Amino acids structure

Configuration of Amino Acids

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

Different types of amino acids 1)Aliphatic Side-Chain Amino Acids 2)Hydroxy-Containing Amino Acids 3)Sulfur-Containing Amino Acids 4)Acidic Amino Acids 5)Amides Amino Acids 6)Basic Amino Acids 7)Cyclic amino acids

Aliphatic Side-Chain Amino Acids glycinealanine valineleucine isoleucine

Hydroxy-Containing Amino Acids Sulfur-Containing Amino Acids serinethreonine cysteine methionine Methyl donor

Acidic Amino Acids Amides of Acidic Amino Acids aspartatic acid glutamic acid asparagineglutamine Amine transfer Amoniac tranfer

Basic Amino Acids lysine Arginine (guanidino) Ornithine, citruline

Benzene-Containing Amino Acids phenylalaninetyrosine

Heterocyclic Amino Acids 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 at which it has no net charge

The pI of an amino acid that has an ionizable side chain is the average of the pK a 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 overall shape of a protein

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

Continue 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 ( 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 can also be determined by Edman degradation

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

The first step in determining the sequence of amino acids in a peptide or protein is to cleave the disulfide bridges cys oxidation Cysteic acid COOH turin HO 3 S-CH 2 -CH 2 -NH 3

The next step is to determine the number and kinds of amino acids in the peptide or protein proteinamino acids 6 N HCl 100 ° C 24 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.