: Entry of amino acids to TCA cycle
 
QUICK REVIEW POINTS FOR NATIONAL BOARD PATTERN OF EXAMS
  • Amino acid that absorbs UV light-Tryptophan, Phenylalanine, Tyrosine
  • Amino acid with no asymmetric carbon atom-Glycine
  • Beta Alanine is derived from Uracil and Cytosine
  • Amino acid at isoelectric pH has no net charge
  • Most common amino acid that undergo oxidative deamination is Glutamate
  • Coenzyme for transamination reaction is Pyridoxal Phosphate (PLP)
  • Amino acid that transport ammonia from most organs including the brain is Glutamine35
  • Amino acid that transport ammonia from skeletal muscle is Alanine
  • The nitrogen atoms of Urea are contributed by Ammonia and Aspartate
  • The rate limiting step of Urea Cycle is Carbamoyl Phosphate Synthetase I
  • Most common urea cycle disorder is Hyperammonemia Type II (Ornithine Transcarbamoylase Defect)
  • Polyamines are derived from Ornithine, Methionine and Lysine
  • Amino acid involved in Cahill Cycle is Alanine
  • Amino acid that play an important role during Starvation as a gluconeogenic AA is Alanine
  • Transamination concentrate amino group as Glutamate
  • Precursor of carnitine is Lysine and Methionine
  • Selenocysteine is derived from Serine
  • Glutamic acid is decarboxylated to GABA
  • Glutamic acid is deaminated to Alpha Ketoglutarate
  • Folate trap traps the THFA as its Methyl Derivative.
  • Amino acids that enter TCA Cycle as Succinyl Choline is Valine, Isoleucine and Methionine.
 
Metabolic Disorder and Biochemical Defect
Metabolic disorder
Biochemical defect
Hyperammonemia Type I
Carbamoyl Phosphate Synthetase I
Hyperammonemia Type II
Ornithine Transcarbamoylase
Citrullinemia Type I
Arginino Succinate Synthetase
Citrullinemia Type II
Citrin (Aspartate-Glutamate) Transporter
Arginino Succinic Aciduria
Arginino Succinate Lyase
Argininemia
Argininase
HHH syndrome
ORNT-I defect (Ornithine Permease)
Classic Phenyl Ketonuria
Phenylalanine Hydroxylase
Alkaptonuria
Homogentisate Oxidase
Tyrosinemia Type I
Fumarylaceto Acetate Hydrolase
Tyrosinemia Type II
Tyrosine Transaminase
Tyrosinemia Type III
Para Hydroxyphenylpyruvate hydroxylase/Para hydroxyl Phenylpyruvate-Dioxygenase
Hawkinsinuria
Para Hydroxyphenylpyruvate hydroxylase/Para hydroxylphenylpyruvate Dioxygenase is mutant, so that it catalyzes only partial reaction.
Segawa Syndrome
GTP Cyclohydrolase
Albinism
Tyrosinase
Pheochromocytoma
Excess production of Catecholamines
Carcinoid Syndrome
Excess production of Serotonin
Hartnup's Disease
Defective absorption of Tryptophan and other neutral amino acids from renal tubules and intestines
Primary Hyperoxaluria Type I
Alanine–Glyoxylate Aminotransferase
Primary Hyperoxaluria Type II
D–Glycerate Dehydrogenase/Glyoxylate reductase Enzyme Complex
Nonketotic Hyperglycinemia
Glycine Cleavage System
Classic Homocystinuria
Cystathionine Beta Synthase
Nonclassic Homocystinuria
I. Methylcobalamin formation defect II. Methylene THFA Reductase
Cystathioninuria
Cystathionase
Cystinuria
Defective reabsorption of Cystine, Ornithine, Lysine and Arginine
Oasthouse Syndrome
Malabsorption of Methionine and other neutral amino acids
Type IA MSUD
E1α gene that codes for Branched Chain Keto acid Decarboxylase component of Branched Chain Ketoacid Dehydrogenase Complex
Type IB MSUD
E1β gene that codes for Branched Chain Keto acid Decarboxylase component of Branched Chain Ketoacid Dehydrogenase Complex
Type II MSUD
E2 gene that codes for Dihydrolipoyl Transacylase component of Branched Chain Ketoacid Dehydrogenase Complex
Type IV MSUD
E1α gene that codes Dihydrolipomide Dehydrogenase component of Branched Chain Keto acid Dehydrogenase Complex
Isovaleric Aciduria
Isovaleryl CoA Dehydrogenase
Canavan Disease
N Asparto Acylase
 
Specialized Products from Amino Acids
Amino acid
Metabolic products
Tyrosine
  • Melanin
  • Catecholamines (Epinephrine, Norepinephrine, Dopamine)
  • Thyroxine
Tryptophan
  • Serotonin
  • Melatonin
  • Niacin
Cysteine
  • Cystine
  • Taurine
  • Glutathione
  • Betamercaptoethanolamine
Glycine
  • Purine
  • Heme
  • Glutathione
  • Creatinine
36
Arginine
  • Nitric oxide
  • Arginine
  • Arginine splits to Ornithine and Urea
  • Creatine
Histidine
  • FIGLU
  • Histamine
Glutamate
  • N acetyl Glutamate Glutathione
  • Gamma Amino Butyric Acid
Glutamine
  • N3 and N9 of Purine
  • N3 of Pyrimidine
Aspartate
  • Purine
  • Pyrimidine
  • Urea Synthesis
 
Peculiar Odors in Different Amino Acidurias
Inborn error of Metabolism
Urine odor
Glutaric acidemia (type II)
Sweaty feet, acrid
Hawkinsinuria
Swimming pool
Isovaleric Acidemia
Sweaty feet, acrid
3-Hydroxy-3-methylglutaric aciduria
Cat urine
Maple syrup urine disease
Maple syrup
Hypermethioninemia
Boiled cabbage
Multiple carboxylase deficiency
Tomcat urine
Oasthouse urine disease
Hops-like
Phenylketonuria
Mousey or musty
Trimethylaminuria
Rotting fish
Tyrosinemia
Boiled cabbage, rancid butter
REVIEW QUESTIONS
 
CLASSIFICATION OF AMINO ACIDS
1. Selenocysteine is coded by:   (AIIMS Nov 2015)
  1. UAG
  2. UGA
  3. UAA
  4. GUA
Ans. b. UGA
  • Stop codon UGA codes Selenocysteine
  • Stop codon UAG codes Pyrrolysine
2. All of the following are essential amino acids except: (AIIMS May 2006)
  1. Methionine
  2. Lysine
  3. Alanine
  4. Leucine
Ans. c. Alanine
(Ref: Harper 30/e p282, Table 27-1)
Based on nutritional requirement amino acids classified into:
  • Essential: Those amino acids which cannot be synthesized in the body. Hence these amino acids are to be supplied in the diet.
  • Semiessential: Growing children require them in the food, but not essential in adults.
  • Nonessential: Amino acids which can be synthesized in the body, hence not required in the diet.
Essential (MettVilPhly Read As Met Will Fly)
All the other amino acid
Nonessential
Methionine
Arginine
All the other amino acid
Threonine
Tryptophan
Valine
Isoleucine
Leucine
Phenylalanine
Lysine
3. Polar amino acids is/are: (PGI May    2012)
  1. Serine
  2. Tryptophan
  3. Tyrosine
  4. Valine
  5. Lysine
Ans. a., e. Serine, Lysine
(Ref: Harper 30/e p18, Table 3-2)
Classification of amino acids based on side chain characteristics (polarity)
  • Polar Amino Acids (Hydrophilic):
    • Uncharged amino acids are Serine, Threonine, Glutamine, Asparagine, Cysteine, Glycine Charged Amino Acids are Aspartic Acid, Glutamic Acid, Histidine, Arginine, Lysine.
  • Nonpolar Amino Acid (Hydrophobic)
    • Alanine, Leucine, Isoleucine, Valine, Phenyl Alanine, Tyrosine, Tryptophan, Proline, Methionine.37
4. Nonpolar Amino acids are:   (PGI Nov 2010)
  1. Alanine
  2. Tryptophan
  3. Isoleucine
  4. Lysine
  5. Tyrosine
Ans. a, b, c, e   (Ref: Harper 30/e p18 table 3-2)
5. Hydrophobic amino acids are: (PGI May 2010)
  1. Methionine
  2. Isoleucine
  3. Tyrosine
  4. Alanine
  5. Asparagine
Ans. a, b, c, d (Ref: Harper 30/e p18, table 3-2)
6. Basic amino acids is/are:
  1. Leucine
  2. Arginine
  3. Lysine
  4. Histidine
Ans. b, c, d (Ref: Harper 30/e p17, Table 3-1)
  • Basic amino acids are Histidine, Arginine and Lysine
  • Acidic amino acids are Aspartic Acid (Aspartate), Glutamic Acid (Glutamate)
7. Guanidinium group is associated with:   (PGI June 2009)
  1. Tyrosine
  2. Arginine
  3. Histidine
  4. Lysine
  5. Tryptophan
Ans. b. Arginine
(Ref: Harper 30/e page 19)
 
