Amino Acid Structure

Amino acid
 Amino Acids are the building units of

proteins. Proteins are polymers of amino
acids linked together by what is called “
Peptide bond” (see latter).
 There are about 300 amino acids occur in
nature. Only 20 of them occur in proteins.
 The first to be discovered was asparagine, in

1806.
 Each amino acid has 4 different groups

attached to α- carbon ( which is C-atom next
to COOH). These 4 groups are : amino
group, COOH gp, Hydrogen atom and side
Chain (R)
Chiral center (alpha carbon)
Common structure of amino acid

Nomenclature(20 amino acids
A Ala Alanine
C Cys Cysteine
D Asp Aspartic acid (Aspartate)
E Glu Glutamic acid (Glutamate)
F Phe Phenylalanine
G Gly Glycine
H His Histidine
I Ile Isoleucine
K Lys Lysine
L Leu Leucine
M Met Methionine
N Asn Asparagine
P Pro Proline
Q Gln Glutamine
R Arg Arginine
S Ser Serine
T Thr Threonine
V Val Valine
W Trp Tryptophan
Y Tyr Tyrosine
D/L Nomenclature
proposed by Emil Fischer in,1891
Levorotatory (rotating
planepolarized light to the left)
Dextrorotatory (rotating light

to the right).
Stereoisomerism of amino acids
 They are nonsuperposable mirror images of each other , the two

forms represent a class of stereoisomers called enantiomers.
 Amino acid residues in protein molecules are exclusively L
stereoisomers.
 Cells are able to specifically synthesize the L isomers of amino acids
because the active sites of enzymes are asymmetric, causing the
reactions they catalyze to be stereospecific.
Classification of amino acids based on R group
 Nonpolar, Aliphatic R Groups
 Aromatic R Groups
 Polar, Uncharged R Groups
 Positively Charged (Basic) R Groups
 Negatively Charged (Acidic) R Groups
Nutritional classification
Essential amino acids: These amino acids can’t be formed in the body and so, it is essential
to be taken in diet. Their deficiency affects growth, health and protein synthesis.
Nine essesntial amino acid: histidine, isoleucine, leucine, lysine, methionine,

phenylalanine, threonine, tryptophan, and valine
Non essential amino acids: These are the rest of amino acids that are formed in the body in
amount enough for adults and children.
They are the remaining 11 amino acids: arginine, glutamine, tyrosine, cysteine,
glycine, proline, serine, ornithine, alanine, asparagine, and aspartate
The conditional amino acids: arginine, glutamine, tyrosine, cysteine, glycine,

proline, serine, and ornithine
Uncommon amino acids
1. 4-hydroxy proline
2. 5-hydroxy lysine
3. Gamma carboxyglutamate
Amino acid acts as acid and base
 Amphoteric properties of amino acids:
They have both basic and acidic groups
and so can act as base or acid. Neutral
amino acids (monobasic, monocarboxylic)
exist in aqueous solution as “ Zwitter ion”
i.e. contain both positive and negative
charge. Zwitter ion is electrically neutral
and can’t migrate into electric field.
 Isoelectric point (IEP) = is the pH at

which the zwitter ion is formed. e.g IEP of
alanine is 6
Isoeleetric point (pI)
pI= (Pk1+ pK2)/2
pI of glycine= 2.34+ 9.6/2=5.97

Titration curve of amino acid
The larger the number
is, the more hydrophobic
the amino acid. The
most hydrophobic amino
acids are isoleucine (4.5)
and valine (4.2). The
most hydrophilic ones
are arginine (-4.5)
and lysine (-3.9).
Peptides and Proteins
20 amino acids are commonly found in protein.
These 20 amino acids are linked together through “peptide bond forming peptides
and proteins (what’s the difference?).
- The chains containing less than 50 amino acids are called “peptides”, while those
containing greater than 50 amino acids are called “proteins”.
Peptide bond formation:

