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Chemistry of Amino Acids(AᾹs)
Amino AcidsWhat are amino acids ??Amino acids are organic compounds.
Organic compounds are the substances that are made up of Hydrocarbon (Hydrogen and Carbon) and its derivatives.
Contents• Definition• History• General Structure• Classification• Properties
– Physical– Isomerism– Optical activity and stereoisomerism– Spectroscopic property of amino acid– Iso-electric point– Chemical Reactions– Color reactions
• Biosynthesis• Catabolism• Separation and analysis of amino acid mixture• Functions• References
Definition
The basic monomeric structural unit of proteins organic in nature whose constituent are two functional groups, an amino group (-NH2) which is basic in nature and a carboxylic group (-COOH) which is acidic in nature are called as amino acids.
History
1700
1750
1800
1850
1900
1950
1806, Asparagine was isolated by Pierre-Jean Robiquet and Louis Nicolas Vauquelin from as-paragus juice.
1935, Threonine William Cum-ming Rose
1819, Leucine from cheese
1820, Glycine by Henri Bracon-not from gelatin by acid hydroly-sis
1922, J H Muller and Odake found Methionine
1849, Justus von Leibig found ty-rosine form cheese
1904, Isoleucine by Ehrlich
1901, Valine by Emil Fischer from caesin and trypto-phan by Fredrick Hopkins from pan-creatic digest of caesin
1850, Alalnine by Adolph Strecker from ac-etaldehyde
1900, Proline by Willstatter
1896, Histidine by Albert Kos-sel & Sven Hedin
1889, Lysine by Drechsel isolated it from casein
1886, Arginine by Ernst Schulze from lupine seedling
1865, Serine by Cramer from Silk
1866, Glutamic acid fromwheat gluten by Karl Ritthausen
1883, Cysteine and Glutamine by Schulze from beet juice
1879, Phenylalanine from Lupinus Zuteus seedling by Schulze & Barbeiri
1868, Aspartic acid from legume in plant seed
General Structure of an Amino Acid
Amino group Hydrogen Side-chainCarboxylic group
α Carbon
Classification
A. Based on structure
B. Based on metabolic fate
C. Based on side chain characters
D. Based on nutritional requirement
A. Based on structure1. Aliphatic amino acids
a) Monoamino monocarboxylic acidi. Simple AĀs - Gly, Ala.ii. Branched chain AĀs – Val, Ile, Leu.iii. Hydroxy AĀs – Ser, Thr.iv. Sulphur containing AĀs – Cys, Met.v. AĀs with amide group – Asn, Gln.
b) Monoamino dicarboxylic acid – Asp, Glu.c) Dibasic monocarboxylic acid – Lys, Arg.
2. Aromatic AĀs – Phe, Tyr.3. Heterocyclic AĀs – Trp, His.4. Imino acids – Pro, hydroxyproline5. Derived AĀs
a) Derieved AĀs found in protein – hydroxyproline, hydroxylysineb) Derieved amino acids not seen in proteins – ornithine, citrulline, homocysteine.c) Non alpha AĀs – GABA.
B. Based on metabolic fate
1. Purely Ketogenic
Leu.
Sometimes Lys is also considered
2. Ketogenic & Glucogenic
Lys, Ile, Phe, Tyr, Trp.
3. Purely Glucogenic
All the remaining 14.
C. Based on side chain Characters
1. Hydrophilic or polar AĀs
Charged hydrophilic
-vely charged – Asp, Glu
+vely charged – Lys, Arg, His
Uncharged hydrophilic
Thr, Ser with OH side chain
Asn, Gln with amide side chain
Cys with SH side chain
Gly with hydrogen also considered
2. Hydrophobic or non polar AĀs
Hydrophobic with aliphatic side chain
Val, Ala, Ile, Leu
Hydrophobic with aromatic side chain
Phe, Tyr, Trp
C. Based on side chain Characters
D. Based on nutritional requirement
1. Essential/Indispensable
Ile, Leu, Thr, Lys, Met, Phy, Trp, Val.