Special Groups Present in Amino Acids
Amino acid
Special group
Arginine
GuanidiniumQ
Phenylalanine
Benzene
Tyrosine
Phenol
Histidine
ImidazoleQ
Proline
Pyrrolidine
Methionine
Thioether Linkage
Tryptophan
Indole
Cysteine
Thioalcohol (SH)
8. Amino acid produced by adding hydroxyl group to benzene ring chain of phenylalanine:   (Kerala 2011)
  1. Threonine
  2. Histidine
  3. Tyrosine
  4. Serine
Ans. c. Tyrosine   (Ref: Harper 30/e page 19 table 3-2)
  • Special group in phenylalanine is benzene ring
  • Special group in Tyrosine is Phenol ring
  • The enzyme that hydroxylate Phenylalanine to Tyrosine is Phenylalanine Hydroxylase
9. Sulfur containing amino acid is:   (Ker 2009)
  1. Cysteine
  2. Leucine
  3. Arginine
  4. Threonine
Ans. a. Cysteine
  • Sulur containing amino acids are Cysteine and Methionine.
  • The Sulphur of Cysteine is provided by Methionine.
  • Special group in Cysteine is Sulfhydryl group (Thioalcohol (-SH)
  • Special group in Methionine is Thioalcohol (C-S-C)
10. Which of the following is a nonaromatic amino acid with a hydroxyl R-group?   (Kerala 2012)
  1. Phenylalanine
  2. Lysine
  3. Threonine
  4. Methionine
Ans. c. Threonine   (Ref: Harper 30/e p17, Table 3.1)
  • Aromatic amino acid with hydroxyl group-Tyrosine
  • Nonaromatic amino acid with hydroxyl group are Serine and Threonine
11. Which is not an essential amino acid?   (Kerala 2006)
  1. Tryptophan
  2. Threonine
  3. Histidine
  4. Cysteine
Ans. d. Cysteine   (Ref: Harper 30/e p282)
Essential Amino acids are Methionine, Threonine, Tryptophan, Valine, Isoleucine, Leucine, Phenylalanine, Lysine (Mnemonic MeTT VIL PhLy) and Histidine
Semiessential Amino acids is Arginine.
12. Which of the following is not an aromatic amino acid?
  1. Phenylalanine
  2. Tyrosine
  3. Tryptophan
  4. Valine
Ans. d. Valine   (Ref: Harper 30/e p17, Table 3-1)38
Aromatic amino acids are
  • Histidine (with Imidazole ring)
  • Phenyl Alanine (Benzene ring)
  • Tyrosine (Phenol ring)
  • Tryptophan (Indole ring)
13. Which of the following side chains is least polar?   (AI 2009)
  1. Methyl
  2. Carboxyl
  3. Amino
  4. Phosphate
Ans. a. Methyl
14. Which of the following group contains only nonessential amino acid?   (NBE pattern Q)
  1. Acidic Amino Acid
  2. Basic Amino Acid
  3. Aromatic Amino Acid
  4. Branched chain amino Acid
Ans. a. Acidic Amino acid   (Ref: Harper 30/e p282)
  • Group of amino acid that contain only essential amino acid is Branched chain amino acids (Leucine, Isoleucine, Valine)
  • Group of amino acid that contain only nonessential amino acid is Acidic Amino acids, Amide group containing amino acids, Imino acid, Simple amino acids
15. Amide group containing amino acid is:   (NBE Pattern Q)
  1. Glutamate
  2. Glutamic acid
  3. Glutamine
  4. Aspartate
Ans. c. Glutamine
  • Glutamine and Asparagine are Amide group containing amino acids.
  • Aspartate and Glutamate are Acidic amino acid.
16. Semiessential amino acids are:   (PGI 94)
  1. Arginine
  2. Histidine
  3. Glycine
  4. Phenylalanine
Ans. a. Arginine   (Ref: Harper 30/e p282, Table 27-1)
Semiessential Amino acid-Arginine
17. Aminoacyl t-RNA is required for all except:   (AI 2000)
  1. Hydroxyproline
  2. Methionine
  3. Cysteine
  4. Lysine
Ans. a. Hydroxyproline
  • Derived amino acids do not require Aminoacyl tRNA.
  • Among the above options Hydroxyproline is a derived amino acid
 
Derived Amino Acid Seen in ProteinQ
4-Hydroxy Proline
  • Found in Collagen
  • Vitamin C is needed for hydroxylation.
5-Hydroxy Lysine
Methyl lysine
  • Found in Myosin
Gamma carboxy glutamate
  • Found in clotting factors, like Prothrombin that bind Ca2+
  • Vitamin K is needed for Gamma carboxylation.
Cystine
  • Found in proteins with disulphide bond.Q 2014 DNB
  • Two cysteine molecules join to form cystine e.g., Insulin, Immunoglobulin
Desmosine
  • Found in ElastinQ AIIMS Nov 2014
 
Derived Amino Acid Not seen in ProteinQ
Ornithine
Intermediates of Urea Cycle
Arginosuccinate
Citrulline
Homocysteine
Derived from MethionineQ
Homoserine
Product of Cysteine Biosynthesis
Glutamate-γ semialdehyde
Serine Catabolite
 
Properties of Amino Acids
18. Replacing alanine by which amino acid will increase UV absorbance of protein at 280 nm wavelength:   (AIIMS Nov 2008)
  1. Leucine
  2. Proline
  3. Arginine
  4. Tryptophan
Ans. d. Tryptophan   (Ref: Harper 30/e p21, 22)
Amino Acid Absorb UV Light
Amino Acids which absorb 250–290 nm (Maximum at 280 nm) UV light are tryptophan, phenylalanine, tyrosine.
Maximum absorption of UV light by tryptophan.
19. Which of the following proteins cannot be phosphorylated using Protein kinase in prokaryotic organisms?    (AI 2012)
  1. Threonine
  2. Tyrosine
  3. Serine
  4. Asparagine
Ans. d. Asparagine    (Ref: Harper 30/e p93, Chapter 9)39
Protein kinases phosphorylate proteins by catalyzing transfer of the terminal phosphoryl group of ATP to the hydroxyl groups of seryl, threonyl, or tyrosyl residues, forming O-phosphoseryl, O-phosphothreonyl, or O-phosphotyrosyl residues, respectively
  • Commonest site of phosphorylation is Serine and Threonine followed by Tyrosine.
20. Carboxylation of clotting factors by vitamin K is required to be biologically active. Which of the following amino acid is carboxylated?     (AIIMS Nov 2008)
  1. Histidine
  2. Histamine
  3. Glutamate
  4. Aspartate
Ans. c. Glutamate    (Ref: Harper 30/e p717)
  • The Vitamin that act as coenzyme for carboxylation is Biotin
  • The vitamin that act as coenzyme for gamma carboxylation is Vitamin K
  • The Proteins that are gamma carboxylated by Vitamin K are:
    • Factor II (Prothrombin),
    • Factor VII (Proconvertin or Serum Prothrombin conversion Accelerator, SPCA),
    • Factor IX (Antihemophilic factor or Christmas factor),
    • Factor X (Stuart Prower factor),
    • Protein C, Protein S,
    • Osteocalcin, Nephrocalcin
    • Product of gene gas 6
21. Which of the following is/are not optically inactive amino acids?    (PGI May 2014)
  1. Threonine
  2. Tyrosine
  3. Valine
  4. Glycine
  5. Serine
Ans. a, b, c, e.     (Ref: Harper 30/e p19)
  • Glycine is the only optically inactive amino acid
22. Property of photochromisity is seen amongst the following amino acids:    (AI 1997)
  1. Unsaturated amino acid
  2. Aromatic amino acid
  3. Monocarboxylic acid
  4. Dicarboxylic acid
Ans. b. Aromatic amino acid
(Ref: Harper 30/e p21, 22)
Amino Acid Absorb UV Light
Amino Acids which absorb 250–290 nm (Maximum at 280 nm) UV light are tryptophan, phenylalanine, tyrosine.
Maximum absorption of UV light by tryptophan.
23. The property of proteins to absorb ultraviolet rays of light is due to:    (AIIMS June 99)
  1. Peptide bond
  2. Imino group
  3. Disulfide bond
  4. Aromatic amino acid
Ans. d. Aromatic amino acid
(Ref: Harper 30/e p21, 22)
24. All biologically active amino acids are:
  1. L-forms
  2. D-forms
  3. Mostly D-forms
  4. D- and L-forms
Ans. a. L forms    (Refe: Harper 30/e p18)
  • Amino acids mostly exists in L forms
  • Carbohydrates exists in D forms
25. Optically inactive amino acid is:    (AI 99)
  1. Proline
  2. Glycine
  3. Lysine
  4. Leucine
Ans. b. Glycine
  • Only optically inactive amino acid is Glycine
26. Flexibility of protein depends on:   (AI 1994)
  1. Glycine
  2. Tryptophan
  3. Phenylalanine
  4. Histidine
Ans. a. Glycine     (Ref: Harper 30/e p39)
  • Glycine having the smallest R group fit in to small spaces and induces bends in the alpha helix.
  • Glycine is usually present in beta turns.
27. Which amino acid can protonate and deprotonate at neutral pH?     (AIIMS May 95)
  1. Histidine
  2. Leucine
  3. Glycine
  4. Arginine
Ans. a. Histidine40
  • Amino acid which can protonate and deprotonate means those which can act as buffer.
  • Amino acid whose pKa = pH of the medium has maximum buffering capacity.
  • pKa of imidazole group of histidine is 6.5–7.4.
  • At pH = 7, Imidazole group of histidine can act as buffer.
28. Phosphorylation of amino acid by: (PGI June 98)
  1. Serine
  2. Tyrosine
  3. Leucine
  4. Tryptophan
Ans. a. Serine, b. Tyrosine
(Ref: Harper 30/e p93, Chapter 9)
29. Which of the following amino acid is purely Glucogenic?     (NBE Pattern Q)
  1. Valine
  2. Lysine
  3. Alanine
  4. Glycine
Ans. c. Alanine > Valine/Glycine
  • Lysine is both ketogenic and gluco(glyco)genic
  • Glycine, Alanine and Valine are purely Glucogenic.
  • But Alanine is the principal Glucogenic amino acid.
 
