biochemistry

1. Prof. Dr. Alam Sher
HOD Biochemistry
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2. AMINO ACIDS
 CLASSIFICATION AND STRUCTURE OF AMINO
ACIDS
 Amino acids can be classified into 3 groups depending
on their reaction in solution.
 A. Neutral
 B. Acidic and
 C. Basic.
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3. A. NEUTRAL AMINO ACIDS:
This is the largest group of amino acids and can be further
subdivided into aliphatic,aromatic, heterocyclic and S-
containing amino acids.
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4. All of the above are simple monoamino monocarboxy-lic acids. The
next from the neutral group of amino acidsare hydroxy amino acids.
Since they contain – OH group in their side chains.
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5. 5

6. 6

7. 7

8. 8

9. 9

10. 10

11. 11

12. 12

13. 13

14. 14

15. NON-STANDARD AMINO ACIDS
A. The compounds similar to basic structure of amino acids but
do not occur in proteins. Examples of some of those are:
 • β-alanine: They found in coenzyme A.
 • Taurine: They found in bile acids
 • Ornithine and citrulline: They are intermediates in urea
cycle
 • Thyroxine (T4) and Tri-iodo Thyronine (T3): Thyroid
hormones synthesised from tyrosine.
 • γ-aminobutyric acid (GABA): A neurotransmitter
produced from glutamic acid.
 • β-amino isobutyric acid: These are end product of
pyrimidine metabolism.
 • δ-aminolaevulinic acid (δ-ALA): These are inter-mediate
in haem synthesis.
 • S-adenosyl methionine (SAM): These are methyl donor
formed from L-methionine
 • 3, 4-dihydroxy phenyl alanine (DOPA): A precursor of
mela nine pigment. 15

16. B. D-AMINO ACIDS:
These are non-standard amino acids—Amino acids
normally isolated from animal and plants are L-amino acids.
But certain D-amino acids are found in bacteria and
antibiotics and in brain tissues of animals.
 • D-glutamic acid and D-Alanine are constituents of
bacterial cell walls.
 • D-amino acids are found in certain antibiotics, e.g.
gramicidin-S, Actinomycin-D.
 • Animal tissues contain L-amino acids which are
deaminated by L-amino acid oxidase.
 But there is also present D-amino acid oxidase the
function of which was not known.
 Now D-amino acids like D-aspartate and D-serine
have been found in brain tissue.
 This explains the existence of D-amino acid oxidase.
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17. FUNCTIONS OF AMINO ACIDS
 Apart from being the monomeric constituents of proteins
and peptides, amino acids serve variety of functions.
 (a) Some amino acids are converted to carbohydrates and
 are called as glucogenic amino acids.
 (b) Specific amino acids give rise to specialised products,
e.g.
 • Tyrosine forms hormones such as thyroid hormones,(T3,
T4), epinephrine and norepinephrine and a pigment
called melanin.
 • Tryptophan can synthesise a vitamin called niacin.
 • Glycine, arginine and methionine synthesise creatine.
 • Glycine and cysteine help in synthesis of Bile salts.
 • Glutamate, cysteine and glycine synthesise glutathione.
 • Histidine changes to histamine on decarboxylation.
 • Serotonin is formed from tryptophan.
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18.  Glycine is used for the synthesis of haem.
 Pyrimidines and purines use several amino acids for their
synthesis such as aspartate and glutamine for pyrimidines
and glycine, aspartic acid.
 (c) Some amino acids such as glycine and cysteine are
used as detoxicants of specific substances.
 (d) Methionine acts as “active” methionine (S-adenosyl-
methionine) and transfers methyl group to various
substances by transmethylation.
 (e) Cystine and methionine are sources of sulphur.,
Glutamine and serine for purin synthesis.
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19.  ESSENTIAL AMINO ACIDS
 Nutritionally, amino acids are of two types: (a) Essential
and
(b) Non-essential. (c) There is also a third group of semi-
essential amino acids.
 (a) Essential amino acids:
 These are the ones which are not synthesised by the body
and must be taken in diet.
 They include valine, leucine, isoleucine, phenylalanine,
threonine, tryptophan, methionine and lysine.
 For remembering the following formula is used—MATT VIL
PHLY.
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20. (B) NON-ESSENTIAL AMINO ACIDS:
 They can be synthesised by the body and may not be
the requisite components of the diet.
 (c) Semi-essential amino acids:
 These are growth promoting factors since they are not
synthesised insufficient quantity during growth.
 They include arginine and histidine.
 They become essential in growing children,pregnancy
and lactating women.
 Occurrence of amino acids:
 All the standard amino acids mentioned above occur in
almost all proteins.
 Cereals are rich in acidic amino acids Asp and Glu
while collagen is rich in basic amino acids and also
proline and hydroxy-proline.
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21. NEW AMINO ACIDS
 In addition to 20 L-amino acids that take part in protein
synthesis, recently two more new amino acids described. They
are:
 A. Selenocysteine - 21st amino acids B. Pyrrolysine - 22nd
amino acid
 A. Selenocysteine It is recently introduced as 21st amino
acid.
 Selenocysteine occurs at the “active site” of several enzymes.
 Examples include:
 • Thioredoxin reductase
 • Glutathione peroxidase which scavenges peroxides,
 • De-iodinase that converts thyroxine to tri-iodothyronine
 • Glycine reductase
 • Selenoprotein P, a glycoprotein containing 10
selenocysteine residues, found in mammalian blood.
 It has an antioxidant function and its concentration falls in
selenium deficiency. 21