2. Semi-essential
His, Arg
3. Non-essential
Remaining 10
alanine valine leucine
isoleucineproline phenylalanine tyrosine
tryptophan methionine serine threonine
cysteineasparagine glutamine
aspartate glutamate
lysine
histidine
PropertiesPhysical– Colourless, crystalline substances– Taste • Sweet: Gly, Ala, Val, Ser, Trp, His & Pro.• Tasteless: Leu.• Bitter: Ile & Arg.• Artificial sweetener: Aspartame contains Asp & Phy.
– Melting point: above 200˚C.– High dielectric constant– Solubility• Water: mostly all.• Alcohol(polar solvent): mostly all.• Benzene(non-polar solvent): none.• Tyr is soluble in hot water.
defined as the product of magnitude of charge & distance of separation between the charges.
• Asymmetric carbon
• Chirality
• Enantiomer
• Stereoisomerism
• Plane polarised light
• Zwitterion
Isomerism• Of the standard α- AĀs, all but Gly can exist in either of two optical
isomers, called L or D AĀs, which are mirror images of each other.
• L-amino acids represent all of the AĀs found in proteins
• D- AĀs are found in some proteins
– as in exotic sea-dwelling organisms such as cone snails,
– are also abundant components of the peptidoglycan cell walls of
bacteria,
– D-serine may act as a neurotransmitter in the brain.
• The isomers are of two types
– Optical isomer
– Stereoisomer
Optical activity and stereochemistry of amino acids– With the exception of Gly, all the 19 other common AĀs
have a uniquely different functional group on the central tetrahedral alpha carbon(α-C)
– The α-C is termed "chiral" to indicate there are four different constituents and that the α-C is asymmetric
– Since the α-C is asymmetric there exists two possible, non-superimposable, mirror images of the amino acids
The D, L system
•When looking down the H-Ca bond towards the α-C there is a
mnemonic to identify the L-enantiomer of Aās
•L-enantiomer, CORN.
•CONR (a silly, meaningless word) for the D-enantiomer.
Stereoisomerism of Amino Acids
Levo-rotatory
Dextro-rotatory
• Enantiomeric molecules have an optical
property known as optical activity - the ability
to rotate the plane of plane polarized light
• Clockwise: dextrorotatoy
• Counterclockwise: levorotatory
• All common AĀs are the L-enantiomer
• However, not all AĀs are Levorotatory, some are actually Dextrorotatory with
regard to their optical activity
• To (attempt) to avoid confusion, the optical activities are given as (+) for
dextrorotatory, and (-) for levorotatory
• L(+)-alanine
• L(-)-serine
Spectroscopic properties of AĀs
• This refers to the ability of AĀs to absorb or emit electromagnetic energy at
different wavelengths (i.e. energies)
• No AĀs absorb light in the visible spectrum (i.e. they are "colorless").
• All AĀs absorb in the IR (longer wavelengths, weaker energy than visible light)
• Some AĀs absorb in the UV spectrum (shorter wavelengths, higher energy
than visible light)
– Absorption occurs as electrons rise to higher energy states
– Electrons in aromatic ring structures absorb in the UV. spectrum. Such
structures comprise the side chains of Trp, Tyr & Phy.
Isoelectric point
• Isoelectric point (pI) is the pH at which a particular molecule or surface carries no
net electrical charge or the negative(-ve) and positive(+ve) charges are equal.
• Zwitterions contain both +ve and -ve charges depending on the functional group.
• Net charge on the molecule is affected by pH of their surrounding & can become
more +vely or -vely charged d/t loss or gain of protons (H+).
Calculating pI values
• For an AĀs with only one amine and one carboxyl group, the pI can be calculated
from the mean of the pKas of this molecule.
Glycine has two ionizable groups: a COOH group and NH2 group, with pKa values of 2.34 and 9.6 respectively.pI =(2.34+9.6)/2 = 5.97
• For simple AĀs such as Ala, the pI is an average of the pKa's
of the carboxyl (2.34) and ammonium (9.69) groups.
• Thus, the pI for Ala is calculated to be: (2.34 + 9.69)/2 = 6.02.