GENERAL AMINO ACID METABOLISM
 
Digestion and Absorption of Proteins, Transamination and Transport of Amino Acids
30. Increased alanine during prolonged fasting represents:     (AIIMS Nov 2011)
  1. Increased breakdown of muscle proteins
  2. Impaired renal function
  3. Decreased utilization of amino acid from Gluconeogenesis
  4. Leakage of amino acids from cells due to plasma membrane damage
Ans. a. Increased break down of muscle protein
During prolonged fasting, there is increased gluconeogenesis. Alanine provided by muscle is one of the substrates for gluconeogenesis.
This is called Glucose Alanine Cycle or Cahill Cycle.
So plasma level of Alanine rises in prolonged starvation.
31. Transfer of an amino group from an amino acid to an alpha keto acid is done by:     (AI 2011)
  1. Transaminases
  2. Aminases
  3. Transketolases
  4. Deaminases
Ans. a. Transaminases    (Ref: Harper 30/e p290)
Keypoints transamination
  • Interconvert pair of α amino acids and α Ketoacid.
    • Ketoacid formed by transamination from Alanine is Pyruvate
    • Ketoacid formed by transamination from Aspartate is Oxaloacetate.
    • Ketoacid formed by transamination from Glutamate is α Keto Glutarate
  • Freely reversible.
  • Transmination concentrate α amino group of nitrogen as L-Glutamate.
  • L-Glutamate is the only enzyme that undergo significant amount of oxidative deamination in mammals.
  • Takes place via ping pong mechanism.
  • Takes an important role in biosynthesis of nutritionally nonessential amino acids.
  • Specific for one pair of substrate but nonspecific for other pair of substrates.
  • Pyridoxal Phosphate is the coenzyme
32. The amino acid which serves as a carrier of ammonia from skeletal muscle to liver is:    (AI 2006)
  1. Alanine
  2. Methionine
  3. Arginine
  4. Glutamine
Ans. a. Alanine    (Ref: Lippincott 6/e p253)
  • Transport form of Ammonia from most tissues including brain is Glutamine
  • Transport form of Ammonia from skeletal muscle is Alanine.
33. Glutamine in blood acts as:    (PGI Dec 98)
  1. NH3 transporter
  2. Toxic element
  3. Stored energy
  4. Abnormal metabolite
Ans. a. Ammonia transporter
Transport form of ammonia from brain and most other tissues41
34. Amino acid absorption is by:    (NBE Pattern qn)
  1. Facilitated transport
  2. Passive transport
  3. Active transport
  4. Pinocytosis
Ans. c. Active Transport    (Ref: Harper 30/e p539)
Free amino acids are absorbed across the intestinal mucosa by sodium-dependent active transport. There are several different amino acid transporters, with specificity for the nature of the amino acid side-chain.
Transporters of Amino Acids
  • For Neutral Amino Acids
  • For Basic Amino acids and Cysteine
  • For Imino Acids and Glycine
  • For Acidic Amino Acids
  • For Beta Amino Acids (Beta Alanine)
Meisters Cycle
  • For absorption of Neutral Amino acids from Intestines, Kidney tubules and brain.
  • The main role is played by Glutathione. (GSH)
  • For transport of 1 amino acid and regeneration of GSH 3 ATPs are required.
Disorders associated with Meister's Cycle Oxoprolinuria
  • 5 Oxoprolinase deficiency leads to Oxoprolinuria
 
Disorders Associated with Absorption of Amino acids
Hartnup's Disease
Malabsorption of neutral amino acids, including the essential amino acid tryptophan
SLC6A19, which is the major luminal sodium-dependent neutral amino acid transporter of small intestine and renal tubules, has been identified as the defective protein
Blue Diaper Syndrome or Drummond Syndrome Indicanuria
Tryptophan is specifically malabsorbed and the defect is expressed only in the intestine and not in the kidney. Intestinal bacteria convert the unabsorbed tryptophan to indican, which is responsible for the bluish discoloration of the urine after its hydrolysis and oxidation
Cystinuria
Dibasic amino acids, including cystine, ornithine, lysine, and arginine are taken up by the Na-independent SLC3A1/SLC7A9, in the apical membrane which is defective in cystinuria
Most common disorder associated with Amino acid malabsorption.
Lysinuric Protein Intolerance
(SLC7A7) carrier at the basolateral membrane of the intestinal and renal epithelium is affected, with failure to deliver cytosolic dibasic cationic amino acids into the paracellular space in exchange for Na+ and neutral amino acids.
Oasthouse Urine Disease
(Smith Strang Disease)
A methionine-preferring transporter in the small intestine was suggested to be affected. Cabbage-like odor, containing 2-hydroxybutyric acid, valine, and leucine.
Iminoglycinuria
Malabsorption of proline, hydroxyproline, and glycine due to the proton amino acid transporter SLC36A2 defect
Dicarboxylic Aciduria
Excitatory amino acid carrier SLC1A1 is affected.
Associated with neurologic symptoms such as POLIP (polyneuropathy, ophthalmoplegia, leukoencephalopathy, intestinal pseudo-obstruction
35. Nontoxic form of storage and transportation of ammonia:    (NBE Pattern Q)
  1. Aspartic acid
  2. Glutamic acid
  3. Glutamine
  4. Glutamate
Ans. c. Glutamine
  • Transport form of Ammonia from most tissues is Glutamine.
  • The enzyme responsible is called Glutamine Synthetase.
  • Belong to Ligase class.
  • Require ATP.
 
Urea Cycle
36. Urea cycle enzymes are:   (PGI May 2010)
  1. Glutaminase
  2. Asparginase
  3. Argininosuccinate synthetase
  4. Ornithine transcarbamoylase
  5. Glutamate dehydrogenase
Ans. c. Argininosuccinate synthetase, d. Ornithine transcarbamoylase    (Ref: Harper 30/e p293)
Reactions of Urea Cycle
The first two reaction takes place in the mitochondria. The rest of the reactions takes place in the cytoplasm.
Carbamoyl Phosphate Synthetase–I (CPS-I)
  • Carbamoyl Phosphate is formed from the condensation of CO2, Ammonia and ATP.
  • CPS-I is the rate limiting (pacemaker) enzyme in this pathway42
  • CPS-I is active only in the presence of N-Acetyl Glutamate, an allosteric activator.
  • This step require 2 mols of ATPs.
 
