Amino acids structure

Configuration of Amino Acids

Peptides and proteins are polymers of amino acids linkedtogether by amide bonds (peptide bond)

Different types of amino acids

1)Aliphatic Side-Chain Amino Acids2)Hydroxy-Containing Amino Acids3)Sulfur-Containing Amino Acids4)Acidic Amino Acids5)Amides Amino Acids6)Basic Amino Acids7)Cyclic amino acids

Aliphatic Side-Chain Amino Acids

+H3N CH C

H

O-

O

+H3N CH C

CH3

O-

O

+H3N CH C

CH

O-

O

CH3

CH3

+H3N CH C

CH2

O-

O

CH CH3

CH3

+H3N CH C

CH

O-

O

CH3

CH2

CH3

glycine alanine

valine leucine isoleucine

Hydroxy-Containing Amino Acids

Sulfur-Containing Amino Acids

+H3N CH C

CH

O-

O

OH

CH3

+H3N CH C

CH2

O-

O

OH

serine threonine

+H3N CH C

CH2

O-

O

SH

+H3N CH C

CH2

O-

O

CH2

S

CH3cysteine methionine

Methyl donor

Acidic Amino Acids

Amides of Acidic Amino Acids

+H3N CH C

CH2

O-

O

C

O-

O

+H3N CH C

CH2

O-

O

CH2

C

O-

Oaspartatic acid glutamic acid

+H3N CH C

CH2

O-

O

CH2

C

NH2

O

+H3N CH C

CH2

O-

O

C

NH2

O

asparagine glutamine

Amine transfer

Amoniac tranfer

Basic Amino Acids

+H3N CH C

CH2

O-

O

CH2

CH2

CH2

NH3+

+H3N CH C

CH2

O-

O

CH2

CH2

NH

C

NH2

NH2+

lysine Arginine (guanidino)

Ornithine, citruline

Benzene-Containing Amino Acids

+H3N CH C

CH2

O-

O

+H3N CH C

CH2

O-

O

OH

phenylalanine tyrosine

Heterocyclic Amino Acids

+H2N

C O-

O

+H3N CH C

CH2

O-

O

N

NH

+H3N CH C

CH2

O-

O

HN

Proline(secondary amine) histidine (imidazole) tryptophan

Polar and non-Polar

• 1- Non polar (hydrophobic) R groups:• Ala, Val, Leu, Iso, pro (imino acid), Met,

phe, Trp• 2- polar but unchrged R groups:

Gly ?, Ser, Thr, Cys, Tyr, Asn, Gln• Negatively charged R groups:

Asp, Glu• Positively charged R groups: • Lys, Arg, His

• Non essential amino acids: Ala, Arg, Asn, Asp, Cys, Glu, , Ser, Gln, Gly, Pro, Tyr

• Essential amino acids: His, Ile, leu, Lys, Meth, Phe, Thr, Tryp, Val

Acid–Base Properties of Amino Acids

An amino acid can never exist as an uncharged compound

The isoelectric point (pI) of an amino acid is the pH atwhich it has no net charge

The pI of an amino acid that has an ionizable side chainis the average of the pKa values of the similarly ionizing groups

Some amino acids have ionizable hydrogens on their side chains

A mixture of amino acids can be separated by electrophoresis on the basis of their pI values

Ninhydrin is used to detect the individual amino acids

Protein construction

• When two amino acids join together they form a dipeptide.

• When many amino acids are joined together a long-chain polypeptide is formed.

• Organisms join amino acids in different linear sequences to form a variety of polypeptides in to complex molecules, the proteins.

Formation of a Peptide

Peptide Bond

phi

psi

Formation of Disulfide Bonds

ß-mercaptoethanol (SH-C2H5-OH) reductive agent: S-S SH

The disulfide bridge in proteins contributes to the overallshape of a protein

Because amino acids have two functional groups, a problem arises when one attempts to make a particular peptide

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• Glycyl- Alanine

• Lysyl– leucyl- tyrosyl- glutamine, the-ine ending on glutamine indicates that its alpha-carboxyl groups is not involved in peptide bond formation.

Absorbance of amino acids

• Amino acids do not absorb visible light and thus , are colorless. However, phenyl alanine, tyrosine and tryptophan absorb high- wavelength (250-290 nm) ultraviolet. Tryptophan therefore makes the major contribution to the ability of most proteins to absorb light in the region of 280 nm.

The C-terminal amino acid can be identified by treating the protein with carboxypeptidase

Sanger method, dinitro fluore benzene, reacts with amino acid in N-terminal and Lys, Arg in the middle of poly peptide.

Edman method, phenyl iso thiocyanate reacts only with amino acid in N-terminal. Dancyl chloride to label the amino terminal residue (are more easily detectable)

The N-terminal amino acid of a peptide or a protein canalso be determined by Edman degradation

Cyanogen bromide causes the hydrolysis of the amidebond on the C-side of a methionine residue

The first step in determining the sequence of amino acidsin a peptide or protein is to cleave the disulfide bridges

cysoxidation

Cysteic acid

COOH

turin

HO3S-CH2-CH2-NH3

The next step is to determine the number and kinds of amino acids in the peptide or protein

protein amino acids6 N HCl

100°C24 h

Determination of amino acid composition: different amino acids can be

separated by ion-exchange chromatography. Buffers of increasing PH are used to elute the amino acids from the column. The amount of each amino acids present is determined from the absorbance. Aspartate, which has an acidic side chain, is first to emerge, where as arginine,

which has a basic side chain, is the last.