• In the case of Asp, the similar acids are the alpha-carboxyl
function (pKa = 2.1) and the side-chain carboxyl function (pKa
= 3.9), so pI = (2.1 + 3.9)/2 = 3.0.
• For Arg, the similar acids are the guanidinium species on the
side-chain (pKa = 12.5) and the alpha-ammonium function
(pKa = 9.0), so the calculated pI = (12.5 + 9.0)/2 = 10.75.
Chemical ReactionsA. Reactions due to –COOH group1. Decarboxylation. • Histidine Histamine +CO2• Tyrosine Tyramine + CO2• Lysine Cadavarine + CO2
2. Formation of amides
• -COOH group of dicarboxylic AĀs can combine with ammonia to from the
corresponding amide.
• Aspartic acid + NH3 Asaparagine
3. Reduction to amino alcohol
• Achieved in presence of lithium aluminium hydride
4. Formations of esters
• Can form esters with alcohols
• The –COOH group can be esterfied with alcohol
• Treatment with Na2CO3 solution in cold releases free ester from ester
hydrochloride.
B. Reactions due to –NH2 group1. Transamination• α amino group of AĀ can be transferred to α keto acid to form
new AĀ and α keto acid.• Important reaction in the synthesis of non essential AĀ.
amino acid α-keto acid Amino acid α-keto acid
Fig: Oxidative deamination
2. Oxidative deamination• α amino group is removed from the AĀ to
form corresponding keto acid and ammonia.• In body glutamic acid is the most common AĀ
to undergo oxidative deamination
3. Formation of carbamino compound
• Carbondioxide adds to α amino group of AĀs to form
carbamino compound.
• Occurs at alkaline pH
• Serves as the mechanism for transport of CO2 from tissues to
lungs by Hb.
C. Reactions due to side chain1. Transmethylation• The methyl group of Met, after activation, may be transferred to
an acceptor which becomes methylated• Met + acceptor methylated acceptor + homocystiene
2. Ester formation by OH group• The hydroxy AĀs can form ester with phosphoric acid• Ser & Thr are involved in the formation of phosphoprotein• Similarly, these hydroxl group can form O-glycosidic bonds
with carbohydrate residues to form glycoprotein.
3. Reaction of the amide group• The amide group of Gln & Asn can form N-glycosidic bond
with with carbohydrate residues to form glycoproteins.
4. Reaction of SH group• Cys has a sulfhydryl(SH) group & it can form a disulphide
bond (S-S)with another Cys residue• The two Cys residue can connect two polypeptide chain by
the formation of interchain disulphide bonds & links.• The dimer formed by the two Cys residue is called cystine or
Dicysteine.
D. Peptide bond formation– Mistakenly called amino bond– covalent bond– formed b/w 2 molecules when the carboxyl group of
one molecule reacts with the amino group of the another molecule, releasing a molecule of H2O.
– resulting CO-NH bond is the peptide bond, & resulting mol is an amide.
– peptide bond c/b broken down by hydrolysis – peptide bonds formed within proteins have tendency to
break when subjected to the +nce of H2O (metastable bonds)
Peptide bond Elimination of water
E. Property due to both –COOH group and –NH2 group• Formation of chelated co-ordination complexes with certain
heavy metals and other ions• These include Cu++, Co++, Mn++ & Ca++.• O=C-O -O-C=O
Ca++
H2C-NH2 NH2-CH2
• chelates are non ionic –used to remove calcium from bones and teeth
Color reaction of AᾹs• Ninhydrin reaction– Adopted for qualitative & quantitative estimation– Used for detection of AᾹs in chromatography– AᾹs + 2 mols. Of Ninhydrin aldehyde with 1 C atom less +
color complex– Color complex: pink/ purple/ blue (c/a Ruhemann’s purple)– Pro, hydroxy-Pro – yellow– Gln, Asn(AᾹs with amide group) – brown
• Xanthoproteic test– Nitration rxn undergone by concņ HNO3
– Rings in Phe, Tyr & Trp– End product yellow, intensified by alkaline medium– Rxn causes the yellow stain in skin by HNO3