Ornithine Transcarbamoylase (OTC)
Transfer carbamoyl group of Carbamoyl Phosphate to Ornithine forming Citrulline. Subsequent steps takes place in the cytoplasm.
Argininosuccinate Synthetase
  • Links Amino nitrogen of Aspartate to Citrulline and provides second nitrogen of Urea
  • This reaction requires ATP.
  • Two inorganic phosphates are utilized.
Argininosuccinate Lyase
Cleavage of Arginiosuccinate to Arginine and Fumarate.
ArginaseQ
Hydrolytic cleavage of Arginine, releases Urea and reforms Ornithine which reenter into mitochondria
37. Which enzymes are part of urea cycle?    (PGI 2012)
  1. Ornithine Transcarbamoylase
  2. Asparaginase
  3. Glutamate Synthase
  4. Arginosuccinase.
Ans. a. Ornithine Transcarbamoylase, d. Arginosuccinase   (Ref: Harper 30/e p293)
Enzymes of urea cycle and its classes
Enzymes name
Class of enzyme it belongs
Carbamoyl-phosphate synthase I
Class 6 (Ligase)
Ornithine carbamoyl transferase
Class 2 (Transferase)
Argininosuccinate synthase
Class 6 (Ligase)
Argininosuccinate lyase (Arginino-Succinase)
Class 4 (Lyase)
Arginase
Class 3 (Hydrolase)
38. Urea cycle occurs in:    (AI 2011)
  1. Liver
  2. GIT
  3. Spleen
  4. Kidney
Ans. a. Liver
  • Site of urea synthesis in liver mitochondria and cytosol.
  • Derived amino acids which has almost exclusive role in urea cycle are Ornithine, Citrulline, Arginino-succinate.
  • Four amino acids which has no net loss or gain in urea cycle is ornithine, citrulline, arginino succinate, arginine.
39. In which of the following condition there is increased level of ammonia in blood?(Ker 2008)
  1. Ornithine transcarbamoylase deficiency
  2. Galactosemia
  3. Histidinemia
  4. Phenyl ketonuria
Ans. a. Ornitine transcarbamoylase
Increased ammonia in blood is suggestive of a urea cycle disorder. So answer is an enzyme of urea cycle.
 
Hyperammonemia Type II (OTC Deficiency)
  • Most common Urea Cycle disorderQ
  • Disorder with X-linked partially dominant inheritance (All other Urea Cycle Disorders are Autosomal Recessive)
  • Urea cycle disorder with Orotic Aciduria
  • Marked elevations of plasma concentrations of glutamine and alanine with low levels of citrulline and arginine
  • Orotate may precipitate in urine as a pink colored gravel or stones.
40. Urea cycle occurs in:    (Ker 2008)
  1. Cytoplasm
  2. Mitochondria
  3. Both
  4. Endoplasmic reticulum
Ans. c. Both
The pathways that takes place in two compartments are:
  • Heme Synthesis
  • Urea Cycle
  • Gluconeogenesis
41. Which of the following enzymes(s) is/are not involved in Urea Cycle?    (PGI May 2012)
  1. Glutamate Dehydrogenase
  2. Argininosuccinate Synthetase
  3. α Ketoglutarate Dehydrogenase
  4. Isocitrate Dehydrogenase
  5. Fumarase
Ans. a, c, d, e  (Ref: Harper 30/e p276, 277)
  • Glutamate Dehydrogenase-Oxidative deamination
  • Argininosuccinate Synthetase-Urea Cycle
  • Alpha Keto Glutarate Dehydrogenase and Isocitrate Dehydrogenase-TCA Cycle
  • Fumarase-TCA Cycle
43
42. Glutamate dehydrogenase in mitochondria is activated by:   (NBE pattern Q)
  1. ATP
  2. GTP
  3. NADH
  4. ADP
Ans. d. ADP   (Ref: Harper 30/e p291)
  • Glutamate Dehydrogenase (GDH)
  • Liver Glutamate Dehydrogenase (GDH) is allosterically inhibited by ATP, GTP, NADH.
  • Liver Glutamate Dehydrogenase (GDH) is allosterically activated by ADP
  • Reversible reaction but strongly favor Glutamate formation
  • Can use either NAD+ or NADP+.
43. Nitrogen atoms of Urea contributed by:     (NBE pattern Q)
  1. Ammonium and Aspartate
  2. Ammonium and Glutamate
  3. Ammonium and Glycine
  4. Ammonium and Asparagine
Ans. a. Ammonium and Aspartate
(Ref: Harper 30/e p293)
  • First nitrogen by Ammonium ion—by the reaction CPS-I
  • Second nitrogen by Aspartate—by the reaction Argininosuccinate Synthetase
44. A 6-month-old boy admitted with failure to thrive with high glutamine and Uracil in urine Hypoglycemia, high blood ammonia. Treatment given for 2 months. At 8 months again admitted for failure to gain weight. Gastric tube feeding was not tolerated Child became comatose. Parenteral Dextrose given. Child recovered from coma within 24 hours. What is the enzyme defect?    (AIIMS May 2015)
  1. CPS1
  2. Ornitine transcarbamoylase
  3. Arginase
  4. Argininosuccinate Synthetase
Ans. b. Ornithine transcarbamoylase
(Ref: Nelson: Defects in metabolism of amino acids page 672)
 
Urea Cycle Disorders
zoom view
44
In the given case clue to diagnosis are:
  • High glutamine: Usually seen in hyperammonemia. Because Ammonia is the transport form of ammonia from brain and most other tissues. So in hyperammonemia Glutamine level is elevated.
  • Increased uracil in urine can be seen in Ornithine Transcarbamoylase defect because as OTC defective, carbamoyl phosphate in mitochondria spills to cytoplasm. Then it enters into Pyrimidine synthesis. Pyrimidine intermediates and pyrimidines can accumulate. Hence, Uracil in urine.
45. Which of the following is true in relation of urea cycle?    (PGI Dec 05)
  1. First 2 steps in cytoplasm
  2. First 2 steps in mitochondria
  3. Defect of enzyme of any step can cause deficiency disease
  4. Urea is formed by NH3, glutamic acid and CO2
  5. Citrulline is formed by combination of carbamoyl phosphate and L. ornithine
Ans. b. First 2 steps in mitochondria, c. Defect of enzyme of any step can cause deficiency disease e. Citruline is formed by combination of carbomoyl phosphate and L. ornithine
Urea Cycle
  • First two steps in mitochondria, rest three steps in the cytoplasm.
  • Ornithine condenses with Carbamoyl Phosphate to form citrulline by the action of the enzyme OTC.
  • Disorder is associated with all the steps of urea cycle disorders
Urea cycle disorders due to enzyme deficiency
Disorder
Enzyme defective
Hyperammonemia Type I
Carbamoyl Phosphate Synthetase I (CPS-I)
Hyperammonemia type -II
Ornithine Transcarbamoylase (OTC)
Citrullinemia Type I (Classic Citrullinemia)
Argininosuccinate synthetase
Arginosuccinic aciduria
Argininosuccinate lyase
Hyperargininemia
Arginase
Urea Cycle Disorders due to Transporter Defect
Citrullinemia Type II
Citrin (Transport Aspartate and Glutamate) Defect
Hyperammonemia Hyperornithinemia Homocitrullinuria (HHH) Syndrome
Ornithine Transporter Defect
46. A baby presents with refusal to feed, skin lesions, seizures, ketosis, organic acids in urine with normal ammonia; likely diagnosis:    (AI 2001)
  1. Proprionic aciduria
  2. Multiple carboxylase deficiency
  3. Maple syrup urine disease
  4. Urea cycle enzyme deficiency
Ans. b. Multiple Carboxylase deficiency
(Ref: Nelson: Defects in Amino acid metabolism page 650)
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45
47. True about urea cycle:    (PGI May 2015)
  1. Nitrogen of the urea comes from alanine and ammonia
  2. Uses ATP during conversion of argininosuccinate to arginine
  3. On consumption of high amount of protein, excess urea is formed.
  4. Occur mainly in cytoplasm
  5. Synthesis of argininosuccinate consumes energy
Ans. c. On consumption of high amount of protein, excess urea is formed, d. Occur mainly in cytoplasm, e. Synthesis of argininosuccinate consumes energy
  • Nitrogen of urea comes from Ammonia and Aspartate
  • ATP is required for CPS-I and Argininosuccinate Synthetase
  • Out of the 5 reactions, 3 reactions occur in cytoplasm. So occur mainly in the cytoplasm.
  • On consumption of high protein, urea synthesis is increased.
48. All are true regarding urea cycle except:    (PGI Nov 2014)
  1. Urea is formed from ammonia
  2. Rate limiting enzyme is Ornthine transcarbamoylase
  3. Require energy expenditure
  4. Malate is a byproduct of urea cycle
  5. One nitrogen of urea comes from Aspartate
Ans. a. Urea is formed from ammonia, c. Require energy expenditure, e. One nitrogen comes from Aspartate
  • Nitrogen of urea are contributed by Ammonia and Aspartate.
  • 3 ATPs are directly required for urea cycle
  • Rate limiting step is Carbamoyl Phosphate Synthase-I
  • Fumarate is a byproduct of urea cycle.
49. Enzyme involved in nonoxidative deamination is:   (NBE Pattern Q)
  1. L-amino acid Oxidase
  2. Glutamate Dehydrogenase
  3. Glutaminase
  4. Amino acid Dehydrases
Ans. d. Amino acid Dehydrases
 
