The document summarizes the structure of proteins at different levels: - Primary structure is the specific sequence of amino acids in the protein backbone. - Secondary structure describes segments of the backbone chain forming regular structures like alpha helices or beta pleated sheets. - Tertiary structure is the overall 3D shape of the protein formed by interactions between amino acid side chains. - Quaternary structure refers to proteins with multiple polypeptide chains interacting to form a complex.

1. Structure of Protein
Anas Bahnassi

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

3. Formation of Peptide Bond

4. Peptide Bond

5. Primary Structure of Proteins
The particular sequence of amino acids that is the
backbone of a peptide chain or protein
Ala-Leu-Cys-Met CH3
CH3 S
CH CH3 SH CH2
CH3 O
+ CH O CH2 O CH2 O
-
H3N CH C N CH C N CH C N CH C O
H H H

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

7. Formation of Disulfide Bonds
Disulfides can be reduced to thiols

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

9. Strategy for Making a Specific Peptide Bond

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

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

15. An Improved Peptide Synthesis Strategy

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

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

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

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

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

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

29. 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.

30. 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”

31. The a-Helix Is Stabilized by Hydrogen Bonds
Prolines are helix breakers

32. 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

33. Two Types of b-Pleated Sheets

34. Tertiary Structure
• Specific overall shape of a protein
• Cross links between R groups of amino acids in
chain
disulfide –S–S–
ionic –COO– H 3 N +–
H bonds C=O HO–
hydrophobic –CH3 H3C–

35. 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.

36. Globular and Fibrous Proteins
Globular proteins Fibrous proteins
“spherical” shape long, thin fibers
Insulin Hair
Hemoglobin Wool
Enzymes Skin
Antibodies Nails

37. Most globular proteins have coil
conformations

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

39. 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

40. 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

41. 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

42. 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

43. Pharmaceutical
Biotechnology
Anas Bahnassi PhD RPh
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