• Millon’s test– Phenol group of tyrosine + HgSO4
H2SO4+NaNO3
red color mercuric phenolate– HgNO3/Hg(NO3)2 in HNO3 c/b used– Cl- interferes with the rxn so not suitable for tyrosine in
urine samples– Tapoica(deficient in Phe & Tyr) give –ve Millon’s &
Xanthoproteic test• Sakaguchi’s test for Arg:– Arg + α-napthol + alk. Hypobromite bright red
color– This is d/t guanidium group
• Aldehyde test for Trp:– Hopkins-Cole test:
• Trp + glyoxylic acid (mix)• Mix layered over H2SO4
• Violet ring at interface shows the +nce of indole ring– Acree-Rosenheim rxn:
• Formaldehyde & HgSO4 is used
– Ehrlich’s rxn:• Para-dimethyl-amino-benzaldehyde & strong HCl• Gives dark blue color• Gelatin with limited Trp content do not give this test
• Pauly’s test for His/Tyr:– Diazo-benzene sulfonic acid + imidazole group of His
alkaline condition
Diazotised product (cherry red color)– Gives orange red color with phenol
• Sulphur test for Cys:
– Cys boiled with strong alkali: organic S splits & forms
Na2S, which on addition of Pb-acetate produces
PbS( black ppt)
– Met doesn’t give this test as S in Met is in thio-ester
linkage which is difficult to break
Biosynthesis
• Nitrogen is first assimilated into organic compounds in the
form of glutamate, formed from alpha-ketoglutarate and
ammonia in the mitochondrion.
• In order to form other AĀs, transaminase is used to move
the amino group to another alpha-keto carboxylic acid.
• Eg, aspartate aminotransferase converts glutamate and
oxaloacetate to alpha-ketoglutarate and aspartate.
• Nonstandard AĀs are usually formed through
modifications to standard AĀs.
• Eg, Homocysteine is formed through the transsulfuration
pathway or by the demethylation of methionine via the
intermediate metabolite S-adenosyl methionine.
• Hydroxyproline is made by a posttranslational modification
of proline.
• Microorganisms and plants can synthesize many
uncommon AĀs.
Catabolism
• AĀs can be:
– Glucogenic
– Ketogenic
– Both glucogenic and ketogenic
• Degradation of AĀs often involve deamination by moving
its amino group to alpha-ketoglutarate, forming glutamate.
• This process involves transaminases, often the same as
those used in amination during synthesis.
• In many vertebrates, the amino group is then removed
through the urea cycle and is excreted in the form of urea.
Separation & analysis of AᾹs mixtures
The 20 common AĀs differ from one another in
several important ways. Here are just two:
• Mass
• Isoelectric point
• In looking at the isoelectric point of the different AĀs it
seems that they will have different partial charges at a
given pH.
• Eg, at pH 6.0 some will be -vely charged, and some +vely
charged.
• For those that are -vely charged, some will be slightly -ve,
and others strongly -ve. Similarly, for those that are +vely
charged, some will be slightly +ve, and others strongly +ve
• The charge differences of the AĀs means that they will
have different affinities for other cationic or anionic
charges
Ion Exchange Chromatography :• Basis • If the immobile surface was coated with anions, then the
chromatography would be termed "cation exchange" chromatography (and cations would selectively bind and be removed from the solution flowing through).
• Strength of binding can be affected by pH & salt
concn of the buffer. The ionic species "stuck" to the
column can be removed & collected by changing
one of these conditions.
• We could lower the pH of the buffer & protonate anions,
this would eliminate their electrostatic attraction to the
immobilized cation surface.
• Or, we could ↑se the salt concentration of the buffer, the
anions in the salt would "compete off" bound anions on
the cation surface.