Some examples of Nonoxidative DeaminationQ NBE pattern
  • Amino acid Dehydrases for amino acids with hydroxyl group (Serine, Threonine)
  • Histidase for histidine
  • Amino acid Desulfhydrases for amino acids with sulfhydryl group, Cysteine and Homocysteine
50. Which of these is a conservative mutation:    (AIIMS Dec 98)
  1. Glutamic acid-glutamine
  2. Histidine-glycine
  3. Alanine-leucine
  4. Arginine-aspartic acid
Ans. c. Alanine-leucine
Conservative mutation means an amino acid replaced by another amino acid of same characteristics.
Glutamic acid: Negatively Charged Polar
Glutamine: Uncharged Polar
Histidine: Positively Charged Polar
Glycine: Uncharged Nonpolar
Alanine-Uncharged Nonpolar
Leucine: Uncharged Nonpolar
Arginine: Positively Charged Polar
Aspartic Acid: Negatively Charged Polar
 
INDIVIDUAL AMINO ACID METABOLISM
 
Aromatic Amino Acids
51. Which is elevated in PLP deficiency?    (NBE Pattern Q)
  1. FIGLU
  2. Xanthurenic acid
  3. Methylmalonic acid
  4. Homocystine
Ans. b. Xanthurenic acid
  • Urinary metabolite in Vitamin B6 deficiency: Xanthurenic acid
  • Urinary Metabolite in Folic Acid Deficiency: Formimino Glutamic acid, Homocystine
  • Urinary metabolite in Vitamin B12 deficiency: Homocystine, Methyl Malonic Acid
52. Dopamine is synthesized from:   (NBE Pattern Q)
  1. Tryptophan
  2. Threonine
  3. Tyrosine
  4. Lysine
Ans. c. Tyrosine
Metabolic products formed from Tyrosine are:
  • Melanin
  • Thyroxine
  • Catecholamines (Dopamine, Epinephrine, Norepinephrine)
46
53. In Phenylketonuria the main aim of first line therapy is:    (AIIMS Nov 2010)
  1. Replacement of the defective enzyme
  2. Replacement of the deficient product
  3. Limiting the substrate for deficient enzyme
  4. Giving the missing amino acid by diet
Ans. c. Limiting substrate for the deficient enzyme
(Ref: Nelson: Defects in metabolism of Amino acids 20/e page 638)
  • The primary goal of therapy is to reduce phenylalanine levels in the plasma and brain.
Treatment of Classical PKU
  • A low–phenylalanine diet
  • Administration of large neutral amino acids (LNAAs) is another approach to diet therapy.
  • Sapropterin dihydrochloride (Kuvan), a synthetic form of BH4, which acts as a cofactor in patients with residual PAH activity, is approved by the FDA to reduce phenylalanine levels in PKU.
Preliminary trials with recombinant phenylalanine ammonia lyase have been encouraging and demonstrated reduced blood levels of phenylalanine during treatment
54. A 40-year-old woman presents with progressive palmoplantar pigmentation X-ray spine shows calcification of IV disk. On adding benedicts reagent to urine, it gives greenish brown precipitate and blue-black supernatant fluid. What is the diagnosis?   (AIIMS Nov 2008)
  1. Phenylketonuria
  2. Alkaptonuria
  3. Tyrosinemia type 2
  4. Argininosuccinic aciduria
Ans. b. Alkaptonuria
(Ref: Nelson: Defects in metabolism of Amino acids 20/e page 642)
Alkaptonuria
  • Autosomal Recessive Disorder is due to a deficiency of Homogentisic Acid Oxidase
  • First inborn error detected.
  • Belongs to Garrod's Tetrad *Alkaptonuria, Albinism, Pentosuria, Cystinuria+
Biochemical defect
Homogentisate Oxidase deficiency leads to accumulation of Homogentisic Acid (Homogentisate) which polymerises to form Alkaptone bodies.
Clinical presentation
  • Normal Life till 3rd or 4th decade.
  • Urine Darkens on standing is the only manifestation in children.
  • In adults Ochronosis: Alkaptone Bodies in Intervertebral Disk, cartilage of nose, pinna etc.
Laboratory Diagnosis
  • Alkalanization increase darkening of urine.
  • Benedicts test positive in urine because homogentisic acid is reducing agent.
  • Ferric Chloride test positive
  • Silver Nitrate Test positive.
  • No Mental Retardation
Treatment
  • New Drug is Nitisinone [NTBC] which inhibit para Hydroxyl Phenyl Pyruvate hydroxylase which prevent the accumulation of homogentisic acid.
  • Symptomatic Treatment
55. Dopamine hydroxylase catalyse:   (Ker 2007)
  1. Dopamine to Norepinephrine
  2. Dopa to Dopamine
  3. Norepinephrine to Epinephrine
  4. Tyrosine to Dopa
Ans. a. Dopamine to Norepinephrine
(Ref: Harper 30/e p320)
Conversion of Tyrosine to Epinephrine involves 4 sequential steps
  1. Ring Hydroxylation
  2. Decarboxylation
  3. Side chain hydroxylation
  4. N-Methylation
56. Type I Tyrosinemia is caused by:   (NBE pattern Question)
  1. Tyrosine Transaminase
  2. Fumaryl Acetoacetate Hydrolase
  3. 4-Hydroxy Phenylpyruvate Hydroxylase
  4. Maleylacetoacetate Isomerase
Ans. b. Fumaryl Acetoacetate Hydrolase
(Ref: Nelson: Defects in metabolism of Amino acids 20/e page 640)
Amino acidurias and enzyme defect
Classic Phenyl Ketonuria
Phenylalanine Hydroxylase
Alkaptonuria
Homogentisate Oxidase
Tyrosinemia Type I
Fumaryl Acetoacetate Hydrolase
Tyrosinemia Type II
Tyrosine Transaminase47
Tyrosinemia Type III
Parahydroxyphenylpyruvate hydroxylase/Parahydroxyl Phenyl Pyruvate Dioxygenase
Hawkinsinuria
Para Hydroxy Phenyl Pyruvate hydroxylase/Parahydroxylphenyl pyruvate dioxygenase is mutant, so that it catalyzes only partial reaction
Segawa Syndrome
GTP Cyclohydrolase
Albinism
Tyrosinase
57. Terminal product of Phenylalanine metabolism is:   (PGI May 2014)
  1. Fumarate
  2. Acetyl CoA
  3. Oxaloacetate
Ans. a. Fumarate, b. Acetyl CoA
(Ref: Harper 30/e p304)
  • Terminal end products of Phenyl Alanine and Tyrosine metabolism is Fumarate, acetate and Acetyl CoA
Amino acid
Terminal end products
Asparagine, Aspartate
Oxaloacetate
Glutamine, Glutamate
α Ketoglutarate
Proline
α Ketoglutarate
Arginine, Ornithine
α Ketoglutarate
Histidine
α Ketoglutarate
Glycine, Serine
CO2, NH3, N5N10 Methylene THFA or Pyruvate
Alanine
Pyruvate
Threonine
Glycine, Acetaldehyde
Methionine
Cysteine, Succinyl CoA
Cysteine
Pyruvate, 3 Mercaptolacetate
Phenylalanine, Tyrosine
Fumarate, Acetyl CoA, Acetate
Tryptophan
Acetyl CoA
Leucine
Acetoacetate, Acetyl - CoA
Isoleucine
Acetyl CoA, Succinyl CoA
Valine
Succinyl CoA, β Aminoisobutyrate
58. Enzyme deficiency in albinism is:
  1. Tyrosinase
  2. Tyrosine hydroxylase
  3. Phenylalanine hydroxylase
  4. Homogentisate oxidase
Ans. a. Tyrosinase
(Ref: Nelson: Defects in metabolism of Amino acids 20/e page 642)
Aminoaciduria
Enzyme deficiency
Albinism
Tyrosinase
Phenyl Ketonuria
Phenylalanine hydroxylase
Alkaptonuria
Homogentisate oxidase
Homocystinuria
Cystathionine Beta Synthase
Maple syrup Urine Disease
Branched Chain Ketoacid Dehydrogenase
59. Mousy body odor is due to:    (JIPMER May 2015)
  1. Phenylalanine
  2. Phenylacetate
  3. Phenylbutazone
  4. Phenylacetylglutamine
Ans. b. Phenylacetate
(Ref: Nelson: Defects in metabolism of Amino acids 20/e page 637, 638)
Clinical Manifestations of PKU
  • The affected infant is normal at birth. Profound mental retardation develops gradually if the infant remains untreated. Cognitive delay may not be evident for the 1st few months.
