Structure of Protein

Anas Bahnassi

Peptides and proteins are polymers of amino acids linked together by amide bonds

Formation of Peptide Bond

Peptide Bond

Primary Structure of Proteins

The particular sequence of amino acids that is the backbone of a peptide chain or protein

H3N CH

CH3

C

O

N

H

CH C

O

N

H

CH C

O

N

H

CH C O-

OCH

CH CH3

CH3

CH2

SH

CH2

CH2

S

CH3

+

Ala-Leu-Cys-Met

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

Disulfides can be reduced to thiols

Formation of Disulfide Bonds

The disulfide bridge in proteins contributes to the overall shape of a protein

Strategy for Making a Specific Peptide Bond

Amino acids can be added to the growing C-terminal end by repeating these two steps

When the desired number of amino acids has been added to the chain, the protecting group can be removed

An Improved Peptide Synthesis Strategy

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

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

protein amino acids

6 N HCl

100°C 24 h

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

The particular PTH-amino acid can be identified by chromatography using known standards

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

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

Secondary Structure of Protein

• Describe the conformation of segments of the backbone chain of a peptide or protein

• Identified by the following factors:

• Regional planarity about each peptide bond

• Maximization of the number of peptide groups that engage in hydrogen bonding

• Adequate separation between nearby R groups.

Secondary Structure – Alpha Helix

• Three-dimensional arrangement of amino acids with the polypeptide chain in a corkscrew shape

• Held by H bonds between the H of –N-H group and the –O of C=O of the fourth amino acid along the chain

• Looks like a coiled “telephone cord”

The a-Helix Is Stabilized by Hydrogen Bonds

Prolines are helix breakers

Secondary Structure – Triple Helix

• Three polypeptide chains woven together

• Glycine, proline, hydroxy proline and hydroxylysine

• H bonding between –OH groups gives a strong structure

• Typical of collagen, connective tissue, skin, tendons, and cartilage

Two Types of b-Pleated Sheets

Tertiary Structure

• Specific overall shape of a protein

• Cross links between R groups of amino acids in chain

disulfide –S–S– ionic –COO– H3N+–

H bonds C=O HO–

hydrophobic –CH3 H3C–

Tertiary Structure

• The tertiary structure is defined by the primary structure.

• The stabilizing interactions include covalent bonds, hydrogen bonds, electrostatic attractions, and hydrophobic interactions.

• Disulfide bonds are the only covalent bonds that can form when a protein folds.

Globular and Fibrous Proteins

Globular proteins Fibrous proteins

“spherical” shape long, thin fibers

Insulin Hair

Hemoglobin Wool

Enzymes Skin

Antibodies Nails

Most globular proteins have coil conformations

The tertiary structure is the three-dimensional arrangement of all the atoms in the protein

Quaternary Structure

• Proteins with two or more chains

• Example is hemoglobin

Carries oxygen in blood

Four polypeptide chains

Each chain has a heme group to

bind oxygen

Test your knowledge

Indicate the type of structure as

(1) primary (2) alpha helix

(3) beta pleated sheet (4) triple helix

A. Polypeptide chain held side by side by H bonds

B. Sequence of amino acids in a polypeptide chain

C. Corkscrew shape with H bonds between amino acids

D. Three peptide chains woven like a rope

Test your knowledge

Select the type of tertiary interaction as

(1) disulfide (2) ionic

(3) H bonds (4) hydrophobic

A. Leucine and valine

B. Two cysteines

C. Aspartic acid and lysine

D. Serine and threonine

Test your knowledge

Identify the level of protein structure

1. Primary 2. Secondary

3. Tertiary 4. Quaternary

A. Beta pleated sheet

B. Order of amino acids in a protein

C. A protein with two or more peptide chains

D. The shape of a globular protein

E. Disulfide bonds between R groups

abahnassi@gmail.com

http://www.linkedin.com/in/abahnassi

attribution – non-commercial – share alike

Anas Bahnassi PhD RPh

Pharmaceutical Biotechnology

http://www.slideshare.net/abahnassi

http://twitter.com/abahnassi

http://www.udemy.com/Biotechnology