Amino acid 3 & 1 letter abbvtn
Mol. weight
Molecular formula
Melting point (◦C)
Properties
Leucine Leu/L 131 C6H13NO2 293 Production of GH
Tyrosine Tyr/Y 181 C9H11NO3 290 ↑ses NTs, DOPA & NEProduction of T3,T4,TSH
Phenylalanine Phe/F 165 C9H11NO2 273 Formation of Ep
Arginine Arg/R 174 C6H14N4O2
223 Precursor of nitric oxide
Lysine Lys/K 146 C5H14N2O2
210 Treatment of HSV
Histidine His/H
155 C6H9N3O2
285 Released in allergic rxn
Valine Val/V 117 C5H11NO2
315 Important in smooth nervous functioning
Tryptophan Trp/W
182 C11h12N2O2
283 Production of serotonin
Isoleucine Ile/I 131 C6H13NO2
287 Isomer of leucine
Methionine Met/M
149 C5H11NO2S
284 Helps reduce the estrogen loadprevents Ca
Amino acid
3 & 1 letter abbvtn
Molecular weight
Molecular formula
Melting point
Properties
Threonine Thr/T 119 C4H9NO3 256 Elevates symptoms of multiple sclerosis
Proline Pro/P 115 C5H9NO2 228 Diminishes arteriosclerosis
Glutamine Gln/Q 146 C5H10N2O3
185 Protects GI liningReleases cortisolNeurotoxic effect & cancer prevention
Cysteine Cys/C 121 C3H7NO2S
220 Produces GSH & TaurineRecovery of hair & nail ts.
Aspartic acid
Asp/D 133 C4H7NO4 270 Participates in ornithine cycleImp in function of RNA/DNA
Glutamic acid
Glu/E
147 C5H9NO4
205 Supports brain functionActs as NTs
Serine Ser/S
105 C3H7NO3
222 Production of AbsAbsorption of creatine
Alanine Ala/A
63 C3H7NO2
315 Helps treat benign prostrate hyperplasia
Glycine Gly/G
57 C2H5NO2
233 Protection against cancer by antioxidants⅓ of collagen are glycine
Asparagines
Asn/N
132 C4H8N2O3
235 Biosynthesis of glycoproteins
Selenocysteine :
• The 21st amino acid
• Abbreviated as Sec or U
• +nt in enzymes (eg glutathione peroxidases, tetraiodothyronine 5'
deiodinases, glycine reductases)
• has a structure similar to that of cysteine, but with an atom of
selenium taking the place of the usual sulfur, forming a selenol group.
• Proteins contain one or more selenocysteine residues are called
selenoproteins
• encoded in a special way by UGA codon, which is normally a stop
codon.
Pyrrolysine:
• abbreviated as Pyl or O
• is a naturally occurring, genetically coded amino acid used by
some methanogenic archaea.
• It is similar to lysine, but with an added pyrroline ring linked
to the end of the lysine side chain.
• Produced by a specific tRNA and aminoacyl tRNA synthetase,
it forms part of an unusual genetic cod
• is considered the 22nd proteinogenic amino acid.
• encoded in mRNA by the UAG codon
Functions • Over 300 AĀs +nt & only 22 found in human body.• Tyr forms hormones such as T3, T4, TSH, Ep, NE &
pigment melanin• Trp can synthesise Niacin• Gly, Arg & Met can synthesise creatine• Gly & Cys– helps in synthesis of bile salts– Used as detoxicants
• Glu, Cys & Gly synthesise glutathione
• His changes to histamine on decarboxylation
• Serotonin is formed from Trp
• Gly is used in synthesis of heme
• Met acts as active methionine & helps in transmethylation
• Cys & Met are sources of sulphur
• Asp & Gln for pyramidine synthesis
• Asn & Glu for purine synthesis
References:1. Biochemistry by DM Vasudevan,Sreekumari S, 4th edition.
2. Tietz Fundamentals of Clinical Chemistry, 6th edition by Carl A. Burtis,
Edward R. Ashwood, and David E. Bruns, editors. St Louis.
3. Devlin's Textbook of Biochemistry,4th Edition by Thomas M Devlin.
4. Textbook of biochemistry by Satyanarayana, 4th edition.
5. Garrett & Grisham, Biochemistry, 4th edition.
6. Textbook Of Medical Biochemistry, Jaypee, Mn Chatterjee, Rana Shinde.
7. Biochemistry by Pankaja Naik, Pankaja, Ph.D. Jaypee, 3rd edition.
8. World wide web.
To hold, as it were the mirror up to nature.-William Shakespeare
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