  • Vomiting, sometimes severe enough to be misdiagnosed as pyloric stenosis, may be an early symptom.
  • The infants are lighter in their complexion than unaffected siblings.
  • Some may have a seborrheic or eczematoid rash, which is usually mild and disappears as the child grows older.
  • These children have an unpleasant odor of phenylacetic acid, which has been described as musty or mousey.
  • Neurologic signs include seizures (≈25%), spasticity, hyperreflexia, and tremors; more than 50% have electroencephalographic abnormalities.
  • Microcephaly, prominent maxillae with widely spaced teeth, enamel hypoplasia, and growth retardation are other common findings in untreated children.
60. The amino acid that can be converted into a vitamin:   (Kerala 91)
  1. Glycine
  2. Tryptophan
  3. Phenyalalanine
  4. Lysine
Ans. b. Tryptophan
  • Tryptophan can be converted to Niacin.
  • The rate limiting enzyme in Niacin synthesis is Quinolinate Phosphoribosyl Transferase (QPRTase)
48
Specialized products of Tryptophan
  • Serotonin (5 Hydroxy Tryptamine)
  • Melatonin
  • Niacin
61. Which of the following amino acids is involved in the synthesis of thyroxine?   (Karnat 97)
  1. Glycine
  2. Methionine
  3. Threonine
  4. Tyrosine
Ans. d. Tyrosine
Specialized products of Tyrosine are Melanin, Thyroxine, Catecholamines (Dopamine, Epinephrine, Norepinephrine)
62. Tyrosinemics are more susceptible to develop:    (AIIMS Feb 97)
  1. Adenocarcinoma colon
  2. Melanoma
  3. Retinoblastoma
  4. Hepatic carcinoma
Ans. d. Hepatic carcinoma
(Ref: Nelson: Defects in metabolism of Amino acids 20/e page 642)
Tyrosinemia Type I (Tyrosinosis, Hereditary Tyrosinemia, Hepatorenal Tyrosinemia) Clinical Manifestations of Tyrosinemia Type I
  • Untreated, the affected infant appears normal at birth and typically presents between 2 and 6 mo of age
  • An acute hepatic crisis commonly heralds the onset of the disease and is usually precipitated by an intercurrent illness that produces a catabolic state. Fever, irritability, vomiting, hemorrhage, hepatomegaly, jaundice, elevated levels of serum transaminases, and hypoglycemia are common. An odor resembling boiled cabbage may be present, due to increased methionine metabolites. Cirrhosis and eventually hepatocellular carcinoma occur with increasing age. Carcinoma is unusual before two year of age.
  • Episodes of acute peripheral neuropathy resembling acute porphyria occur in ≈40% of affected children. These crises, often triggered by a minor infection, are characterized by severe pain, often in the legs, associated with hypertonic posturing of the head and trunk, vomiting, paralytic ileus, and, occasionally, self-induced injuries of the tongue or buccal mucosa.
  • Renal involvement is manifested as a Fanconi-like syndrome with normal anion gap metabolic acidosis, hyperphosphaturia, hypophosphatemia, and vitamin D-resistant rickets. Nephromegaly and nephrocalcinosis may be present on ultrasound examination.
  • Hypertrophic cardiomyopathy and hyperinsulinism are seen in some infants.
63. Metabolites of tryptophan can give rise to:    (PGI June 02)
  1. Diarrhea
  2. Vasoconstriction
  3. Flushing
  4. Can predispose to albinism
  5. Phenylketonuria
Ans. a, b, c. Diarhea, Vasoconstriction, Flushing
Actions of Serotonin (Metabolite of Tryptophan) are:
  • Neurotransmitter in the Brain
  • Mood Elevation
  • GI Motility
  • Temp Regulation
  • Cutaneous flushing due to vasoconstriction
64. Correct combination of Urine odor in various metabolic disorder:   (PGI Nov 2013)
  1. Phenylketonuria: Mousy body odor
  2. Tyrosinemia: Rotten cabbage
  3. Hawkinsinuria: Potato smell
  4. Maple syrup disease: Rotten tomato
  5. Alkaptonuria: Rotten egg
Ans. a. Phenylketonuria: Mousy body odor, b. Tyrosinemia: Rotten cabbage
Peculiar odors in different Amino acidurias
Inborn error of metabolism
Urine odor
Glutaricacidemia (type II)
Sweaty feet, acrid
Hawkinsinuria
Swimming pool
Isovaleric acidemia
Sweaty feet, acrid
3-Hydroxy-3-methylglutaric aciduria
Cat urine
Maple syrup urine disease
Maple syrup
Hypermethioninemia
Boiled cabbage
Multiple carboxylase deficiency
Tomcat urine
Oasthouse urine disease
Hops-like
Phenylketonuria
Mousey or musty
Trimethylaminuria
Rotting fish
Tyrosinemia
Boiled cabbage, rancid butter49
65. Which of the following is true regarding Phenyl Ketonuria?   (PGI nov 2014)
  1. Dietary Phenyl Alanine restriction is used as a treatment
  2. Occur due to deficiency of Phenylalanine Hydroxylase
  3. Occur due to increase activity of phenylalanine hydroxylase
  4. Diet should contain high phenylalanine containing food items
  5. Tyrosine should be supplied in the diet
Ans. a, b, e
  • Phenylketonuria is due to deficiency of Phenyl Alanine Hydroxylase
  • Dietary restriction of Phenylalanine with supplementation of Tyrosine is needed as Tyrosine is a nonessential amino acid synthesized from Phenylalanine by the action of Phenylalanine Hydroxylase.
 
Simple Amino acids
66. Which of the following is true about glycine?   (Ker 2008)
  1. Glycine is an essential amino acid
  2. Sulphur containing at 4th position
  3. Has a guanidine group
  4. Optically inactive
Ans. d. Optically Inactive    (Ref: Harper 30/e p19)
  • Glycine is the only optically inactive amino acid.
  • Sulfur containing amino acids are Cysteine and Methionine
  • Guanidinium group is present in Arginine.
  • Glycine is a nonessential amino acid
67. Which of the following would not act as source of glycine by transamination?   (NBE pattern Question)
  1. Alanine
  2. Aspartate
  3. Glutamate
  4. Glyoxylate
Ans. b. Aspartate   (Ref: Harper 30/e p283)
Biosynthesis of Glycine
  • Glycine Amino Transferase catalyse the synthesis of Glycine from Glyoxylate, Glutamate and AlanineQ
  • From Serine by Serine Hydroxy Methyl Transferase. This is a reversible reaction.
Serine hydroxyl Methyltransferase
zoom view
Fig. 1.44: Conversion of Serine to Glycine
  • By Glycine Synthase System in Invertebrates
  • From Threonine by Threonine Aldolase
68. Glycine cleavage system in liver mitochondria is associated with which enzyme?   (NBE pattern Question)
  1. Glycine Dehydrogenase
  2. Glycine Transaminase
  3. Glycine Decarboxylase
  4. Glycine Dehydratase
Ans. a. Glycine Dehydrogenase
(Ref: Harper 30/e p302)
Glycine Cleavage system consists of three enzymes and an H Protein that has covalently attached Dihydrolipoyl moiety. The three enzymes are:
  1. Glycine Dehydrogenase
  2. Amino methyl Transferase
  3. Dihydrolipomide Dehydrogenase
69. Guanidoacetic acid is formed in……from……   (JIPMER 2000, DNB 98)
  1. Kidney; Arginine + Glycine
  2. Liver; Methionine + Glycine
  3. Liver; Cysteine + Arginine
  4. Muscle; Citrulline + Aspartate
Ans. a. Kidney; Arginine + Glycine
 
