3.1 PROTEIN CHEMISTRY (3.1.1 Polypeptide backbone, covalent and non

covalent interaction , end group analysis by chemical and enzymatic methods, conformation and

configuration)

PRESENTED BYJYOTI DEVENDRA ADALA

PEPTIDE BOND

Two amino acid molecules can be covalently joinedthrough a substituted amide linkage, termed a peptidebond, to yield a dipeptide.

POLYPEPTIDE BACKBONEThree amino acids can be joined by two peptide bonds to form a tripeptide. When a few amino acids are joined in this fashion, the structure is called an oligopeptide. When many amino acids are joined, the product is called a polypeptide.

Covalent interactions in proteins

A covalent compound is formed by the mutual sharing of electrons among the combining atoms of the same or different elements. In this process both atoms attain noble gas configuration.

1) Peptide bond2) Disulfide bonds

Electrostatic Interactions in Proteins

Figure shows an electrostatic interaction between a positively charged lysine amino group and a negatively charged glutamate carboxyl group.

HYDROGEN BONDS IN PROTEINS

A weak electrostatic force of attraction between the covalently bonded hydrogen atom of one molecule and a highly electronegative atom of other molecule is called hydrogen bond.

This is generally represented by a dotted line.

Hydrophobic interactions in proteins

Interaction between uncharged substituents on different molecules without a sharing of electrons or protons.

Interaction of (unionizable) hydrocarbon molecules forced together because of stronger water interaction.

Van der Waals forces in proteins

The van der Waals forces is the sum of the attractive or repulsive forces between molecules (or between parts of the same molecule with one another).

End group analysis

Number of chains can be determined by identifying the number of N and C terminal. N-TERMINAL ANALYSIS -Dansyl chloride -Edmans degradation -Treatment with Sanger reagent C-TERMINAL ANALYSIS -Carboxypeptidases

Reaction with Dansyl chlorideDansyl chloride ( 1,1 dimethyl amino naphalene-5-sulfonyl chloride) reacts with N-terminal amino acid to form dansyl amino acid derivative .

Edman degradationThis method utilizes phenylisothiocyanate to react with the N-terminal residue under alkaline conditions. The reaction results in the released N-terminal residue to a phenylthiohydantoin derivative.Advantage :- The remaining peptides are intact.

Treatment with Sanger’s reagent

Sanger’s reagent is 1-fluoro-2,4-dinitrobenzene (FNDB). FNDB specifically binds with N-terminal amino acid to form dinitrophenyl (DNP) derivative of peptide. On hydrolysis yield DNP amino acid and free amino acid from rest of peptide.

C- Terminal Analysis

- Carboxypeptidase A: cleaves all except Arg, Lys, and Proline– Carboxypeptidase B: cleaves C-terminal Arg and Lys if the next residue is not Proline.– Carboxypeptidase C: cleaves C-terminal residues

Any of the spatial arrangements of a molecule that can be obtained by rotation of the atoms about a single bond. The alternative structures of the same protein are referred to as different CONFORMATION.

The CONFIGURATION is a concept that is related to the order by which different substituents linked to the same central atom establish covalent bonds.

-LEHNINGER FOURTH EDITION

-NCERT CHEMISTRY BOOK

References