Peptide Bond Amino acids are linked together by peptide bonds to form polypepetide chain.

Peptide Bond

Peptide Bond

 Amino acids are linked together by peptide bonds to form polypepetide chain .

+ H₂O

2

 Peptide bonds are strong and not broken by conditions that denature

proteins, such as heating.

Prolonged exposure to a strong acid or base at elevated temperatures is

required to hydrolyze these bonds

nonenzymically .

--

is, it is shorter than a single bond, and is rigid and planar . --This prevents free rotation around the bond between the

carbonyl carbon and the nitrogen of the peptide bond.

--However, the bonds between the α-carbons and the α-amino or α-carboxyl groups can be freely rotated.

--This allows the polypeptide chain to assume a variety of possible configurations.

Polarity of the peptide bond

 the -C=O and -NH groups of the peptide bond are uncharged, but they are polar and involved in hydrogen bonding in secondary

structure

Characteristics of the peptide bond

Typical Bond Lengths Within a Peptide Unit

The C-N distance in a peptide bond is typically 1.32 Å, which is between the values expected for a C-N single bond (1.49 Å) and a C = N double bond (1.27 Å) .

Resonance of peptide bond

C H

C R₁ H₂N

O

N C H

C H

R₂ O

OH C

H C R₁ H₂N

O^-

OH O

R₂ H

C H

N⁺ C

The peptide bond is rigid. It has a partial double bond character .

 The other bonds in the peptide backbone are not rigid. They are free to rotate

 The amide tautomerism that causes the peptide bond to have a partial double bond character .

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Resonance structure of the peptide bond

(a) Peptide bond shown as a C-N single bond

(b) Peptide bond shown as a double bond

(c) Actual structure is a hybrid of the two resonance forms.

Electrons are delocalized over

three atoms: O, C, N

Peptide Bonds Are Planar. In a pair of linked amino acids, six atoms (α C , C, O, N, H, and α C ) lie in a plane . Side chains are shown as green

 Thus, for a pair of amino acids linked by a

peptide bond, six atoms lie in the same plane: the α-carbon atom and CO group from the first amino acid and the NH group and α-carbon atom from the second amino acid.

The peptide bond is essentially Planar

Planar peptide groups in a polypeptide chain

• Rotation around C-N bond is restricted due to the double-bond nature of the resonance hybrid form

• Peptide groups (blue planes) are therefore planar

Trans and Cis Peptide Bonds

 Two configurations are possible for a planar peptide bond.

--1- In the trans configuration, the two α-carbon atoms are on opposite sides of the peptide bond.

--2-In the cis configuration, these groups are on the same side of the peptide bond.

Almost all peptide bonds in proteins are trans.

Characteristics of Peptide bond

Polypeptides and Proteins

Polypeptide Chain

• Polypeptides are long chains of amino acids linked by peptide bonds.

• Formation of peptide bonds eliminates the ionizable a- carboxyl and a-amino groups of the free amino acids

• Proteins are made up of one or more polypeptide chains .

• Name comes from peptide group –CONH-

Polypeptide

• the free amino end of the peptide chain (N- terminal) is written to the left and the free carboxyl end (C-terminal) to the right

• Therefore, all amino acid sequences are read

from the N- to the C-terminal end of the peptide.

For example, in Fig, the order of the amino acids is “valine, alanine.”

• Linkage of many amino acids through peptide

bonds results in an unbranched chain called a

polypeptide.

dipeptide valylalanine

Polypeptide

• Each component amino acid in a polypeptide is called a “residue” because it is the portion of the amino acid remaining after the atoms of water are lost in the formation of the peptide bond .

• When a polypeptide is named, all amino acid

residues have their suffixes (-ine, -an, -ic, or -ate) changed to -yl, with the exception of the C-

terminal amino acid.

• For example, a tripeptide composed of an N-

terminal valine, a glycine, and a C-terminal

leucine is called valylglycylleucine.

 Peptides made of small numbers of amino acids (<10) are called oligopeptides or simply peptides.

 Chains that are between 10-50 amino acids are referred to as

polypeptide chains . ---Most natural polypeptide chains contain between 50 and 2000

amino acid residues and are commonly referred to as proteins.

 The mean molecular weight of an amino acid residue is about 110, and so the molecular weights of most proteins are between 5500

and 220,000.

---The mass of a protein is expressed also in units of daltons; one dalton is equal to one atomic mass unit. A protein with a molecular weight of 50,000 has a mass of 50,000 daltons, or 50 kd

(kilodaltons).

Structurally, proteins can be organized into four levels :

1-Primary 2-Secondar

3-Tertiar 4-Quaternary structure.

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Levels of Protein Structure

-Primary structure

- Secondary structure

- Tertairy structure

- Quarternary structure

Primary structure

• Primary structure of a protein is simply the linear sequence of amino acid in its polypeptide chain(s) .

• All proteins have their own specific primary structure [a.a sequence], determined by their genes .

• The structure , function and general properties of the protein are all determined by the sequence of amino acids that make up its primary sequence

• The linear sequence of the linked amino acids contains the information necessary to generate a protein molecule with a unique three-dimensional shape

• It is the arrangement or sequence (order) of amino acids in the polypeptide chain.

• The peptide:

NH

-leu-gly-thr-val-arg-asp-his-COOH

has a different primary structure from that of the peptide

NH

-val-his-asp-leu-gly-arg-thr-COOH

even though both have the same number and kind of a.a.

Primary structure