α-carboxyl group of one amino acid (with side chain R1) forms a covalent
peptide bond with α-amino group of another amino acid ( with the side chain R2)
by removal of a molecule of water. The result is : Dipeptide ( i.e. Two amino acids
linked by one peptide bond). By the same way, the dipeptide can then forms a
second peptide bond with a third amino acid (with side chain R3) to give Tripeptide.
Repetition of this process generates a polypeptide or protein of specific amino acid
sequence.
Peptide bond formation:
- Each polypeptide chain starts on the left side by free amino group of
the first amino acid enter in chain formation . It is termed (N- terminus).
- Each polypeptide chain ends on the right side by free COOH group of
the last amino acid and termed (C-terminus).
Isolation of protein
 Crude extract
 Isolation of organelle
Separation of protein
Charge :
1. Ion excange
2. Electrophoresis
3. Isoelectric focusing
Polarity:
1. Adsorption chromatgraphy
2. Paper chromatography
3. Reverse-phase chromatography
4. Hydrophobic interaction chromatography
Size:
1. Dialysis and ultrafiltration
2. 2. Gel electrophoresis
3. Gel filtration chromatograpy
4. Ultracentrifugation
Specficity
1, Affinity chromatography
Ion-exchange chromatography
1. pH of the solution
2. Con of salt solution
DEAE-cellullose –CH2Ch2N(C2H5)2 - acidic

DEAE-Sephadex- CH2COOH- basic
Dialysis (Molecular Filtration)
Dialysis is a process that separates molecules according to size through the use of
semipermeable membranes containing pores of less than macromolecular dimensions.
Cellophane (cellulose acetate) is the most commonly used dialysis material, although
several other substances such as cellulose and collodion are similarly employed
Paper chromatography
The paper commonly used consists of highly purified cellulose. Cellulose,
a homopolysaccharide of glucose. Contains several thousand anhydro-glucose
units-linked through oxygen atoms.
Size-exclusion Chromatography
Sephadex G10: 0.05-0.7 KD

Sepharose 2B: 70-40000 KD
Affinity Chromatography
A striking characteristic of many proteins is their ability to bind specific molecules tightly
but noncovalently. This property can be used to purify such proteins by affinity
Chromatography.
Reverse-phase chromatography
Stationary phase : silica substituted with nalkyl chains

such as C8 and C18,
Mobile phase: More polar liquid.
Proteins hydrophobically interact with the nonpolar

groups on animmobilized matrix.
High-performance Liquid
Chromatography
Separation may be based on adsorption, ion exchange, size exclusion, HIC, or RPC
as previously described
The narrow and relatively long columns are packed with a noncompressible matrix
of fine (1–10 µm in diameter) silica beads, whose available hydroxyl groups can be
derivatized with many of the commonly usedfunctional groups of ion exchange
chromatography, RPC, HIC, or affinity chromatography.
SDS PAGE
separation of proteins is based on the migration of charged proteins in an electric
field, a process called electrophoresis.
Two-dimensional Gel Electrophoresis
Isoelectric Focusing
Expression and purification of protein
Detection of protein by Western blot
Identification of protein
by MS/MS
MALDI-TOF Mass Spectrometry

Amino Acid Structure

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Amino Acid Structure

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Amino acid

 Amino Acids are the building units of

 The first to be discovered was asparagine, in

 Each amino acid has 4 different groups

Chiral center (alpha carbon)

Common structure of amino acid

Dextrorotatory (rotating light

Stereoisomerism of amino acids

 They are nonsuperposable mirror images of each other , the two

Nine essesntial amino acid: histidine, isoleucine, leucine, lysine, methionine,

The conditional amino acids: arginine, glutamine, tyrosine, cysteine, glycine,

 Isoelectric point (IEP) = is the pH at

pI= (Pk1+ pK2)/2

pI of glycine= 2.34+ 9.6/2=5.97

Peptide bond formation:

DEAE-cellullose –CH2Ch2N(C2H5)2 - acidic

Sephadex G10: 0.05-0.7 KD

Stationary phase : silica substituted with nalkyl chains

Proteins hydrophobically interact with the nonpolar

MALDI-TOF Mass Spectrometry

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