Steps of synthesis of Creatinine
Step I Glycine Arginine Amidotransferase
  • First step in the Kidney.
  • Guanidino group of Arginine is transferred to Glycine to form Guanidinoacetic Acid.
Step II Guanidinoacetate Methyltransferase
  • Second step in the Liver
  • Creatine is formed
  • S Adenosyl Methionine is the methyl donor
Step III Creatine Kinase
  • Third step in the Muscle
  • Creatine Phosphate is formed
50
Step IV
  • Occur spontaneously
  • Creatinine is formed.
70. Conversion of glycine to serine requires:   (PGI Dec 02)
  1. Folic acid
  2. Thiamine
  3. Vit C
  4. Fe2+
  5. Pyridoxal phosphate
Ans. a. Folic acid, e. Pyridoxal Phosphate
  • Glycine is converted to Serine by Serine Hydroxy methyl Transferase
  • Coenzymes required are Folic acid, Pyridoxal Phosphate
71. N Methyl Glycine is known as: (NBE Pattern Q)
  1. Ergothionine
  2. Sarcosine
  3. Carnosine
  4. Betaine
Ans. b. Sarcosine
Sarcosine
N Methyl Glycine
Betaine
Trimethylglycine
Choline
Trimethylethanolamine
Ethanolamine
Serine on decarboxylation
Ergothionine
Derivative of Histidine
Betamercaptoethanolamine
Cysteine on decarboxylation
Carnosine
Beta Alanyl Histidine
Anserine
Carnosine on Methylation
Homo Carnosine
GABA + Histidine
Serotonin
5 Hydroxy Tryptamine
72. What is the metabolic defect in Primary Oxaluria Type II?   (NBE Pattern Q)
  1. Glycine cleavage system
  2. Alanine Glyoxalate Amino Transferase
  3. D Glycerate Dehydrogenase
  4. Excess Vitamin C
Ans. c. D Glycerate Dehydrogenase
Primary Hyperoxaluria Type I
  • The most common form of Primary hyperoxaluria.
  • It is due to a deficiency of the peroxisomal enzyme alanine-glyoxylate aminotransferase, (expressed only in the liver peroxisomes and requires pyridoxine (vitamin B6) as its cofactor)
  • Protein targeting defect.
Primary Hyperoxaluria Type II (Glyceric Aciduria)
  • Due to a deficiency of D-glycerate dehydrogenase (glyoxylate reductase enzyme complex)
Secondary Hyperoxaluria
  • Pyridoxine deficiency (cofactor for alanine-glyoxylate aminotransferase)
  • After ingestion of ethylene glycol
  • High doses of vitamin C
  • After administration of the anesthetic agent metho-xyflurane (which oxidizes directly to oxalic acid)
  • In patients with inflammatory bowel disease or extensive resection of the bowel (enteric hyperoxaluria).
Nonketotic Hyperglycemia
  • Due to a defect in the Glycine Cleavage System
73. All are true about glutathione except:   (AIIMS Nov 2008)
  1. It is a tripeptide
  2. It converts hemoglobin to methemoglobin.
  3. It conjugates xenobiotics
  4. It is co-factor of various enzymes
Ans. b. Glutathione   (Ref: Harper 30/e p23)
Functions of glutathione
Glutathione is a tripeptide
  • Free radical scavenging
  • Transport of Amino acid across cell membrane
  • Keep iron in the ferrous sate, so prevent methmoglobin formation.
  • Act as coenzyme for certain enzymes.
Phase II Xenobiotic reaction in Conjugation
 
Sulfur Containing Amino Acids
74. Sulfur of cysteine are not used/utilized in the body for the following process/product:   (PGI May 2015)
  1. Help in the conversion of cyanide to thiocyanate
  2. Thiosulfate formation
  3. Introduction of sulfur in methionine
  4. Disulfide bond formation between two adjacent peptide
Ans. c. Introduction of sulfur in methionine
Methionine is an essential amino acid, so it cannot be synthesized from Cysteine.
  • But Sulfur of cysteine is donated by sulfur of methionine.
  • This is called transsulfuration reaction.
  • PLP is the coenzyme of transrulfuration.51
  • The reaction is catalyzed by Cystathionine beta Synthase and Cystathionase enzyme.
75. Cysteine is abundantly found in:   (Ker 2008)
  1. Keratin
  2. Chondroitin Sulfate
  3. Creatine
  4. Spermine
Ans. a. Keratin
  • The more the disulfide bond harder the keratin is.
  • Cysteine contributes to the disulfide bond.
76. N-acetyl-cysteine replenishes:   (JIPMER 2012)
  1. Glutathione
  2. Glycine
  3. Glutamate
  4. GABA
Ans. a. Glutathione
  • The active part of both Glutathione and N-Acetyl Cysteine is Sulfhydryl group of Cysteine. So N-Acetyl Cysteine replenishes Glutathione.
77. Which of the following is true about Glutathione?   (PGI 2000)
  1. Contain sulfhydral group
  2. Forms met Hb from Hb
  3. It does not detoxify superoxide radicals
  4. Transport aminoacid across cell membrane
  5. Part of enzymes
Ans. a. Contain sulfhydral group, d. Transport aminoacid across cell membrane, e. Part of enzymes
Functions of glutathione
  • Free radical scavenging
  • Transport of Amino acid across cell membrane
  • Keep iron in the ferrous sate, so prevent methmoglobin formation.
  • Act as coenzyme for certain enzymes.
78. In glutathione which amino acid is reducing agent?   (AIIMS June 1997)
  1. Glutamic acid
  2. Glycine
  3. Cysteine
  4. Alanine
Ans. c. Cysteine   (Ref: Harper 30/e p23)
  • Glutathione is a tripeptide (Gamma Glutamic acid + Cysteine + Glycine)
  • Gamma glutamyl cysteinyl Glycine
  • Atypical peptide bond is present between Gamma Glutamic acid and cysteine.
  • -SH (Sulfhydryl) group of cysteine is the active part of glutathione.
 
Acidic and Basic Amino acids
79. Nitric Oxide synthesized from?   (NBE pattern Question)
  1. Arginine
  2. Citrulline
  3. Alanine
  4. Cysteine
Ans. a. Arginine   (Ref: Harper 30/e p661)
Synthesis of Nitric Oxide
zoom view
Fig. 1.45: Synthesis of nitric oxide
80. Histidine load test is used for:   (NBE pattern Question)
  1. Folate Deficiency
  2. Histidine Deficiency
  3. Histamine deficiency
Ans. a. Folate Deficiency   (Ref: Harper 30/e p299)
Important Points of the histidine metabolism pathway
  • Urocanate is a derivative of Histidine.
  • FIGLU is Formiminoglutamic acid
  • FIGLU is derived from Histidine.
  • In Folic Acid deficiency FIGLU is excreted in Urine.
Histidine Load Test
  • To identify Folic Acid Deficiency.
  • FIGLU excreted in urine is measured following a Histidine load.
81. True about Nitric Oxide are all except:   (NBE pattern Question)
  1. Produced from arginine
  2. Nitric Oxide Synthase has three isoforms
  3. Otherwise called Endothelium derived Relaxing Factor
  4. Acts through c AMP
Ans. d. Acts through cAMP   (Ref: Harper 30/e p661)
  • Nitric Oxide acts through cGMP
  • Formed from Arginine
  • iNOS, eNOS, nNOS are three isoforms of Nitric Oxide Synthase
Nitric Oxide
Uncharged molecule having an unpaired electron, so it is highly reactive, free radical.
  • Very short half life (0.1 seconds)52
  • Formerly called Endothelium Derived Relaxing Factor.
  • Gaseous molecule.
  • Second messenger is cGMP.
Functions of Nitric Oxide
  • Potent Vasodilator.
  • Involved in Penile erection
  • Neurotransmitter in brain and Peripheral Nervous System.
  • Low level of NO involved in Pylorospasm in Congenital Hypertrophic Pyloric Stenosis.
  • Inhibit adhesion, activation and aggregation of Platelets.
82. Creatinine is formed from:   (PGI June 06)
  1. Arginine
  2. Lysine
  3. Leucine
  4. Histamine
Ans. a. Arginine   (Ref: Harper 30/e p320)
Three amino acids from which Creatine and creatinine is synthesized are
  1. Glycine
  2. Arginine
  3. Methionine
83. Histidine is converted to Histamine by which reaction:   (NBE Pattern Q)
  1. Carboxylation
  2. Oxidation
  3. Decarboxylation
  4. Amination
Ans. c. Decarboxylation
  • Amino acid is converted to ketoacid by Deamination or transamination.
  • Amino acid converted to biological amines by decarboxylation.
Amino acid
Biologic amines
Histidine
Histamine
Tyrosine
Tyramine
Tryptophan
Tryptamine
Lysine
Cadaverine
Glutamic AcidQ
Gamma Aminobutyric Acid (GABA)
Serine
Ethanolamine
Cysteine
Betamercapto Ethanolamine
 