22.  Selenocysteine arises co-translationally during its
incorporation into peptides.The UGA anticodon of the
unusual tRNA designated tRNAsec, normally signals STOP.
 The ability of the protein synthesising apparatus to identify a
selenocysteine specific UGA codon involves the
selenocysteine insertion element, a stem-loop structure
in the untranslated region of the m-RNA.
 Selenocysteine-tRNAsec is first charged with serine by the
Ligase that charges tRNAsec.Subsequent replacement of
the serine oxygen by selenium involves seleno-phosphate
formed by Selenophosphate synthetase.
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23. B. Pyrrolysine—the 22nd Amino Acid Recently it has been claimed as
22nd amino acid by some scientists. The STOP codon UAG can code for
pyrrolysine.
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24.  PROPERTIES OF AMINO ACIDS
 A. Isomerism: Two types of isomerism are shown by
amino acids basically due to the presence of asymmetric
carbon atom. Glycine has no asymmetric carbon atom in
its structure hence is optically inactive.
 (a) Stereoisomerism: All amino acids except glycine
exist in D and L isomers. As described in the chapter on
carbo-hydrates it is an absolute configuration.
 In D-amino acids– NH2 group is on the right hand while
in L-amino acids it is oriented to the left. It is the same
orientation of – OH group of the central carbon of
glyceraldehyde.
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25.  Natural proteins of animals and plants generally contain L-
amino acids. D-amino acids occur in bacteria.
 (b) Optical Isomerism: All amino acids except glycine
have asymmetric carbon atom. Few amino acids like
isoleucine and threonine have an additional asymmetric
carbon in their structures.
 Consequently all but glycine exhibit ‘optical’ activities and
rotate the plane of plane polarised light and exist as
dextrorotatory (d) or laevorotatory (l) isomers. Optical
activity depends on the pH and side chain.
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26.  B. AMPHOTERIC NATURE AND ISOELECTRIC pH:
 The -NH2 and -COOH groups of amino acids are ionizable
groups. Further, charged polar side chains of few amino
acids also ionise.
 Depending on the pH of the solution these groups act as
proton donors (acids) or proton acceptors (bases).
 This property is called as amphoteric and therefore amino
acids are called as ampholytes.
 At a specific pH the ami11no acid carries both the charges
in
equal number and exists as dipolar ion or “Zwitterion”.
 At this point the net charge on it is zero, i.e. positive charges
and negative charges on the protein/amino acid molecule
equalizes.
 The pH at which it occurs without any charge on it is called
pI or isoelectric pH. On the acidic side of its pI amino acids
exist as a cation by accepting a proton and on alkaline as
anion by donating a proton.
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27.  C. PHYSICAL PROPERTIES:
 They are colourless, crystalline substances,
more soluble in water than in polar solvents.
 Tyrosine is soluble in hot water.
 They have high melting point usually more
than 200°C.
 They have a high dielectric constant.
 They possess a large dipole moment.
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28.  D. CHEMICAL PROPERTIES
 I. Due to Carboxylic (—COOH) Group
 1. Formation of esters: They can form esters with
alcohols.The COOH group can be esterified with
alcohol.Treatment with Na2CO3 solution in cold releases the
free ester from ester hydrochloride.
 2. Reduction to amino alcohol: This is achieved in pre-
sence of lithium aluminium hydride.
 3. Formation of amines by decarboxylation: Action of
specific amino acid decarboxylases, dry distillation or heating
with Ba(OH)2 or with diphenylamine evolves CO2 from the —
COOH group and changes the amino acid into its amine.
 In vivo, the amino acids can be decarboxylated by the
enzyme decarboxylase and forms the corresponding amines.
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29. 4. FORMATION OF AMIDES:
 Anhydrous NH3 may replace alcohol from its combination
with an amino acid in an amino acid ester so that an amide
of amino acid and a molecule of free alcohol is produced.
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30. II. PROPERTIES DUE TO AMINO (–NH2) GROUP
 1. Salt formation with acids:
 The basic amino group reacts with mineral acids such as
HCl to form salts like hydrochlorides.
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31. 2. FORMATION OF ACYL DERIVATIVES:
 Amino group reacts with acyl anhydride or acyl halides
such as benzoyl chloride and give acyl amino acids like
benzoyl glycine (hippuric acid).
 Incidentally, this is one of the mechanisms of
detoxication in which glycine is used and this also
forms the basis of one of the liver function tests.
3.Oxidation: Potassium permanganate or H2O2
oxidises the NH2 group and converts the amino acid
into imino acid which reacts with water to form NH3 and
α-keto- acid.
4.Reaction with HNO2: Like other primary amines, the
amino acids except proline and hydroxyproline react
with HNO2 (nitrous acid) libering N2 from NH2 group.
 This forms the basis of Van Slyke’s method for
determining -NH2 group (Nitrogen).
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32. 5. REACTION WITH CO2:
 The amino acid anion present in an alkaline solution
may react with CO2 through NH2 group to form a
carbaminoacid anion.
6. Reaction with formaldehyde:Formaldehyde
reacts with the-NH2 group to form a methylene
compound.
 Application: Because of the presence of free basic
amino group in the amino acid molecule its amount
cannot be estimated directly by titration with a standard
alkali.
 On addition of neutral formaldehyde it combines with
the amino group to form either methylene amino acid
or dimethylol amino acid.
 Both these products are strong acids and may be
estimatedby titration with a standard alkali.
 This is known as “Sorensen’s” formol titration method. 32

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