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PROTEIN CHEMISTRY - I
By Dr ANURAG YADAVModerator Dr ARUN KUMAR K
Content :
Definition of amino acids
Definition of peptide bond
General structure of amino acids
Numbering of amino acids
Nomenclature of amino acids.
Classification of amino acids.
Properties of amino acids.
Biological importance of amino acid
derivatives.
OVERVIEW:
Proteins are most abundant & functionally
diverse molecule in living system.
Virtually every life process
depends on this class of molecules.
Enzymes & polypeptide hormones direct &
regulate body metabolism.
In bone, protein collagen forms a frame work
for deposition of salts.
Immunoglobulin's fight against infectious
bacteria & viruses
DEFINITION Amino acids are group of organic compounds
containing two functional groups – amino and carboxyl.
PEPTIDE BOND
Is chemical bond formed between the α-carboxyl groups and α-amino group of next amino acid.
It’s the primary linkage of all protein structures.
NON STANDARD AMINO ACIDS:
Amino acids can b classed as standard amino acids and non standard amino acids.
Of 300 amino acids human body codes 20 amino acids.
These although never incorporated into structure of protein , but play several biological role.
These include :
D-amino acids: bact cell wall, antibiotics
Non-protein amino acids: taurine,homocysteine.etc.,
Amino acid derivatives: GABA, DOPA, hydroxy proline & hydroxy lysine.
AMINO ACIDS
They are monomer unit of proteins
All major structural and functional aspect of body
are carried out by the proteins
20 amino acids are seen in humans.
Most of amino acids are in α-amino acids except
proline
General structure
NUMBERING OF AMINO ACID:
ABBREVIATIONS & SYMBOLS FOR AMINO ACIDS
a) Unique letters first: if only one amino acid begins with particular letter , than letter is used as symbol.(I=Isoleucine).
b) Most commonly occurring Amino Acid have priority if more than one amino acid begin with particular letter & it receive that letter as symbol (Glycine>Glutamate; so G=Glycine.
c) Similar sounding names : F-Phenylalanine.W-tryptophan.
d) Letter close to initial letter: is assigned as symbol which is close to first letter as close .
Eg: k- lysine
CLASSIFICATION OF AMINO ACIDS:
Based on structure
Based on side chain
Based on metabolic fate
Based on nutritional requirement
BASED ON STRUCTURE:
Aliphatic amino acids.
Aromatic amino acids.
Heterocyclic amino acids.
Imino acids.
Derived amino acids.
ALIPHATIC AMINO ACIDS:
Monoamino monocarboxylic acids
Monoamino dicarboxylic acids
Dibasic monocarboxylic acids
Simple amino acid: Glycine. Alanine.
Branched chain amino acids: Valine. Leucine. Isoleucine.
Hydroxyamino acids: Serine.
Threonine.
Sulfur containing amino acids: Cysteine.
methionine.
Amino acid with Amide group: Glutamine. Asparagine.
Monoamino dicarboxylic acids: Aspartic acid. Glutamic acid.
Dibasic monocarboxylic acids: Lysine. Arginine.
AROMATIC AMINO ACIDS:
Phenylalanine, Tyrosine.
HETEROCYCLIC AMINO ACIDS:
Tryptophan
Histidine
IMINO ACID: Proline.
Tryptophan(Trp)(W) with indole group
Derived amino acids :
• Derived amino acid found in proteins:
Hydroxyproline
• Derived amino acid not found in proteins:
Ornithine and citrulline.
• Non alpha amino acids: GABA, βalanine.
SPECIAL GROUPS IN AMINO ACIDS:
Arginine Guanidinium group
Phenylalanine Benzene group
Tyrosine Phenol group
Tryptophan Indole group
Histidine Imidazole group
Proline Pyrrolidine group
BASED ON SIDE CHAIN:
Amino acids having Non-polar side chain:
Has an Non-polar side chain that doesnot gain/lose proton/particiate in hydrogen/ionic bond.
They are usually hydrophobic.
LOCATION: The side chain tends to cluster
together in interior of protein & this phenomenon is called as hydrophobic effect.
Eg: Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan.
Amino acids with uncharged/Non-ionic polar:
These are with ZERO net charge at neutral pH .
These amino acids are hydrophilic. eg: Glycine, Serine, Threonine & Asparagine.
Amino acids having charged/Ionic polar side chain:
a)Acidic amino acid: they are negatively charge on R group. Eg: Aspartic acid.
Glutamic acid.
b) Basic amino acids: they have positive charge on R group. Eg: Lysine.
Argenine. Histidine.
BASED ON METABOLIC FATE:
a) Purely ketogenic: converted to ketone bodies (fat can be synthesized from these amino acids). Eg:Leucine
b) Both ketogenic & glucogenic: Lysine, isoleucine, Phenylalanine, Tyrosine, Tryptophan are partially ketogenic & glucogenic.
c) Purely glucogenic: all remaining 14 amino acids are glucogenic as they enter only into the glucogenic pathway.
BASED ON NUTRITIONAL REQUIREMENT:
Essential/indispensable
Cannot be synthesized by
the body.
Needed to be supplied in
diet.
Phenylalanine, Valine,
Threonine, Trptophan,
lsoleucine, Methionine,
Leusine, Lysine
Non-essential
they can be synthesized
by body & need not to be
supplemented.
Alanine, Aspargine,
Aspartate, Glutamate,
Glutamine, Tyrosine,
Serine, Proline, Glycine,
Cysteine.