Branched Chain Amino Acid
84. Branched chain ketoacid decarboxylation is defective in:   (AI 2010)
  1. Maple Syrup urine disease
  2. Hartnup disease
  3. Alkaptonuria
  4. GMI Gangliosidosis
Ans. a. Maple Syrup urine disease
(Ref: Harper 30/e p276-278)
Maple Syrup Urine Disease
Biochemical defect
  • Deficiency of the enzyme Branched Chain Ketoacid Dehydrogenase.
  • Defective reaction is Defective Decarboxylation.
Clinical features
  • Mental Retardation
  • Convulsion
  • Acidosis, Coma
  • Smell of Burnt Sugar [Maple Syrup]
Tests for MSUD
  • Di Nitro Phenyl Hydrazine Test (DNPH Test)
  • Rothera's Test
  • Enzyme Analysis
Treatment
  • Restrict Branched Chain Amino Acid
  • Give high doses Thiamine.
85. MSUD type I A is due to mutation of:   (NBE pattern Question)
  1. E I α
  2. E I β
  3. E 2
  4. E 3
Ans. a. E1 α
(Ref: Nelson Defects in metabolism of Amino acids 20/e page 649; Harper 30/e p311)
  • Types of MSUDQ
    Gene
    Component
    MSUD Types
    E1α
    Branched Chain α Keto acid decarboxylase (contains TPP)
    Type I A MSUD
    E1β
    Branched Chain α Keto acid decarboxylase
    Type I B MSUD
    E2
    Dihydrolipoyl Transacylase (contains Lipomide)
    Type II MSUD
    E3
    Dihydrolipomide Dehydrogenase (Contains FAD)
    Type III MSUD
53
86. Which is not formed from branched chain amino acid?   (Latest Q)
  1. Xanthurenate
  2. Tiglyl CoA
  3. Acetoacetyl CoA and Acetyl CoA
  4. Acetyl CoA and Succinyl CoA
Ans. a. Xanthurenate   (Ref: Harper 30/e p309)
  • Xanthurenate is formed from Tryptophan if Kynureninase enzyme is defective.
87. Treatment used in Isovaleric Aciduria:   (Latest Q)
  1. Arginine
  2. Lysine
  3. Glycine
  4. Methionine
Ans. c. Glycine
(Ref: Nelson's textbook of Pediatrics 20/e chapter 79.6)
Treatment of Isovaleric Acidemia
Hydration
Reversal of the catabolic state (by providing adequate calories orally or intravenously), correction of metabolic acidosis (by infusing sodium bicarbonate)
Removal of the excess isovaleric acid.
By Administering Glycine
Because isovalerylglycine has a high urinary clearance, administration of glycine (250 mg/kg/24 hr) is recommended to enhance formation of isovalerylglycine.
By administering L-Carnitine
L-carnitine (100 mg/kg/24 hr orally) also increases removal of isovaleric acid by forming isovalerylcarnitine, which is excreted in the urine.
88. Which of the following amino acid is excreted in urine in maple syrup urine disease:   (AI 1999)
  1. Tryptophan
  2. Phenyl alanine
  3. Leucine
  4. Arginine
Ans. c. Leucine
Lab Diagnosis of MSUD
  • Plasma shows marked elevation of leucine, isoleucine, valine, and alloisoleucine (a stereoisomer of isoleucine not normally found in blood)
  • Urine contains high levels of leucine, isoleucine, and valine and their respective ketoacids
89. Diseases of branched chain amino acid includes:   (PGI Nov 2013)
  1. Phenylketonuria
  2. Maple Syrup Urine Disease
  3. Tay-Sachs disease
  4. Isovaleric Acidemia
  5. Niemann Pick disease
Ans. b. MSUD, d. Isovaleric Acidemia
  • Phenylketonuria associated with Aromatic Amino acid
  • Tay-Sach's Disease and Niemann Pick disease are Sphingolipidoses
 
Other Amino acids and Entry of Amino Acid to TCA Cycle
90. The nitrogen atom of aspartate formed from asparagines using enzyme asparaginase is from:   (NBE pattern Question)
  1. Ammonium
  2. Glutamate
  3. Glutamine
  4. Alpha Ketoglutarate
Ans. c. Glutamine   (Ref: Harper 30/e p267)
Asparagine Synthetase
  • Asparagine Synthetase is analogous to Glutamine Synthetase
  • In Asparagine Synthetase, Glutamine rather than ammonium ions, provides nitrogen
  • Hence cannot fix ammonia like Glutamine Synthetase
  • Bacterial Asparagine Synthetase can however, also use ammonium ion
91. Oxaloacetate is formed from:   (NBE pattern Question)
  1. Proline
  2. Histidine and Arginine
  3. Glutamate and Glutamine
  4. Aspartate and Asparagine
54
Ans. d. Aspartate and Asparagine
(Ref: Harper 30/e p298)
zoom view
Fig. 1.46: Entry of amino acids into TCA cycle
92. Amino acid responsible for Thioredoxin reductase activation: (NBE pattern Question)
  1. Serine
  2. Selenocysteine
  3. Cysteine
  4. Alanine
Ans. b. Selenocysteine   (Ref: Harper 30/e p16)
Selenocysteine is seen in the active site of following Enzymes and ProteinsQ
  • Thioredoxin reductase
  • Glutathione Peroxidase
  • Iodothyronine Deiodinase
  • Selenoprotein P
93. Oxaloacetate is derived from which amino acids:   (NBE pattern Question)
  1. Glutamine and glutamate
  2. Asparagine and aspartate
  3. Histidine and arginine
  4. Glutamine and Proline
Ans. b. Asparagine and Aspartate
(Ref: Harper 30/e p299)
  • Asparagine and aspartate forms oxaloacetate
  • Glutamine and Glutamate forms alpha Ketoglutarate.
94. Smell of sweaty feet is seen in:   (NBE pattern Q)
  1. MSUD
  2. Phenylketonuria
  3. Homocystinuria
  4. Glutaric Acidemia
Ans. d. Glutaric Acidemia
(Ref: Nelson's textbook of Pediatrics 20/e page 635 table 84.3)
Peculiar odors in different Amino acidurias
Inborn error of metabolism
Urine odor
Glutaric acidemia (type II)
Sweaty feet, acrid
Hawkinsinuria
Swimming pool
Isovaleric Acidemia
Sweaty feet, Acrid
3-Hydroxy-3-methylglutaric aciduria
Cat urine
Maple syrup urine disease
Maple syrup
Hypermethioninemia
Boiled cabbage
Multiple carboxylase deficiency
Tomcat urine
Oasthouse urine disease
Hops-like
Phenylketonuria
Mousey or musty
Trimethylaminuria
Rotting fish
Tyrosinemia
Boiled cabbage, rancid butter
95. During the formation of hydroxyl proline and hydroxyl lysine, the essential factors required is/are:   (PGI Dec 2003)55
  1. Pyridoxal phosphate
  2. Ascorbic acid
  3. Thiamine pyrophosphate
  4. Methylcobalamine
  5. Biotin
Ans. b. Ascorbic acid
  • Hydroxylation of Proline and Lysine
  • Enzyme: Prolyl and Lysyl Hydroxylase
  • Coenzyme is Vitamin C
96. Succinyl CoA is formed by:   (PGI June 1998)
  1. Histidine
  2. Leucine
  3. Valine
  4. Lysine
Ans. c. Valine
  • Succinyl CoA is formed by Valine, Leucine, Methionine
97. In one carbon metabolism Serine loses which carbon atom?   (NBE Pattern Q)
  1. Alpha
  2. Beta
  3. Gamma
  4. Delta
Ans. b. Beta    (Ref: Harper 30/e p284)
zoom view
Enzyme is Serine Hydroxymethyltransferase
Serine loses the beta Carbon atom to form Glycine and Methylene THFA.