1. Levels of Protein Structure
Primary: Ultimately determines the 3D structure of the protein
Secondary: Individual amino acids’ backbone functional groups forming H bonds
Tertiary: Intermolecular forces between the R groups of different amino acids
Quaternary: Interaction between all the individual chains of a protein

2. Primary Structure Amino acids Amino end 1 5 10 30 25 20 15
Figure 5.18aa
Amino acid acids bonded between the C terminus and the N terminus = peptide bond
Specific type and order of amino acids determines the overall structure of the protein.
So, a change in one amino acid may alter the polypeptide structure and later the functional protein.
Primary Structure
Amino
acids 1 5 10
Amino end
Figure 5.18aa Exploring levels of protein structure (part 1a: primary, detail) 30 25 20 15
Something about the illustration:
Only the N terminus is shown; There are 32 amino acids in this polypeptide chain;
Abbreviations for different amino acids shown
Gene mutation may cause the polypeptide’s sequence of amino acid to change.

3. Second Level of Protein structure
Figure 5.18ba
Notice how the polypeptide chain interacts with itself.
Helical or pleated conformations occur. Why? Hydrogen bond formation. Where?
Secondary
Structure
𝛂 helix
Hydrogen bond
𝛃 strand
Hydrogen
bond
Figure 5.18ba Exploring levels of protein structure (part 2a: secondary)
𝛃 pleated sheet
Second Level of Protein structure

4. However these bonds are between specific areas of the polypeptide
Alpha – H bond between every 4th amino acid
Beta – H bond between parallel segments
However these bonds are between specific areas of the polypeptide
H bonding between the repeating constituents of the polypeptide's backbone

5. More Intermolecular Interactions
This now coiled and pleated polypeptide chain begins to fold on itself because the structure of the different R groups.
How many polypeptide chains on the slide?
More Intermolecular Interactions

6. Hydrogen bond Hydrophobic interactions and Van der Waals interactions
Figure 5.18d
Hydrogen
bond
Hydrophobic
interactions and
Van der Waals
interactions
Disulfide
bridge
Ionic bond
Figure 5.18d Exploring levels of protein structure (part 4: tertiary stabilization)
Polypeptide
backbone

7. The Fourth Level of Structure: Forms the protein
Here are two functional proteins. One protein is 2 chains and the hemoglobin is 4 chains.
The Fourth Level of Structure: Forms the protein

8. Product of Translation: the transthyretin polypeptide
Figure 5.18a
Primary Structure
Amino
acids 1 5 10
Amino end
Product of Translation: the transthyretin polypeptide 30 25 20 15 35 40 45 50
Primary structure of transthyretin 55 70 65 60
Figure 5.18a Exploring levels of protein structure (part 1: primary) 75 80 85 90 95
115
110
105
100
120
125
Carboxyl end

9. What does transthyretin do?
Figure 5.18b
What does transthyretin do?
Secondary
Structure
Tertiary
Structure
Quaternary
Structure
𝛂 helix
Hydrogen bond
𝛃 strand
Hydrogen
bond
Transthyretin
polypeptide
Transthyretin
protein
Figure 5.18b Exploring levels of protein structure (part 2: secondary through quaternary)
𝛃 pleated sheet

10. Another Way to Illustrate Hemoglobin: Ribbon Model- Find the chains
Figure 5.18f
Another Way to Illustrate Hemoglobin:
Ribbon Model- Find the chains
Heme
Iron
𝛃 subunit
𝛂 subunit
Figure 5.18f Exploring levels of protein structure (part 6: hemoglobin)
𝛂 subunit
𝛃 subunit
Hemoglobin

11. Real World Protein Structure
Figure 5.19
Real World Protein Structure
Secondary
and Tertiary
Structures
Primary
Structure
Quaternary
Structure
Red Blood Cell
Shape
Function 1
Normal 𝛃
subunit
Normal
hemoglobin
Proteins do not associate
with one another; each
carries oxygen. 2 3 𝛃 4
Normal 𝛂 5 6 7
5 µm 𝛃 𝛂
Sickle-cell 𝛃
subunit
Sickle-cell
hemoglobin
Proteins aggregate into a
fiber; capacity to
carry oxygen
is reduced. 1 2
Figure 5.19 A single amino acid substitution in a protein causes sickle-cell disease 3 𝛃 4
Sickle-cell 5 𝛂 6 7
5 µm 𝛂 𝛃
Hemoglobin shape is changed because of one amino acid change: structure altered.

12. A protein’s structure determines how it works The function of a protein usually depends on its ability to recognize and bind to some other molecule. The antibody interacts with the virus’ protein coat.
Antibody protein
Protein from flu virus

13. Can explain protein structure and function?