Semi-essential amino acids: they are synthesized
by the adults , but the growing children need to be
supplemented in food . They
are :Arginine Histidine.
Conditional essential amino acids: when person
suffers from chronic illness he lose ability to
manufacture enough Non-essential amino acids &
hence need to be supplemented.
- Arginine, Glycine, Cysteine, Tyrosine, Proline,
Glutamine & Taurine.
SELENOCYSTEINE- 21ST AMINO ACID
21st amino acid
Derivative of serine
Structure similar to cysteine,
but with an atom of
selenium(SeH) taking place of
sulphadryl (SH).
Stop codon: UGA
It’s present in active site of
several enzymes like
glutathione peroxidase.
PYRROLYSINE:
22nd amino acid.
• lysine derivative
encoded by UAG codon
• Used by some
prokaryotes.
• Present in methyl
transferase enzyme of
bacteria.
PROPERTIES OF AMINO ACIDS:
Physical properties :
They are colourless.
Taste varies( glycine-sweet, leucine-tasteless,
arginine-bitter).
Soluble in water .
Melting point is higher >200°c.
Optical activity.
Ampholyte & Isoelectric point.
OPTICAL ACTIVITY:
All amino acids have
asymmetric carbon atom
hence show optical
isomers.
Except glycine.
The mirror image are
produced with reference
to α-carbon atom as D &
L isomers.
D & L ISOMERS
L amino acid occur in nature & therefore called as Natural amino acid
D-amino acids are found in antibiotics & bacterial cell wall.
AMPHOTERIC NATURE & ISOELECTRIC POINT
At physiological pH amino acids exists as ions.
They act as ampholyte/ zwitter ion in solution
depending on pH of the medium.
In acidic medium acts as cations & in alkaline
medium as anion.
All groups are ionized but cancel eachother
At this particular pH the molecule carry no net charge is known as Isolectric point & these are called zwitter ions.
hence there will be no mobility in an electrical field.
Solubility & buffering capacity will be minimum.
TITRATION CURVE FOR AMINO ACID
pI= pK1 + pK2
2
In case of amino acid having more than two
ionizable groups, correspondingly there will
be more pK values , eg: aspartic acid
Features of a molecule at iso-electric
point:
molecule minimally soluble & maximally
precipitated.
Viscosity of substance is minimum.
Buffering capacity is at its minimum.
The conductivity & osmotic pressure are at
minimum.
Molecule is electrically neutral.
CHEMICAL REACTIONS
Due to carboxyl group:1. amino acids form salts (COONa) with bases
& ester (-COOR’ ) with alcohol.
2. Decarboxylation: form corresponding amine.
1. Histidine histamine + CO2
2. Tyrosine tyramine + CO2
3. Tryptophan tryptamine + CO2
4. Lysine cadaverine + CO2
5. Glutamic acid GABA + CO2
Reactions with ammonia: the carboxyl
group of dicarboxylic AA other than α-
carboxyl combine with ammonia to form
corresponding amide.
Aspartic acid +NH3 =
Asparagine. glutamic acid +NH3=
Glutamine.
REACTIONS DUE TO AMINO GROUP:
Transamination : α-amino group transferred to α-keto acid to form new amino acid & α-keto acid.
Oxidative deamination: removal of α-amino group to form α-keto acids and ammonia.
Formation of carbamino compound: in
alkaline pH CO2 adds to α-amino group to
form carbamino compound. It serves
transport of CO2 by hemoglobin.
Hb-NH2 Hb-NH-COOH
REACTIONS DUE TO SIDE CHAIN:
Transmethylation: the methyl group is transferrred;
Eg: methionine + acceptor methylated acceptor
+ homocysteine.
Ester formation by OH group:
Serine(OH)+Phosphoric acid Phosphoproteins
and also forms glycoproteins.
Reactions of amide group: glycoprotein is
formed when amide group of Glutamine &
Asparagine forms N-glycosidic bonds with
carbohydrate.
Reaction of SH group: cysteine has a sulfhydryl
group it can form disulfide bond with another
residue. Can also connect two polypeptide
chains forming interchain disulfide bonds.
COLOR REACTIONS OF AMINO ACIDS & PROTEINS
1.Ninhydrin Alpha amino group
2.Biuret reaction Peptide bonds
3.Xanthoproteic test Benzene ring(Phe,Tyr,Trp)
4.Millon’s test Phenol(Tyrosine)
5.Aldehyde test Indole(Tryptophan)
6.Sakaguchi’s test Guanidinium(Arginine)
7.Sulfur test Sulfhydryl(Cysteine)
8.Nitroprusside test Sulfhydryl(Cysteine)
9.Pauly’s test Imidazole(Histidine)
AMINO ACID DERIVATIVES OF IMPORTANCE
GABA: Derivative of glutamic acid & dopamine. A neurotransmitter GABA pentin can pass BBB & form GABA in
brain.
Hitamine: Synthesized from histidine. Mediator in allergic reactions.
Thyroxine: From tyrosine. An thyroid hormone.
Cycloserine: Derivative of serine As an antituberculous drug
Histidine: Important in buffering.
Ornithine: & citrulline are derivative of arginine, essential for
urea synthesis.
REFERENCES:
Text book of biochemistry- DM Vasudevan. Lippincott’s illustrated biochemistry. Biochemistry – U Satyanarayana.
Thank you