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Peptide Bond

Proteins form by the condensation polymerization of amino acids. There are two functional groups present in amino acid molecule, carboxyl group (-COOH) and amino group (-NH2). On the basis of position of these two functional groups amino acids can be different types :
$\alpha$ -amino acid
$\beta$-amino acid
$\gamma$-amino acid
and so on.

Out of these all, only $\alpha$-amino acids involve in the formation of proteins. There are total twenty amino acids which involve in protein formation through different combinations. In $\alpha$-amino acids, both functional groups bonded on same carbon atom, $\alpha$-carbon atom. Because of opposite nature of both functional groups, acidic group (-COOH) lose proton and convert in carboxylate ion.
At the same time one of the proton accepted by basic group (-NH2) convert in NH4+ ion. Hence $\alpha$-amino group exists in the form of an ion having two opposite charges on same molecule and known as zwitterion. The alkyl group (-R) bonded on alpha carbon atom vary in all amino acids.

Amino Acid

 

Whatis Peptide Bond?

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All twenty amino acids involve in various protein formation through peptide bond.

Essential amino acid 3-letter abbreviation 1-letter code Structure Properties
Histidine His H  Histidine
Essential amino acid with heterocyclic ring
Isoleucine Ile I Isoleucine
Essential amino acid
Leucine Leu L Leucine Essential amino acid
Lysine Lys K Lysine
Essential amino acid, basis in nature with amino group
Methionine Met M Methionine
Essential amino acid with sulpher atom
Phenylalanine Phe F
Phenylalanine
Essential amino acid, aromatic amino acid
Threonine Thr T
Threonine
Essential amino acid with hydroxyl group
Tryptophan Trp W Tryptophan
Aromatic essential amino acid
Valine Val V Valine
Non-polar essential amino acid
Alanine Ala A Alanine
Non-polar and Non-essential amino acid
Arginine* Arg R Arginine Non-essential amino acid, but become essential in some conditions
Asparagine Asn N Asparagine
Non-essential amino acid with amide group
Aspartic acid Asp D Aspartic acid
Acidic amino acid with two carboxyl group and Non-essential amino acid
Cysteine* Cys C Cysteine
Non-essential amino acid with sulpher atom , becomes essential in some conditions
Glutamic acid Glu E Glutamic acid
Acidic , Non-essential amino acid
Glutamine* Gln Q Glutamine
Non-essential amino acid with amide group
Glycine Gly G Glycine
Non-polar, Non-essential amino acid
Proline* Pro P Proline
Non-essential amino acid with imine group. Become essential in some condition
Selenocysteine* Sec U Selenocysteine
Non-essential amino acid with selenium
Serine* Ser S Serine
Non-essential amino acid with hydroxyl group
Taurine* Tau - Taurine
Non-essential amino acid with sulphonic acid group
Tyrosine* Tyr Y Tyrosine
Non-essential amino acid with phenolic group
Ornithine* Orn - Ornithine Non-essential amino acid involve in urea cycle
In protein formation, amino acids condensed together through their amino group and carboxyl group. The condensation of amino group of one $\alpha$-amino acid with the carboxyl group of another molecule of same or different $\alpha$-amino acid with the elimination of a water molecule forms an amide linkage between molecules.
 
This amide linkage (-C(=O)NH-) between two $\alpha$-amino acids is termed as peptide bond or peptide linkage. The dimer formed due to this linkage is called as dipeptide.

Dipeptide

Peptide Bond Formation

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The amide linkage (-C(=O)NH-) between $\alpha$-amino acid is called as peptide bond.
For example:
when carboxyl group (-COOH) group of glycine react with the amino group (-NH2) group of Alanine, it forms a dipeptide, glycylalanine (Gly-Ala).

Similarly the peptide linkage between two glycine (CH2(NH2)COOH) amino acid to form glycylglycine (Gly-gly).

Peptide Bond

The configuration of peptide depends upon the configuration of amino acids involve in peptide bond formation. If the amino group (-NH2) bonded at chiral carbon atom lies on the left side as in L-glyceraldehyde, the amino acid is said to belong to L-series and the location of amino group at right side belongs to D-series.

Similarly amino acids bonded in a chain to form a long chain to form polymer, called as polypeptide. In each polypeptide chain more than thousand amino acids liked together through peptide linkage through condensation reaction.

Polypeptide

Polypeptide chain has the free amino group at one end and a free carboxyl group at another end. The amino acid unit having free amino group is known as N-terminal end whereas the unit with free carbon. The amino acid unit having free amino group is known as N-terminal end whereas the unit with free carboxyl group is called as C-terminal end.

Polypeptide Chain

The structure of polypeptide written is in such a way that the free amino group is written on the left side of the polypeptide chain and free carboxyl group on right side on chain. During writing the name of polypeptide chain, the name is starting from the N-terminal end to the C-terminal end. The amino acid at N-terminal written first with the suffix "ine" is replaced by "yl" like glycyl for glycine followed by name of amino acid residues of polypeptide chain. Three letter abbreviation or one letter code can also be used for nomenclature of polypeptide chains.

Peptide Linkage

PeptideBond Mechanism

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The peptide bond between is a simple amide linkage between amino group and carboxyl group of same of different amino acids. However it's a biochemical reaction, takes place under certain temperature and in the presence of some other biochemical compounds. Reaction required some amount of energy which provided by adenosine triphosphate (ATP) which is an energy center for biochemical reactions. The peptide bond formation completed in three steps.
  1. Carboxylate Activation
  2. Nucleophilic Addition and Formation of the tetrahedral intermediate
  3. Decomposition of the tetrahedral intermediate to form product
1. Carboxylate Activation:

Since amino acids exits as a dipolar ion also known as zwitterion in which carboxyl group (-COOH) exists as carboxylate ion (-COO-) and amino group (-NH2) as -NH3+ ion. The lone pair on oxygen atom of carboxylate ion reacts with phosphate group of ATP molecule through SN2 mechanism and form a transition state which proceeds by the formation of ADP molecule and removal of hydroxyl group from carboxylate ion with the formation of a new phosphate ester.

2. Nucleophilic Addition and Formation of the tetrahedral intermediate:

In second step, the lone pair of nitrogen atom of the amino-terminus of second amino acid reacts with the carbonyl carbon of the phosphate ester formed in previous step and form a tetrahedral intermediate which has four substituents on the carbonyl carbon. Finally, the amine nucleophile gets deprotonated and converts in to a neutral state.

3. Decomposition of the tetrahedral intermediate to form product:

Out of four group on carbonyl carbon atom of tetrahedral intermediate, one is oxylate ion which get collapses and inorganic phosphate moves as a leaving group to form amide linkage, that is peptide bond between two amino acids.

Peptide Bond Mechanism

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